Life cycle energy and GHG emissions of PET recycling: change-oriented effects

Purpose  

The demand of PET bottles has increased rapidly in the past decades. The purpose of this study is to understand the environmental impact of PET recycling system, in which used bottles are recycled into both fibre and bottles, and to compare the recycling system with single-use PET.     

PepBank - a database of peptides based on sequence text mining and public peptide data sources

Background  

Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated biological data. Rather, peptide sequences still have to be mined from abstracts and full-length articles, and/or obtained from the fragmented public sources.     

Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

Background  

Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.     

Exploration of phylogenetic data using a global sequence analysis method

Background  

Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.     

Assembling and gap filling of unordered genome sequences through gene checking

Background  

The first draft of human genome sequencing is complete. A large amount of DNA sequences are already available in the database but these are not ordered and assembled. In many cases, these sequences are shorter sequences (ranging from 10kb to 100kb) and are separated by "NNNNNN". Also a considerable amount of gaps are to be filled in the subsequent years. Even after generating raw data, properly ordered, finished available sequences, are enormous tasks and expected to take another 2 years.     

The Average Mutual Information Profile as a Genomic Signature

Background  

Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also provide the means for identifying and discriminating organisms using genomic data. Species specific genomic signatures are useful in a variety of contexts such as evolutionary analysis, assembly and classification of genomic sequences from large uncultivated microbial communities and a rapid identification system in health hazard situations.     

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

Background  

The alignment of biological sequences is of chief importance to most evolutionary and comparative genomics studies, yet the two main approaches used to assess alignment accuracy have flaws: reference alignments are derived from the biased sample of proteins with known structure, and simulated data lack realism.     

Évaluation de la TEP au 18F-FDG dans la tuberculose extrapulmonaire : premiers résultats d’une étude pilote observationnelle

Aim

Extrapulmonary tuberculosis treatment is difficult to assess and there is a need for new tools. The aim of this observational pilot study is to evaluate the potential role of 18F-FDG PET/CT in the initial staging and treatment evaluation of extrapulmonary tuberculosis.

Methods

Twenty-eight patients were included between January 2009 and 2010. Twenty-three had a 18F-FDG PET/CT before treatment and/or during and/or after treatment. All patients will be followed for 18 months after the end of treatment. A control group of five patients with previous history of tuberculosis was also included and PET/CT was performed.

Results

Three cases of differential diagnosis were excluded of the study. The initial PET for staging showed additional lesions in 8/10 patients compared to conventional imaging. At the end of treatment, 6/11 patients had a negative PET, and 5/11 patients had a positive PET. PET had a significant clinical impact for 3/10 patients at initial staging (guiding biopsy or increase of planned treatment duration), and for 3/16 during follow up (extend or early interruption of the treatment). All PET scans in the control group were negative.

Conclusion

18F-FDG PET has an excellent sensitivity for the detection of extrapulmonary tuberculosis lesion and excellent negative predictive values. The impact of initial PET staging seems significant. The interest of 18F-FDG PET for the evaluation of response to treatment remains to be assessed and will be correlated with patients’ follow up in a second phase of this study.     

Micro-Mar: a database for dynamic representation of marine microbial biodiversity

Background  

The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes.     

Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

Background  

Phylogenetic analyses of angiosperm relationships have used only a small percentage of available sequence data, but phylogenetic data matrices often can be augmented with existing data, especially if one allows missing characters. We explore the effects on phylogenetic analyses of adding 378 matK sequences and 240 26S rDNA sequences to the complete 3-gene, 567-taxon angiosperm phylogenetic matrix of Soltis et al.     

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics

Background  

Phylogenetic studies using expressed sequence tags (EST) are becoming a standard approach to answer evolutionary questions. Such studies are usually based on large sets of newly generated, unannotated, and error-prone EST sequences from different species. A first crucial step in EST-based phylogeny reconstruction is to identify groups of orthologous sequences. From these data sets, appropriate target genes are selected, and redundant sequences are eliminated to obtain suitable sequence sets as input data for tree-reconstruction software. Generating such data sets manually can be very time consuming. Thus, software tools are needed that carry out these steps automatically.     

Empirical codon substitution matrix

Background  

Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution.     

An Intra-Individual Comparison of MRI, [18F]-FET and [18F]-FLT PET in Patients with High-Grade Gliomas

Objectives

Intra-individual spatial overlap analysis of tumor volumes assessed by MRI, the amino acid PET tracer [¹⁸F]-FET and the nucleoside PET tracer [¹⁸F]-FLT in high-grade gliomas (HGG).

Methods

MRI, [¹⁸F]-FET and [¹⁸F]-FLT PET data sets were retrospectively analyzed in 23 HGG patients. Morphologic tumor volumes on MRI (post-contrast T1 (cT1) and T2 images) were calculated using a semi-automatic image segmentation method. Metabolic tumor volumes for [¹⁸F]-FET and [¹⁸F]-FLT PETs were determined by image segmentation using a threshold-based volume of interest analysis. After co-registration with MRI the morphologic and metabolic tumor volumes were compared on an intra-individual basis in order to estimate spatial overlaps using the Spearman''s rank correlation coefficient and the Mann-Whitney U test.

Results

[¹⁸F]-FLT uptake was negative in tumors with no or only moderate contrast enhancement on MRI, detecting only 21 of 23 (91%) HGG. In addition, [¹⁸F]-FLT uptake was mainly restricted to cT1 tumor areas on MRI and [¹⁸F]-FLT volumes strongly correlated with cT1 volumes (r = 0.841, p<0.001). In contrast, [¹⁸F]-FET PET detected 22 of 23 (96%) HGG. [¹⁸F]-FET uptake beyond areas of cT1 was found in 61% of cases and [¹⁸F]-FET volumes showed only a moderate correlation with cT1 volumes (r = 0.573, p<0.001). Metabolic tumor volumes beyond cT1 tumor areas were significantly larger for [¹⁸F]-FET compared to [¹⁸F]-FLT tracer uptake (8.3 vs. 2.7 cm³, p<0.001).

Conclusion

In HGG [¹⁸F]-FET but not [¹⁸F]-FLT PET was able to detect metabolic active tumor tissue beyond contrast enhancing tumor on MRI. In contrast to [¹⁸F]-FET, blood-brain barrier breakdown seems to be a prerequisite for [¹⁸F]-FLT tracer uptake.     

Genetic variation in <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> surface and immune evasion genes is lineage associated: implications for vaccine design and host-pathogen interactions

Background  

S. aureus is a coloniser and pathogen of humans and mammals. Whole genome sequences of 58 strains of S. aureus in the public domain and data from multi-strain microarrays were compared to assess variation in the sequence of proteins known or putatively interacting with host.     

Mining metadata from unidentified ITS sequences in GenBank: A case study in <Emphasis Type="Italic">Inocybe</Emphasis> (<Emphasis Type="Italic">Basidiomycota</Emphasis>)

Background  

The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified Inocybe sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to that of other mycorrhizal genera.     

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

Background  

Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets.