OmicsVis: an interactive tool for visually analyzing metabolomics data

When analyzing metabolomics data, cancer care researchers are searching for differences between known healthy samples and unhealthy samples. By analyzing and understanding these differences, researchers hope to identify cancer biomarkers. Due to the size and complexity of the data produced, however, analysis can still be very slow and time consuming. This is further complicated by the fact that datasets obtained will exhibit incidental differences in intensity and retention time, not related to actual chemical differences in the samples being evaluated. Additionally, automated tools to correct these errors do not always produce reliable results. This work presents a new analytics system that enables interactive comparative visualization and analytics of metabolomics data obtained by two-dimensional gas chromatography-mass spectrometry (GC × GC-MS). The key features of this system are the ability to produce visualizations of multiple GC × GC-MS data sets, and to explore those data sets interactively, allowing a user to discover differences and features in real time. The system provides statistical support in the form of difference, standard deviation, and kernel density estimation calculations to aid users in identifying meaningful differences between samples. These are combined with novel transfer functions and multiform, linked visualizations in order to provide researchers with a powerful new tool for GC × GC-MS exploration and bio-marker discovery

Survival of dental implants in patients with oral cancer treated by surgery and radiotherapy: a retrospective study

BACKGROUND: The aim of this retrospective study was to evaluate the survival of dental implants placed after ablative surgery, in patients affected by oral cancer treated with or without radiotherapy. METHODS: We collected data for 34 subjects (22 females, 12 males; mean age: 51 ± 19) with malignant oral tumors who had been treated with ablative surgery and received dental implant rehabilitation between 2007 and 2012. Postoperative radiation therapy (less than 50 Gy) was delivered before implant placement in 12 patients. A total of 144 titanium implants were placed, at a minimum interval of 12 months, in irradiated and non-irradiated residual bone. RESULTS: Implant loss was dependent on the position and location of the implants (P = 0.05-0.1). Moreover, implant survival was dependent on whether the patient had received radiotherapy. This result was highly statistically significant (P < 0.01). Whether the implant was loaded is another highly significant (P < 0.01) factor determinin

Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70

Various subsets of invariant natural killer T (iNKT) cells with different cytokine productions develop in the mouse thymus, but the factors driving their differentiation remain unclear. Here we show that hypomorphic alleles of Zap70 or chemical inhibition of Zap70 catalysis leads to an increase of IFN-gamma-producing iNKT cells (NKT1 cells), suggesting that NKT1 cells may require a lower TCR signal threshold. Zap70 mutant mice develop IL-17-dependent arthritis. In a mouse experimental arthritis model, NKT17 cells are increased as the disease progresses, while NKT1 numbers negatively correlates with disease severity, with this protective effect of NKT1 linked to their IFN-gamma expression. NKT1 cells are also present in the synovial fluid of arthritis patients. Our data therefore suggest that TCR signal strength during thymic differentiation may influence not only IFN-gamma production, but also the protective function of iNKT cells in arthritis

Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration

Chromosome-level design-build-test-learn cycles (chrDBTLs) allow systematic combinatorial reconfiguration of chromosomes with ease. Here, we established chrDBTL with a redesigned synthetic Saccharomyces cerevisiae chromosome XV, synXV. We designed and built synXV to harbor strategically inserted features, modified elements, and synonymously recoded genes throughout the chromosome. Based on the recoded chromosome, we developed a method to enable chrDBTL: CRISPR-Cas9-mediated mitotic recombination with endoreduplication (CRIMiRE). CRIMiRE allowed the creation of customized wild-type/synthetic combinations, accelerating genotype-phenotype mapping and synthetic chromosome redesign. We also leveraged synXV as a "build-to-learn" model organism for translation studies by ribosome profiling. We conducted a locus-to-locus comparison of ribosome occupancy between synXV and the wild-type chromosome, providing insight into the effects of codon changes and redesigned features on translation dynamics in vivo. Overall, we established synXV as a versatile reconfigurable system that advances chrDBTL for understanding biological mechanisms and engineering strains. </p

Religio-ethical discussions on organ donation among Muslims in Europe: an example of transnational Islamic bioethics

This article analyzes the religio-ethical discussions of Muslim religious scholars, which took place in Europe specifically in the UK and the Netherlands, on organ donation. After introductory notes on fatwas (Islamic religious guidelines) relevant to biomedical ethics and the socio-political context in which discussions on organ donation took place, the article studies three specific fatwas issued in Europe whose analysis has escaped the attention of modern academic researchers. In 2000 the European Council for Fatwa and Research (ECFR) issued a fatwa on organ donation. Besides this “European” fatwa, two other fatwas were issued respectively in the UK by the Muslim Law (Shariah) Council in 1995 and in the Netherlands by the Moroccan religious scholar Muṣṭafā Ben Ḥamza during a conference on “Islam and Organ Donation” held in March 2006. The three fatwas show that a great number of Muslim religious scholars permit organ donation and this holds true for donating organs to non-Muslims as well. Further, they demonstrate that transnationalism is one of the main characteristics of contemporary Islamic bioethics. In a bid to develop their own standpoints towards organ donation, Muslims living in the West rely heavily on fatwas imported from the Muslim world

Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing

Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated (PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias

A fast and robust hepatocyte quantification algorithm including vein processing

<p>Abstract</p> <p>Background</p> <p>Quantification of different types of cells is often needed for analysis of histological images. In our project, we compute the relative number of proliferating hepatocytes for the evaluation of the regeneration process after partial hepatectomy in normal rat livers.</p> <p>Results</p> <p>Our presented automatic approach for hepatocyte (HC) quantification is suitable for the analysis of an entire digitized histological section given in form of a series of images. It is the main part of an automatic hepatocyte quantification tool that allows for the computation of the ratio between the number of proliferating HC-nuclei and the total number of all HC-nuclei for a series of images in one processing run. The processing pipeline allows us to obtain desired and valuable results for a wide range of images with different properties without additional parameter adjustment. Comparing the obtained segmentation results with a manually retrieved segmentation mask which is considered to be the ground truth, we achieve results with sensitivity above 90% and false positive fraction below 15%.</p> <p>Conclusions</p> <p>The proposed automatic procedure gives results with high sensitivity and low false positive fraction and can be applied to process entire stained sections.</p

Bovine GDF10 gene polymorphism analysis and its association with body measurement traits in Chinese indigenous cattle

The objective of this research was to detect bovine GDF10 gene polymorphism and analyze its association with body measurement traits (BMT) of animals sampled from 6 different Chinese indigenous cattle populations. The populations included Xuelong (Xl), Luxi (Lx), Qinchuan (Qc), Jiaxian red (Jx), Xianang (Xn) and Nanyang (Ny). Blood samples were taken from a total of 417 female animals stratified into age categories of 12–36 months. Polymerase chain reaction–single strand conformation polymorphism (PCR–SSCP) was employed to find out GDF10 single polymorphism nucleotide (SNPs) and explore their possible association with BMT. Sequence analysis of GDF10 gene revealed 3 SNPs in total: 1 in exon1 (G142A) and 2 in exon3 (A11471G, and T12495C). G142A and T12495C SNPs are both synonymous mutation. They showed 2 genotypes namely respectively (GG, GA) and (PP and PB). A11471G SNP is a missense mutation leading to the change of Alanine to Threonine amino acid. It showed three genotypes namely AA, BB and AB. Analysis of association of polymorphism with body measurement traits at the three locus showed that there were significant effects on BMT in Qc, Jx and Ny cattle population. These results suggest that the GDF10 gene might have potential effects on body measurement traits in the above mentioned cattle populations and could be used for marker-assisted selection