Essential parameters needed for a U-Net-based segmentation of individual bones on planning CT images in the head and neck region using limited datasets for radiotherapy application.

Objective.The field of radiotherapy is highly marked by the lack of datasets even with the availability of public datasets. Our study uses a very limited dataset to provide insights on essential parameters needed to automatically and accurately segment individual bones on planning CT images of head and neck cancer patients.Approach.The study was conducted using 30 planning CT images of real patients acquired from 5 different cohorts. 15 cases from 4 cohorts were randomly selected as training and validation datasets while the remaining were used as test datasets. Four experimental sets were formulated to explore parameters such as background patch reduction, class-dependent augmentation and incorporation of a weight map on the loss function.Main results.Our best experimental scenario resulted in a mean Dice score of 0.93 ± 0.06 for other bones (skull, mandible, scapulae, clavicles, humeri and hyoid), 0.93 ± 0.02 for ribs and 0.88 ± 0.03 for vertebrae on 7 test cases from the same cohorts as the training datasets. We compared our proposed solution approach to a retrained nnU-Net and obtained comparable results for vertebral bones while outperforming in the correct identification of the left and right instances of ribs, scapulae, humeri and clavicles. Furthermore, we evaluated the generalization capability of our proposed model on a new cohort and the mean Dice score yielded 0.96 ± 0.10 for other bones, 0.95 ± 0.07 for ribs and 0.81 ± 0.19 for vertebrae on 8 test cases.Significance.With these insights, we are challenging the utilization of an automatic and accurate bone segmentation tool into the clinical routine of radiotherapy despite the limited training datasets.

Segmentation of 71 Anatomical Structures Necessary for the Evaluation of Guideline-Conforming Clinical Target Volumes in Head and Neck Cancers.

The delineation of the clinical target volumes (CTVs) for radiation therapy is time-consuming, requires intensive training and shows high inter-observer variability. Supervised deep-learning methods depend heavily on consistent training data; thus, State-of-the-Art research focuses on making CTV labels more homogeneous and strictly bounding them to current standards. International consensus expert guidelines standardize CTV delineation by conditioning the extension of the clinical target volume on the surrounding anatomical structures. Training strategies that directly follow the construction rules given in the expert guidelines or the possibility of quantifying the conformance of manually drawn contours to the guidelines are still missing. Seventy-one anatomical structures that are relevant to CTV delineation in head- and neck-cancer patients, according to the expert guidelines, were segmented on 104 computed tomography scans, to assess the possibility of automating their segmentation by State-of-the-Art deep learning methods. All 71 anatomical structures were subdivided into three subsets of non-overlapping structures, and a 3D nnU-Net model with five-fold cross-validation was trained for each subset, to automatically segment the structures on planning computed tomography scans. We report the DICE, Hausdorff distance and surface DICE for 71 + 5 anatomical structures, for most of which no previous segmentation accuracies have been reported. For those structures for which prediction values have been reported, our segmentation accuracy matched or exceeded the reported values. The predictions from our models were always better than those predicted by the TotalSegmentator. The sDICE with 2 mm margin was larger than 80% for almost all the structures. Individual structures with decreased segmentation accuracy are analyzed and discussed with respect to their impact on the CTV delineation following the expert guidelines. No deviation is expected to affect the rule-based automation of the CTV delineation.

Photochemical Desaturation and Epoxidation with Oxygen by Sequential Flavin Catalysis.

Catalytic desaturations are important strategies for the functionalization of organic molecules. In nature, flavoenzymes mediate the formation of α,ß-unsaturated carbonyl compounds by concomitant cofactor reduction. Contrary to many laboratory methods for these reactions, such as the Saegusa-Ito oxidation, no transition metal reagents or catalysts are required. However, a molecular flavin-mediated variant has not been reported so far. We disclose a photochemical approach for silyl enol ether oxidation, which leads to α,ß-unsaturated ketones (13 examples) in very good yields. The flavin catalysts are stable throughout the desaturation reaction, and we successfully applied them in a subsequent aerobic epoxidation by simply changing the reaction conditions. This protocol allowed us to directly convert silyl enol ethers into α,ß-epoxyketones in a one-pot fashion (12 examples). Sequential flavin catalysis is not limited to one specific reactivity combination and can, inter alia, couple the photochemical oxidation with radical additions. We anticipate that flavin-catalyzed desaturation will be applicable to other substrate classes and that its sequential catalytic activity will enable rapid substrate diversification.

Biofidelic image registration for head and neck region utilizing an in-silico articulated skeleton as a transformation model.

Objective.We propose an integration scheme for a biomechanical motion model into a deformable image registration. We demonstrate its accuracy and reproducibility for adaptive radiation therapy in the head and neck region.Approach. The novel registration scheme for the bony structures in the head and neck regions is based on a previously developed articulated kinematic skeleton model. The realized iterative single-bone optimization process directly triggers posture changes of the articulated skeleton, exchanging the transformation model within the deformable image registration process. Accuracy in terms of target registration errors in the bones is evaluated for 18 vector fields of three patients between each planning CT and six fraction CT scans distributed along the treatment course.Main results. The median of target registration error distribution of the landmark pairs is 1.4 ± 0.3 mm. This is sufficient accuracy for adaptive radiation therapy. The registration performs equally well for all three patients and no degradation of the registration accuracy can be observed throughout the treatment.Significance. Deformable image registration, despite its known residual uncertainties, is until now the tool of choice towards online re-planning automation. By introducing a biofidelic motion model into the optimization, we provide a viable way towards an in-build quality assurance.

Molecular flavin catalysts for C-H functionalisation and derivatisation of dehydroamino acids.

In nature, the isoalloxazine heterocycle of flavin cofactors undergoes reversible covalent bond formation with a variety of different reaction partners. These intermediates play a crucial role inter alia as the signalling states and in selective catalysis reactions. In the organic laboratory, covalent adducts with a new carbon-carbon bond have been observed with photochemically excited flavins but have, so far, only been regarded as dead-end side products. We have identified a series of molecular flavins that form adducts resulting in a new C-C bond at the C4a-position through allylic C-H activation and dehydroamino acid oxidation. Typically, these reactions are of radical nature and a stepwise pathway is assumed. We could demonstrate that these adducts are no dead-end and that the labile C-C bond can be cleaved by adding the persistent radical TEMPO leading to flavin regeneration and alkoxyamine-functionalised substrates. Our method allows for the catalytic oxidation of dehydroamino acids (16 examples) and we show that the acylimine products serve as versatile starting points for diversification. The present results are envisioned to stimulate the design of further catalytic reactions involving intermediates at the flavin C4a-position and their reactivity towards metal complexes or other persistent organic radicals. Our method for dehydrobutyrine derivatisation is orthogonal to the currently used methods (i.e., nucleophilic attack or radical addition) and offers new perspectives for peptide natural product diversification.

Reduced Molecular Flavins as Single-Electron Reductants after Photoexcitation.

Flavoenzymes mediate a multitude of chemical reactions and are catalytically active both in different oxidation states and in covalent adducts with reagents. The transfer of such reactivity to the organic laboratory using simplified molecular flavins is highly desirable, and such applications in (photo)oxidation reactions are already established. However, molecular flavins have not been used for the reduction of organic substrates yet, although this activity is known and well-studied for DNA photolyase enzymes. We report a catalytic method using reduced molecular flavins as photoreductants and γ-terpinene as a sacrificial reductant. Additionally, we present our design for air-stable, reduced flavin catalysts, which is based on a conformational bias strategy and circumvents the otherwise rapid reduction of O2 from air. Using our catalytic strategy, we were able to replace superstoichiometric amounts of the rare-earth reductant SmI2 in a 5-exo-trig cyclization of substituted barbituric acid derivatives. Such flavin-catalyzed reductions are anticipated to be beneficial for other transformations as well and their straightforward synthesis indicates future use in stereo- as well as site-selective transformations.

Synthetic C6-Functionalized Aminoflavin Catalysts Enable Aerobic Bromination of Oxidation-Prone Substrates.

Flavoenzymes catalyze oxidations via hydroperoxide intermediates that result from activation of molecular O2 . These reactions-such as hydroxylation and halogenation-depend on the additional catalytic activity of functional groups in the peptide environment of the flavin cofactor. We report synthetic flavin catalysts that contain C6 amino modifications at the isoalloxazine core and are consequently capable of mediating halogenations outside the peptide surrounding. The catalysts are competent in the selective, biomimetic bromination of oxidation-prone phenols, flavones, and flavanones using a halide salt in combination with 2,6-lutidinium oxalate as a flavin reductant under visible-light irradiation. Our studies show the beneficial effect of stacked bisflavins as well as the catalytic activity of the flavin modifications. The designed flavin catalysts outperform isolated natural (-)-riboflavin and contribute to the continuing search for tailored flavins in oxidation reactions.

Food-Related Contact Dermatitis, Contact Urticaria, and Atopy Patch Test with Food.

A wide variety of foods may cause or aggravate skin diseases such as contact dermatitis, contact urticaria, or atopic dermatitis (AD), both in occupational and private settings. The mechanism of action underlying allergic disease to food, food additives, and spices may be immunologic and non-immunologic. The classification and understanding of these reactions is a complex field, and knowledge of the possible reaction patterns and appropriate diagnostic test methods is essential. In addition, certain foods may cause worsening of atopic dermatitis lesions in children. The atopy patch test (APT) is a well-established, clinically useful tool for assessing delayed type reactions to protein allergens in patients and may be useful to detect protein allergens relevant for certain skin diseases. The APT may even detect sensitization against allergens in intrinsic atopic dermatitis patients, who show negative skin prick test and negative in vitro IgE test results against these allergens. Native foods, SPT solutions on filter paper, and purified allergens in petrolatum have been used for APT. The European Task Force on Atopic Dermatitis (ETFAD) has worked on standardizing this test in the context of AD patients, who are allergic to aeroallergens and food. This recommended, standardized technique involves test application at the upper back of children and adults; use of large, 12-mm Finn chambers; avoidance of any pre-treatment such as tape stripping or delipidation; standardized amounts of purified allergens in petrolatum; and use of the standardized ETFAD reading key. The APT may not be the best working or best standardized of all possible skin tests, but it is the best test that we currently have available in this niche.

Dupilumab for treatment of atopic dermatitis.

INTRODUCTION: Dupilumab is a new treatment option for patients with moderate-to-severe atopic dermatitis. It blocks IL-4/IL13-signaling and thereby inhibits receptor signaling downstream the JAK-STAT-pathway. Three of the main disease mechanisms of atopic dermatitis are affected by blocking this pathway; the decrease of skin barrier function, the class switch to IgE and the TH2-differentiation. Areas Covered: Dupilumab showed promising results in clinical trials of phase I-III. Clinical outcome parameters such as SCORAD, EASI, IGA and BSA improved with dupilumab. A positive effect on patient-reported outcomes like DLQI or pruritus-rating-scales was also demonstrated. The safety profile of dupilumab is superior to conventional immunosuppressive drugs, such as cyclosporine or methotrexate. Injection-site reactions and conjunctivitis were the most relevant side-effects. Skin infections were less frequently observed compared to placebo. Data on the use of dupilumab during pregnancy or in children are not published to date. Expert Commentary: Dupilumab was approved by the FDA in April 2017 for the treatment of adult patients with moderate-to-severe atopic dermatitis whose disease is not adequately controlled with topical prescription therapies or when those therapies are not advisable.

Mathematical model of the MenD-catalyzed 1,4-addition (Stetter reaction) of α-ketoglutaric acid to acrylonitrile.

The Stetter reaction, a conjugate umpolung reaction, is well known for cyanide-catalyzed transformations of mostly aromatic aldehydes. Enzymatic Stetter reactions, however, have been largely unexplored, especially with respect to preparative transformations. We have investigated the kinetics of the MenD-catalyzed 1,4-addition of α-ketoglutaric acid to acrylonitrile which has shown that acrylonitrile, while an interesting candidate, is a poor substrate for MenD due to low affinity of the enzyme for this substrate. The kinetic model of the reaction was simplified to double substrate Michaelis-Menten kinetics where the reaction rate linearly depends on acrylonitrile concentration. Experiments at different initial concentrations of acrylonitrile under batch, repetitive batch, and fed-batch reactor conditions were carried out to validate the developed mathematical model. Thiamine diphosphate dependent MenD proved to be quite a robust enzyme; nevertheless, enzyme operational stability decay occurs in the reactor. The spontaneous reactivity of acrylonitrile towards polymerization was also taken into account during mathematical modeling. Almost quantitative conversion of acrylonitrile was achieved in all batch reactor experiments, while the yield of the desired product was dependent on initial acrylonitrile concentration (i.e., the concentration of the stabilizer additive). Using the optimized reactor parameters, it was possible to synthesize the product, 6-cyano-4-oxohexanoic acid, in a concentration of 250 mM. The highest concentration of product was achieved in a repetitive batch reactor experiment. A fed-batch reactor experiment also delivered promising results, especially regarding the short reaction time needed to achieve a 200 mM concentration of product. Hence, the enzymatic Stetter reaction with a highly reactive acceptor substrate can be performed on a preparative scale, which should enable similar transformations with acrylate, methacrylate, and methyl vinyl ketone.

Discovery of inhibitors of Schistosoma mansoni HDAC8 by combining homology modeling, virtual screening, and in vitro validation.

Schistosomiasis, caused by S. mansoni, is a tropical disease that affects over 200 million people worldwide. A novel approach for targeting eukaryotic parasites is to tackle their dynamic epigenetic machinery that is necessary for the extensive phenotypic changes during their life cycle. We recently identified S. mansoni histone deacetylase 8 (smHDAC8) as a potential target for antiparasitic therapy. Here we present results from a virtual screening campaign on smHDAC8. Besides hydroxamates, several sulfonamide-thiazole derivatives were identified by a target-based virtual screening using a homology model of smHDAC8. In vitro testing of 75 compounds identified 8 hydroxamates as potent and lead-like inhibitors of the parasitic HDAC8. Solving of the crystal structure of smHDAC8 with two of the virtual screening hits confirmed the predicted binding mode.

Single-case design evaluation of compression therapy for edema of the stroke-affected hand.

OBJECTIVE. To explore the efficacy of low- and high-stretch compression bandaging for edema management in the stroke-affected upper limb. METHOD. A single-case, ABA-design study was conducted with 8 participants alternately allocated to receive low- or high-stretch bandaging. Edema was measured with circumferential tape at four specified points from the hand to the mid-forearm. All measurements were represented graphically for visual analysis, and celeration lines were calculated to indicate the degree of slope in each phase. RESULTS. Visual analysis indicated fluctuating edema volume in the first baseline phase, decreasing edema volume in the intervention phase, and increasing edema volume in the second baseline phase. The results did not clearly distinguish between the two bandaging groups. CONCLUSION. Compression bandaging may have benefits in the management of edema after stroke. Further research is required to identify factors contributing to the long-term maintenance of reductions gained after compression bandaging.

Molecular basis for the antiparasitic activity of a mercaptoacetamide derivative that inhibits histone deacetylase 8 (HDAC8) from the human pathogen schistosoma mansoni.

Schistosomiasis, caused by the parasitic flatworm Schistosoma mansoni and related species, is a tropical disease that affects over 200 million people worldwide. A new approach for targeting eukaryotic parasites is to tackle their dynamic epigenetic machinery that is necessary for the extensive phenotypic changes during the life cycle of the parasite. Recently, we identified S. mansoni histone deacetylase 8 (smHDAC8) as a potential target for antiparasitic therapy. Here, we present results on the investigations of a focused set of HDAC (histone deacetylase) inhibitors on smHDAC8. Besides several active hydroxamates, we identified a thiol-based inhibitor that inhibited smHDAC8 activity in the micromolar range with unexpected selectivity over the human isotype, which has not been observed so far. The crystal structure of smHDAC8 complexed with the thiol derivative revealed that the inhibitor is accommodated in the catalytic pocket, where it interacts with both the catalytic zinc ion and the essential catalytic tyrosine (Y341) residue via its mercaptoacetamide warhead. To our knowledge, this is the first complex crystal structure of any HDAC inhibited by a mercaptoacetamide inhibitor, and therefore, this finding offers a rationale for further improvement. Finally, an ester prodrug of the thiol HDAC inhibitor exhibited antiparasitic activity on cultured schistosomes in a dose-dependent manner.

Association between NAD(P)H: quinone oxidoreductase 1 (NQ01) inactivating C609T polymorphism and adenocarcinoma of the upper gastrointestinal tract.

NQO1 is an antioxidant enzyme, important in the detoxification of environmental carcinogens. A single nucleotide polymorphism (C-->T) at position 609 of the NQO1 cDNA has been associated with susceptibility to tumours induced by chemical carcinogens. In our case-control study, we determined the prevalence of the C609T NQO1 polymorphism by PCR-RFLP analysis in Caucasian patients with oesophageal adenocarcinoma (OAC; n=61), cardiac adenocarcinoma (CAC; n=120) or gastric adenocarcinoma (GAC; n=203) vs. a control group that consisted of 252 healthy blood donors. Additionally, NQO1 mRNA expression and NQO1 protein expression were determined by RT-PCR and immunohistochemistry in a subset of cases. The NQO1 C609T genotype distribution was significantly different among controls (C/C, 73.4%; C/T, 25.0%; T/T, 1.6%) as compared to OAC patients (C/C, 49.2%; C/T, 47.5%; T/T, 3.3%; p=0.0004), CAC patients (C/C, 55.8%; C/T, 40.0%; T/T, 4.2%; p=0.0005) and with GAC patients (C/C, 65.5%; C/T; 30.6%, T/T; 3.9%; p=0.0377). The 609T allele overall frequency was 0.141 in controls, 0.270 in OAC patients, 0.241 in CAC patients and 0.192 in GAC patients. Individuals carrying 1 or 2 609T alleles had a 2.85-fold higher risk (95% CI: 1.61-5.07; p=0.0003) for the development of OAC and a 2.18-fold higher risk (95% CI: 1.38-3.44; p=0.0007) for the development of CAC than wild-type gene homozygotes. Immunohistochemical analysis showed NQO1 protein expression in 133 carcinomas, whereas 17 carcinomas were negative. Negativity for NQO1 protein expression correlated strongly with the NQO1 genotype being present in 3.9% of cases with C/C, 13.9% of cases with C/T and 62.5% of cases with T/T genotype (p<0.001). In contrast, NQO1 mRNA expression was detectable irrespective of underlying genotype. In conclusion, determination of the NQO1 genotype may gain importance as a stratification marker in future prevention trials for adenocarcinoma of upper gastrointestinal tract.