Biomedical subjects

Xiaohui Liu

Publications and source records attributed to Xiaohui Liu.

15 recordsLinked to original sources

PubMed2026

The Znf711-Phf8 complex functions as a transcriptional rheostat essential for neutrophil development.

Neutrophil differentiation is governed by a precise transcriptional and epigenetic program. Here, we identify the zinc finger protein 711 (Znf711) and its partner, the histone demethylase PHD finger protein 8 (Phf8), as essential regulators of terminal granulopoiesis. Contrary to their established role as a transcriptional activator-co-activator pair, we found that the Znf711- Phf8 complex operates through a repressive mechanism. Znf711 promotes neutrophil maturation in a DNA-binding-independent manner by sequestering Phf8. Upon loss of Znf711, Phf8 is recruited by the growth factor independent 1 transcription repressor (Gfi1aa) to the promoter of the master regulator c/ebpα, where SUMOylated Phf8 acts as a corepressor to inhibit its transcription. Furthermore, we delineate a positive feedback loop wherein C/ebpα directly activates znf711 expression, ensuring a high level of c/ebpα at the onset of differentiation. Our findings define the Znf711-Phf8 complex as a critical transcriptional rheostat in neutrophil development.

Humans↗

PubMed2005

Synthesis, crystal structure, and properties of MnNCN, the first carbodiimide of a magnetic transition metal.

Synthesis, single-crystal structure determination, and magnetic properties are reported for manganese carbodiimide, MnNCN. The presumably unstable but inert phase adopts the trigonal system (R3m) with a = 3.3583(4) A, c = 14.347(2) A, V = 140.13(3) A3, and Z = 3. Divalent manganese is octahedrally coordinated by nitrogen atoms at 2.26 A, and the NCN(2-) unit adopts the linear [N=C=N](2-) carbodiimide shape with two C=N double bonds of 1.23 A. MnNCN contains high-spin Mn(II) with five unpaired electrons and behaves like an antiferromagnet with an ordering temperature below 30 K.

Journal Article↗

PubMed2005

A spatio-temporal Bayesian network classifier for understanding visual field deterioration.

OBJECTIVE: Progressive loss of the field of vision is characteristic of a number of eye diseases such as glaucoma which is a leading cause of irreversible blindness in the world. Recently, there has been an explosion in the amount of data being stored on patients who suffer from visual deterioration including field test data, retinal image data and patient demographic data. However, there has been relatively little work in modelling the spatial and temporal relationships common to such data. In this paper we introduce a novel method for classifying visual field (VF) data that explicitly models these spatial and temporal relationships. METHODOLOGY: We carry out an analysis of our proposed spatio-temporal Bayesian classifier and compare it to a number of classifiers from the machine learning and statistical communities. These are all tested on two datasets of VF and clinical data. We investigate the receiver operating characteristics curves, the resulting network structures and also make use of existing anatomical knowledge of the eye in order to validate the discovered models. RESULTS: Results are very encouraging showing that our classifiers are comparable to existing statistical models whilst also facilitating the understanding of underlying spatial and temporal relationships within VF data. The results reveal the potential of using such models for knowledge discovery within ophthalmic databases, such as networks reflecting the 'nasal step', an early indicator of the onset of glaucoma. CONCLUSION: The results outlined in this paper pave the way for a substantial program of study involving many other spatial and temporal datasets, including retinal image and clinical data.

Algorithms↗

PubMed2005

State estimation for delayed neural networks.

In this letter, the state estimation problem is studied for neural networks with time-varying delays. The interconnection matrix and the activation functions are assumed to be norm-bounded. The problem addressed is to estimate the neuron states, through available output measurements, such that for all admissible time-delays, the dynamics of the estimation error is globally exponentially stable. An effective linear matrix inequality approach is developed to solve the neuron state estimation problem. In particular, we derive the conditions for the existence of the desired estimators for the delayed neural networks. We also parameterize the explicit expression of the set of desired estimators in terms of linear matrix inequalities (LMIs). Finally, it is shown that the main results can be easily extended to cope with the traditional stability analysis problem for delayed neural networks. Numerical examples are included to illustrate the applicability of the proposed design method.

Algorithms↗

PubMed2004

Consensus clustering and functional interpretation of gene-expression data.

Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFkappaB and the unfolded protein response in certain B-cell lymphomas.

Cluster Analysis↗

PubMed2004

Preparation of single rice chromosome for construction of a DNA library using a laser microbeam trap.

We report the development of a laser micromanipulation system and its application in the isolation of individual rice chromosomes directly from a metaphase cell. Microdissection and flow sorting are two major methods for the isolation of single chromosome. These methods are dependent on the techniques of chromosome spread and chromosome suspension, respectively. In the development of this system, we avoided using chromosome spread and cell suspension was used instead. The cell wall of metaphase rice cell was cut by optical scissors. The released single chromosome was captured by an optical trap and transported to an area without cell debris. The isolated single chromosome was then collected and specific library was constructed by linker adaptor PCR. The average insert size of the library was about 300 bp. Two hundred inserts of chromosome 4 library were sequenced, and 96.5% were aligned to the corresponding sequences of rice chromosome 4. These results suggest the possible application of this method for the preparation of other subcellular structures and for the cloning of single macromolecule through a laser microbeam trap.

Chromosomes, Plant↗

PubMed2003

Experimental and quantum-chemical studies on the thermochemical stabilities of mercury carbodiimide and mercury cyanamide.

Calorimetric dissolution measurements of the solid compounds mercury carbodiimide HgNCN(I) and mercury cyanamide HgNCN(II) in aqueous HCl that targeted at their thermochemical stabilities show the cyanamide species HgNCN(II) to be the more stable phase in terms of both enthalpy and Gibbs energy with an enthalpy difference of 2-3 kJ mol-1. While the stability ranking of HgNCN(I) and HgNCN(II) thus perfectly matches Pearson's HSAB concept, quantum-chemical stability predictions using common parametrizations of density functional theory appear to be fundamentally flawed. An analysis of the error is attempted on the basis of correlated wave functions for related molecules.

Journal Article↗

PubMed2003

c-Myc transformation domain recruits the human STAGA complex and requires TRRAP and GCN5 acetylase activity for transcription activation.

Deregulation of the c-Myc oncoprotein (Myc) is implicated in many types of cancer. Myc is a sequence-specific transcription factor that regulates transcription of genes involved in the control of cell proliferation and apoptosis via mechanisms that are still poorly understood. Cell transformation by Myc involves its association with the transformation-transactivation domain-associated protein (TRRAP) and the human histone acetyltransferase (HAT) GCN5. TRRAP and GCN5 are components of a variety of shared and distinct multiprotein HAT complexes with diverse functions. Myc induces TRRAP recruitment and histone hyperacetylation at specific Myc-activated genes in vivo. However, the identity of the HAT complexes recruited by Myc and the roles of TRRAP and GCN5 in Myc function are still unclear. Here we show that Myc co-recruits TRRAP and GCN5 via direct physical interactions of its N-terminal activation/transformation domain with the human STAGA (SPT3-TAF-GCN5 acetylase) coactivator complex. We demonstrate that GCN5 and TRRAP cooperate to enhance transcription activation by the N-terminal activation domain of Myc in vivo and that this synergy requires both the SPT3/GCN5 interaction domain of TRRAP and the HAT activity of GCN5. Thus, TRRAP might function as an adaptor within the STAGA complex, which helps recruit GCN5 HAT activity to Myc during transcription activation.

Acetylation↗

PubMed2003

Improved processing of microarray data using image reconstruction techniques.

Spotted cDNA microarray data analysis suffers from various problems such as noise from a variety of sources, missing data, inconsistency, and, of course, the presence of outliers. This paper introduces a new method that dramatically reduces the noise when processing the original image data. The proposed approach recreates the microarray slide image, as it would have been with all the genes removed. By subtracting this background recreation from the original, the gene ratios can be calculated with more precision and less influence from outliers and other artifacts that would normally make the analysis of this data more difficult. The new technique is also beneficial, as it does not rely on the accurate fitting of a region to each gene, with its only requirement being an approximate coordinate. In experiments conducted, the new method was tested against one of the mainstream methods of processing spotted microarray images. Our method is shown to produce much less variation in gene measurements. This evidence is supported by clustering results that show a marked improvement in accuracy.

Algorithms↗

PubMed2003

Relationships among apolipoprotein A1 gene polymorphisms, lipid levels and coronary atherosclerosis disease.

OBJECTIVE: To investigate the relationship among -75 bp/+83 bp polymorphism in apolipoprotein A1 (apo A1) gene, lipids levels and the occurrence of coronary atherosclerosis disease (CAD). METHODS: We determined distributions of two MspI polymorphisms of the apo A1 gene at -75 bp and +83 bp, and blood lipids levels among 137 Chinese patients (92 with CAD and 45 in the control group) in relation to circulating lipids and coronary angiography. RESULTS: The demographic information for 137 subjects showed that subjects with CAD tended to have more unfavorable lipoprotein variables. Genotype distributions at both sites were different between the CAD and control groups. Furthermore, the control group had higher M1-/M2- frequencies than the CAD group (M1: P < 0.005; M2: P < 0.05) and the "M1-" (A) and "M2-" alleles were associated with increased high-density lipoprotein cholesterol (HDL-C) (M1-: P < 0.0001; M2-: P < 0.05) and apo A1 (M1-: P < 0.0001; M2-: P < 0.05) levels. "M1-" and "M2-" were significantly negatively correlated with CAD (P < 0.01 and P < 0.05, respectively). CONCLUSIONS: Our results suggest that changes from G to A at the -75 bp site and from C to T or G to A at the +83 bp site do increase circulating levels of apo A1 and HDL-C. And those individuals with these changes are likely to have a lower risk of developing CAD.

Apolipoprotein A-I↗

PubMed2003

Lipid-lowering efficacy and safety of varying doses of Simvastatin in patients with early stage acute coronary syndromes: one-year follow-up study.

OBJECTIVE: To investigate whether patients, who are at risk of major acute coronary events, are safe to undergo and benefit from early intervention after using simvastatin. METHODS: The study was a randomized, open, two-dosage-controlled trial to evaluate the safety and benefits of simvastatin administered to 197 patients (10 mg group, n = 98 and 20 mg group, n = 99), within 48 hours of hospitalization for a diagnosis of unstable angina or acute myocardial infarction (MI), with total cholesterol (TC) >/= 180 mg/dL or low-density lipoprotein cholesterol (LDL-C) >/= 100 mg/dL. Lipid levels were measured immediately, followed by the 3rd, 6th and 12th month after admission and all adverse events were recorded during follow-up. RESULTS: TC levels fell by 10.15% and 14.52% in the 10 mg and 20 mg groups (P < 0.05), and LDL-C levels fell 13.87% and 19.38% in the 10 mg and 20 mg groups, respectively (P < 0.01), 12 months after using simvastatin. The rates of achieving target TC reached 26.3% and 36.5% in the 10 mg and 20 mg groups (P < 0.01), and that of LDL-C reached 28.2% and 40.3% in the 10 mg and 20 mg groups, respectively (P < 0.01). There were higher rates of MI and re-hospitalization resulting from angina pectoris and revascularization in the 10 mg group compared with the 20 mg group. CONCLUSIONS: The results suggest that early intervention with the HMG-CoA reductase inhibitor, simvastatin, in acute coronary syndromes is possible and safe. It also indicates that the clinical dosage of simvastatin are relatively smaller than that for satisfactory lipid control in patients with acute coronary syndromes.

Acute Disease↗

PubMed2002

Sequence and analysis of rice chromosome 4.

Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.

Arabidopsis↗

PubMed2002

Synthesis, structure determination, and quantum-chemical characterization of an alternate HgNCN polymorph.

A novel, possibly metastable form of HgNCN, designated HgNCN(II), is accessible under soft-chemical reaction conditions, and its existence has been established from combined X-ray/neutron Rietveld refinements (P2(1)/a, a = 6.8521(4) A, b = 6.9797(4) A, c = 5.5516(4) A, beta = 113.212(4) degrees ), vibrational spectroscopy investigations, and plane-wave DFT calculations utilizing pseudopotentials. In contrast to the known mercury carbodiimide HgNCN(I) with two practically identical N-C double bonds of 1.22 A, the true cyanamide HgNCN(II) is characterized by a short ("triple") N-C bond (1.12 A) and a long ("single") C-N bond (1.35 A); two Hg atoms coordinate the asymmetrically shaped NCN(2)(-) unit only on the side of the C-N "single" bond. Mercury carbodiimide HgNCN(I) and mercury cyanamide HgNCN(II) are thermochemically separated from each other by such a high energy barrier that thermal decomposition prevents structural interconversion. The structure-chemical relationship of the two HgNCN phases is discussed in terms of bond-stretch and linkage isomerism.

Journal Article↗

PubMed2002

Predicting glaucomatous visual field deterioration through short multivariate time series modelling.

In bio-medical domains there are many applications involving the modelling of multivariate time series (MTS) data. One area that has been largely overlooked so far is the particular type of time series where the dataset consists of a large number of variables but with a small number of observations. In this paper, we describe the development of a novel computational method based on genetic algorithms that bypasses the size restrictions of traditional statistical MTS methods, makes no distribution assumptions, and also locates the order and associated parameters as a whole step. We apply this method to the prediction and modelling of glaucomatous visual field deterioration.

Algorithms↗

PubMed2002

A fine physical map of the rice chromosome 4.

As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies.

Chromosomes↗