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Vision Transformers (ViTs) and Swin Transformers (Swin) are currently state-of-the-art in computational pathology. However, domain experts are still reluctant to use these models due to their lack of interpretability. This is not surprising, as critical decisions need to be transparent and understandable. The most common approach to understanding transformers is to visualize their attention. However, attention maps of ViTs are often fragmented, leading to unsatisfactory explanations. Here, we introduce a novel architecture called the B-cos Vision Transformer (BvT) that is designed to be more interpretable. It replaces all linear transformations with the B-cos transform to promote weight-input alignment. In a blinded study, medical experts clearly ranked BvTs above ViTs, suggesting that our network is better at capturing biomedically relevant structures. This is also true for the B-cos Swin Transformer (Bwin). Compared to the Swin Transformer, it even improves the F1-score by up to 4.7% on two public datasets., Comment: Accepted at MICCAI 2023 (oral). Camera-ready available at https://doi.org/10.1007/978-3-031-43993-3_50

Three institutes of the Universities of Applied Sciences that are active in Chemistry and Life Sciences present a selection of their activities in the field of environmental sciences. These projects include analytical monitoring, removal of micropollutants, waste reduction and valorization.

Short-chain chlorinated paraffins (SCCPs) are listed as persistent organic pollutants (POPs) under the Stockholm Convention. Such substances are toxic, bioaccumulating, transported over long distances and degrade slowly in the environment. Certain bacterial strains of the Sphingomonadacea family are able to degrade POPs, such as hexachlorocyclohexanes (HCHs) and hexabromocyclododecanes (HBCDs). The haloalkane dehalogenase LinB, expressed in certain Sphingomonadacea, is able to catalyze the transformation of haloalkanes to hydroxylated compounds. Therefore, LinB is a promising candidate for conversion of SCCPs. Hence, a mixture of chlorinated tridecanes was exposed in vitro to LinB, which was obtained through heterologous expression in Escherichia coli. Liquid chromatography mass spectrometry (LC-MS) was used to analyze chlorinated tridecanes and their transformation products. A chloride-enhanced soft ionization method, which favors the formation of chloride adducts [M+Cl]- without fragmentation, was applied. Mathematical deconvolution was used to distinguish interfering mass spectra of paraffinic, mono-olefinic and di-olefinic compounds. Several mono- and di-hydroxylated products including paraffinic, mono-olefinic and di-olefinic compounds were found after LinB exposure. Mono- (rt = 5.9-6.9 min) and di-hydroxylated (rt = 3.2-4.5 min) compounds were separated from starting material (rt = 7.7-8.5 min) by reversed phase LC. Chlorination degrees of chlorinated tridecanes increased during LinB-exposure from nCl = 8.80 to 9.07, indicating a preferential transformation of lower chlorinated (Cl<9) tridecanes. Thus, LinB indeed catalyzed a dehalohydroxylation of chlorinated tridecanes, tridecenes and tridecadienes. The observed hydroxylated compounds are relevant CP transformation products whose environmental and toxicological effects should be further investigated.

The haloalkane dehalogenase LinB from Sphingobium indicum B90A converts β-hexachlorocyclohexane (β-HCH), the most persistent HCH stereoisomer, to mono- and dihydroxylated metabolites. Recently, we reported that LinB also transforms α-, β- and γ-hexabromocyclododecanes (HBCDs), which are structurally related to HCHs. Here, we show that LinB catalyzes the hydroxylation of δ-HBCD to two pentabromocyclododecanols (PBCDOHs) and two tetrabromocyclododecadiols (TBCDDOHs). The stereochemistry of this enzymatic transformation was deduced from XRD crystal structure data of the substrate δ-HBCD and α(2)-PBCDOH, one of the biotransformation products. Five stereocenters of δ-HBCD are unchanged but the one at C6 is converted to an alcohol with inversion from S- to R-configuration in a nucleophilic, S(N)2-like substitution reaction. Only α(2)-PBCDOH with the 1R,2R,5S,6R,9R,10S-configuration is obtained but not its enantiomer. With only two of the 64 PBCDOHs formed, these transformations indeed are regio- and stereoselective. A conformational analysis revealed that the triple-turn motive, which is predominant in δ-HBCD and in several other HBCD stereoisomers, is also found in the product. This shows that LinB preferentially converted reactive bromine atoms but not those in the conserved triple-turn motive. The widespread contamination with HCHs triggered the bacterial evolution of dehalogenases which acquired the ability to convert these pollutants and their metabolites. We here demonstrate that LinB of S. indicum also transforms HBCDs regio- and stereoselectively following a similar mechanism.

Hexabromocyclododecanes (HBCDs) and hexachlorocyclohexanes (HCHs) are lipophilic, polyhalogenated hydrocarbons with comparable stereochemistry. Bacterial evolution in HCH-contaminated soils resulted in the development of several Spingomonadaceae which express a series of HCH-converting enzymes. We showed that LinB, a haloalkane dehalogenase from Sphingobium indicum B90A, also transforms various HBCDs besides HCHs. Here we present evidence that LinA2, another dehalogenase from S. indicum also converts certain HBCDs to pentabromocyclododecenes (PBCDEs). Racemic mixtures of α-, β-, γ-HBCDs, a mixture of them, and δ-HBCD, a meso form, were exposed to LinA2. Substantial conversion of (-)β-HBCD was observed, but all other stereoisomers were not transformed significantly. The enantiomeric excess (EE) of β-HBCDs increased up to 60% in 32 h, whereas EE values of α- and γ-HBCDs were not affected. Substrate conversion and product formation were described with second-order kinetic models. One major (P1β) and possibly two minor (P2β, P3β) metabolites were detected. Respective mass spectra showed the characteristic isotope pattern of PBCDEs, the HBr elimination products of HBCDs. Michaelis-Menten parameters KM=0.47 ± 0.07 μM and vmax=0.17 ± 0.01 μmoll(-1)h(-1) were deduced from exposure data with varying enzyme/substrate ratios. LinA2 is more substrate specific than LinB, the latter converted all tested HBCDs, LinA2 only one. The widespread HCH pollution favored the selection and evolution of bacteria converting these compounds. We found that LinA2 and LinB, two of these HCH-converting enzymes expressed in S. indicum B90A, also dehalogenate HBCDs to lower brominated compounds, indicating that structural similarities of both classes of compounds are recognized at the level of substrate-protein interactions.