PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data

BACKGROUND: We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments raised a new set of bioinformatics challenges, including how to extract PETs from raw sequence reads, and correctly yet efficiently map PETs to reference genome sequences. To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable. RESULTS: We designed an integrated computation program package, PET-Tool, to automatically process PET sequences and map them to the genome sequences. The Tool was implemented as a web-based application composed of four modules: the Extractor module for PET extraction; the Examiner module for analytic evaluation of PET sequence quality; the Mapper module for locating PET sequences in the genome sequences; and the ProjectManager module for data organization. The performance of PET-Tool was evaluated through the analyses of 2.7 million PET sequences. It was demonstrated that PET-Tool is accurate and efficient in extracting PET sequences and removing artifacts from large volume dataset. Using optimized mapping criteria, over 70% of quality PET sequences were mapped specifically to the genome sequences. With a 2.4 GHz LINUX machine, it takes approximately six hours to process one million PETs from extraction to mapping. CONCLUSION: The speed, accuracy, and comprehensiveness have proved that PET-Tool is an important and useful component in PET experiments, and can be extended to accommodate other related analyses of paired-end sequences. The Tool also provides user-friendly functions for data quality check and system for multi-layer data management

High negative predictive value of 68Ga PSMA PET-CT for local lymph node metastases in high risk primary prostate cancer with histopathological correlation

Background: Current guidelines highlight the importance of accurate staging in the management and prognostication of high risk primary prostate cancer. Conventional radiologic imaging techniques are insufficient to reliably detect lymph node metastases in prostate cancer. Despite promising results, there is limited published data on the diagnostic accuracy of PSMA PET-CT to assess local nodal metastases prior to radical prostatectomy. This study aims to assess the diagnostic efficacy of 68Ga PSMA PET-CT in local lymph node staging of high risk primary prostate cancer when compared to histopathological findings following radical prostatectomy with pelvic lymph node dissection. Methods: We retrospectively analysed consecutive patients with high risk primary prostate cancer referred by urologists for primary staging PSMA PET-CT using a 68Ga-labeled PSMA ligand, Glu-NH-CO-NHLys-(Ahx)-[HBEDDCC], from October 2015 to October 2017. The scans of patients who underwent radical prostatectomy with pelvic lymph node dissection were interpreted by the consensus reading of two experienced nuclear medicine physicians blinded to clinical and histopathological data. The contemporaneous records of the referring urologists were retrospectively reviewed for noteworthy unexpected PET findings that altered their personal preference for surgical management. Results: Seventy-one patients were recruited and analysed. PSMA PET-CT showed findings compatible with local disease in 47 patients (66.2%), lymph node metastases in 10 patients (14.1%) and distant metastases in 14 patients (19.7%). Twenty-eight patients (twenty-seven of whom had local disease only) underwent surgery yielding 214 lymph nodes, all of which were negative on histopathological analysis. On a node-based analysis, 213 of 214 lymph nodes were accurately identified as negative for disease with a negative predictive value of 100%. 11 patients had unexpected PET findings contemporaneously documented by urologists to alter their preference for surgical management. Conclusions: PSMA PET-CT appears to have a high negative predictive value for local lymph node metastases in high risk primary prostate cancer when compared to histopathological findings following radical prostatectomy with pelvic lymph node dissection

Global Trends and Gaps in Research Related to Latent Tuberculosis Infection

Background There is a global commitment to eliminating tuberculosis (TB). It is critical to detect and treat cases of latent TB infection (LTBI), the reservoir of new TB cases. Our study assesses trends in publication of LTBI-related research. Methods We used the keywords (“latent tuberculosis” OR “LTBI” OR “latent TB”) to search the Web of Science for LTBI-related articles published 1995–2018, then classified the results into three research areas: laboratory sciences, clinical research, and public health. We calculated the proportions of LTBI-related articles in each area to three areas combined, the average rates of LTBI-related to all scientific and TB-related articles, and the average annual percent changes (AAPC) in rates for all countries and for the top 13 countries individually and combined publishing LTBI research. Results The proportion of LTBI-related articles increased over time in all research areas, with the highest AAPC in laboratory (38.2%/yr), followed by public health (22.9%/yr) and clinical (15.1%/yr). South Africa (rate ratio [RR] = 8.28, 95% CI 5.68 to 12.08) and India (RR = 2.53, 95% CI 1.74 to 3.69) had higher RRs of overall TB-related articles to all articles, but did not outperform the average of the top 13 countries in the RRs of LTBI-related articles to TB-related articles. Italy (RR = 1.95, 95% CI 1.45 to 2.63), Canada (RR = 1.73, 95% CI 1.28 to 2.34), and Spain (RR = 1.53, 95% CI 1.13 to 2.07) had higher RRs of LTBI-related articles to TB-related articles. Conclusions High TB burden countries (TB incidence \u3e 100 per 100,000 population) published more overall TB-related research, whereas low TB burden countries showed greater focus on LTBI. Given the potential benefits, high TB burden countries should consider increasing their emphasis on LTBI-related research

Photoinduced charge separation in donor-acceptor spiro compounds at metal and metal oxide surfaces: Application in dye-sensitized solar cell

Modulated charge separation has been investigated by surface photovoltage spectroscopy in the fixed capacitor arrangement for four different fluorene compounds adsorbed from highly diluted solutions at ultra-thin nanoporous TiO 2 (np-TiO 2), Au and ITO surfaces. Donor (-N(C 6H 5) 2) and acceptor moieties (-CN, -COOH) were linked by fluorene or spirobisfluorene cores and the chain length has been changed by introducing thiophene. Modulated charge separation by electron injection and intramolecular transport has been separated and directed adsorption of spiro compounds at Au surfaces has been demonstrated. Striking differences between the interaction of linking -CN and -COOH groups and the different substrates were observed. The capability as TiO 2 spectral sensitizer of spirobisfluorene donor-acceptor molecules with extended conjugation has been demonstrated. Solar cells exhibit 5.6% energy conversion efficiency, confirming that spiro-configured geometry is a promising route to the design of metal free dyes. © 2012 The Royal Society of Chemistry.Fil: Macor, Lorena Paola. Universidad Nacional de Río Cuarto; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados; ArgentinaFil: Gervaldo, Miguel Andres. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados; Argentina. Universidad Nacional de Río Cuarto; ArgentinaFil: Fungo, Fernando Gabriel. Universidad Nacional de Río Cuarto; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados; ArgentinaFil: Otero, Luis Albert. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados; Argentina. Universidad Nacional de Río Cuarto; ArgentinaFil: Dittrich, Thomas. Helmholtz Center Berlin for Materials and Energy, Institute of Heterogeneous Materials; AlemaniaFil: Lin, Chih-Yen. National Taiwan University; República de ChinaFil: Chi, Liang-Chen. National Taiwan University; República de ChinaFil: Fang, Fu-Chuan. National Taiwan University; República de ChinaFil: Lii, Shu-Woei. National Taiwan University; República de ChinaFil: Wong, Ken-Tsung. National Taiwan University; República de ChinaFil: Tsai, Chih-Hung. National Taiwan University; República de ChinaFil: Wu, Chung-Chih. National Taiwan University; República de Chin

In vitro test of external Qigong

BACKGROUND: Practitioners of the alternative medical practice 'external Qigong' generally claim the ability to emit or direct "healing energy" to treat patients. We investigated the ability of experienced Qigong practitioners to enhance the healthy growth of cultured human cells in a series of studies, each following a rigorously designed protocol with randomization, blinding and controls for variability. METHODS: Qigong practitioners directed healing intentionality toward normal brain cell cultures in a basic science laboratory. Qigong treatments were delivered for 20 minutes from a minimum distance of 10 centimeters. Cell proliferation was measured by a standard colony-forming efficiency (CFE) assay and a CFE ratio (CFE for treated samples/CFE for sham samples) was the dependent measure for each experiment. RESULTS: During a pilot study (8 experiments), a trend of increased cell proliferation in Qigong-treated samples (CFE Qigong/sham ratios > 1.0) was observed (P = 0.162). In a formal study (28 experiments), a similar trend was observed, with Qigong-treated samples showing on average more colony formation than sham samples (P = 0.036). In a replication study (60 experiments), no significant difference between Qigong-treated samples and sham samples was observed (P = 0.465). CONCLUSION: We observed an apparent increase in the proliferation of cultured cells following external Qigong treatment by practitioners under strictly controlled conditions, but we did not observe this effect in a replication study. These results suggest the need for more controlled and thorough investigation of external Qigong before scientific validation is claimed

Oviposition Site Selection by the Dengue Vector Aedes aegypti and Its Implications for Dengue Control

Controlling the mosquito Aedes aegypti is of public health importance because, at present, it is the only means to stop dengue virus transmission. Implementing successful mosquito control programs requires understanding what factors regulate population abundance, as well as anticipating how mosquitoes may adapt to control measures. In some species of mosquitoes, females choose egg-laying sites to improve the survival and growth of their offspring, a behavior that ultimately influences population distribution and abundance. In the current study, we tested whether Ae. aegypti actively choose the containers in which they lay their eggs and determined what cues are most relevant to that process. We also explored whether females select containers that provide the most food for their larval progeny. Surprisingly, egg-laying females were most attracted to sites containing other immature Ae. aegypti, rather than to sites containing the most food. We propose that this behavior may contribute to density-dependent competition for food among larvae and play a larger role than previously thought in regulating Ae. aegypti populations. We recommend that accounting for, and even taking advantage of, this natural behavior will lead to more effective strategies for dengue prevention

Focal dose escalation using FDG-PET-guided intensity-modulated radiation therapy boost for postoperative local recurrent rectal cancer: a planning study with comparison of DVH and NTCP

<p>Abstract</p> <p>Background</p> <p>To evaluate the safety of focal dose escalation to regions with standardized uptake value (SUV) >2.0 using intensity-modulated radiation therapy (IMRT) by comparison of radiotherapy plans using dose-volume histograms (DVHs) and normal tissue complication probability (NTCP) for postoperative local recurrent rectal cancer</p> <p>Methods</p> <p>First, we performed conventional radiotherapy with 40 Gy/20 fr. (CRT 40 Gy) for 12 patients with postoperative local recurrent rectal cancer, and then we performed FDG-PET/CT radiotherapy planning for those patients. We defined the regions with SUV > 2.0 as biological target volume (BTV) and made three boost plans for each patient: 1) CRT boost plan, 2) IMRT without dose-painting boost plan, and 3) IMRT with dose-painting boost plan. The total boost dose was 20 Gy. In IMRT with dose-painting boost plan, we increased the dose for BTV+5 mm by 30% of the prescribed dose. We added CRT boost plan to CRT 40 Gy (<it>summed plan 1</it>), IMRT without dose-painting boost plan to CRT 40 Gy (<it>summed plan 2</it>) and IMRT with dose-painting boost plan to CRT 40 Gy (<it>summed plan 3</it>), and we compared those plans using DVHs and NTCP.</p> <p>Results</p> <p>D_meanof PTV-PET and that of PTV-CT were 26.5 Gy and 21.3 Gy, respectively. V₅₀of small bowel PRV in <it>summed plan 1 </it>was significantly higher than those in other plans ((<it>summed plan 1 </it>vs. <it>summed plan 2 </it>vs. <it>summed plan 3</it>: 47.11 ± 45.33 cm³vs. 40.63 ± 39.13 cm³vs. 41.25 ± 39.96 cm³(p < 0.01, respectively)). There were no significant differences in V₃₀, V₄₀, V₆₀, D_meanor NTCP of small bowel PRV.</p> <p>Conclusions</p> <p>FDG-PET-guided IMRT can facilitate focal dose-escalation to regions with SUV above 2.0 for postoperative local recurrent rectal cancer.</p

2017 HRS/EHRA/ECAS/APHRS/SOLAECE expert consensus statement on catheter and surgical ablation of atrial fibrillation: executive summary.

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2017 HRS/EHRA/ECAS/APHRS/SOLAECE expert consensus statement on catheter and surgical ablation of atrial fibrillation: executive summary.

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withdrawn 2017 hrs ehra ecas aphrs solaece expert consensus statement on catheter and surgical ablation of atrial fibrillation

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