Extracting transcription factor binding sites from unaligned gene sequences with statistical models

<p>Abstract</p> <p>Background</p> <p>Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA interaction loci within 1–2 kb resolution. To find out the exact binding motifs, it is necessary to build a computational method to examine the ChIP-chip array binding sequences and search for possible motifs representing the transcription factor binding sites.</p> <p>Results</p> <p>We developed a program to find out accurate motif sites from a set of unaligned DNA sequences in the yeast genome. Compared with MDscan, the prediction results suggest that, overall, our algorithm outperforms MDscan since the predicted motifs are more consistent with previously known specificities reported in the literature and have better prediction ranks. Our program also outperforms the constraint-less Cosmo program, especially in the elimination of false positives.</p> <p>Conclusion</p> <p>In this study, an improved sampling algorithm is proposed to incorporate the binomial probability model to build significant initial candidate motif sets. By investigating the statistical dependence between base positions in TFBSs, the method of dependency graphs and their expanded Bayesian networks is combined. The results show that our program satisfactorily extract transcription factor binding sites from unaligned gene sequences.</p

Web-based computer adaptive assessment of individual perceptions of job satisfaction for hospital workplace employees

<p>Abstract</p> <p>Background</p> <p>To develop a web-based computer adaptive testing (CAT) application for efficiently collecting data regarding workers' perceptions of job satisfaction, we examined whether a 37-item Job Content Questionnaire (JCQ-37) could evaluate the job satisfaction of individual employees as a single construct.</p> <p>Methods</p> <p>The JCQ-37 makes data collection via CAT on the internet easy, viable and fast. A Rasch rating scale model was applied to analyze data from 300 randomly selected hospital employees who participated in job-satisfaction surveys in 2008 and 2009 via non-adaptive and computer-adaptive testing, respectively.</p> <p>Results</p> <p>Of the 37 items on the questionnaire, 24 items fit the model fairly well. Person-separation reliability for the 2008 surveys was 0.88. Measures from both years and item-8 job satisfaction for groups were successfully evaluated through item-by-item analyses by using <it>t</it>-test. Workers aged 26 - 35 felt that job satisfaction was significantly worse in 2009 than in 2008.</p> <p>Conclusions</p> <p>A Web-CAT developed in the present paper was shown to be more efficient than traditional computer-based or pen-and-paper assessments at collecting data regarding workers' perceptions of job content.</p

Orthogonal Constant-Amplitude Sequence Families for System Parameter Identification in Spectrally Compact OFDM

In rectangularly-pulsed orthogonal frequency division multiplexing (OFDM) systems, constant-amplitude (CA) sequences are desirable to construct preamble/pilot waveforms to facilitate system parameter identification (SPI). Orthogonal CA sequences are generally preferred in various SPI applications like random-access channel identification. However, the number of conventional orthogonal CA sequences (e.g., Zadoff-Chu sequences) that can be adopted in cellular communication without causing sequence identification ambiguity is insufficient. Such insufficiency causes heavy performance degradation for SPI requiring a large number of identification sequences. Moreover, rectangularly-pulsed OFDM preamble/pilot waveforms carrying conventional CA sequences suffer from large power spectral sidelobes and thus exhibit low spectral compactness. This paper is thus motivated to develop several order-I CA sequence families which contain more orthogonal CA sequences while endowing the corresponding OFDM preamble/pilot waveforms with fast-decaying spectral sidelobes. Since more orthogonal sequences are provided, the developed order-I CA sequence families can enhance the performance characteristics in SPI requiring a large number of identification sequences over multipath channels exhibiting short-delay channel profiles, while composing spectrally compact OFDM preamble/pilot waveforms.Comment: 15 pages, 4 figure

Multi-domain vertical alignment liquid crystal displays with improved angular dependent gamma curves.

Methods, systems and apparatus for a liquid crystal display panel having a first substrate with a color filter, an over-coating and a common electrode. The second substrate includes an insulating layer surface facing the first substrate, a pixel electrode, a plurality of common and pixel domain guides formed on the common and the pixel electrodes, a plurality of electric shields on one of the common or pixel electrodes and a liquid crystal layer vertically aligned between the first and second substrates. The panel also includes a drive circuit for applying a voltage to generate an electric field to control liquid crystal molecule orientation corresponding to the plurality of domain guides and electric shields to form a multi-domain liquid crystal display panel device. The plural domain guides are either protrusions or slits formed in the common electrode and the pixel electrode to form the multi-domain vertical alignment liquid crystal device

The association of dimethylarginine dimethylaminohydrolase 1 gene polymorphism with type 2 diabetes: a cohort study

<p>Abstract</p> <p>Background</p> <p>Elevated plasma levels of asymmetric dimethylarginine (ADMA) has been reported to be associated with insulin resistance and micro/macrovascular diabetic complications, and may predict cardiovascular events in type 2 diabetic patients. Dimethylarginine dimethylaminohydrolase 1 (DDAH1) is the major enzyme eliminating ADMA in humans, but the effect of genetic variations in <it>DDAH1 </it>on type 2 diabetes and its long-term outcome are unknown.</p> <p>Methods</p> <p>From July 2006 to June 2009, we assessed the association between polymorphisms in <it>DDAH1 </it>and type 2 diabetes in 814 consecutive unrelated subjects, including 309 type 2 diabetic patients and 505 non-diabetic individuals. Six single nucleotide polymorphisms (SNPs) in <it>DDAH1</it>, rs233112, rs1498373, rs1498374, rs587843, rs1403956, and rs1241321 were analyzed. Plasma ADMA levels were determined by high performance liquid chromatography. Insulin sensitivity was assessed by the homeostasis model assessment of insulin resistance (HOMA-IR).</p> <p>Results</p> <p>Among the 6 SNPs, only rs1241321 was significantly associated with a decreased risk of type 2 diabetes (AA <it>vs </it>GG+AG, OR = 0.64, 95% CI 0.47-0.86, p = 0.004). The association remained unchanged after adjustment for plasma ADMA level. The fasting plasma glucose and log HOMA-IR tended to be lower in subjects carrying the homozygous AA genotype of rs1241321 compared with the GG+AG genotypes. Over a median follow-up period of 28.2 months, there were 44 all-cause mortality and 50 major adverse cardiovascular events (MACE, including cardiovascular death, non-fatal myocardial infarction and stroke). Compared with the GG and AG genotypes, the AA genotype of rs1241321 was associated with reduced risk of MACE (HR = 0.31, 95% CI: 0.11-0.90, p = 0.03) and all-cause mortality (HR = 0.18, 95% CI: 0.04-0.80, p = 0.02) only in subgroup with type 2 diabetes. One common haplotype (GGCAGC) was found to be significantly associated with a decreased risk of type 2 diabetes (OR = 0.67, 95% CI = 0.46-0.98, p = 0.04).</p> <p>Conclusions</p> <p>Our results provide the first evidence that SNP rs1241321 in <it>DDAH1 </it>is associated with type 2 diabetes and its long-term outcome.</p

A probabilistic evaluation of pier-scour potential in the Gaoping River Basin of Taiwan

A probabilistic approach is used to create a preliminary inspection evaluation form (PIEF) for scour potential at bridge sites. In Taiwan, the risk of pier scour is often evaluated using a two-step procedure. First, a bridge is visually inspected based on a PIEF. An advanced scour risk analysis is conducted for a bridge with a high PIEF score. Because a PIEF can quickly evaluate scour potential, it can be used to build a maintenance sequence for a group of bridges. However, a PIEF is often created based on only engineers’ experience; the accuracy and reliability of PIEFs have not been examined systematically. Thus, a probabilistic-based PIEF is constructed by establishing a close correlation between the PIEF score and scour potential via Taguchi method. The scour potential is evaluated by Bayesian network (BN) that incorporates experts’ judgments and results of reliability analyses. For example, the conditional probabilities (CP) in the proposed BN are calculated based on an existing PIEF and results of a stability-based reliability analysis. Thus, the proposed PIEF implicitly considers the probabilistic characteristics in the scour potential, which will provide an efficient and accurate evaluation of scour potential and assist in establishing maintenance priorities of existing bridges in Taiwan