Biomedical subjects

Xin Zhou

Publications and source records attributed to Xin Zhou.

At least 19 recordsLinked to original sources

PubMed2026

Integrating genetic predictors into subsequent breast cancer risk prediction in survivors of childhood cancer.

PURPOSE: Female survivors of childhood cancer are at high risk for developing breast cancer. The contributions of most general population primary breast cancer genetic predictors to this risk have not been explored. METHODS: Analyses included females who survived ≥5 years after their childhood cancer diagnosis with available array (N = 2096, subsequent breast cancer [SBC]=218) or whole-genome sequencing (WGS; N = 3292, SBC=101) data from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. We computed 99 externally-validated primary breast cancer polygenic risk scores (PRS). Using deep-coverage WGS, ClinVar-annotated pathogenic/likely pathogenic (P/LP) variants in breast cancer susceptibility genes were identified. Cox proportional hazards models assessed associations with SBC risk, adjusting for treatments and genetic ancestry. RESULTS: Among 5388 female survivors (genetic ancestry, European: N = 4,752; African: N = 444; East Asian: N = 192), 319 developed SBC. Most (90.9%) PRSs were nominally associated with SBC risk (P < 0.05), but effect sizes varied substantially. PRSs with superior discriminatory ability had greater genome-wide coverage (e.g., 6.4 million-variant PRS, HR per SD = 1.71, 95% CI = 1.43 to 2.05; P = 4.2x10-9) and 7.7-fold higher odds (P = 7.0x10-4) of including variants in multiple DNA damage repair pathways compared with PRSs with weaker risk associations. Among survivors with WGS, 1.6% carried P/LP variants in clinical testing panel genes, which was associated with a 7.4-fold greater risk (95% CI = 3.16 to 17.19). Including genetic factors improved SBC risk prediction by age 40 (P < 0.001) compared to treatment exposures alone. CONCLUSIONS: Externally-validated primary breast cancer genetic susceptibility predictors are relevant for SBC risk prediction and should be prioritized for risk stratification in survivors.

Journal Article↗

PubMed2026

The ASH HematOmics Program supports integrative analysis of genomic and clinical data in hematologic diseases.

The increasing availability of genomic and transcriptomic sequencing has uncovered diverse genomic alterations and distinct gene expression profiles driving hematologic diseases, yet a data integration and sharing platform dedicated to hematology remains lacking. We developed the American Society of Hematology (ASH) HematOmics Program (ASHOP; ashop.hematology.org), a resource for exploring somatic alterations and gene fusions, transcriptomic results, and clinical data from 5960 patients spanning B-cell precursor and T-cell acute lymphoblastic leukemia, acute myeloid leukemia, myelodysplastic syndromes, and chronic lymphocytic leukemia. Users can explore genomic alteration landscapes and comutation patterns via lollipop and matrix plots and analyze significantly altered genes in user-defined subcohorts. Transcriptomes can be explored through interactive uniform manifold approximation and projections, clustering, differential expression, and pathway enrichment. Genomic, transcriptomic features, and clinical outcomes can be correlated in a user-driven manner or combined to precisely define study cohorts. We illustrate the following 4 use cases of ASHOP: (1) stratification of DUX4-rearranged B-cell leukemias into Early/Multipotent and Committed subgroups with distinct outcomes, (2) characterization of HOXA/HOXB expression patterns in acute myeloid leukemias, (3) correlating mutational burden with mismatch repair deficiency and mutational signatures, and (4) investigation of TP53 alteration landscape. ASHOP is an open-access resource to inform genomic and transcriptomic data interpretation for hematologic malignancies and will expand to support additional diseases and data modalities from the ASH community.

Humans↗

PubMed2026

Non-destructive prediction of lead content in oilseed rape leaves by fluorescence hyperspectral technology based on neural network.

Based on fluorescence hyperspectral imaging (FHSI), this study targeted rapid, non-destructive quantification of lead (Pb) content in oilseed rape leaves treated with varying silicon (Si) concentrations, acquiring fluorescence spectra over the 484.43-1001.61 nm wavelength range. To optimize spectral data quality, preprocessing methods (Savitzky-Golay smoothing, first derivative, detrending) were comprehensively compared. Characteristic wavelengths were then selected via interval variable iterative shrinkage, which effectively compressed data dimensionality and reduced computational load. A hybrid SE-CL1DA model, fusing a 1D convolutional neural network, a long short-term memory network and SE attention mechanism was constructed, with Bayesian optimization tuning hyperparameters to boost stability. The BO-SE-CL1DA outperformed both traditional machine learning and insufficiently optimized deep learning model (Rp2=0.9609, RMSE = 0.0377 mg/kg, RPD = 5.1736), thus enabling accurate Pb estimation, supporting Si-regulated heavy metal stress management and facilitating agricultural contamination monitoring.

Plant Leaves↗

PubMed2025

Uncovering parental exposure risks of TCPP: Impaired development and metabolic homeostasis in zebrafish offspring.

As brominated flame retardants are phased out, tris (1‑chloro-2-propyl) phosphate (TCPP), a phosphorus-based flame retardant, has emerged as a prominent detectable flame retardant in the environment. However, TCPP has been found to exhibit endocrine-disrupting effects on organisms, raising significant safety concerns. In our study, we utilized the zebrafish model to explore the toxic effects of parental TCPP exposure on offspring and uncover its regulatory mechanisms through metabolomics analysis. Moreover, the impact on the nervous system and lipid metabolism was examined through behavioral analysis and specific staining. Our findings demonstrated that both embryonic and parental TCPP exposure induced developmental disorders in larvae, along with decreased locomotor activity and disordered lipid metabolism homeostasis. Parental exposure to TCPP, exhibiting stronger developmental toxicity than direct embryonic exposure, notably led to reductions in crucial energy substrates such as amino acids and carbohydrates. Meanwhile, embryonic TCPP exposure primarily affected the endogenous lipid-related metabolites including phospholipids, lipid-soluble vitamins, steroids and fatty acids, promoting lipid accumulation in larval liver and subcutaneous tissue. What's more, continuously parental and embryonic exposure showed the most pronounced effects on zebrafish development and metabolic regulation. Our study highlights the risk posed by parental exposure to TCPP on offspring zebrafish, underscoring the need for comprehensive consideration of the impact from parental exposure in pollutants regulation.

Animals↗

PubMed2025

The landscape of structural variation in pediatric cancer.

Structural variants (SVs) account for over 60% of the driver variants in pediatric cancer, and in many cases act as the cancer initiating event. To study SVs from a pan-cancer perspective, we analyzed 1,616 pediatric cancer genomes in 16 major cancer types of hematological malignancies (n = 908), brain tumors (n = 183), and solid tumors (n = 525) and compared their profiles to those of 2,203 adult cancers. The SV burden varied ~100-fold across pediatric cancer types and demonstrated an 8- to 16-fold reduction compared to adult brain and solid tumors but was comparable in pediatric versus adult hematological malignancies. Recurrent SV hotspots occurred uniquely in pediatric acute lymphoblastic leukemias (ALLs) in proximity to RAG-mediated recombination signal sequences (RSS) and disrupted multiple immune-related loci as well as 69 genes, which often involved cryptic RSS sites. By contrast, such hotspots affected only immune-related loci but not driver genes in adult lymphoid cancers. Eight SV signatures extracted from the cohort had varying distributions across cancer types, with clustered translocations reflecting templated insertions in osteosarcoma, and medium-sized deletions (10 kb to 1 Mb) enriched in cancers with RAG-mediated deletions. Intra-patient evolutionary analysis in 13 patients with multiple spatiotemporally distinct samples revealed that RAG-mediated recombination in leukemia and complex rearrangements in solid tumors occurred both early in disease initiation and continuously during later diversification, contributing to clonal heterogeneity. Finally, we found that both driver genes and fragile sites were the two genomic regions most frequently disrupted by SVs. The unique and diverse SV landscapes that emerged from this comprehensive analysis expand the scope of RSS-mediated mutagenesis in pediatric ALL and will be a valuable resource for guiding future functional studies and the design of clinical genomic testing in pediatric cancer.

Journal Article↗

PubMed2019

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants.

Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE), a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in variant call format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4000 pediatric cancer patients and serves as a repository for the expert-reviewed results. PeCanPIE was originally developed for pediatric cancer but can be easily extended for use for nonpediatric cancers and noncancer genetic diseases. Although PeCanPIE's web-based interface was designed to be accessible to non-bioinformaticians, its back-end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.

Child↗

PubMed2007

Electronic structures and spectroscopic properties of mono- and binuclear d(8) complexes: a theoretical exploration on promising phosphorescent materials.

The structures of trans-[M(2)(CN)(4)(PH(2)CH(2)PH(2))(2)] (M = Pt (1), Pd (2), and Ni (3)), trans-[Pt(2)X(4)(PH(2)CH(2)PH(2))(2)] (X = Cl (4) and Br (5)), and trans-[M(CN)(2)(PH(3))(2)] (M = Pt (6), Pd (7), and Ni (8)) in the ground state were optimized using the MP2 method. Frequency calculations reveal that the weak metal-metal interaction is essentially attractive for 1, 2, 4, and 5 but not for 3. The TD-DFT calculations associated with the polarized continuum model (PCM) were performed to predict absorption spectra in CH(2)Cl(2) solution. Experimental spectra are well reproduced by our results. With respect to analogous mononuclear d(8) complexes (6-8), a large red shift of the absorption wavelength was calculated for the binuclear d(8) complexes (1-3). Relative to 1 with unsaturated CN- donors, introduction of saturated halogen donors into 4 and 5 changes their electronic structures, especially the HOMO and LUMO. The TD-DFT and subsequent unrestricted MP2 calculations predict that 1 produces the lowest-energy d --> p emission while 2-5 favor the d --> d emissions, agreeing with experimental observations.

Journal Article↗

PubMed2007

Phosphoramidate pronucleotides: a comparison of the phosphoramidase substrate specificity of human and Escherichia coli histidine triad nucleotide binding proteins.

To facilitate the delivery of nucleotide-based therapeutics to cells and tissues, a variety of pronucleotide approaches have been developed. Our laboratory and others have demonstrated that nucleoside phosphoramidates can be activated intracellularly to the corresponding 5'-monophosphate nucleotide and that histidine triad nucleotide binding proteins (Hints) are potentially responsible for their bioactivation. Hints are conserved and ubiquitous enzymes that hydrolyze phosphoramidate bonds between nucleoside 5'-monophosphate and an amine leaving group. On the basis of the ability of nucleosides to quench the fluorescence of covalently linked amines containing indole, a sensitive, continuous fluorescence-based assay was developed. A series of substrates linking the naturally fluorogenic indole derivatives to nucleoside 5'-monophosphates were synthesized, and their steady state kinetic parameters of hydrolysis by human Hint1 and Escherichia coli hinT were evaluated. To characterize the elemental and stereochemical effect on the reaction, two P-diastereoisomers of adenosine or guanosine phosphoramidothioates were synthesized and studied to reveal a 15-200-fold decrease in the specificity constant (kcat/Km) when the phosphoryl oxygen is replaced with sulfur. While a stereochemical preference was not observed for E. coli hinT, hHint1 exhibited a 300-fold preference for d-tryptophan phosphoramidates over l-isomers. The most efficient substrates evaluated to date are those that contain the less sterically hindering amine leaving group, tryptamine, with kcat and Km values comparable to those found for adenosine kinase. The apparent second-order rate constants (kcat/Km) for adenosine tryptamine phosphoramidate monoester were found to be 107 M-1 s-1 for hHint1 and 106 M-1 s-1 for E. coli hinT. Both the human and E. coli enzymes preferred purine over pyrimidine analogues. Consistent with observed hydrogen bonding between the 2'-OH group of adenosine monophosphate and the active site residue, Asp43, the second-order rate constant (kcat/Km) for thymidine tryptamine phosphoramidate was found to be 3-4 orders of magnitude smaller than that for uridine tryptamine phosphoramidate for hHint1 and 2 orders of magnitude smaller than that for E. coli hinT. Ara-A tryptamine phosphoramidate was, however, shown to be a good substrate with a specificity constant (kcat/Km) only 10-fold lower than the value for adenosine tryptamine phosphoramidate. Consequently, nucleoside phosphoramidates containing unhindered primary amines and either an alpha or beta 2'-OH group should be easily bioactivated by Hints with efficiencies rivaling those for the 5'-monophosphorylation of nucleosides by nucleoside kinases. The differential substrate specificity observed for human and E. coli enzymes represents a potential therapeutic rationale for the development of selective antibiotic phosphoramidate pronucleotides.

Amides↗

PubMed2006

Enhancement of endogenous defenses against ROS by supra-nutritional level of selenium is more safe and effective than antioxidant supplementation in reducing hypertensive target organ damage.

Hypertension-induced target organ damage (TOD), is one of the leading causes of morbidity and mortality. Reactive oxygen species (ROS) play an important role in the pathogenesis and development of hypertension. It has been suggested that hypertension-induced TOD is related to the level of oxidative stress, but is in part independent of the level of blood pressure. Therefore, in addition to anti-hypertensive drug therapy, novel strategies against ROS, will provide additional benefits to patient with hypertension. Vitamin E has long been supplemented as an effective antioxidant. However, the potential hazardous effects of vitamin E supplementation as antioxidant revealed by recent studies make its clinical and routine use prudent. Therefore, novel approaches capable of enhancing endogenous system to defend against ROS are required. Here, we propose that enhancement of intrinsic defenses against ROS by supra-nutritional level of selenium is more safe and effective than antioxidant supplementation in reducing hypertensive target organ damage, owing to its role in activating and constitution of native vital proteins and/or enzymes against oxidative stress, and the fact that scarcity of selenium can not be supplemented by normal food, and potentially extra benefits by supra-normal intake.

Antioxidants↗

PubMed2006

Novel mutations found in mitochondrial diabetes in Chinese Han population.

Mitochondria provide cells with most of the energy in the form of ATP. Mutations in mitochondrial DNA (mtDNA) are associated with type 2 diabetes mellitus (T2DM) because ATP plays a critical role in the production and the release of insulin. To systematically determine mutant loci and to investigate their association with T2DM in Chinese Han population, 17 commonly reported mutant loci were screened in 236 cases of T2DM and 240 normal controls by PCR-RFLP, allele-specific PCR (AS-PCR) and DNA sequencing methods. Biological softwares were used to analyze the secondary structure of DNA, RNA and the corresponding proteins for missense mutations. Sixteen mutant loci were detected in total, of which five were novel, GenBank accession nos. were DQ092356, DQ473644 and DQ473645; they were mainly in16S rRNA, ND1 and ND4 gene. There was significant difference between the two groups for ND1 and ND4 genes mutation frequencies (ND1: P=0.001, OR=3.944, 95% CI 1.671-9.306; ND4: P=0.010, OR=5.818, 95% CI 1.275-26.537). No significant association was observed between the two groups for 5178A/C polymorphisms (P=0.418). Our study suggested that T3394C and A12026G might be associated with T2DM in Chinese Han population, and T2DM with mtDNA variant should be considered mitochondrial diabetes.

Adult↗

PubMed2006

Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings.

Full-length cDNAs are very important for genome annotation and functional analysis of genes. The number of full-length cDNAs from maize (Zea mays L.) remains limited. Here we report the construction of a full-length enriched cDNA library from osmotically stressed maize seedlings by using the modified CAP trapper method. From this library, 2073 full-length cDNAs were collected and further analyzed by sequencing from both the 5'- and 3'-ends. A total of 1728 (83.4%) sequences did not match known maize mRNA and full-length cDNA sequences in the GenBank database and represent new full-length genes. After alignment of the 2073 full-length cDNAs with 448 maize BAC sequences, it was found that 84 full-length cDNAs could be mapped to the BACs. Of these, 43 genes (51.2%) have been correctly annotated from the BAC clones, 37 genes (44.0%) have been annotated with a different exon-intron structure from our cDNA, and four genes (4.76%) had no annotations in the TIGR database. Expression analysis of 2073 full-length maize cDNAs using a cDNA macroarray led to the identification of 79 genes upregulated by stress treatments and 329 downregulated genes. Of the 79 stress-inducible genes, 30 genes contain ABRE, DRE, MYB, MYC core sequences or other abiotic-responsive cis-acting elements in their promoters. These results suggest that these cis-acting elements and the corresponding transcription factors take part in plant responses to osmotic stress either cooperatively or independently. Additionally, the data suggest that an ethylene signaling pathway may be involved in the maize response to drought stress.

DNA, Complementary↗

PubMed2006

[Development of a DNA chip screening mitochondrial DNA mutations in patients with diabetes mellitus].

OBJECTIVE: To establish a rapid and precise high-throughput mitochondrial (mt) DNA chip and to investigate the relationship between mtDNA tRNA Leu (UUR) and ND1 gene mutations and diabetes mellitus. METHODS: A wild-type and mutant probes of 28 loci in tRNA Leu (UUR) and ND1 gene were immobilized on the Hybond N + nylon membrane by UV-crosslinking, then the mtDNA chips were used to detect 28 loci mutation in 200 cases of type 2 diabetes mellitus and 210 matched healthy controls. All the mutations were further confirmed by DNA sequencing. Mfold and Antherprot softwares were used to predict the secondary structures of the mutant gene and protein. RESULTS: The mtDNA chip, which could detect 28 loci mutations, was successfully developed. In diabetic group, there were 2 (1.0%) cases of T3 290C mutation, 6 (3.0%) of G3 316A (Ala-->Thr) mutation, 5 (2.5%) of T 3 394C (Tyr-->His) mutation, 1 (0.5%) of T3 593 C (Val-->Ala) mutation, 1 (0.5%) of A3 606G (Leu-->Leu) mutation, 8 (4.0%) of A4 164G (Met-->Met) mutation, 2 (1.0%) of T4 216C (Met-->His) mutation. In the controls, 1 (0.5%) carrier of G3 316A mutation and 5 (2.4%) carriers of A4 164G mutation were found. There was significant difference between two groups for T3 394C mutation frequencies (P = 0.027). The secondary structures of the mutant proteins of G3 316A, T3 394C, T3 593C and T4 216C mutations were all different from those of the wild-types'. CONCLUSION: mtDNA chip is a rapid and reliable high-throughput method for mutations detection, and T3 394C mutation in ND1 gene might contribute to the pathogenesis of mitochondrial diabetes.

Adult↗

PubMed2006

Abdominal aortic aneurysm and cerebral aneurysm present different pathological evolutions and responses to pharmacological therapy.

Over-degradation of extracellular components by matrix metalloproteinases (MMPs) has been implicated as an important characteristic during the pathological evolution of the abdominal aortic aneurysm (AAA) and cerebral aneurysm (CA), which contribute to progressive dilation of vascular wall. However, mRNA and protein expression of local rennin-angiotensin system (RAS) components are found down-regulated in CA walls, which is contrary to long-holding concept that local RAS will be activated in response to increased hemodynamic stress and contributes to thickening of arterial wall. Similarly, MMPs inhibition by doxycycline effectively ameliorate AAA expansion in basic and clinical researches, but can not reduce the incidence of CA formation in rat. These evidences may suggest that suppression of RAS favors the regression of AAA, but at an increased risk of CA rupture. As the strategies of RAS blockade have became the optimal antihypertensive drugs of choice in clinical arena, the discrepant responses to pharmacologic intervention of AAA and CA should be received considerable attentions, due to their high prevalence in hypertensive population. Here we proposed that AAA and CA, outward remodeling of elastic and muscular arteries respectively, presented with different pathological evolutions and distinct responses to drug intervention, i.e., RAS and MMPs inhibition. It can not be excluded that the potentially deleterious effects of RAS inhibition on CA may be masked by the beneficial action of controlled blood pressure, and the propagation of CA will be exacerbated once suboptimal dose have been prescribed, or under the condition of stress, even drug withdrawal. If the paradoxical outcomes of these two kinds of arterial remodeling were proven true in basic research, clinical use of RAS blockade should be prudent in hypertensive patients, and routine procedures to detect the existence of CA should be considered. Therefore, in depth investigation in their responses to pharmacological approaches will provide us with more insights into the pathogenesis of arterial aneurysm.

Aorta, Abdominal↗

PubMed2006

Rapid analysis of the essential oils from dried Illicium verum Hook. f. and Zingiber officinale Rosc. by improved solvent-free microwave extraction with three types of microwave-absorption medium.

A new method of extracting essential oils from dried plant materials has been studied. By adding a microwave-absorption medium (MAM) to a reactor, solvent-free microwave extraction (SFME) was improved and can be used to extract essential oils from dried plant material without pretreatment. With a microwave irradiation power of 85 W it took only approximately 30 min to extract the essential oils completely. The whole extraction process is simple, rapid, and economical. Three types of MAM, iron carbonyl powder (ICP), graphite powder (GP), and activated carbon powder (ACP), and two types of dried plant material, Illicium verum Hook. f. and Zingiber officinale Rosc., were studied. The results were compared with those obtained by use of conventional SFME, microwave-assisted hydrodistillation (MAHD), and conventional hydrodistillation (HD), and the conclusion drawn was that improved SFME was a feasible means of extracting essential oils from dried plant materials, because there were few differences between the composition of the essential oils extracted by improved SFME and by the other methods.

Adsorption↗

PubMed2006

Polyethylene glycol fractionation improved detection of low-abundant proteins by two-dimensional electrophoresis analysis of plant proteome.

Poor detection of low-abundant proteins is a common problem in two-dimensional electrophoresis (2-DE) for separation of proteins in a proteome analysis. This is attributed partially, at least, to the existence of high-abundant proteins, e.g. ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in plants. They engage a large proportion of the whole-cell proteins and thus prevent low-abundant proteins from being up-taken by immobilized pH gradient (IPG) strip, consequently making the latter poorly detectable by 2-DE. In this work, we report a straightforward protocol for preparation of whole-cell proteins through differential polyethylene glycol (PEG) precipitation aiming at elimination of Rubisco from plant protein samples. In comparison with 2-DE analysis of protein samples prepared using a conventional TCA/acetone method, a relatively high reproducibility of proteins was achieved using a PEG fractionation protocol in terms of protein yield and protein species. As expected, the large subunit of Rubisco was precipitated predominantly in the 16% PEG fraction. This allowed proteins of the Rubisco-containing fraction to be analyzed separately from those of other PEG fractions. After taking into account the overlapping protein spots among 2-DE gels of all fractions through image and statistical analyses, we detected with this protocol a total 5077 protein spots, among which ca. 80% are proteins undetectable with the TCA/acetone method, while the rest of proteins exhibited a significant increase in their abundance. This protocol was developed using Arabidopsis as a source of protein and thus may also be applicable to protein preparations of other plants.

Arabidopsis↗

PubMed2006

Hyperdynamics for entropic systems: time-space compression and pair correlation function approximation.

We develop a generalized hyperdynamics method that is able to simulate slow dynamics in atomistic general (both energy- and entropy-dominated) systems. We show that a few functionals of the pair correlation function, involving two-body entropy, form a low-dimensional collective space, which is a good approximation that is able to distinguish stable and transitional conformations. A bias potential, which raises the energy in stable regions, is constructed on the fly. We examine the slow nucleation processes of a Lennard-Jones gas and show that our method can generate correct long-time dynamics without prior knowledge.

Journal Article↗

PubMed2006

Analysis of volatile components of Curcuma sichuanensis X. X. Chen by gas chromatography-mass spectrometry.

Volatile components of Curcuma sichuanensis X. X. Chen growing in Sichuan, China, were extracted by steam distillation and analyzed by using gas chromatography and gas chromatography-mass spectrometry. A total of 44 volatile essential oil components were identified in the extract of C. sichuanensis X. X. Chen, representing 87.1% of the total integrated chromatographic peaks. The major compounds were found to be epi-curzerenone (26.9%), germacrone (12.4%), isocurcumenol (9.7%), beta-elemene (6.4%) and curzerene (6.2%). The results of semi-quantitative analysis indicated that levels of total sesquiterpene fraction (85.4%) were more than 55 times higher than those of monoterpene components (1.5%).

China↗

PubMed2006

The ties problem resulting from counting-based error estimators and its impact on gene selection algorithms.

MOTIVATION: Feature selection approaches, such as filter and wrapper, have been applied to address the gene selection problem in the literature of microarray data analysis. In wrapper methods, the classification error is usually used as the evaluation criterion of feature subsets. Due to the nature of high dimensionality and small sample size of microarray data, however, counting-based error estimation may not necessarily be an ideal criterion for gene selection problem. RESULTS: Our study reveals that evaluating genes in terms of counting-based error estimators such as resubstitution error, leave-one-out error, cross-validation error and bootstrap error may encounter severe ties problem, i.e. two or more gene subsets score equally, and this in turn results in uncertainty in gene selection. Our analysis finds that the ties problem is caused by the discrete nature of counting-based error estimators and could be avoided by using continuous evaluation criteria instead. Experiment results show that continuous evaluation criteria such as generalised the absolute value of w2 measure for support vector machines and modified Relief's measure for k-nearest neighbors produce improved gene selection compared with counting-based error estimators. AVAILABILITY: The companion website is at http://www.ntu.edu.sg/home5/pg02776030/wrappers/ The website contains (1) the source code of all the gene selection algorithms and (2) the complete set of tables and figures of experiments.

Algorithms↗