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Yong Zhang

Publications and source records attributed to Yong Zhang.

At least 55 records · Page 3Linked to original sources
PubMed2006

NATsDB: Natural Antisense Transcripts DataBase.

Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense partners. They regulate sense genes at multiple levels and are implicated in various diseases. Using an improved whole-genome computational pipeline, we identified abundant cis-encoded exon-overlapping sense-antisense (SA) gene pairs in human (7356), mouse (6806), fly (1554), and eight other eukaryotic species (total 6534). We developed NATsDB (Natural Antisense Transcripts DataBase, http://natsdb.cbi.pku.edu.cn/) to enable efficient browsing, searching and downloading of this currently most comprehensive collection of SA genes, grouped into six classes based on their overlapping patterns. NATsDB also includes non-exon-overlapping bidirectional (NOB) genes and non-bidirectional (NBD) genes. To facilitate the study of functions, regulations and possible pathological implications, NATsDB includes extensive information about gene structures, poly(A) signals and tails, phastCons conservation, homologues in other species, repeat elements, expressed sequence tag (EST) expression profiles and OMIM disease association. NATsDB supports interactive graphical display of the alignment of all supporting EST and mRNA transcripts of the SA and NOB genes to the genomic loci. It supports advanced search by species, gene name, sequence accession number, chromosome location, coding potential, OMIM association and sequence similarity.

Animals↗
PubMed2006

Molecular dynamics study of the fibril elongation of the prion protein fragment PrP106-126.

The present paper aims at exploring the elongation of the PrP106-126 fibril under acid environments through molecular dynamics simulation. It shows that influenced by the edge strands of the fibril, single PrP106-126 peptide forms beta-sheet and becomes a new element of the fibril. Under acidic condition, single PrP106-126 fragment presents a much larger variety of conformations than it does under neural condition. However, acidic condition does not largely affect the stability of the PrP106-126 fibril. Consequently, the speed of the fibril elongation can be dramatically increased by lowering the pH value of the solution. The pH values are adjusted by either altering the protonation state of the residues or adding hydronium ions or hydroxyl ions.

Computer Simulation↗
PubMed2006

Gradient distribution of persistent organic contaminants along northern slope of central-Himalayas, China.

High mountains may serve as condenser for persistent organic pollutants (POPs) and the vegetation in remote areas has been used as a means to characterized atmospheric concentrations of air pollutants. In this study, organochlorine pesticides (OCPs) and polycyclic aromatic hydrocarbons (PAHs) in Himalayan spruce needle samples from Zhangmu-Nyalam region (central-Himalayas) were analyzed and the altitudinal gradient of these pollutants was investigated. Total HCHs and DDTs concentration in needles were in the range of 1.3-2.9 ng g(-1) dry weight and 1.7-11 ng g(-1) dry weight, which were lower than concentrations reported in spruce needles from Alps, however higher than concentrations in conifer needles from mountain areas of Alberta. Total Himalayan spruce needle PAHs was below 600 ng g(-1) and fluorene, phenanthrene and acenaphthene were abundant individual compounds measured. The ratios of alpha-HCH/gamma-HCH in pine needles were similar with the usual values for technical HCH, implying technical HCHs might be used in this region. The high ratios of o-p'-DDT/p-p'-DDT and no p-p'-DDE measured in this study led to the suspicion that a new source of o-p'-DDT and/or p-p'-DDT existed in this region. In addition, higher ratios of low molecular weight-/high molecular weight-PAHs in this region indicated that petroleum combustion, vehicle emission and low-temperature combustion might be the major contributions of PAH source. To examine the POPs distillation, the analyte concentrations were correlated with altitude. The more volatile OCPs, alpha-HCH, gamma-HCH, aldrin and alpha-endosulfan positively correlated with altitude, however, less volatile OCPs (DDT and DDD) inversely related with elevation. Almost all PAHs detected in this area showed positive correlations with altitude. It is worthy to note that heavy PAHs (Benzo[k] fluoranthene and Benzo[a]anthracene) displayed positive correlation, which implied the sources of PAHs were near the sampling sites. The distillation of POPs was strongly affected by the proximity between sampling sites and contaminant sources. If the contaminant sources are close to the mountains, it may be the dominant factor that controls the concentration gradient.

Air Pollutants↗
PubMed2006

Solid-state NMR of a paramagnetic DIAD-FeII catalyst: sensitivity, resolution enhancement, and structure-based assignments.

A general protocol for the structural characterization of paramagnetic molecular solids using solid-state NMR is provided and illustrated by the characterization of a high-spin Fe(II) catalyst precursor. We show how good NMR performance can be obtained on a molecular powder sample at natural abundance by using very fast (>30 kHz) magic angle spinning (MAS), even though the individual NMR resonances have highly anisotropic shifts and very short relaxation times. The results include the optimization of broadband heteronuclear (proton-carbon) recoupling sequences for polarization transfer; the observation of single or multiple quantum correlation spectra between coupled spins as a tool for removing the inhomogeneous bulk magnetic susceptibility (BMS) broadening; and the combination of NMR experiments and density functional theory calculations, to yield assignments.

Algorithms↗
PubMed2006

Catena-poly[[diisothiocyanatocadmium(II)]-bis[mu-1,3-bis(1,2,4-triazol-1-ylmethyl)benzene-kappa2N4:N4']]: a double-chain coordination polymer.

The coordination geometry of the CdII atom in the title complex, [Cd(NCS)2(C12H12N6)2]n or [Cd(NCS)2(mbtz)2]n, where mbtz is 1,3-bis(1,2,4-triazol-1-ylmethyl)benzene, is a distorted compressed octahedron in which the CdII atom lies on an inversion centre, coordinated by four N atoms from the triazole rings of four mbtz ligands and two N atoms from two monodentate NCS- ligands. The structure is polymeric, with 24-membered spiro-fused rings extending along [100] and with the 24-membered ring containing two inversion-related mbtz molecules.

Crystallography, X-Ray↗
PubMed2006

A novel tracing algorithm for high throughput imaging Screening of neuron-based assays.

High throughput neuron image processing is an important method for drug screening and quantitative neurobiological studies. The method usually includes detection of neurite structures, feature extraction, quantification, and statistical analysis. In this paper, we present a new algorithm for fast and automatic extraction of neurite structures in microscopy neuron images. The algorithm is based on novel methods for soma segmentation, seed point detection, recursive center-line detection, and 2D curve smoothing. The algorithm is fully automatic without any human interaction, and robust enough for usage on images with poor quality, such as those with low contrast or low signal-to-noise ratio. It is able to completely and accurately extract neurite segments in neuron images with highly complicated neurite structures. Robustness comes from the use of 2D smoothening techniques and the idea of center-line extraction by estimating the surrounding edges. Efficiency is achieved by processing only pixels that are close enough to the line structures, and by carefully chosen stopping conditions. These make the proposed approach suitable for demanding image processing tasks in high throughput screening of neuron-based assays. Detailed results on experimental validation of the proposed method and on its comparative performance with other proposed schemes are included.

Algorithms↗
PubMed2006

Sequential treatment with lamivudine and interferon-alpha monotherapies in hepatitis B e antigen-negative Chinese patients and its suppression of lamivudine-resistant mutations.

OBJECTIVES: To assess the efficacy of sequential treatment with lamivudine and interferon-alpha monotherapies in Chinese patients with hepatitis B e antigen (HBeAg)-negative chronic hepatitis B. METHODS: One hundred and sixty-two patients with HBeAg-negative chronic hepatitis B were included in this study. Ninety-eight were treated with lamivudine alone (100 mg per day) for 48 weeks (group B). Sixty-four were treated with lamivudine alone (100 mg per day) for 20 weeks, then combined with interferon-alpha-2b (5 million units three times per week) for 4 weeks and then treated for another 24 weeks with interferon-alpha-2b alone (5 million units three times per week) (group A). All patients were followed for an additional 24 weeks. RESULTS: After 48 weeks of treatment, the percentage of patients with normalization of alanine aminotransferase (ALT) levels or hepatitis B virus (HBV) DNA levels below 1000 copies/mL was not significantly different between the lamivudine monotherapy group (55.10% and 55.10%, respectively) and the sequential treatment group (59.36% and 56.25%, respectively). The percentage of patients with normalized ALT levels was significantly higher in group A (53%) than in group B (36%) at week 72 (P<0.05). The percentage of patients with lamivudine-resistant mutations was significantly higher with lamivudine monotherapy (22.45%) than with sequential therapy (P<0.05). CONCLUSIONS: Sequential treatment of chronic hepatitis B with lamivudine and interferon-alpha monotherapies is as effective as lamivudine-alone treatment in Chinese patients. However, sequential treatment can significantly suppress the emergence of lamivudine-resistant mutations.

Adult↗
PubMed2006

Toward rational construction of gold, gold-silver, and gold-mercury string complexes: syntheses, structures, and properties of [Au(Tab)2]2L2 (L = I and PF6), {[(Tab)2M][Au(CN)2]}2 (M = Au and Ag), and {[Hg(Tab)2][Au(CN)2]2} [Tab = 4-(trimethylammonio)benzenethiolate].

The reaction of AuI with 2 equiv of TabHPF6 [TabH = 4-(trimethylammonio)benzenethiol] in the presence of excess Et3N in dimethylformamide (DMF)/MeOH afforded a binuclear gold(I) complex [Au(Tab)2]2I2.2H2O (1). Anion exchange of 1 with NH4PF6 in DMF gave rise to the more soluble complex [Au(Tab)2]2(PF6)2 (2). Treatment of 2 with K[Au(CN)2] produced a tetranuclear gold(I) complex {[(Tab)2Au][Au(CN)2]}2 (3). Analogous reactions of two known mononuclear complexes [Ag(Tab)2](PF6) (4) and [Hg(Tab)2](PF6)2 (5) with 1 or 2 equiv of K[Au(CN)2] generated one Ag2Au2 complex {[(Tab)2Ag][Au(CN)2]}2 (6) and one Au/Hg complex {[Hg(Tab)2][Au(CN)2]2} (7), respectively. Compounds 1-3, 6, and 7 were fully characterized by elemental analysis, IR spectra, UV-vis spectra, 1H NMR, and single-crystal X-ray crystallography. 1 and 2 have a similar [Au(Tab)2]2(2+) dimeric structure in which the two [Au(Tab)2]+ cations are connected via one Au-Au aurophilic interaction. In the structure of 3 or 6, each of the two pairs of [M(Tab)2]+ cation and [Au(CN)2]- anion is held together via ionic interactions to form a {[(Tab)2M][Au(CN)2]} species (M = Au, 3; Ag, 6). Two such species are further connected by one Au-Au aurophilic bonding interaction to form an uncommon Au(4) or Ag2Au2 linear string structure with three ligand-unsupported metal-metal bonds. For 7, the [Hg(Tab)2]2+ dication and the [Au(CN)2]2(2-) dianion are interconnected by the secondary Hg...N(CN) interactions to form a 1D chain structure. The thermal and luminescent properties of 1-3, 6, and 7 in solid state were also investigated.

Journal Article↗
PubMed2006

Asymmetric heat conduction in nonlinear lattices.

In this Letter, we conduct an extensive study of the two-segment Frenkel-Kontorova model. We show that the rectification effect of the heat flux reported in recent literature is possible only in the weak interfacial coupling limit. The rectification effect will be reversed when the properties of the interface and the system size change. These two types of asymmetric heat conduction are governed by different mechanisms though both are induced by nonlinearity. An intuitive physical picture is proposed to interpret the reversal of the rectification effect. Since asymmetric heat conduction depends critically on the properties of the interface and the system size, it is probably not an easy task to fabricate a thermal rectifier or thermal diode in practice.

Journal Article↗
PubMed2006

[The animal research of recombinant adenovirus controlled by human telomerase reverse transcriptase promoter in the treatment of human prostate cancer].

OBJECTIVE: To approach the treatment efficiency of replication defective adenovirus carrying HSV-tk gene under control of the human telomerase reverse transcriptase (hTERT) promoter in a mouse xenografts model of prostate cancer. METHODS: It was erected that the model of human prostate cancer in BALB/C nude mouse followed by locally injecting Ad-hTERT-HSV-tk and peritoneal injection of GCV. The anti-tumor efficacy was evaluated by index of tumor volume, tumor weight, relative tumor curative, and tumor growth curve. Afterwards, the TUNEL and transmission electron microscope to overview apoptosis of tumor cells were used. Finally, immunohistochemistry for detecting PCNA of tumor cells were applied. RESULTS: Compared with the control group, all viruses treatment groups demonstrated tumor growth inhibition. Among 3 treatment groups, antitumoral effect of Ad-hTERT-HSV-tk/GCV was much stronger than other two groups (P < 0.05). Obvious necrosis and apoptosis was observed by TUNEL, and PCNA was detected by immunohistochemistry in tumor tissues in all viruses treatment group. CONCLUSIONS: Ad-hTERT-HSV-tk/GCV system is highly efficacious to inhabit the growth of human prostate cancer.

Adenoviridae↗
PubMed2006

Random walk approximation of fractional-order multiscaling anomalous diffusion.

Random walks are developed to approximate the solutions of multiscaling, fractional-order, anomalous diffusion equations. The essential elements of the diffusion are described by the matrix-order scaling indexes and the mixing measure, which describes the diffusion coefficient in every direction. Two forms of the governing equation (also called the multiscaling fractional diffusion equation), based on fractional flux and fractional divergence, are considered, where the diffusion coefficient and the drift vary in space. The particle-tracking algorithm is also extended to approximate anomalous diffusion with a streamline-dependent mixing measure, using a streamline-projection technique. In this and other general cases, the random walk method is the only known way to solve the nonhomogeneous equations. Five numerical examples demonstrate the flexibility, simplicity, and efficiency of the random walk method.

Journal Article↗
PubMed2006

Long-term immunogenicity after single and booster dose of a live attenuated hepatitis A vaccine: results from 8-year follow-up.

Live, attenuated hepatitis A vaccines are used widely in China but there is uncertainty regarding the persistence of vaccine-induced anti-HAV antibodies after single dose and booster dose administrated at month 12. A large scale clinical trial to evaluate the live, attenuated hepatitis A vaccine was conducted in Hebei province between 1996 and 1999. Five years after the trials, children in single dose and booster dose groups were bled and followed. Seventy two percent (61/85) of children who received a single trial dose had detectable anti-HAV antibodies for 96 months (GMC at 96 months: 89.0 mIU/mL). In the booster group 98% (48/49) children remained anti-HAV positive with GMC of 262.8 mIU/mL at month 96. The reinjection with live attenuated HAV vaccine can elicit a booster effect. Results from single dose group seems not to support the need for booster doses of live attenuated hepatitis A vaccine in immunocompetent individuals regarding the persisting anti-HAV and anamnestic response of a single dose vaccine. Continued monitoring of anti-HAV antibodies is needed for a rational hepatitis A immunization strategy in China.

Alanine Transaminase↗
PubMed2006

Potential solution processible phosphorescent iridium complexes toward applications in doped light-emitting diodes: rapid syntheses and optical and morphological characterizations.

A series of carbazol-9-yl end-capped red-emitting heteroleptic iridium complexes was readily synthesized using post Suzuki coupling. The appealing solubility, photoluminescent characteristics, and morphological stability enabled the current heteroleptic iridium complexes to be highly desirable phosphorescent dopant emitters in doped light-emitting diodes for the purpose of resisting molecular aggregations in the doped emitting layers.

Journal Article↗
PubMed2006

An outbreak of poliomyelitis caused by type 1 vaccine-derived poliovirus in China.

BACKGROUND: In May-July 2004, type 1 vaccine-derived poliovirus (VDPV) was isolated from 2 case patients with polio and a contact of a third case patient in Guizhou Province. METHODS: We conducted a field investigation of the outbreak, characterized outbreak isolates, and retrospectively reviewed national polio surveillance data for other VDPVs. RESULTS: Case patients were unimmunized children, 0.9-3.2 years old, living in 2 villages 40 km apart. Immunization coverage in the affected villages was very low. Isolates differed from the Sabin 1 type by 9-11 VP1 nucleotides (1.0%-1.2%); which indicated, on the basis of known rates of mutation of Sabin strains, that they had been circulating for <1 year. A province-wide immunization response targeting all children <5 years old was initiated in August, and the strain has not been isolated since. During 1997-2004, 10 VDPV strains (5 of type 2, 3 of type 1, and 2 of type 3) were isolated from >50,000 children with acute flaccid paralysis and their contacts; 8 (80%) were found in southern provinces, and 9 (90%) spontaneously disappeared. CONCLUSION: This is the first polio outbreak in China in over a decade and the first due to VDPV. The short duration of circulation demonstrates the rapidity with which attenuated Sabin strains can revert to a wild phenotype. One to two VDPVs have been identified each year, primarily in densely populated subtropical regions of southern China. This outbreak highlights the need to consider risks of paralysis from vaccine-derived strains in development of national poliomyelitis immunization policy.

Child, Preschool↗
PubMed2006

Preparation of porous materials with ordered hole structure.

This review paper investigates the synthesis of porous structures with controlled hole pattern and provides an overall view of the various factors involved when synthesizing such porous materials. The following factors are discussed: 1) various methods of synthesis to produce the porous structures; 2) materials which the porous structures are made of; 3) control of the pore structure; 4) various applications of such porous materials. The materials of the porous structures and the control of the pore structure will also be discussed separately under each different method, as these two factors are closely dependent on the method of fabrication.

Animals↗
PubMed2006

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to find overlapping transcripts and combining information from coding sequence, poly(A) signal, poly(A) tail and splicing sites to deduce transcription orientation. We identified cis-NATs in 10 eukaryotic species, including 7830 candidate sense-antisense (SA) genes in 3915 SA pairs in human. The abundance of SA genes is remarkably low in worm and does not seem to be caused by the prevalence of operons. Hundreds of SA pairs are conserved across different species, even maintaining the same overlapping patterns. The convergent SA class is prevalent in fly, worm and sea squirt, but not in human or mouse as reported previously. The percentage of SA genes among imprinted genes in human and mouse is 24-47%, a range between the two previous reports. There is significant shortage of SA genes on Chromosome X in human and mouse but not in fly or worm, supporting X-inactivation in mammals as a possible cause. SA genes are over-represented in the catalytic activities and basic metabolism functions. All candidate cis-NATs can be downloaded from http://nats.cbi.pku.edu.cn/download/.

Animals↗
PubMed2006

Survivin stable knockdown by siRNA inhibits tumor cell growth and angiogenesis in breast and cervical cancers.

Increased resistance to apoptosis is a hallmark of many tumor cells. Survivin, a member of IAP family protein, is expressed in many human cancers and plays an important role in protecting cells from apoptosis. Here we show that vector-based small interfering RNAs (siRNA) stably knockdown survivin expression in several cancer cell lines, leading to increased apoptotic rate in response to different proapoptotic stimuli, such as doxorubicin or TNF-alpha. The apoptotic susceptibility was dependent on divergent levels of survivin expression. The stable transfectants exhibited abnormal morphology, suppressed cell growth, enhanced spontaneous apoptosis and cell cycle hindrance. Furthermore, in nude mice xenografts of survivin-positive tumors, cells expressing survivin-targeted siRNAs exhibited decreased tumor formation and reduced angiogenesis. Results from these studies: (1) provide direct evidence that intracellular silencing of survivin by siRNA sensitizes human tumor cells to apoptosis; (2) define survivin as a promising molecular target for cancer therapy; and (3) suggest the potential applicability of survivin-targeted siRNA for treating human tumors, probably in combination with chemotherapy.

Animals↗