A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage

BACKGROUND: The allele frequencies of single-nucleotide polymorphisms (SNPs) are needed to select an optimal subset of common SNPs for use in association studies. Sequence-based methods for finding SNPs with allele frequencies may need to handle thousands of sequences from the same genome location (sequences of deep coverage). RESULTS: We describe a computational method for finding common SNPs with allele frequencies in single-pass sequences of deep coverage. The method enhances a widely used program named PolyBayes in several aspects. We present results from our method and PolyBayes on eighteen data sets of human expressed sequence tags (ESTs) with deep coverage. The results indicate that our method used almost all single-pass sequences in computation of the allele frequencies of SNPs. CONCLUSION: The new method is able to handle single-pass sequences of deep coverage efficiently. Our work shows that it is possible to analyze sequences of deep coverage by using pairwise alignments of the sequences with the finished genome sequence, instead of multiple sequence alignments

Permanence and periodicity of a delayed ratio-dependent predator–prey model with Holling type functional response and stage structure

AbstractA periodic and delayed ratio-dependent predator–prey system with Holling type III functional response and stage structure for both prey and predator is investigated. It is assumed that immature predator and mature individuals of each species are divided by a fixed age, and immature predator do not have the ability to attack prey. Sufficient conditions are derived for the permanence and existence of positive periodic solution of the model. Numerical simulations are presented to illustrate the feasibility of our main results

Modeling and Dynamic Characteristic Analysis of a Ball Screw Feed Drive System Based on Receptance Coupling

Modeling and modal analysis method based on receptance coupling are proposed for a vibration mode of a ball screw feed drive system, which cannot be determined by axial and torsional modal shape curves through a traditional method. In this study, the mathematical model for ball screw feed drive system is obtained by improved receptance coupling. The natural frequencies of different assembly states are calculated in the modeling process. The vibration modes of the feed drive system are determined by comparing the natural frequency distributions of different assembly states for a detailed analysis of the dynamic characteristics of the feed drive system. In the proposed method, a self-developed ball screw feed drive system is selected to study the influence of worktable position, worktable mass, and screw lead on the dynamic characteristics of the ball screw feed drive system. A change in the worktable position mainly affects the vibration of the ball screw itself. A change in the worktable mass mainly affects the coupling vibration between the ball screw and the rotor or bearing. The screw lead has an opposite influence on axial and torsional vibrations of the feed drive system, and the stability of the feed drive system improves with the screw lead. The validity of the proposed method is verified by the case study

Multi-Position Identification of Joint Parameters in Ball Screw Feed System Based on Response Coupling

Existing methods of parameters identification do not consider the torsion characteristics of a ball screw and the worktable position simultaneously. Therefore, this paper proposes a multi-position identification method based on receptance coupling. Firstly, the mathematical model of the feed drive system is established by the improved receptance coupling, and this model considers both axial and torsional vibration of the ball screw. Secondly, the identification equation is established by minimum error of the modal parameters of multiple worktable position, and differential evolution algorithm is used to calculate the stiffness and damping of the joint. Finally, the self-developed ball screw feed drive system is used for experimental study. The maximum error of the first four orders of natural frequencies predicted through multi-position identification results is 2.95%, and the multi-position method is more robust than the common method identification at one position. The experiment study showed that the proposed method is accuracy and necessity

Modeling Heavy Metal Uptake by Sludge Particulates in the Presense of Dissolved Organic Matter

The uptake of the seven heavy metal ions Cd(II), Co(II), Cr(III), Cu(II), Ni(II), Pb(II), and Zn(II) by sludge particulates in single-metal systems was investigated. Results showed that under acidic and neutral pH conditions, the uptake of all heavy metals by sludge particulates increases with the increase of pH. However, in the alkaline pH region, the uptake of Cu(II), Ni(II), and Co(II) decreases with the increase of pH, primarily due to the high dissolved organic matter (DOM) concentration in high pH conditions. Based on chemical reactions among heavy metal, sludge solids, and DOM, a mathematical model describing metal uptake as functions of DOM and pH was developed. the stability constants of metal-sludge and metal-DOM complexes can be determined using this model in conjunction with experimental metal uptake data. Results showed that, for the secondary sludge sample collected from Baltimore Back River Wastewater Treatment plant on March 1997, the stability constants of Cu(II)-sludge complex (log KS) and Cu(II)-DOM complex (log KL) are 5.3±0.2 and 4.7±0.3, respectively; for Ni(II), they are 4.0±0.2 and 3.9±0.2, respectively. Results also showed that under neutral and low pH conditions (pH\u3c8), the DOM effects on metal uptake for all heavy metals are insignificant. Therefore, the DOM term in the model can be ignored. Results showed that, for the secondary sludge sample collected from Baltimore Back River Wastewater Treatment plant on December 1996, the estimated log KS values of metal-sludge complexes for Cd(II), Co(II), Cr(III), Cu(II), Ni(II), Pb(II), and Zn(II) are, respectively, 3.6±0.2, 3.0±0.1, 5.5±0.1, 4.8±0.1, 3.1±0.1, 5.1±0.1, and 4.4±0.3

A homoharringtonine-based induction regimen for the treatment of elderly patients with acute myeloid leukemia: a single center experience from China

<p>Abstract</p> <p>Background and purpose</p> <p>The response to remission induction in elderly patients with acute myeloid leukemia (AML) remains poor. The purpose of this paper is to evaluate the efficacy and toxicity of a plant alkaloid, homoharringtonine, in combination with cytarabine as an induction therapy for AML in elderly patients (≥60 years).</p> <p>Results</p> <p>Twenty-three patients were treated with the HA regimen consisting of homoharringtonine (2 mg/m²/day for 7 days) and cytarabine (Ara-C, 100 mg/m²/day for 7 days). The overall response rate was 56.5% with complete remission (CR) rate of 39.1% and partial remission of 17.4%. There was no early death in this cohort of patients. The estimated median overall survival (OS) time of all patients was (12.0 ± 3.0) months. The estimated OS time of the CR patients was 15 months. The estimated one-year OS rate of all patients treated with HA protocol was (49.3 ± 13.5) %. The estimated one-year OS rate of the CR patients was (62.5 ± 17.1) %.</p> <p>Conclusion</p> <p>HA is a suitable induction regimen for elderly patients with AML, with relatively low toxicity and reasonable response rate.</p

PCAP: A Whole-Genome Assembly Program

We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple processors are used to perform most time-consuming computations in assembly. A more sensitive method is used to avoid missing overlaps caused by sequencing errors. Repetitive regions of reads are detected on the basis of many overlaps with other reads, instead of many shorter word matches with other reads. Contaminated end regions of reads are identified and removed. Generation of a consensus sequence for a contig is based on an alignment of reads in the contig, in which both base quality values and coverage information are used to determine every consensus base. The PCAP program was tested on a mouse whole-genome data set of 30 million reads and a human Chromosome 20 data set of 1.7 million reads. The program is freely available for academic use