Data pre-processing for more effective gene clustering

The high-throughput experimental data from the new gene microarray technology has spurred numerous efforts to find effective ways of processing microarray data for revealing real biological relationships among genes. This work proposes an innovative data pre-processing approach to identify noise data in the data sets and eliminate or reduce the impact of the noise data on gene clustering, With the proposed algorithm, the pre-processed data sets make the clustering results stable across clustering algorithms with different similarity metrics, the important information of genes and features is kept, and the clustering quality is improved. The primary evaluation on real microarray data sets has shown the effectiveness of the proposed algorithm.<br /

Content exploration for e-learning using XML Web services

Obtaining high quality content in an e-learning portal is critical to maximise the learning experience. For e-learning portals the content specialists are the publishers. Typically, publishers are nominated by portal administrators to make their content available to instructors. Instructors subsequently customise the portal by selecting content according to their requirements. The choice of content is limited to that provided by the publishers. This is a rigid system owing to the fact that instructors do not have access to an exhaustive range of content. We propose a system based on XML Web services which can be adopted by publishers in adherence with a number of emerging Web standards including SOAP and UDDI to disseminate their content. This system can be leveraged by portals to preview and subsequently acquire content which best suits the requirements as determined by instructors. <br /

Video-thoracoscopic enucleation of esophageal leiomyoma

<p>Abstract</p> <p>Background</p> <p>Leiomyoma is the most common benign tumor of the esophagus. Surgical enucleation is indicated in case of symptoms or an unclear diagnosis, and open thoracotomy has long been the standard approach for this procedure. However, enucleation through video assisted thoracoscopic surgery (VATS) has been developed as a preferred approach for most lesions in recent years.</p> <p>Method</p> <p>Herein we report our twelve patients (seven men and five women, with median age of 42 years) from 2001 to 2009, who underwent enucleation through VATS for esophageal leiomyomas, with a size from 1 to 8 cm in diameter (median: 5), and at different locations, from the thoracic outlet to near the diaphragmatic level of the thoracic esophagus. Intraoperative fiberoptic esophagoscopy was performed in two patients for localization by illumination. A right-sided approach was performed in eight cases (upper two thirds of esophagus) and the left-sided in another four cases (lower third of esophagus).</p> <p>Result</p> <p>The median operative time was 95 minutes (70 to 230 minutes). Four of them required small utility incisions (4-6 cm) for better exploration and manipulation. There were no major complications, such as death or empyema due to leaks from mucosal tears, and the presenting symptoms were improved during the follow-up period, from 12 to 98 months.</p> <p>Conclusion</p> <p>VATS can be considered as an initial approach for most patients with esophageal leiomyomas, even large in size, irregular in shape, or at unfavorable location. It is a safe, minimally invasive, and effective treatment. However, conversion to open thoracotomy should be required for the sake of clinical or technical concern.</p

Cloning and selection of reference genes for gene expression studies in Ananas comosus

Full length mRNA sequences of Ac-β-actin and Ac-gapdh, and partial mRNA sequences of Ac-18SrRNA and Ac-ubiquitin were cloned from pineapple in this study. The four genes were tested as housekeeping genes in three experimental sets. GeNorm and NormFinder analysis revealed that β-actin was the most appropriate reference gene for qPCR analysis of callus under induction conditions and in different tissue types, meanwhile, 18SrRNA was the most stable reference gene during organ development. Gapdh was the most unstable gene in all tested experimental sets. Transcript level analysis result of AcSERK1 in stressed callus normalized by β-actin and 18SrRNA further confirmed that reference genes selected in this study were suitable for transcript level analysis of pineapple. The expression pattern of AcSERK1 during somatic embryogenesis normalized by β-actin coincided with the cytological features of calluses during somatic embryogenesis. These results will enable more accurate and reliable normalization of qPCR results for transcription analysis in pineapple. Keywords: Reference genes, qPCR, pineapple, geNorm, NormFinder African Journal of Biotechnology Vol. 11(29), pp. 7424-7433, 10 April, 201

Effective-stress finite element analysis of spudcan penetration with lattice leg in clay

10.1063/1.4826009AIP Conference Proceedings15582337-234

Clinicopathologic Evaluation of Prognostic Factors for Squamous Cell Carcinoma of the Buccal Mucosa

BackgroundThe purpose of this research was to evaluate the prognostic significance of clinicopathologic variables on the survival rate for squamous cell carcinoma of the buccal mucosa (BMSCC). We analyzed the outcomes of surgical therapy for this aggressive cancer and compared these results with those in the literature.MethodsWe reviewed the medical charts of 172 patients treated in our institution between 1990 and 2005. There were 22 patients excluded from our studies: 20 patients with advanced tumors who received no treatment or palliative treatment, and 2 patients who had received preoperative radiotherapy (RT). The remaining 150 patients were treated with surgeries and among them, 56 patients had undergone postoperative RT. The influence of clinicopathologic factors on the survival rate was analyzed with the Kaplan-Meier method and log-rank test. Multivariate analysis was assessed with Cox's regression model.ResultsThere were 148 males and 2 females, with a mean age of 53.5 years. The prevalence rate of habitual betel quid chewing documented in charts among 113 patients was 75%. The 5-year overall survival rate and disease-specific survival rate for all patients were 64% and 69%, respectively. For patients with stages I, II, III, and IV disease, the 5-year disease-specific survival rates were 90%, 77%, 52%, and 47%, respectively (p< 0.001). According to the multivariate analysis, the pathologic staging and histologic grading of the tumor were independently the important prognostic factors affecting survival rate. There were 80 patients who developed locoregional recurrence in lymph nodes in the follow-up diagnoses. Distant metastases occurred in 14 patients, with 11 of them also having locoregional recurrence. The distant metastases were found in the lungs (8/14), T-spine (3/14), liver (2/14) and brain (1/14).ConclusionPathologic stage and histologic grade are the most important prognostic factors

Validation of bidimensional measurement in nasopharyngeal carcinoma

<p>Abstract</p> <p>Background</p> <p>Our previous study showed a close relationship between computed tomography (CT)-derived bidimensional measurement of primary tumor and retropharyngeal nodes (BDMprn) and gross tumor volume of primary tumor and retropharyngeal nodes (GTVprn) in nasopharyngeal carcinoma (NPC) and better prognosis for NPC patients with smaller BDMprn. In this study, we report the results on of a study to validate the use of BDM in a separate cohort of NPC patients.</p> <p>Methods</p> <p>We retrospectively reviewed 103 newly diagnosed NPC cases who were treated with radiotherapy/concurrent chemoradiotherapy (CCRT) or CCRT with adjuvant chemotherapy from 2002 to 2009. We used magnetic resonance imaging (MRI) to measure BDMprn. We calculated overall survival, recurrence-free and distant metastasis-free survival curves and set a BDMprn cut off point to categorize patients into a high- or low-risk group. We then used Cox proportional hazard model to evaluate the prognostic influence of BDMprn after correcting age, gender and chemotherapy status.</p> <p>Results</p> <p>After adjusting for age, gender, and chemotherapy status, BDMprn remained an independent prognostic factor for distant metastasis [Hazard ratio (HR) = 1.046; <it>P </it>= 0.042] and overall survival (HR = 1.012; <it>P </it>= 0.012). Patients with BDMprn < 15 cm²had a greater 3-year overall survival rate than those with BDMprn ≧ 15 cm²(92.3% vs. 73.7%; <it>P </it>= 0.009). They also had a greater 3-year distant metastasis-free survival (94% vs.75%; <it>P </it>= 0.034).</p> <p>Conclusion</p> <p>The predictive ability of BDMprn was validated in a separate NPC cohort. A BDMprn of 15 cm²can be used to separate NPC patients into high- and low-risk groups and predict survival rates and metastasis potential. It can, therefore, be used as a reference to design clinical trials, predict prognosis, and make treatment decisions.</p

Identification and characterization of a novel subtype of Tula virus in Microtus arvalis obscurus voles sampled from Xinjiang, China

Although most of Arvicolinae associated hantaviruses can not cause disease in humans, hemorrhagic fever with renal syndrome (HFRS) cases caused by Tula virus (TULV) have been described in Europe since 2002. In addition to Europe, TULV was also identified in the Microtus arvalis obscurus voles sampled from Kazakhstan, which shares borders with China. To gain more insight into the molecular epidemiology of TULV, a total of 365 rodents representing 7 species of 4 subfamily (Arvicolinae, Murinae, Gerbillinae, and Cricetinae) were captured in Qapqal county, Xinjiang, northwest China. Hantavirus RNA was recovered from 40 lung tissue samples of M. arvalis obscurus, with the prevalence of 10.96%. Genetic analysis revealed that all recovered viral sequences were most closely related to those of TULV, but exhibited >11% nucleotide differences from all currently known TULV, suggesting that they may represent a new subtype of TULV. In the S tree, the newly identified viruses formed a distinct lineage and showed a close evolutionary relationship with those sampled from Southwestern Siberia and Kazakhstan. However, they exhibited a different clustering pattern in both the M and the L trees, suggesting the possibility of genetic reassortment. Finally, the recombination event was also observed in Xinjiang TULV viruses. In sum, all these data reveal a complex evolutionary history of TULV in Central Asia.Peer reviewe

Topographic Study of Extracted Molars with Advanced Furcation Involvement: Furcation Entrance Dimension and Molar Type

This study investigated the topography of the furcation entrance dimension (FED) on molars with advanced furcation involvement (FI). The sample pool consisted of 169 maxillary and mandibular molars from a group of 165 individuals with severely advanced periodontal destruction. The subjects included men and women aged 24 to 84 years (mean, 47.8 ± 7.2 years). The FEDs of the maxillary buccal, mesial, and distal surfaces as well as the mandibular buccal and lingual surfaces were measured under a stereomicroscope and clarified into grades I (FED < 0.55 mm), II (0.55-0.75 mm), and III (> 0.75 mm) using automatic grading system software designed by our research associates. The differences and relationships among molar location, furcation site, and FED grade were analyzed using the chi-square test. There was a significant difference among buccal (BFED), mesial (MFED), and distal (DFED) FEDs in both the maxillary first (χ24 = 58.915, p < 0.001) and second (χ24 = 66.839, p < 0.001) molars. The relationship between molar type and FED grade was statistically significant for both the BFED (p < 0.001) and the DFED (p < 0.001) of maxillary molars, as well as for both the BFED (p < 0.0001) and LFED (p < 0.0001). The difference in FED grade between the first and second molars was statistically significant in both maxillary (p < 0.001) and mandibular (p < 0.0001) molars. There was a significant relationship between FED grade and tooth location at molars with advanced FI

Neurotization of free gracilis transfer with the brachialis branch of the musculocutaneous nerve to restore finger and thumb flexion in lower trunk brachial plexus injury: an anatomical study and case report

OBJECTIVE: To investigate the feasibility of using free gracilis muscle transfer along with the brachialis muscle branch of the musculocutaneous nerve to restore finger and thumb flexion in lower trunk brachial plexus injury according to an anatomical study and a case report. METHODS: Thirty formalin-fixed upper extremities from 15 adult cadavers were used in this study. The distance from the point at which the brachialis muscle branch of the musculocutaneous nerve originates to the midpoint of the humeral condylar was measured, as well as the length, diameter, course and branch type of the brachialis muscle branch of the musculocutaneous nerve. An 18-year-old male who sustained an injury to the left brachial plexus underwent free gracilis transfer using the brachialis muscle branch of the musculocutaneous nerve as the donor nerve to restore finger and thumb flexion. Elbow flexion power and hand grip strength were recorded according to British Medical Research Council standards. Postoperative measures of the total active motion of the fingers were obtained monthly. RESULTS: The mean length and diameter of the brachialis muscle branch of the musculocutaneous nerve were 52.66±6.45 and 1.39±0.09 mm, respectively, and three branching types were observed. For the patient, the first gracilis contraction occurred during the 4th month. A noticeable improvement was observed in digit flexion one year later; the muscle power was M4, and the total active motion of the fingers was 209°. CONCLUSIONS: Repairing injury to the lower trunk of the brachial plexus by transferring the brachialis muscle branch of the musculocutaneous nerve to the anterior branch of the obturator nerve using a tension-free direct suture is technically feasible, and the clinical outcome was satisfactory in a single surgical patient