Transferability of Deep Learning Algorithms for Malignancy Detection in Confocal Laser Endomicroscopy Images from Different Anatomical Locations of the Upper Gastrointestinal Tract

Squamous Cell Carcinoma (SCC) is the most common cancer type of the epithelium and is often detected at a late stage. Besides invasive diagnosis of SCC by means of biopsy and histo-pathologic assessment, Confocal Laser Endomicroscopy (CLE) has emerged as noninvasive method that was successfully used to diagnose SCC in vivo. For interpretation of CLE images, however, extensive training is required, which limits its applicability and use in clinical practice of the method. To aid diagnosis of SCC in a broader scope, automatic detection methods have been proposed. This work compares two methods with regard to their applicability in a transfer learning sense, i.e. training on one tissue type (from one clinical team) and applying the learnt classification system to another entity (different anatomy, different clinical team). Besides a previously proposed, patch-based method based on convolutional neural networks, a novel classification method on image level (based on a pre-trained Inception V.3 network with dedicated preprocessing and interpretation of class activation maps) is proposed and evaluated. The newly presented approach improves recognition performance, yielding accuracies of 91.63% on the first data set (oral cavity) and 92.63% on a joint data set. The generalization from oral cavity to the second data set (vocal folds) lead to similar area-under-the-ROC curve values than a direct training on the vocal folds data set, indicating good generalization.Comment: Erratum for version 1, correcting the number of CLE image sequences used in one data se

Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955

Background The thermophile Geobacillus thermoglucosidasius has considerable attraction as a chassis for the production of chemicals and fuels. It utilises a wide range of sugars and oligosaccharides typical of those derived from lignocellulose and grows at elevated temperatures. The latter improves the rate of feed conversion, reduces fermentation cooling costs and minimises the risks of contamination. Full exploitation of its potential has been hindered by a dearth of effective gene tools. Results Here we designed and tested a collection of vectors (pMTL60000 series) in G. thermoglucosidasius NCIMB 11955 equivalent to the widely used clostridial pMTL80000 modular plasmid series. By combining a temperature-sensitive replicon and a heterologous pyrE gene from Geobacillus kaustophilus as a counter-selection marker, a highly effective and rapid gene knock-out/knock-in system was established. Its use required the initial creation of uracil auxotroph through deletion of pyrE using allele-coupled exchange (ACE) and selection for resistance to 5-fluoroorotic acid. The turnaround time for the construction of further mutants in this pyrE minus strain was typically 5 days. Following the creation of the desired mutant, the pyrE allele was restored to wild type, within 3 days, using ACE and selection for uracil prototrophy. Concomitant with this process, cargo DNA (pheB) could be readily integrated at the pyrE locus. The system’s utility was demonstrated through the generation in just 30 days of three independently engineered strains equivalent to a previously constructed ethanol production strain, TM242. This involved the creation of two in-frame deletions (ldh and pfl) and the replacement of a promoter region of a third gene (pdh) with an up-regulated variant. In no case did the production of ethanol match that of TM242. Genome sequencing of the parental strain, TM242, and constructed mutant derivatives suggested that NCIMB 11955 is prone to the emergence of random mutations which can dramatically affect phenotype. Conclusions The procedures and principles developed for clostridia, based on the use of pyrE alleles and ACE, may be readily deployed in G. thermoglucosidasius. Marker-less, in-frame deletion mutants can be rapidly generated in 5 days. However, ancillary mutations frequently arise, which can influence phenotype. This observation emphasises the need for improved screening and selection procedures at each step of the engineering processes, based on the generation of multiple, independent strains and whole-genome sequencing

Prokayrotic Ubiquitin-Like Protein (Pup) Proteome of Mycobacterium tuberculosis

Prokaryotic ubiquitin-like protein (Pup) in Mycobacterium tuberculosis (Mtb) is the first known post-translational small protein modifier in prokaryotes, and targets several proteins for degradation by a bacterial proteasome in a manner akin to ubiquitin (Ub) mediated proteolysis in eukaryotes. To determine the extent of pupylation in Mtb, we used tandem affinity purification to identify its “pupylome”. Mass spectrometry identified 55 out of 604 purified proteins with confirmed pupylation sites. Forty-four proteins, including those with and without identified pupylation sites, were tested as substrates of proteolysis in Mtb. Under steady state conditions, the majority of the test proteins did not accumulate in degradation mutants, suggesting not all targets of pupylation are necessarily substrates of the proteasome under steady state conditions. Four proteins implicated in Mtb pathogenesis, Icl (isocitrate lyase), Ino1 (inositol-1-phosphate synthase), MtrA (Mtb response regulator A) and PhoP (phosphate response regulator P), showed altered levels in degradation defective Mtb. Icl, Ino1 and MtrA accumulated in Mtb degradation mutants, suggesting these proteins are targeted to the proteasome. Unexpectedly, PhoP was present in wild type Mtb but undetectable in the degradation mutants. Taken together, these data demonstrate that pupylation regulates numerous proteins in Mtb and may not always lead to degradation

The Role of Reflection in Maturing Organizational Know-how

Abstract. The Knowledge Maturing Phase Model has been presented as a model aligning knowledge management and organizational learning. The core argument underlying the present paper is that maturing organizational knowhow requires individual and collaborative reflection at work. We present an explorative interview study that analyzes reflection at the workplace in four organizations in different European countries. Our qualitative findings suggest that reflection is not equally self-evident in different settings. A deeper analysis of the findings leads to the hypothesis that different levels of maturity of processes come along with different expectations towards the workers with regard to compliance and flexibility, and to different ways of how learning at work takes place. Furthermore, reflection in situations where the processes are in early maturing phases seems to lead to consolidation of best practice, while reflection in situations where processes are highly standardized may lead to a modification of these standard processes. Therefore, in order to support the maturing of organizational know-how by providing reflection support, one should take into account the degree of standardisation of the processes in the target group

Wood day capacitance is related to water content, wood density, and anatomy across 30 temperate tree species

Water released from wood during transpiration (capacitance) can meaningfully affect daily water use and drought response. To provide context for better understanding of capacitance mechanisms, we investigated links between capacitance and wood anatomy. On twigs of 30 temperate angiosperm tree species, we measured day capacitance (between predawn and midday), water content, wood density, and anatomical traits, that is, vessel dimensions, tissue fractions, and vessel–tissue contact fractions (fraction of vessel circumference in contact with other tissues). Across all species, wood density (WD) and predawn lumen volumetric water content (VWCL-pd) together were the strongest predictors of day capacitance (r2adj =.44). Vessel–tissue contact fractions explained an additional ~10% of the variation in day capacitance. Regression models were not improved by including tissue lumen fractions. Among diffuse-porous species, VWCL-pd and vessel–ray contact fraction together were the best predictors of day capacitance, whereas among semi/ring-porous species, VWCL-pd, WD and vessel–fibre contact fraction were the best predictors. At predawn, wood was less than fully saturated for all species (lumen relative water content = 0.52 ± 0.17). Our findings imply that day capacitance depends on the amount of stored water, tissue connectivity and the bulk wood properties arising from WD (e.g., elasticity), rather than the fraction of any particular tissue

Expanding the repertoire of gene tools for precise manipulation of the Clostridium difficile genome: allelic exchange using pyrE alleles

Sophisticated genetic tools to modify essential biological processes at the molecular level are pivotal in elucidating the molecular pathogenesis of Clostridium difficile, a major cause of healthcare associated disease. Here we have developed an efficient procedure for making precise alterations to the C. difficile genome by pyrE-based allelic exchange. The robustness and reliability of the method was demonstrated through the creation of in-frame deletions in three genes (spo0A, cwp84, and mtlD) in the non-epidemic strain 630Δerm and two genes (spo0A and cwp84) in the epidemic PCR Ribotype 027 strain, R20291. The system is reliant on the initial creation of a pyrE deletion mutant, using Allele Coupled Exchange (ACE), that is auxotrophic for uracil and resistant to fluoroorotic acid (FOA). This enables the subsequent modification of target genes by allelic exchange using a heterologous pyrE allele from Clostridium sporogenes as a counter-/negative-selection marker in the presence of FOA. Following modification of the target gene, the strain created is rapidly returned to uracil prototrophy using ACE, allowing mutant phenotypes to be characterised in a PyrE proficient background. Crucially, wild-type copies of the inactivated gene may be introduced into the genome using ACE concomitant with correction of the pyrE allele. This allows complementation studies to be undertaken at an appropriate gene dosage, as opposed to the use of multicopy autonomous plasmids. The rapidity of the ‘correction’ method (5–7 days) makes pyrE− strains attractive hosts for mutagenesis studies