Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool

Pipelines of pooled library screen analysis. Table S1. Public library sets of shRNA, sgRNA and deletion mutant strains. Figure S2. A list of wrong barcodes from 1,230 shRNAs of TRC library. Table S2. Sequences of 25 barcodes with abnormally increased mapping counts by imperfect matching. Table S3. A list of the used options for each tool. Table S4. Comparison of mapping results and speed by three tools. (PDF 7691 kb

Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells

Spermatogonial stem cells (SSCs) are germline stem cells located along the basement membrane of seminiferous tubules in testes. Recently, SSCs were shown to be reprogrammed into multipotent SSCs (mSSCs). However, both the key factors and biological networks underlying this reprogramming remain elusive. Here, we present transcriptional regulatory networks (TRNs) that control cellular processes related to the SSC-to-mSSC reprogramming. Previously, we established intermediate SSCs (iSSCs) undergoing the transition to mSSCs and generated gene expression profiles of SSCs, iSSCs and mSSCs. By comparing these profiles, we identified 2643 genes that were up-regulated during the reprogramming process and 15 key transcription factors (TFs) that regulate these genes. Using the TF-target relationships, we developed TRNs describing how these TFs regulate three pluripotency-related processes (cell proliferation, stem cell maintenance and epigenetic regulation) during the reprogramming. The TRNs showed that 4 of the 15 TFs (Oct4/Pou5f1, Cux1, Zfp143 and E2f4) regulated cell proliferation during the early stages of reprogramming, whereas 11 TFs (Oct4/Pou5f1, Foxm1, Cux1, Zfp143, Trp53, E2f4, Esrrb, Nfyb, Nanog, Sox2 and Klf4) regulated the three pluripotency-related processes during the late stages of reprogramming. Our TRNs provide a model for the temporally coordinated transcriptional regulation of pluripotency-related processes during the SSC-to-mSSC reprogramming, which can be further tested in detailed functional studies.111Ysciescopuskc

Nb-doped TiO2 air-electrode for advanced Li-air batteries

As new substrate materials to replace a conventional carbon substrate, TiO2 and Nb-doped TiO2 air-electrodes for Li-air batteries were investigated. Through a simple two-step process, we successfully synthesized anatase Nb-doped TiO2 nanoparticles and demonstrated the potential applicability of TiO2-based materials for use in Li-air battery electrode. An air-electrode with Nb-doped TiO2 nanoparticles could deliver a higher discharge capacity than a bare TiO2 electrode due to the enhanced conductivity, which implies the importance of facile electron transport during the discharge process. © 2014 The Ceramic Society of Japan and the Korean Ceramic Society.

Leadership Succession Planning: An Examination of Sole Proprietor Estate Surveying and Valuation Firms in Lagos Metropolis, Nigeria

This paper reports the results from a survey of 38 small sole- proprietor estate surveying and valuation firms in Lagos, Nigeria. A 45% questionnaire retrieval rate was achieved while CEOs/owners of estate surveying and valuation firms were interviewed. Descriptive statistics were used to analyze the respondents‟ general characteristics as well as their attitude toward business succession planning. The study found that sole-proprietor firm owners desired that their firms outlive them through transferring of the firms‟ businesses to their next generation. However, majority of these sole proprietors‟ next generation were not keen on pursuing real estate business related courses in their undergraduate days in view of their exposure to modern technology and the influence of peers. Also, the study found that the owners of these firms have not, as a matter of policy, planned for their succession because of the cultural and attitudinal beliefs and values, which forbid thoughts about death or incapacitation about a living soul. As a result, the study indicated that only 5% of sole proprietor estate surveying and valuation firms in this category have continued to the second generation in the study area. This outcome has serious implications for small professional service businesses‟ economic and job creation potential for Nigeria

Elevated Neutrophil to Lymphocyte Ratio Predicts Poor Prognosis in Non-muscle Invasive Bladder Cancer Patients: Initial Intravesical Bacillus Calmette-Guerin Treatment After Transurethral Resection of Bladder Tumor Setting

The objective of this study was to investigate pretreatment systemic inflammatory response (SIR) markers in patients who underwent initial intravesical treatment for high-risk non-muscle invasive bladder cancer (NMIBC). A total of 385 patients who underwent initial intravesical Bacillus Calmette-Guerin treatment after transurethral resection of bladder tumor (TURB) were included. We analyzed the relationship between oncological outcomes and ratios of SIR markers, including neutrophil-to-lymphocyte ratio (NLR), derived neutrophil-to-lymphocyte ratio (dNLR), and platelet-to-lymphocyte ratio (PLR). Each SIR marker was used for analysis. Their cut-off values were determined through receiver operation characteristics curves analysis. Patients were divided into two groups according to pretreatment NLR (<1.5 vs. ≥1.5), dNLR (<1.2 vs. ≥1.2), and PLR values (171< vs. ≥171). Patients with NLR ≥ 1.5 and dNLR ≥ 1.2 were associated with poor prognosis in terms of overall survival and cause-specific survival. However, no serum SIR marker was associated with prognosis in recurrence-free survival or progression-free survival. Cox multivariate analysis revealed that age, NLR, dNLR, hemoglobin, and pathologic T stage were significant factors predicting overall survival. Age, NLR, and pathologic T stage were significant factors predicting cancer-specific survival, NLR and tumor number were the most important predictors of bladder preserving survival. NLR before treatment was correlated with both oncological outcomes and survival outcome in NMIBC patients undergoing initial intravesical BCG treatment after TURB. Increased NLR reflects a poor prognosis of these outcomes

Diagnostic Value of Galectin-3, HBME-1, Cytokeratin 19, High Molecular Weight Cytokeratin, Cyclin D1 and p27kip1 in the Differential Diagnosis of Thyroid Nodules

The distinction between benign and malignant thyroid tumors is critical for the management of patients with thyroid nodules. We applied immunohistochemical staining for galectin-3, HBME-1, cytokeratin 19 (CK19), high molecular weight cytokeratin (HMWCK), cyclin D1 and p27kip1 in 295 thyroid lesions to determine their diagnostic accuracy. The expression of all markers was significantly associated with differentiated thyroid carcinoma (DTC).The sensitivity for the diagnosis of DTC was 94.7% with galectin-3, 91.3% with HBME-1, and 90.3% with CK19. The specificities of these markers were 95.5%, 69.7%, and 83.1%, respectively. Combining these markers, co-expression of galectin-3 and CK19 or galectin-3 and HBME-1 was seen in 93.2% of carcinomas but in none of the benign nodules. Comparing follicular variant of papillary carcinoma (FVPC) with follicular carcinoma (FC), the expression of galectin-3, CK19, and HMWCK was significantly higher in FVPC. When comparing FC with FA, the expression of galectin-3 and HBME-1 was significantly higher in FC. These results suggest that 1) galectin-3 is a useful marker in the distinction between benign and malignant thyroid tumors, 2) the combined use of HBME-1 and CK19 can increase the diagnostic accuracy, and 3) the use of CK19 and HMWCK can aid in the differential diagnosis between PC and FC

Stochastic Particle Flow for Nonlinear High-Dimensional Filtering Problems

A series of novel filters for probabilistic inference that propose an alternative way of performing Bayesian updates, called particle flow filters, have been attracting recent interest. These filters provide approximate solutions to nonlinear filtering problems. They do so by defining a continuum of densities between the prior probability density and the posterior, i.e. the filtering density. Building on these methods' successes, we propose a novel filter. The new filter aims to address the shortcomings of sequential Monte Carlo methods when applied to important nonlinear high-dimensional filtering problems. The novel filter uses equally weighted samples, each of which is associated with a local solution of the Fokker-Planck equation. This hybrid of Monte Carlo and local parametric approximation gives rise to a global approximation of the filtering density of interest. We show that, when compared with state-of-the-art methods, the Gaussian-mixture implementation of the new filtering technique, which we call Stochastic Particle Flow, has utility in the context of benchmark nonlinear high-dimensional filtering problems. In addition, we extend the original particle flow filters for tackling multi-target multi-sensor tracking problems to enable a comparison with the new filter

Endovascular and Clinical Outcomes of Vertebrobasilar Intracranial Atherosclerosis-Related Large Vessel Occlusion

Background and Purpose: Endovascular treatment (EVT) for acute vertebrobasilar intracranial atherosclerosis-related large vessel occlusion (ICAS-LVO) and its outcomes are not well known. We aimed to evaluate endovascular and clinical outcomes of vertebrobasilar ICAS-LVO patients who underwent EVT.Methods: Consecutive acute stroke patients who underwent EVT for vertebrobasilar LVO were retrospectively reviewed. Patients were assigned to the ICAS (+) or the ICAS (–) group based on angiographical findings. Procedural details and clinical outcomes were compared between the ICAS (+) and ICAS (–) groups.Results: This study included 77 patients with acute vertebrobasilar LVO who underwent EVT. Among the study subjects, 24 (31.2%) had an ICAS-LVO. Recanalization was achieved in 19 patients in the ICAS (+) group (79.2%), which was comparable with the ICAS (–) group (84.9%; p = 0.529). However, recanalization using conventional endovascular modalities (stent retriever thrombectomy, contact aspiration thrombectomy, or intra-arterial urokinase infusion) was less successful in the ICAS (+) group (36.8%) than the ICAS (–) group (100.0%; p < 0.001). All the remaining patients in the ICAS (+) group required specific rescue treatments appropriate for ICAS, including balloon angioplasty, stenting, or intra-arterial glycoprotein IIb/IIIa inhibitor infusion to obtain a successful recanalization. Procedural time was not significantly longer in the ICAS (+) group. The rates of favorable outcomes (37.5% vs. 41.5%; p = 0.740), death, and symptomatic intracerebral hemorrhage were not significantly different between the groups.Conclusion: ICAS-LVO was common in patients who underwent EVT for acute vertebrobasilar LVO. Although conventional modalities were often ineffective for vertebrobasilar ICAS-LVO, a comparable recanalization rate could be obtained with ICAS-specific modalities. Recanalization rate and procedural time were comparable, and clinical outcomes did not differ between patients with or without ICAS-LVO