58 research outputs found
Albin F. Irzyk Oral History Interview
No full textAlbin F. Irzyk was the commander of the 8th Tank Battalion, 4th Armored Division, which liberated Ohrdruf on April 4, 1945. In this interview, he gives the highlights of the division\u27s arrival in Europe, experiences during the Battle of the Bulge, and progression through the Rhineland. En route to Dresden, Irzyk received orders to go to Ohrdruf and look for an underground complex which was thought to hold communications equipment. His division bivouacked outside the town for the night and started to hear reports of bodies. The next morning, Irzyk went into the camp to look around, finding over 300 corpses. He describes his reactions to the camp and how it affected him as a commanding officer. Irzyk retired from the army as a brigadier general and is the author of three books about the U.S. military
Брачные контракты в польском и русском законодательстве – сравнительный анализ
No full textThe aim of the following paper is to present the institution of the prenuptial and postnuptial marriage contracts in Polish and Russian law. The Author tries to point out the similarities and differences of both legal systems. In Poland these regimes are regulated in one act – Family and Guardianship Code, in Russia are partly regulated in the Civil Code of the Russian Federation and more widely in the Family Code of the Russian Federation. In both systems legislator admits the contractual property regimes, opposite the statutory property regime. The Author focus on pointing out such issues as conclusion of the marriage contract, its content and the limitations of freedom of concluding the marriage contracts.Цель этой статьи заключается в представлении вопросов брачных контрактов в польском и русском праве. Автором предпринята попытка определить сходства и различия в этих двух правовых системaх. В Польше, институт семейных договор регулируется в Кодексе о семье и опеке, в России вышеуказанный вопрос представлен в Гражданском кодексе и более подробно в Семейным кодексе Российской Федерации. В обеих системах, законодательный орган разрешил режимы брачных контрактов наряду с системой основанной на уставе. Автор сосредоточил внимание на развитии таких понятий, как заключение брачного договора, его содержание и ограничения
Removing noise from pyrosequenced amplicons
No full text<b>Background</b><p></p>
In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR amplicons than ever before. This has revolutionised the study of microbial diversity as it is now possible to sequence a substantial fraction of the 16S rRNA genes in a community. However, there is a growing realisation that because of the large read numbers and the lack of consensus sequences it is vital to distinguish noise from true sequence diversity in this data. Otherwise this leads to inflated estimates of the number of types or operational taxonomic units (OTUs) present. Three sources of error are important: sequencing error, PCR single base substitutions and PCR chimeras. We present AmpliconNoise, a development of the PyroNoise algorithm that is capable of separately removing 454 sequencing errors and PCR single base errors. We also introduce a novel chimera removal program, Perseus, that exploits the sequence abundances associated with pyrosequencing data. We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms. <p></p>
<b>Results</b><p></p>
AmpliconNoise outperforms alternative algorithms substantially reducing per base error rates for both the GS FLX and latest Titanium protocol. All three sources of error lead to inflation of diversity estimates. In particular, chimera formation has a hitherto unrealised importance which varies according to amplification protocol. We show that AmpliconNoise allows accurate estimates of OTU number. Just as importantly AmpliconNoise generates the right OTUs even at low sequence differences. We demonstrate that Perseus has very high sensitivity, able to find 99% of chimeras, which is critical when these are present at high frequencies. <p></p>
<b>Conclusions</b><p></p>
AmpliconNoise followed by Perseus is a very effective pipeline for the removal of noise. In addition the principles behind the algorithms, the inference of true sequences using Expectation-Maximization (EM), and the treatment of chimera detection as a classification or 'supervised learning' problem, will be equally applicable to new sequencing technologies as they appear.<p></p>
TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
No full textDiaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW. TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics. 2009;10(1):56.Background:
Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning.
Results
Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained.
Conclusion:
An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference set can be easily updated as newly sequenced genomes become available. Moreover, the method demonstrated to be competitive when compared to the most current classifier PhyloPythia and has the advantage that it can be locally installed and the reference set can be kept up-to-date.
Background
Antiendothelial Cells Antibodies in Patients with Systemic Sclerosis in Relation to Pulmonary Hypertension and Lung Fibrosis
No full textOptical mapping as a routine tool for bacterial genome sequence finishing
No full textBackground: In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila.
Results: Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished.
Conclusion: Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly
P2606Refined balloon pulmonary angioplasty - a new therapuetic option in patients over 75 years with chronic thromboembolic pulmonary hypertension
No full textStatistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts
No full textAs a fruit of the current revolution in sequencing technology, transcriptomes can now be analyzed at an unprecedented level of detail. These advances have been exploited for detecting differential expressed genes across biological samples and for quantifying the abundances of various RNA transcripts within one gene. However, explicit strategies for detecting the hidden differential abundances of RNA transcripts in biological samples have not been defined. In this work, we present two novel statistical tests to address this issue: a 'gene structure sensitive' Poisson test for detecting differential expression when the transcript structure of the gene is known, and a kernel-based test called Maximum Mean Discrepancy when it is unknown. We analyzed the proposed approaches on simulated read data for two artificial samples as well as on factual reads generated by the Illumina Genome Analyzer for two _C. elegans_ samples. Our analysis shows that the Poisson test identifies genes with differential transcript expression considerably better that previously proposed RNA transcript quantification approaches for this task. The MMD test is able to detect a large fraction (75%) of such differential cases without the knowledge of the annotated transcripts. It is therefore well-suited to analyze RNA-Seq experiments when the genome annotations are incomplete or not available, where other approaches have to fail
Glutathione transferases in soybean glycine max (L.) Merr
No full textGlutathione transferases, also known as Glutathione S-transferases (GSTs), are a diverse group of enzymes that catalyse the conjugation of the tri-peptide glutathione to a wide range of electrophilic substrates. Their biological function in endogenous metabolism in plants is not well characterised, although their role in herbicide metabolism and herbicide selectivity is well documented. Many herbicides used in soybean. Glycine max (L.) Merr., are selective against weeds due to their rapid detoxification in the crop through conjugation with homoglutathione (γ-glu-cys-β-ala), the predominant free thiol in many legumes. However, an in depth characterisation of the GSTs which can potentially catalyse these reactions in soybean has never been performed. This work describes the biochemical and molecular characterisation of GSTs in soybean with emphasis on the identification of specific isoenzymes involved in herbicide metabolism. GST activity toward the chloroacetanilide herbicides acetochlor and metolachlor, the diphenyl ethers acifluorfen and fomesafen and the sulphonyl urea chlorimuron-ethyl were all detected in crude protein extracts from five-day-old suspension cultured soybean cells. GST activity was also determined in five-day-old soybean seedlings, though this activity was significantly lower than that observed with the cell suspension cultures. Treatment of soybean plants with herbicides and herbicide safeners resulted in increased GST activity toward the model substrate l-chloro-2,4-dinitrobenzene (CDNB), but no change in activity toward herbicide substrates. In both plant and cell cultures GST-catalysed conjugation of the diphenyl ethers acifluorfen and fomesafen was over five-fold greater in the presence of homoglutathione as compared with glutathione. The preferential detoxification of these herbicides in the presence of homoglutathione appeared to be an important determinant of their rapid detoxification in soybean and an important factor in herbicide selectivity. GSTs were purified from five-day-old soybean cell cultures using S-hexylglutathione affinity chromatography and anion-exchange chromatography. A combination of reversed-phase HPLC, SDS-PAGE and MALDI-TOF mass spectrometry of the purified fractions indicated the presence of nine putative GST subunits, each with a molecular mass between 25 and 29 kDa. Soybean GST cDNA clones were obtained using a combination of RT-PCR, utilising degenerate oligonucleotides designed to conserved regions within plant GSTs, and screening of cDNA libraries prepared from soybean plants and cell cultures. This process failed to identify any theta-type GSTs, the class associated with herbicide detoxification in maize. In contrast, seven distinct tau-type GSTs were isolated together with a number of clones showing minor variations in individual sequences. Expression of these cDNAs in Escherichia coli showed the purified recombinant GSTs were active toward a diverse range of substrates, and possessed additional glutathione peroxidase activity. GST activities for each recombinant enzyme varied with substrate and thiol type, with a marked preference for homoglutathione with selected substrates. From the work reported in this study it would appear that the tau-type GSTs of soybean are at least as complex as those previously reported in cereals and have an important role in determining herbicide metabolism and selectivity in this major crop
The variation of radiologists' performance over the course of a reading session
No full textThe radiologist's task of reviewing many cases successively is highly repetitive and requires a high level of concentration. Fatigue effects have, for example, been shown in studies comparing performance at different times of day. However, little is known about changes in performance during an individual reading session. During a session reading an enriched case set, performance may be affected by both fatigue (i.e. decreasing performance) and training (i.e. increasing performance) effects. In this paper, we reanalyze 3 datasets from 4 studies for changes in radiologist performance during a reading session. Studies feature 8-20 radiologists reading and assessing 27-60 cases in single, uninterrupted sessions. As the studies were not designed for this analysis, study setups range from bone fractures to mammograms and randomization varies between studies. Thus, they are analyzed separately using mixed-effects models. There is some indication that, as time goes on, specificity increases (shown with p<0.05 for 2 out of 3 datasets, no significant difference for the other) while sensitivity may also increase (p<0.05 for 1 out of 3 datasets). The difficulty of 'normal' (healthy / non-malignant) and 'abnormal' (unhealthy / malignant) cases differs (p<0.05 for 3 out of 3 datasets) and the reader's experience may also be relevant (p<0.05 for 1 out of 3 datasets). These results suggest that careful planning of breaks and session length may help optimize reader performance. Note that the overall results are still inconclusive and a targeted study to investigate fatigue and training effects within a reading session is recommended. © 2013 SPIE
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