Dimension reduction and outlier detection of 3-D shapes derived from multi-organ CT images

BACKGROUND

Unsupervised clustering and outlier detection are important in medical research to understand the distributional composition of a collective of patients. A number of clustering methods exist, also for high-dimensional data after dimension reduction. Clustering and outlier detection may, however, become less robust or contradictory if multiple high-dimensional data sets per patient exist. Such a scenario is given when the focus is on 3-D data of multiple organs per patient, and a high-dimensional feature matrix per organ is extracted.

METHODS

We use principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE) and multiple co-inertia analysis (MCIA) combined with bagplots to study the distribution of multi-organ 3-D data taken by computed tomography scans. After point-set registration of multiple organs from two public data sets, multiple hundred shape features are extracted per organ. While PCA and t-SNE can only be applied to each organ individually, MCIA can project the data of all organs into the same low-dimensional space.

RESULTS

MCIA is the only approach, here, with which data of all organs can be projected into the same low-dimensional space. We studied how frequently (i.e., by how many organs) a patient was classified to belong to the inner or outer 50% of the population, or as an outlier. Outliers could only be detected with MCIA and PCA. MCIA and t-SNE were more robust in judging the distributional location of a patient in contrast to PCA.

CONCLUSIONS

MCIA is more appropriate and robust in judging the distributional location of a patient in the case of multiple high-dimensional data sets per patient. It is still recommendable to apply PCA or t-SNE in parallel to MCIA to study the location of individual organs.

Exploring the potential of incremental feature selection to improve genomic prediction accuracy

BACKGROUND

The ever-increasing availability of high-density genomic markers in the form of single nucleotide polymorphisms (SNPs) enables genomic prediction, i.e. the inference of phenotypes based solely on genomic data, in the field of animal and plant breeding, where it has become an important tool. However, given the limited number of individuals, the abundance of variables (SNPs) can reduce the accuracy of prediction models due to overfitting or irrelevant SNPs. Feature selection can help to reduce the number of irrelevant SNPs and increase the model performance. In this study, we investigated an incremental feature selection approach based on ranking the SNPs according to the results of a genome-wide association study that we combined with random forest as a prediction model, and we applied it on several animal and plant datasets.

RESULTS

Applying our approach to different datasets yielded a wide range of outcomes, i.e. from a substantial increase in prediction accuracy in a few cases to minor improvements when only a fraction of the available SNPs were used. Compared with models using all available SNPs, our approach was able to achieve comparable performances with a considerably reduced number of SNPs in several cases. Our approach showcased state-of-the-art efficiency and performance while having a faster computation time.

CONCLUSIONS

The results of our study suggest that our incremental feature selection approach has the potential to improve prediction accuracy substantially. However, this gain seems to depend on the genomic data used. Even for datasets where the number of markers is smaller than the number of individuals, feature selection may still increase the performance of the genomic prediction. Our approach is implemented in R and is available at https://github.com/FelixHeinrich/GP_with_IFS/ .

High-energy molecular-frame photoelectron angular distributions: a molecular bond-length ruler

We present a study on molecular-frame photoelectron angular distributions (MFPADs) of small molecules using circularly polarized synchrotron light. We find that the main forward-scattering peaks of the MFPADs are slightly tilted with respect to the molecular axis. This tilt angle is directly connected to the molecular bond length by a simple, universal formula. We apply the derived formula to several examples of MFPADs of C 1s and O 1s photoelectrons of CO, which have been measured experimentally or obtained by means of ab initio modeling. In addition, we discuss the influence of the back-scattering contribution that is superimposed over the analyzed forward-scattering peak in the case of homo-nuclear diatomic molecules such as N₂.

Cross-reactive antibodies against Langat virus protect mice from lethal tick-borne encephalitis virus infection

Introduction

Naturally attenuated Langat virus (LGTV) and highly pathogenic tick-borne encephalitis virus (TBEV) share antigenically similar viral proteins and are grouped together in the same flavivirus serocomplex. In the early 1970s, this has encouraged the usage of LGTV as a potential live attenuated vaccine against tick-borne encephalitis (TBE) until cases of encephalitis were reported among vaccinees. Previously, we have shown in a mouse model that immunity induced against LGTV protects mice against lethal TBEV challenge infection. However, the immune correlates of this protection have not been studied.

Methods

We used the strategy of adoptive transfer of either serum or T cells from LGTV infected mice into naïve recipient mice and challenged them with lethal dose of TBEV.

Results

We show that mouse infection with LGTV induced both cross-reactive antibodies and T cells against TBEV. To identify correlates of protection, Monitoring the disease progression in these mice for 16 days post infection, showed that serum from LGTV infected mice efficiently protected from developing severe disease. On the other hand, adoptive transfer of T cells from LGTV infected mice failed to provide protection. Histopathological investigation of infected brains suggested a possible role of microglia and T cells in inflammatory processes within the brain.

Discussion

Our data provide key information regarding the immune correlates of protection induced by LGTV infection of mice which may help design better vaccines against TBEV.

Assessing Outlier Probabilities in Transcriptomics Data When Evaluating a Classifier

Outliers in the training or test set used to fit and evaluate a classifier on transcriptomics data can considerably change the estimated performance of the model. Hence, an either too weak or a too optimistic accuracy is then reported and the estimated model performance cannot be reproduced on independent data. It is then also doubtful whether a classifier qualifies for clinical usage. We estimate classifier performances in simulated gene expression data with artificial outliers and in two real-world datasets. As a new approach, we use two outlier detection methods within a bootstrap procedure to estimate the outlier probability for each sample and evaluate classifiers before and after outlier removal by means of cross-validation. We found that the removal of outliers changed the classification performance notably. For the most part, removing outliers improved the classification results. Taking into account the fact that there are various, sometimes unclear reasons for a sample to be an outlier, we strongly advocate to always report the performance of a transcriptomics classifier with and without outliers in training and test data. This provides a more diverse picture of a classifier's performance and prevents reporting models that later turn out to be not applicable for clinical diagnoses.

Observation of Nondipole-Induced Asymmetry in the Angular Emission Distribution of Photoelectrons from Fixed-in-Space CO Molecules

We investigate experimentally and theoretically the C and O 1s photoionization of fixed-in-space CO molecules at a photon energy of 905 eV. We find a significant dependence of the photoelectron angular distributions on the direction of propagation of the ionizing radiation. It results from an interplay of nondipole effects, on one hand, and molecular effects, on the other. The nondipole effects lead to an increase of the emission probability in the forward direction along the light propagation, and the photoelectron wave being scattered by the molecular potential gives rise to a strong peak in the direction of the atom neighboring the emitter site. These effects can either conspire or extenuate each other, depending on the photoelectron emission direction and molecular orientation in space.

Augmentation of Transcriptomic Data for Improved Classification of Patients with Respiratory Diseases of Viral Origin

To better understand the molecular basis of respiratory diseases of viral origin, high-throughput gene-expression data are frequently taken by means of DNA microarray or RNA-seq technology. Such data can also be useful to classify infected individuals by molecular signatures in the form of machine-learning models with genes as predictor variables. Early diagnosis of patients by molecular signatures could also contribute to better treatments. An approach that has rarely been considered for machine-learning models in the context of transcriptomics is data augmentation. For other data types it has been shown that augmentation can improve classification accuracy and prevent overfitting. Here, we compare three strategies for data augmentation of DNA microarray and RNA-seq data from two selected studies on respiratory diseases of viral origin. The first study involves samples of patients with either viral or bacterial origin of the respiratory disease, the second study involves patients with either SARS-CoV-2 or another respiratory virus as disease origin. Specifically, we reanalyze these public datasets to study whether patient classification by transcriptomic signatures can be improved when adding artificial data for training of the machine-learning models. Our comparison reveals that augmentation of transcriptomic data can improve the classification accuracy and that fewer genes are necessary as explanatory variables in the final models. We also report genes from our signatures that overlap with signatures presented in the original publications of our example data. Due to strict selection criteria, the molecular role of these genes in the context of respiratory infectious diseases is underlined.

Ion and Electron Momentum Distributions from Single and Double Ionization of Helium Induced by Compton Scattering

We present the momentum distributions of the nucleus and of the electrons from double ionization of the helium atom by Compton scattering of photons with hν=40  keV. We find that the doubly charged ion momentum distribution is very close to the Compton profile of the nucleus in the ground state of the helium atom, and the momentum distribution of the singly charged ion to give a precise image of the electron Compton profile. To reproduce these results, nonrelativistic calculations require the use of highly correlated initial- and final-state wave functions.

Investigating charge-up and fragmentation dynamics of oxygen molecules after interaction with strong X-ray free-electron laser pulses

The X-ray-induced charge-up and fragmentation process of a small molecule is examined in great detail by measuring the molecular-frame photoelectron interference pattern in conjunction with other observables in coincidence.

Fourfold Differential Photoelectron Circular Dichroism

We report on a joint experimental and theoretical study of photoelectron circular dichroism (PECD) in methyloxirane. By detecting O 1s photoelectrons in coincidence with fragment ions, we deduce the molecule's orientation and photoelectron emission direction in the laboratory frame. Thereby, we retrieve a fourfold differential PECD clearly beyond 50%. This strong chiral asymmetry is reproduced by ab initio electronic structure calculations. Providing such a pronounced contrast makes PECD of fixed-in-space chiral molecules an even more sensitive tool for chiral recognition in the gas phase.

Recoil-Induced Asymmetry of Nondipole Molecular Frame Photoelectron Angular Distributions in the Hard X-ray Regime

We investigate angular emission distributions of the 1s photoelectrons of N_{2} ionized by linearly polarized synchrotron radiation at hν=40  keV. As expected, nondipole contributions cause a very strong forward-backward asymmetry in the measured emission distributions. In addition, we observe an unexpected asymmetry with respect to the polarization direction, which depends on the direction of the molecular fragmentation. In particular, photoelectrons are predominantly emitted in the direction of the forward nitrogen atom. This observation cannot be explained via asymmetries introduced by the initial bound and final continuum electronic states of the oriented molecule. The present simulations assign this asymmetry to a novel nontrivial effect of the recoil imposed to the nuclei by the fast photoelectrons and high-energy photons, which results in a propensity for the ions to break up along the axis of the recoil momentum. The results are of particular importance for the interpretation of future experiments at x-ray free electron lasers operating in the few tens of keV regime, where such nondipole and recoil effects will be essential.

Photon-Momentum-Induced Molecular Dynamics in Photoionization of N_{2} at hν=40 keV

We investigate K-shell ionization of N_{2} at 40 keV photon energy. Using a cold target recoil ion momentum spectroscopy reaction microscope, we determine the vector momenta of the photoelectron, the Auger electron, and both N^{+} fragments. These fully differential data show that the dissociation process of the N_{2}^{2+} ion is significantly modified not only by the recoil momentum of the photoelectron but also by the photon momentum and the momentum of the emitted Auger electron. We find that the recoil energy introduced by the photon and the photoelectron momentum is partitioned with a ratio of approximately 30∶70 between the Auger electron and fragment ion kinetic energies, respectively. We also observe that the photon momentum induces an additional rotation of the molecular ion.

Measurement of relative lung perfusion with electrical impedance and positron emission tomography: an experimental comparative study in pigs

BACKGROUND

Electrical impedance tomography (EIT) with indicator dilution may be clinically useful to measure relative lung perfusion, but there is limited information on the performance of this technique.

METHODS

Thirteen pigs (50-66 kg) were anaesthetised and mechanically ventilated. Sequential changes in ventilation were made: (i) right-lung ventilation with left-lung collapse, (ii) two-lung ventilation with optimised PEEP, (iii) two-lung ventilation with zero PEEP after saline lung lavage, (iv) two-lung ventilation with maximum PEEP (20/25 cm H₂O to achieve peak airway pressure 45 cm H₂O), and (v) two-lung ventilation under unilateral pulmonary artery occlusion. Relative lung perfusion was assessed with EIT and central venous injection of saline 3%, 5%, and 10% (10 ml) during breath holds. Relative perfusion was determined by positron emission tomography (PET) using ⁶⁸Gallium-labelled microspheres. EIT and PET were compared in eight regions of equal ventro-dorsal height (right, left, ventral, mid-ventral, mid-dorsal, and dorsal), and directional changes in regional perfusion were determined.

RESULTS

Differences between methods were relatively small (95% of values differed by less than 8.7%, 8.9%, and 9.5% for saline 10%, 5%, and 3%, respectively). Compared with PET, EIT underestimated relative perfusion in dependent, and overestimated it in non-dependent, regions. EIT and PET detected the same direction of change in relative lung perfusion in 68.9-95.9% of measurements.

CONCLUSIONS

The agreement between EIT and PET for measuring and tracking changes of relative lung perfusion was satisfactory for clinical purposes. Indicator-based EIT may prove useful for measuring pulmonary perfusion at bedside.

Breakdown of the Spectator Concept in Low-Electron-Energy Resonant Decay Processes

We suggest that low-energy electrons, released by resonant decay processes, experience substantial scattering on the electron density of excited electrons, which remain a spectator during the decay. As a result, the angular emission distribution is altered significantly. This effect is expected to be a common feature of low-energy secondary electron emission. In this Letter, we exemplify our idea by examining the spectator resonant interatomic Coulombic decay of Ne dimers. Our theoretical predictions are confirmed by a corresponding coincidence experiment.

The fermentative production of L-lysine as an animal feed additive

A new and innovative process for the biotechnological production of L-lysine is presented, exemplified here by the fermentative production of the feed additive Biolys60. The novel feature of this product is that the entire manufacturing concept, i.e. the production strain, the raw materials, all process stages and the product specifications have been systematically tailored for optimal environmental compatibility and for minimum resource depletion and waste. The process completely dispenses with the need to discharge residual and waste material and reduces the handling of hazardous materials to a minimum. Since only a few process stages are involved, the method is economical to use and investment outlay is reduced. The process, which also leads to a higher grade product, is thus highly attractive in both ecological and economical terms. By boosting the nutrient value of the plant-based feedstuffs, the product itself makes an cost-effective contribution towards a more sustainable form of animal feeding and by reducing nitrogen emission levels promotes a more environmentally compatible form of animal husbandry.

Specific V beta T cell subsets are associated with cat and birch pollen allergy in humans

Cognate interaction between TCRs and MHC class II molecules plays an important role in initiating the allergen-specific immune response. Therefore, we analyzed the TCR distribution of human PBLs of 56 atopic and nonatopic (NA) individuals, including 4 monozygotic twin pairs, from two extended and four nuclear families. The expression of 23 V beta and 3 V alpha elements was analyzed. The blood samples of symptomatic birch pollen-sensitized individuals that were taken < or = 6 wk after the birch pollen season (n = 8) showed a significantly higher frequency of V beta 16.1+ and V beta 20.1+ T cells compared with the blood samples of birch pollen-sensitized individuals that were obtained out of allergen season (n = 10) or from NA individuals (p < 0.0005 and p < 0.0001, respectively). Allergen-specific lymphocyte proliferation was detected in the allergic individuals, and the distribution of V beta 16.1+ and V beta 20.1+ T cells returned to normal levels after the pollen season. The frequency of these V beta-expressing T cells correlated with the levels of allergen-specific IgE Abs. In addition, cat-sensitized individuals (n = 8) showed a significantly higher frequency of V beta 17.1-expressing T cells than did NA individuals (p < 0.005). Our results indicate restricted TCR-V beta gene usage in cat and birch pollen allergies; we suggest that both genetic and environmental factors contribute to TCR-V beta gene expression and to the development of a specific T cell response.

Intracavernous application of SIN-I in rabbit and man: functional and toxicological results

The mode of action of the active metabolite SIN-I of the vasodilator prodrug molsidomine was studied in vitro and in vivo in corpus cavernosum of rabbit and man. SIN-I produces a dose-dependent relaxation of isolated human cavernous smooth muscle strips. In the rabbit, the intracavernous application of SIN-I increased the intracavernous pressure to a full erection (approximately 100 cm H2O). This response was highly reproductible. SIN-I was also injected intracavernously 6 times in five rabbits over 2 weeks; no inflammatory or fibrotic reactions were found on histology. SIN-I may be a reliable drug for the treatment of impotence without side-effects.

Discrimination of Corynebacterium glutamicum, Brevibacterium flavum and Brevibacterium lactofermentum by restriction pattern analysis of DNA adjacent to the hom gene

Different strains of Corynebacterium glutamicum, Brevibacterium flavum, and Brevibacterium lactofermentum were analysed for restriction fragment length polymorphism using the homoserine dehydrogenase gene (hom) as a probe. The hybridization patterns obtained PvuII- or Asp700-restriction of chromosomal DNA were specific and distinguishable for each of the three species and identical for the different strains of each species. Thus, the method employed allows rapid distinction of Corynebacterium glutamicum, Brevibacterium flavum, and Brevibacterium lactofermentum. The former species could also be discriminated from the latter two by its resistance to 0.5 g/l of the methionine analog ethionine.

Amplification of three threonine biosynthesis genes in Corynebacterium glutamicum and its influence on carbon flux in different strains

The hom-thrB operon (homoserine dehydrogenase/homoserine kinase) and the thrC gene (threonine synthase) of Corynebacterium glutamicum ATCC 13,032 and the homFBR (homoserine dehydrogenase resistant to feedback inhibition by threonine) alone as well as homFBR-thrB operon of C. glutamicum DM 368-3 were cloned separately and in combination in the Escherichia coli/C. glutamicum shuttle vector pEK0 and introduced into different corynebacterial strains. All recombinant strains showed 8- to 20-fold higher specific activities of homoserine dehydrogenase, homoserine kinase, and/or threonine synthase compared to the respective host. In wild-type C. glutamicum, amplification of the threonine genes did not result in secretion of threonine. In the lysine producer C. glutamicum DG 52-5 and in the lysine-plus-threonine producer C. glutamicum DM 368-3 overexpression of hom-thrB resulted in a notable shift of carbon flux from lysine to threonine whereas cloning of homFBR-thrB as well as of homFBR in C. glutamicum DM 368-3 led to a complete shift towards threonine or towards threonine and its precursor homoserine, respectively. Overexpression of thrC alone or in combination with that of homFBR and thrB had no effect on threonine or lysine formation in all recombinant strains tested.

Viability of intramedullary canal bone reamings for continued calcification

The viability of intramedullary canal bone reamings as a potential bone graft material was examined. Intramedullary bone reamings were obtained from the tibia or femur of three patients during intramedullary nailing procedures. Histologic examination showed bone marrow elements with complete disruption of the marrow compartmental organization. Bone trabeculas were present in a randomly scattered fashion with no structural organization. To assess the viability after reaming of the material for continued calcification, implants of the reaming material were placed in a pocket made in the gluteus maximus muscle of 12 rats. After 7 days, the implanted bone spicules showed evidence of tetracycline label uptake, indicating the material obtained after reaming the intramedullary canal was still viable and capable of continued calcification. That the intramedullary canal bone reamings may be a source of bone graft material is interesting. The reamings appear to continue an osteoproductive capacity when used as a graft.

DNA alkylation by mustard gas in yeast strains of different repair capacity

Reaction of the toxic and mutagenic alkylating agent mustard gas with DNA of the yeast Saccharomyces cerevisiae was analyzed qualitatively and quantitatively. Within the dose range tested (2 X 10(-5)-2 X 10(-3) M) DNA in vivo is alkylated dose-proportionally. DNA alkylation and relative distribution of purine derivatives are not influenced by the cell's sensitivity towards the mutagen. At LD37 (4.4 X 10(-4) M) the wild type contains 44 300 purine derivatives: 9200 3-alkyladenines (20%), 29600 7-alkylguanines (67%) and 5500 diguaninyl derivates (13%) per genome. In sensitive strains the number of derivates per genome at LD37 is reduced according to the dose reduction factor. Alkylation at the position O6 of guanine by mustard gas cannot be shown, the method's limit of detection being 0.3% amongst purine derivates.

Biological and chemical effects of mustard gas in yeast

Mustard gas induces inactivation and mutation in yeast. Both effects are dose-proportional, indicating single-hit events. Induction of both effects is influenced by the cell's capacity for DNA dark-repair, whereby the probability of reversion is highest in repair-proficient cells. Binding of mustard gas to cells and probably to DNA is independent of DNA-repair systems. The number of inter-strand cross-links, as determined by assaying for renaturability of alkalidenatured DNA, increases in a dose-proportional manner. At 37% survival an excision-deficient strain contains 55 inter-strand cross-links. Chromatographic analysis yields several alkylation products of DNA. Their relative frequencies resemble the values reported for E. coli and bacteriophage T7.