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Abstract Background Rotavirus is the leading cause of acute gastroenteritis (AGE) and the most frequent cause of severe diarrhoea in children aged less than 5 years. Although the epidemiology of rotavirus gastroenteritis (RVGE) is well documented, there are few data on the impact of RVGE on the families of affected children. Methods Data associated with the burden of RVGE, including number of working days lost, levels of parental stress, the need for alternative childcare arrangements and additional nappies used, were extracted from questionnaires completed by parents of children participating in a prospective, multicentre, observational study (Rotavirus gastroenteritis Epidemiology and Viral types in Europe Accounting for Losses in public health and society, REVEAL), conducted during 2004-2005 in selected areas of Belgium, France, Germany, Italy, Spain, Sweden, and the United Kingdom to estimate the incidence of RVGE in children aged less than 5 years seeking medical care as a result of AGE. Results 1102 children with RVGE were included in the present analysis. The proportion of RVGE cases that required at least one parent or other person to be absent from work was 39%-91% in the hospital setting, 44%-64% in the emergency department, and 20%-64% in primary care. Self-reported levels of parental stress were generally high (mean stress levels, ≥ 5 on a 10-point visual analogue scale). Additional childcare arrangements were required in up to 21% of RVGE episodes. The mean number of nappies used per day during RVGE episodes was approximately double that used when the child was not ill. Conclusions Paediatric RVGE cases cause disruption to families and parental stress. The burden of RVGE on children and their families could be substantially reduced by routine rotavirus vaccination of infants.

Abstract Background In Germany, the first outbreak of highly pathogenic avian influenza A/H5N1 occurred among wild birds on the island of Ruegen between February and April 2006. The aim of this study was to investigate the use of recommended protective measures and to measure H5N1-seroprevalence among personnel tasked with bird collection. Methods Inclusion criteria of our study were participation in collecting wild birds on Ruegen between February and March 2006. Study participants were asked to complete a questionnaire, and to provide blood samples. For evaluation of the use of protective measures, we developed a personal protective equipment (PPE)-score ranging between 0 and 9, where 9 corresponds to a consistent and complete use of PPE. Sera were tested by plaque neutralization (PN) and microneutralization (MN) assays. Reactive sera were reanalysed in the World Health Organization-Collaborating Centre (WHO-CC) using MN assay. Results Of the eligible personnel, consisting of firemen, government workers and veterinarians, 61% (97/154) participated in the study. Of those, 13% reported having always worn all PPE-devices during bird collection (PPE-score: 9). Adherence differed between firemen (mean PPE-score: 6.6) and government workers (mean PPE-score: 4.5; p = 0.006). The proportion of personnel always adherent to wearing PPE was lowest for masks (19%). Of the participants, 18% had received seasonal influenza vaccination prior to the outbreak. There were no reports of influenza-like illness. Five sera initially H5-reactive by PN assay were negative by WHO-CC confirmatory testing. Conclusion Gaps and variability in adherence demonstrate the risk of exposure to avian influenza under conditions of wild bird collection, and justify serological testing and regular training of task personnel.

Abstract Background Current and past pertussis epidemiology in the two parts of Germany is compared in the context of different histories of vaccination recommendations and coverage to better understand patterns of disease transmission. Methods Available regional pertussis surveillance and vaccination coverage data, supplemented by a literature search for published surveys as well as official national hospital and mortality statistics, were analyzed in the context of respective vaccination recommendations from 1964 onwards. Results Routine childhood pertussis vaccination was recommended in the German Democratic Republic (GDR) from 1964 and in former West German states (FWG) from 1969, but withdrawn from 1974–1991 in FWG. Pertussis incidence declined to Conclusion The shift in pertussis morbidity to older age groups observed in FEG is similar to reports from other countries with longstanding vaccination programs and suggests that additional booster vaccination may be necessary beyond adolescence. The high proportion of fully vaccinated cases in older children in FEG suggests waning immunity 5–10 years after primary immunisation in infancy. The higher incidence of pertussis hospitalisations in infants suggests a stronger force of infection in FWG than FEG. Nationwide pertussis reporting is required for better evaluation of transmission patterns and vaccination policy in both parts of Germany.

Background: Current and past pertussis epidemiology in the two parts of Germany is compared in the context of different histories of vaccination recommendations and coverage to better understand patterns of disease transmission.Methods: Available regional pertussis surveillance and vaccination coverage data, supplemented by a literature search for published surveys as well as official national hospital and mortality statistics, were analyzed in the context of respective vaccination recommendations from 1964 onwards.Results: Routine childhood pertussis vaccination was recommended in the German Democratic Republic (GDR) from 1964 and in former West German states (FWG) from 1969, but withdrawn from 1974-1991 in FWG. Pertussis incidence declined to <1 case/100,000 inhabitants in GDR prior to reunification in 1991, while in FWG, where pertussis was not notifiable after 1961, incidence was estimated at 160-180 cases/100,000 inhabitants in the 1970s-1980s. Despite recommendations for universal childhood immunization in 1991, vaccination coverage decreased in former East German States (FEG) and increased only slowly in FWG. After introduction of acellular pertussis vaccines in 1995, vaccination coverage increased markedly among younger children, but remains low in adolescents, especially in FWG, despite introduction of a booster vaccination for 9-17 year olds in 2000. Reported pertussis incidence increased in FEG to 39.3 cases/100,000 inhabitants in 2007, with the proportion of adults increasing from 20% in 1995 to 68% in 2007. From 2004-2007, incidence was highest among 5-14 year-old children, with a high proportion fully vaccinated according to official recommendations, which did not include a preschool booster until 2006. Hospital discharge statistics revealed a ~2-fold higher pertussis morbidity among infants in FWG than FEG.Conclusion: The shift in pertussis morbidity to older age groups observed in FEG is similar to reports from other countries with longstanding vaccination programs and suggests that additional booster vaccination may be necessary beyond adolescence. The high proportion of fully vaccinated cases in older children in FEG suggests waning immunity 5-10 years after primary immunisation in infancy. The higher incidence of pertussis hospitalisations in infants suggests a stronger force of infection in FWG than FEG. Nationwide pertussis reporting is required for better evaluation of transmission patterns and vaccination policy in both parts of Germany. [ABSTRACT FROM AUTHOR]

We present first results from a dark photon dark matter search in the mass range from 44 to 52  μeV (10.7-12.5 GHz) using a room-temperature dish antenna setup called GigaBREAD. Dark photon dark matter converts to ordinary photons on a cylindrical metallic emission surface with area 0.5  m^{2} and is focused by a novel parabolic reflector onto a horn antenna. Signals are read out with a low-noise receiver system. A first data taking run with 24 days of data does not show evidence for dark photon dark matter in this mass range, excluding dark photon photon mixing parameters χ≳10^{-12} in this range at 90% confidence level. This surpasses existing constraints by about 2 orders of magnitude and is the most stringent bound on dark photons in this range below 49  μeV.

The lack of internal polarization fields in cubic group-III nitrides makes them promising arsenic-free contenders for next-generation high-performance electronic and optoelectronic applications. In particular, cubic In x Ga 1- x N semiconductor alloys promise band gap tuning across and beyond the visible spectrum, from the near-ultraviolet to the near-infrared. However, realization across the complete composition range has been deemed impossible due to a miscibility gap corresponding to the amber spectral range. In this study, we use plasma-assisted molecular beam epitaxy (PAMBE) to fabricate cubic In x Ga 1- x N films on c-GaN/AlN/3C-SiC/Si template substrates that overcome this challenge by careful adjustment of the growth conditions, conclusively closing the miscibility gap. X-ray diffraction reveals the composition, phase purity, and strain properties of the In x Ga 1- x N films. Scanning transmission electron microscopy reveals a CuPt-type ordering on the atomistic scale in highly alloyed films with x (In) ≈ 0.5. Layers with much lower and much higher indium content exhibit statistical distributions of the cations Ga and In. Notably, this CuPt-type ordering results in a spectrally narrower emission compared to that of statistically disordered zincblende materials. The emission energies of the films range from 3.24 to 0.69 eV and feature a quadratic bowing parameter of b = 2.4 eV. In contrast, the LO-like phonon modes that are observed by Raman spectroscopy exhibit a one-mode behavior and shift linearly from c-GaN to c-InN.

Breakthrough methods in machine learning (ML), protein structure prediction, and novel ultrafast structural aligners are revolutionizing structural biology. Obtaining accurate models of proteins and annotating their functions on a large scale is no longer limited by time and resources. The most recent method to be top ranked by the Critical Assessment of Structure Prediction (CASP) assessment, AlphaFold 2 (AF2), is capable of building structural models with an accuracy comparable to that of experimental structures. Annotations of 3D models are keeping pace with the deposition of the structures due to advancements in protein language models (pLMs) and structural aligners that help validate these transferred annotations. In this review we describe how recent developments in ML for protein science are making large-scale structural bioinformatics available to the general scientific community., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Deep-learning (DL) methods like DeepMind's AlphaFold2 (AF2) have led to substantial improvements in protein structure prediction. We analyse confident AF2 models from 21 model organisms using a new classification protocol (CATH-Assign) which exploits novel DL methods for structural comparison and classification. Of ~370,000 confident models, 92% can be assigned to 3253 superfamilies in our CATH domain superfamily classification. The remaining cluster into 2367 putative novel superfamilies. Detailed manual analysis on 618 of these, having at least one human relative, reveal extremely remote homologies and further unusual features. Only 25 novel superfamilies could be confirmed. Although most models map to existing superfamilies, AF2 domains expand CATH by 67% and increases the number of unique 'global' folds by 36% and will provide valuable insights on structure function relationships. CATH-Assign will harness the huge expansion in structural data provided by DeepMind to rationalise evolutionary changes driving functional divergence., (© 2023. The Author(s).)

Motivation: CATH is a protein domain classification resource that exploits an automated workflow of structure and sequence comparison alongside expert manual curation to construct a hierarchical classification of evolutionary and structural relationships. The aim of this study was to develop algorithms for detecting remote homologues missed by state-of-the-art hidden Markov model (HMM)-based approaches. The method developed (CATHe) combines a neural network with sequence representations obtained from protein language models. It was assessed using a dataset of remote homologues having less than 20% sequence identity to any domain in the training set., Results: The CATHe models trained on 1773 largest and 50 largest CATH superfamilies had an accuracy of 85.6 ± 0.4% and 98.2 ± 0.3%, respectively. As a further test of the power of CATHe to detect more remote homologues missed by HMMs derived from CATH domains, we used a dataset consisting of protein domains that had annotations in Pfam, but not in CATH. By using highly reliable CATHe predictions (expected error rate <0.5%), we were able to provide CATH annotations for 4.62 million Pfam domains. For a subset of these domains from Homo sapiens, we structurally validated 90.86% of the predictions by comparing their corresponding AlphaFold2 structures with structures from the CATH superfamilies to which they were assigned., Availability and Implementation: The code for the developed models is available on https://github.com/vam-sin/CATHe, and the datasets developed in this study can be accessed on https://zenodo.org/record/6327572., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2023. Published by Oxford University Press.)

The availability of accurate and fast artificial intelligence (AI) solutions predicting aspects of proteins are revolutionizing experimental and computational molecular biology. The webserver LambdaPP aspires to supersede PredictProtein, the first internet server making AI protein predictions available in 1992. Given a protein sequence as input, LambdaPP provides easily accessible visualizations of protein 3D structure, along with predictions at the protein level (GeneOntology, subcellular location), and the residue level (binding to metal ions, small molecules, and nucleotides; conservation; intrinsic disorder; secondary structure; alpha-helical and beta-barrel transmembrane segments; signal-peptides; variant effect) in seconds. The structure prediction provided by LambdaPP-leveraging ColabFold and computed in minutes-is based on MMseqs2 multiple sequence alignments. All other feature prediction methods are based on the pLM ProtT5. Queried by a protein sequence, LambdaPP computes protein and residue predictions almost instantly for various phenotypes, including 3D structure and aspects of protein function. LambdaPP is freely available for everyone to use under embed.predictprotein.org, the interactive results for the case study can be found under https://embed.predictprotein.org/o/Q9NZC2. The frontend of LambdaPP can be found on GitHub (github.com/sacdallago/embed.predictprotein.org), and can be freely used and distributed under the academic free use license (AFL-2). For high-throughput applications, all methods can be executed locally via the bio-embeddings (bioembeddings.com) python package, or docker image at ghcr.io/bioembeddings/bio&#95;embeddings, which also includes the backend of LambdaPP., (© 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

Experimental structures are leveraged through multiple sequence alignments, or more generally through homology-based inference (HBI), facilitating the transfer of information from a protein with known annotation to a query without any annotation. A recent alternative expands the concept of HBI from sequence-distance lookup to embedding-based annotation transfer (EAT). These embeddings are derived from protein Language Models (pLMs). Here, we introduce using single protein representations from pLMs for contrastive learning. This learning procedure creates a new set of embeddings that optimizes constraints captured by hierarchical classifications of protein 3D structures defined by the CATH resource. The approach, dubbed ProtTucker , has an improved ability to recognize distant homologous relationships than more traditional techniques such as threading or fold recognition. Thus, these embeddings have allowed sequence comparison to step into the 'midnight zone' of protein similarity, i.e. the region in which distantly related sequences have a seemingly random pairwise sequence similarity. The novelty of this work is in the particular combination of tools and sampling techniques that ascertained good performance comparable or better to existing state-of-the-art sequence comparison methods. Additionally, since this method does not need to generate alignments it is also orders of magnitudes faster. The code is available at https://github.com/Rostlab/EAT., (© The Author(s) 2022. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)

Introduction: With the increased emergence of SARS-CoV-2 variants, the impact on schools and preschools remains a matter of debate. To ensure that schools and preschools are kept open safely, the identification of factors influencing the extent of outbreaks is of importance. Aim: To monitor dynamics of COVID-19 infections in schools and preschools and identify factors influencing the extent of outbreaks. Methods: In this prospective observational study we analyzed routine surveillance data of Mecklenburg-Western Pomerania, Germany, from calendar week (CW) 32, 2020 to CW19, 2021 regarding SARS-CoV-2 infection events in schools and preschools considering changes in infection control measures over time. A multivariate linear regression model was fitted to evaluate factors influencing the number of students, teachers and staff tested positive following index cases in schools and preschools. Due to an existing multicollinearity in the common multivariate regression model between the variables "face mask obligation for children" and "face mask obligation for adults", two further separate regression models were set up (Multivariate Model Adults and Multivariate Model Children). Results: We observed a significant increase in secondary cases in preschools in the first quarter of 2021 (CW8 to CW15, 2021), and simultaneously a decrease in secondary cases in schools. In multivariate regression analysis, the strongest predictor of the extent of the outbreaks was the teacher/ caregiver mask obligation ( B = -1.9; 95% CI: -2.9 to -1.0; p < 0.001). Furthermore, adult index cases (adult only or child+adult combinations) increased the likelihood of secondary cases ( B = 1.3; 95% CI: 0.9 to 1.8; p < 0.001). The face mask obligation for children also showed a significant reduction in the number of secondary cases ( B = -0.6; 95% CI: -0.9 to -0.2; p = 0.004. Conclusion: The present study indicates that outbreak events at schools and preschools are effectively contained by an obligation for adults and children to wear face masks., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Sombetzki, Lücker, Ehmke, Bock, Littmann, Reisinger, Hoffmann and Kästner.)

One important aspect of protein function is the binding of proteins to ligands, including small molecules, metal ions, and macromolecules such as DNA or RNA. Despite decades of experimental progress many binding sites remain obscure. Here, we proposed bindEmbed21, a method predicting whether a protein residue binds to metal ions, nucleic acids, or small molecules. The Artificial Intelligence (AI)-based method exclusively uses embeddings from the Transformer-based protein Language Model (pLM) ProtT5 as input. Using only single sequences without creating multiple sequence alignments (MSAs), bindEmbed21DL outperformed MSA-based predictions. Combination with homology-based inference increased performance to F1 = 48 ± 3% (95% CI) and MCC = 0.46 ± 0.04 when merging all three ligand classes into one. All results were confirmed by three independent data sets. Focusing on very reliably predicted residues could complement experimental evidence: For the 25% most strongly predicted binding residues, at least 73% were correctly predicted even when ignoring the problem of missing experimental annotations. The new method bindEmbed21 is fast, simple, and broadly applicable-neither using structure nor MSAs. Thereby, it found binding residues in over 42% of all human proteins not otherwise implied in binding and predicted about 6% of all residues as binding to metal ions, nucleic acids, or small molecules., (© 2021. The Author(s).)

Motivation: Classifying proteins into functional families can improve our understanding of protein function and can allow transferring annotations within one family. For this, functional families need to be 'pure', i.e., contain only proteins with identical function. Functional Families (FunFams) cluster proteins within CATH superfamilies into such groups of proteins sharing function. 11% of all FunFams (22 830 of 203 639) contain EC annotations and of those, 7% (1526 of 22 830) have inconsistent functional annotations., Results: We propose an approach to further cluster FunFams into functionally more consistent sub-families by encoding their sequences through embeddings. These embeddings originate from language models transferring knowledge gained from predicting missing amino acids in a sequence (ProtBERT) and have been further optimized to distinguish between proteins belonging to the same or a different CATH superfamily (PB-Tucker). Using distances between embeddings and DBSCAN to cluster FunFams and identify outliers, doubled the number of pure clusters per FunFam compared to random clustering. Our approach was not limited to FunFams but also succeeded on families created using sequence similarity alone. Complementing EC annotations, we observed similar results for binding annotations. Thus, we expect an increased purity also for other aspects of function. Our results can help generating FunFams; the resulting clusters with improved functional consistency allow more reliable inference of annotations. We expect this approach to succeed equally for any other grouping of proteins by their phenotypes., Availability and Implementation: Code and embeddings are available via GitHub: https://github.com/Rostlab/FunFamsClustering., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press.)

Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre for Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. PredictProtein was the first Internet server for protein predictions. It pioneered combining evolutionary information and machine learning. Given a protein sequence as input, the server outputs multiple sequence alignments, predictions of protein structure in 1D and 2D (secondary structure, solvent accessibility, transmembrane segments, disordered regions, protein flexibility, and disulfide bridges) and predictions of protein function (functional effects of sequence variation or point mutations, Gene Ontology (GO) terms, subcellular localization, and protein-, RNA-, and DNA binding). PredictProtein's infrastructure has moved to the LCSB increasing throughput; the use of MMseqs2 sequence search reduced runtime five-fold (apparently without lowering performance of prediction methods); user interface elements improved usability, and new prediction methods were added. PredictProtein recently included predictions from deep learning embeddings (GO and secondary structure) and a method for the prediction of proteins and residues binding DNA, RNA, or other proteins. PredictProtein.org aspires to provide reliable predictions to computational and experimental biologists alike. All scripts and methods are freely available for offline execution in high-throughput settings., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Models from machine learning (ML) or artificial intelligence (AI) increasingly assist in guiding experimental design and decision making in molecular biology and medicine. Recently, Language Models (LMs) have been adapted from Natural Language Processing (NLP) to encode the implicit language written in protein sequences. Protein LMs show enormous potential in generating descriptive representations (embeddings) for proteins from just their sequences, in a fraction of the time with respect to previous approaches, yet with comparable or improved predictive ability. Researchers have trained a variety of protein LMs that are likely to illuminate different angles of the protein language. By leveraging the bio&#95;embeddings pipeline and modules, simple and reproducible workflows can be laid out to generate protein embeddings and rich visualizations. Embeddings can then be leveraged as input features through machine learning libraries to develop methods predicting particular aspects of protein function and structure. Beyond the workflows included here, embeddings have been leveraged as proxies to traditional homology-based inference and even to align similar protein sequences. A wealth of possibilities remain for researchers to harness through the tools provided in the following protocols. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. The following protocols are included in this manuscript: Basic Protocol 1: Generic use of the bio&#95;embeddings pipeline to plot protein sequences and annotations Basic Protocol 2: Generate embeddings from protein sequences using the bio&#95;embeddings pipeline Basic Protocol 3: Overlay sequence annotations onto a protein space visualization Basic Protocol 4: Train a machine learning classifier on protein embeddings Alternate Protocol 1: Generate 3D instead of 2D visualizations Alternate Protocol 2: Visualize protein solubility instead of protein subcellular localization Support Protocol: Join embedding generation and sequence space visualization in a pipeline., (© 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.)

Knowing protein function is crucial to advance molecular and medical biology, yet experimental function annotations through the Gene Ontology (GO) exist for fewer than 0.5% of all known proteins. Computational methods bridge this sequence-annotation gap typically through homology-based annotation transfer by identifying sequence-similar proteins with known function or through prediction methods using evolutionary information. Here, we propose predicting GO terms through annotation transfer based on proximity of proteins in the SeqVec embedding rather than in sequence space. These embeddings originate from deep learned language models (LMs) for protein sequences (SeqVec) transferring the knowledge gained from predicting the next amino acid in 33 million protein sequences. Replicating the conditions of CAFA3, our method reaches an F max of 37 ± 2%, 50 ± 3%, and 57 ± 2% for BPO, MFO, and CCO, respectively. Numerically, this appears close to the top ten CAFA3 methods. When restricting the annotation transfer to proteins with < 20% pairwise sequence identity to the query, performance drops (F max BPO 33 ± 2%, MFO 43 ± 3%, CCO 53 ± 2%); this still outperforms naïve sequence-based transfer. Preliminary results from CAFA4 appear to confirm these findings. Overall, this new concept is likely to change the annotation of proteins, in particular for proteins from smaller families or proteins with intrinsically disordered regions.

Background: In children, the infection with SARS-CoV-2, the cause of COVID-19, tends to be clinically inapparent more often or less severe than in adults. The spread of this infection from children poses a danger to vulnerable adults. Therefore, child care institutions and schools currently are widely closed., Methods: Since the status of infection tends to be congruent in mothers and their children, we tested 401 mothers of children between 1 and 10 years in the city of Rostock (State of Mecklenburg-Westpomerania, northeast of Germany), for the presence of RNA of SARS-CoV-2 in throat swabs, and of antibodies against SARS-CoV-2 in serum., Results: In none of the mothers tested, RNA of this virus was detected in the throat swab. In the ELISA test, IgG antibodies were positive in one serum sample, IgA antibodies were positive in 11, and borderline in 3 serum samples. All 401 sera were negative in the indirect immunofluorescence test (IIFT) with FITC-labeled IgG, IgA, und IgM antibodies., Conclusion: At the time of this study, neither SARS-CoV-2 RNA, nor specific antibodies against SARS-CoV-2 were detectable in the mothers tested in Rostock., Competing Interests: Die Autorinnen/Autoren geben an, dass kein Interessenkonflikt besteht., (© Georg Thieme Verlag KG Stuttgart · New York.)

Following publication of the original article [1], the author reported that an incorrect figure has been published as Figure 2. The correct Figure 2 is shown below.

From June to October 2019, 17 patients (six infected, 11 colonised) with an extensively drug-resistant (XDR) Klebsiella pneumoniae strain were notified from four Western Pomerania medical facilities. The XDR K. pneumoniae produced carbapenemases NDM-1 and OXA-48, and was only susceptible to chloramphenicol, tigecycline and cefiderocol. Synergistic activity was observed for the combination of aztreonam plus ceftazidime-avibactam. Genomic analyses showed all isolates belonged to K. pneumoniae sequence type 307. Control measures and further investigations are ongoing.

Background: The CATH database provides a hierarchical classification of protein domain structures including a sub-classification of superfamilies into functional families (FunFams). We analyzed the similarity of binding site annotations in these FunFams and incorporated FunFams into the prediction of protein binding residues., Results: FunFam members agreed, on average, in 36.9 ± 0.6% of their binding residue annotations. This constituted a 6.7-fold increase over randomly grouped proteins and a 1.2-fold increase (1.1-fold on the same dataset) over proteins with the same enzymatic function (identical Enzyme Commission, EC, number). Mapping de novo binding residue prediction methods (BindPredict-CCS, BindPredict-CC) onto FunFam resulted in consensus predictions for those residues that were aligned and predicted alike (binding/non-binding) within a FunFam. This simple consensus increased the F1-score (for binding) 1.5-fold over the original prediction method. Variation of the threshold for how many proteins in the consensus prediction had to agree provided a convenient control of accuracy/precision and coverage/recall, e.g. reaching a precision as high as 60.8 ± 0.4% for a stringent threshold., Conclusions: The FunFams outperformed even the carefully curated EC numbers in terms of agreement of binding site residues. Additionally, we assume that our proof-of-principle through the prediction of protein binding residues will be relevant for many other solutions profiting from FunFams to infer functional information at the residue level.

Background: Sub-nuclear structures or locations are associated with various nuclear processes. Proteins localized in these substructures are important to understand the interior nuclear mechanisms. Despite advances in high-throughput methods, experimental protein annotations remain limited. Predictions of cellular compartments have become very accurate, largely at the expense of leaving out substructures inside the nucleus making a fine-grained analysis impossible., Results: Here, we present a new method (LocNuclei) that predicts nuclear substructures from sequence alone. LocNuclei used a string-based Profile Kernel with Support Vector Machines (SVMs). It distinguishes sub-nuclear localization in 13 distinct substructures and distinguishes between nuclear proteins confined to the nucleus and those that are also native to other compartments (traveler proteins). High performance was achieved by implicitly leveraging a large biological knowledge-base in creating predictions by homology-based inference through BLAST. Using this approach, the performance reached AUC = 0.70-0.74 and Q13 = 59-65%. Travelling proteins (nucleus and other) were identified at Q2 = 70-74%. A Gene Ontology (GO) analysis of the enrichment of biological processes revealed that the predicted sub-nuclear compartments matched the expected functionality. Analysis of protein-protein interactions (PPI) show that formation of compartments and functionality of proteins in these compartments highly rely on interactions between proteins. This suggested that the LocNuclei predictions carry important information about function. The source code and data sets are available through GitHub: https://github.com/Rostlab/LocNuclei ., Conclusions: LocNuclei predicts subnuclear compartments and traveler proteins accurately. These predictions carry important information about functionality and PPIs.

Passive immunisation with immunoglobulins as post-exposure prophylaxis after contact with measles is recommended by the German Standing Committee on Vaccination (STIKO) particularly for unprotected individuals at high risk of complications for whom active immunization is contraindicated, such as infants <6 months of age, immunocompromised patients and pregnant women. The efficacy of passive immunisation in preventing measles depends on how soon after exposure it is administered, the concentration of measles antibodies in the immunoglobulin products and dosage. Since the global introduction of standard active immunisation against measles and the concomitant reduction in virus circulation, the levels of measles virus (MV)-specific IgG antibodies in the population have dropped. Thus, the concentration of MV-specific antibodies in immunoglobulin products derived from human plasma donors has declined as the proportion of vaccinated donors has increased. The MV-neutralizing capacity of immunoglobulin products is not routinely tested in Germany. No official data exist on the concentrations of MV-specific IgG antibodies in individual batches of immunoglobulins available in Germany and the required minimum level for MV-specific IgG is not stipulated. The STIKO re-evaluated available data and measurements of MV-neutralizing capacities of available immunoglobulin (IgG) products in Germany at the National Reference Centre Measles, Mumps, Rubella at the Robert Koch Institute. Based on the findings, STIKO modified its previous recommendations on the post-exposure use of immunoglobulins (2001), especially with respect to risk groups, application and dosage. STIKO now recommends a single intravenous administration of immunoglobulins (400 mg/kg body weight) as soon as possible, preferably within six days, after exposure to measles, specifically for infants aged <6 months, susceptible pregnant women and immunocompromised patients., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Lyme borreliosis (LB) is the most commonly reported tick-borne disease in Germany. In 9/16 states, notification of erythema migrans (EM), acute neuroborreliosis (NB) and Lyme arthritis (LA) is mandatory. We describe incidence measures, time trends, geographical distribution and frequencies of manifestations to better understand LB epidemiology and target prevention measures. We used cases notified in the 9 states and confirmed by local health offices, 2013-2017, to calculate incidences by time, place and person. Altogether, we observed 56,446 cases. Disease onset peaked yearly in July. Incidence ranged from 26/100,000 (2015) to 41/100,000 (2013) with mean annual incidences 2013-2017 on district level between 0.5/100,000 and 138/100,000. Median age was 54 years with peaks in boys (5-9 years, mean incidence 36/100,000) and women (50-69 years, mean incidence 57/100,000). 95% experienced EM only, 2.7% NB and 2.1% LA. 54% were female, but more men had NB (56%) and LA (53%, p < 0.001). Hospitalisation was recorded for 10% of LA and 71% of NB cases. LB remains an important public health concern in Germany with marked regional variation. To facilitate early diagnosis and treatment, health authorities should raise awareness among physicians and promote prevention strategies among the general population: tick-bite-protection, prompt tick removal and medical consultation.

Studies of the incidence of pertussis in adults have shown that it accounts for only 5-15% cases of prolonged coughing. We assessed the burden of suffering related to prolonged coughing and tried to identify further causative agents. Based on a sentinel study with 35 general practitioners in two German cities (Krefeld, Rostock), with 3,946 patients fulfilling the inclusion criteria, we estimated the incidence of prolonged coughing in adults. In 975 of these outpatients, PCR and/or serology for adenovirus, Bordetella pertussis and B. parapertussis, human metapneumovirus, influenza virus A and rhinovirus, parainfluenza virus, Mycoplasma pneumonia, and respiratory syncytial virus (RSV) were performed. Treatment data were extracted for a subgroup of 138 patients. Descriptive statistics, including Kaplan-Maier curves were generated. Yearly incidence ranged between 1.4 and 2.1% per population in the two cities. Adult patients sought medical attention only after a median of 3 weeks of coughing. Irrespective of smoking and unrelated to the identified pathogens, the median duration of coughing was 6 weeks, with an interquartile range of 4-11 weeks. In 48.3% of patients, possible pathogens were identified, among which adenovirus (15.1%), RSV (7.5%), B. pertussis (5.6%), and influenza viruses (4.0%) were most often found. Symptoms were not indicative of a specific agent and a total of 64% of patients received antibiotics. Prolonged adult coughing requiring medical attention prompts substantial healthcare use. Apart from B. pertussis, a broad range of pathogens was associated with the symptoms. However, patients sought medical attention too late to guide efficacious therapeutic interventions using the diagnostic tests.

Yale science professor Denison Olmsted used crowdsourcing to gather observations from across the United States of the unexpected deluge of meteors on 13 November 1833--more than 72,000/h. He used these observations (and newspaper accounts and correspondence from scientists) to make a commendably accurate interpretation of the meteor storm, overturning 2100 years of erroneous teachings about shooting stars and establishing meteor science as a new branch of astronomy. Olmsted's success was substantially based on his use of newspapers and their practice of news pooling to solicit observations from throughout the country by lay and expert observers professionally unaffiliated with Yale College and him. In today's parlance, Olmsted was a remarkably successful early practitioner of scientific crowdsourcing, also known as citizen science. He may have been the first to use mass media for crowdsourcing in science. He pioneered many of the citizen-science crowdsourcing practices that are still in use today: an open call for citizen participation, a clearly defined task, a large geographical distribution for gathering data and a rapid response to opportunistic events. Olmsted's achievement is not just that he used crowdsourcing in 1833 but that crowdsourcing helped him to advance science significantly., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

The incidence of tick-borne encephalitis has risen in Europe since 1990 and the tick-borne encephalitis virus (TBEV) has been documented to be spreading into regions where it was not previously endemic. In Mecklenburg-West Pomerania, a federal state in Northern Germany, TBEV was not detectable in over 16,000 collected ticks between 1992 and 2004. Until 2004, the last human case of TBE in the region was reported in 1985. Following the occurrence of three autochthonous human cases of TBE after 2004, however, we collected ticks from the areas in which the infections were contracted. To increase the chance of detecting TBEV-RNA, some of the ticks were fed on mice. Using nested RT-PCR, we were able to confirm the presence of TBEV in ticks for the first time after 15 years. A phylogenetic analysis revealed a close relationship between the sequences we obtained and a TBEV sequence from Mecklenburg-East Pomerania published in 1992 and pointed to the reemergence of a natural focus of TBEV after years of low activity. Our results imply that natural foci of TBEV may either persist at low levels of activity for years or reemerge through the agency of migrating birds.

Background: In the German federal state Mecklenburg-Western Pomerania, routine rotavirus (RV) vaccination in infants has been recommended since 2009. The effectiveness of RV vaccination was investigated after an unexpectedly high number of RV infections in fully vaccinated children occurred., Methods: Intensified RV surveillance was performed in Mecklenburg-Western Pomerania between 2010 and 2011. The screening method was applied to assess vaccine effectiveness (VE) in children up to 24 months after vaccination. To identify risk factors for breakthrough infections, a case-control study and genotyping were conducted in vaccinated and unvaccinated RV-infected children., Results: VE for the prevention of RV infection requiring medical attention or hospitalization was 68% (95% confidence interval [CI]: 61-71) and 80% (95% CI: 77-83), respectively. VE for preventing hospitalization but not medical attention remained stable over 2 years. Vaccinated were less often hospitalized (23%) than unvaccinated RV-infected children (61%; P < 0.001). Breastfeeding (odds ratio, 3.99; 95% CI: 1.92-8.27) and attending daycare (odds ratio, 3.42; 95% CI: 1.64-7.12) were independently associated with breakthrough infections. Genotype G1P[8] was detected more frequently in RotaTeq-vaccinated (44% versus 11%; P < 0.03) and G2P[4] in Rotarix-vaccinated children (42% versus 6%; P < 0.02)., Conclusions: RV vaccination protects young children effectively from RV disease and can reduce disease severity. Breastfeeding might impair VE, but further research is needed to identify the critical time window for this interference and to develop appropriate recommendations.

During the autumn wave of the pandemic influenza virus A/(H1N1) 2009 (pIV) the German population was offered an AS03-adjuvanted vaccine. The authors compared results of two methods calculating the effectiveness of the vaccine (VE). The test-negative case-control method used data from virologic surveillance including influenza-positive and negative patients. An innovative case-series methodology explored data from all nationally reported laboratory-confirmed influenza cases. The proportion of reported cases occurring in vaccinees during an assumed unprotected phase after vaccination was compared with that occurring in vaccinees during their assumed protected phase. The test-negative case-control method included 1,749 pIV cases and 2,087 influenza test-negative individuals of whom 6 (0.3%) and 36 (1.7%), respectively, were vaccinated. The case series method included data from 73,280 cases. VE in the two methods was 79% (95% confidence interval (CI) = 35-93%; P = 0.007) and 87% (95% CI = 78-92%; P<0.001) for individuals less than 14 years of age and 70% (95% CI = -45%-94%, P = 0.13) and 74% (95% CI = 64-82%; P<0.001) for individuals above the age of 14. Both methods yielded similar VE in both age groups; and VE for the younger age group seemed to be higher.

A 40-year-old Asian circus elephant developed mouth and trunk ulcers. Three weeks later, her 19-year-old animal warden noticed a vesicle on his forearm, evolving into a scab. Identical cowpox strains were isolated from lesions of the elephant and the warden. Cowpox virus could no longer be isolated after the scab disappeared, but PCR still revealed orthopox DNA. Healing was complete seven weeks later, leaving a 1 cm scar., (Copyright © 2010 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

Tick-borne encephalitis (TBE) was known to have occurred in humans in the area of Mecklenburg-Western Pomerania in Germany, until 1985. Between 1992 and 2004 more than 16,000 ticks were tested and found to be negative for TBE virus in that area of Germany, wich was therefore thought to be free of TBE. But after 19 years three autochthonous cases of human TBE-infections were identified between 2004 and 2006. We subsequently collected ticks from the three areas where the infection had been acquired and tested them for the presence of TBE-virus RNA with a nested reverse transcription polymerase chain reaction (RT-PCR). Since there is evidence that a blood-meal leads to an increase of FSME-RNA in ticks, we tested both, unfed ticks and ticks after a blood-meal. Three unfed and one fed nymph from the area around Lake Woblitz and one unfed and one fed nymph from Thiessow were positive for TBE-virus RNA. A total of six of 250 (2.4%) ticks tested positive for TBE-virus. The emerging of human TBE infections in three regions in Mecklenburg-Western Pomerania shows that the activity of natural TBE virus foci does not cease even after decades, or that TBE-infected ticks could have recolonized these regions., (Georg Thieme Verlag KG Stuttgart, New York.)

Background: Rotavirus is the leading cause of acute gastroenteritis (AGE) and the most frequent cause of severe diarrhoea in children aged less than 5 years. Although the epidemiology of rotavirus gastroenteritis (RVGE) is well documented, there are few data on the impact of RVGE on the families of affected children., Methods: Data associated with the burden of RVGE, including number of working days lost, levels of parental stress, the need for alternative childcare arrangements and additional nappies used, were extracted from questionnaires completed by parents of children participating in a prospective, multicentre, observational study (Rotavirus gastroenteritis Epidemiology and Viral types in Europe Accounting for Losses in public health and society, REVEAL), conducted during 2004-2005 in selected areas of Belgium, France, Germany, Italy, Spain, Sweden, and the United Kingdom to estimate the incidence of RVGE in children aged less than 5 years seeking medical care as a result of AGE., Results: 1102 children with RVGE were included in the present analysis. The proportion of RVGE cases that required at least one parent or other person to be absent from work was 39%-91% in the hospital setting, 44%-64% in the emergency department, and 20%-64% in primary care. Self-reported levels of parental stress were generally high (mean stress levels, > or = 5 on a 10-point visual analogue scale). Additional childcare arrangements were required in up to 21% of RVGE episodes. The mean number of nappies used per day during RVGE episodes was approximately double that used when the child was not ill., Conclusions: Paediatric RVGE cases cause disruption to families and parental stress. The burden of RVGE on children and their families could be substantially reduced by routine rotavirus vaccination of infants.

Background: In Germany, the first outbreak of highly pathogenic avian influenza A/H5N1 occurred among wild birds on the island of Ruegen between February and April 2006. The aim of this study was to investigate the use of recommended protective measures and to measure H5N1-seroprevalence among personnel tasked with bird collection., Methods: Inclusion criteria of our study were participation in collecting wild birds on Ruegen between February and March 2006. Study participants were asked to complete a questionnaire, and to provide blood samples. For evaluation of the use of protective measures, we developed a personal protective equipment (PPE)-score ranging between 0 and 9, where 9 corresponds to a consistent and complete use of PPE. Sera were tested by plaque neutralization (PN) and microneutralization (MN) assays. Reactive sera were reanalyzed in the World Health Organization-Collaborating Centre (WHO-CC) using MN assay., Results: Of the eligible personnel, consisting of firemen, government workers and veterinarians, 61% (97/154) participated in the study. Of those, 13% reported having always worn all PPE-devices during bird collection (PPE-score: 9). Adherence differed between firemen (mean PPE-score: 6.6) and government workers (mean PPE-score: 4.5; p = 0.006). The proportion of personnel always adherent to wearing PPE was lowest for masks (19%). Of the participants, 18% had received seasonal influenza vaccination prior to the outbreak. There were no reports of influenza-like illness. Five sera initially H5-reactive by PN assay were negative by WHO-CC confirmatory testing., Conclusion: Gaps and variability in adherence demonstrate the risk of exposure to avian influenza under conditions of wild bird collection, and justify serological testing and regular training of task personnel.

Dendritic cells (DCs) protect the respiratory epithelium via induction of innate immune responses and priming of naïve T cells during the initiation of adaptive immunity. Streptococcus pneumoniae, a commonly carried asymptomatic member of the human nasopharyngeal microflora, can cause invasive and inflammatory diseases and the cholesterol-dependent cytotoxin pneumolysin is a major pneumococcal virulence factor implicated in compounding tissue damage and mediating inflammatory responses. While most studies examining the impact of pneumolysin have been based on murine models, we have focused this study on human DC responses. We show that expression of haemolytic pneumolysin inhibits human DC maturation, induction of proinflammatory cytokines and activation of the inflammasome. Furthermore, intracellular production of pneumolysin induces caspase-dependent apoptosis in infected DCs. Similarly, clinical isolates with non-haemolytic pneumolysin were more proinflammatory and caused less apoptosis compared to clonally related strains with active pneumolysin. This study describes a novel role of pneumolysin in the evasion of human DC surveillance that could have a profound clinical impact upon inflammatory disease progression and highlights the need to study human responses to human-specific pathogens.

A pertussis outbreak primarily affecting school-age children in Ludwigslust, Germany, was investigated in 2006 to estimate attack rates and relative risk of pertussis according to time since last vaccination, after a complete primary course. Results suggested waning immunity beginning approximately 5 years after the last dose of pertussis vaccination. Most cases could have been prevented by earlier booster vaccination.

Introduction: Pertussis is not just a childhood disease, but a respiratory infection that causes persistent cough in all age groups, from newborns to the elderly., Methods: The authors performed a selective literature search and reviewed national and international recommendations for treatment and vaccination., Results: Pertussis is found principally in young unvaccinated infants, but school-age children, adolescents, and adults are also affected. Up to 1% of infants contract pertussis, and their respiratory symptoms are often accompanied by apnea. School-age children occasionally display the coughing spasms typical of the disease. Annually, 0.2% to 0.5% of all adolescents and adults are infected and suffer from prolonged, frequently non-paroxysmal coughing. Severe and fatal cases of pertussis occur mainly in newborns and infants, and 25% of affected adults experience complications. Bordetella DNA may be detected by polymerase chain reaction (PCR) for four weeks after symptom onset; except in infants, the sensitivity of this diagnostic technique is low. Although the diagnosis can be confirmed by serological tests, the methods are not well standardized. Treatment with a macrolide prevents the spread of infection, but generally does not alleviate the symptoms. Combination vaccines are the most effective means of prophylaxis., Discussion: Pertussis is usually not included in the differential diagnosis of persistent respiratory symptoms. The considerable burden of disease could be reduced in adults and young infants by vaccinating adults with acellular combination vaccines.

Objective: Monitor the long-term immunogenicity of a single dose of acellular pertussis vaccine in health-care workers., Design: German health-care workers and child-care workers received a single dose of a monovalent acellular pertussis vaccine (PAC-Mérieux) in an open-label study. Blood samples were taken before (n=261), 4 weeks after (n=246), 1 year (n=187), 2 years (n=53), 3 years (n=134) and 4 years (n=37) after vaccination. IgG- and IgA-anti-pertussis-toxin (PT), IgG- and IgA-anti-filamentous hemagglutinin (FHA), and IgG-anti-pertactin (PRN) were measured by ELISA., Results: Of all subjects, 97.1%, 99.2% and 97.2% had an antibody response to PT, FHA and PRN, respectively. Four weeks after vaccination the median titres of IgG antibodies to PT, FHA and PRN were 314, 785 and 84 EU/l, respectively, and all vaccinees had an immune response to at least one pertussis antigen. IgA-anti-PT and IgA-anti-FHA responses were found in 63.4% and 96.3% of subjects with a median titre of 30 and 196 EU/ml, respectively. The titre of IgG-anti-PT decreased slowly with a median concentration of 76, 71, 71 and 63 EU/ml after 1, 2, 3 and 4 years, respectively. Secondary titre increases were observed in 0.5%, 3.3%, 5.6% and 12.5% of the vaccinees 1, 2, 3, and 4 years after vaccination., Conclusion: In German health paediatric care workers long-lasting immune responses with high antibody levels could be induced by a single dose of acellular pertussis vaccine. A renewed contact with B. pertussis antigens resulted in a measurable immune response to PT between 0.5% (1 year p.v.) and 12.5% (4 years p.v.).

Background and Objective: A prospective sentinel study into the population-based incidence of pertussis in adults was done between 2001 and 2004 in Rostock (former East Germany) and Krefeld (former West Germany)., Patients and Methods: 971 outpatients, who consulted general practitioners or internists, were included. Clinical inclusion criteria were coughing for one week or more and no chronic respiratory diseases. Bordetella infection was diagnosed by PCR on nasopharyngeal swabs and ELISA for serology (IgG-anti-PT, IgA-anti-PT, IgG-anti-FHA, IgA-anti-FHA)., Results: We found a total of 97 cases of pertussis in this cohort. The main symptom was coughing for a median of 7-8 weeks. Population-based incidence was estimated in Krefeld at 169 cases/100000 population per year, and in Rostock at 160/100000 per year. Resource use was 120 EUR of direct medical cost and 434 euro of indirect medical cost, not including hospitalization in this study., Conclusions: Pertussis is a frequent cause of longer lasting cough in German adults, and it causes significant morbidity and costs.

History: A 61-year-old man was bitten by a tick at Lake Woblitz, near the town of Neustrelitz in former East Germany. Nine days later he saw his general practitioner because of fever and headache. Three weeks after the tick bite he was hospitalized with fever (39.2 degrees C) and mental confusion. Because he had taken a Nile cruise six months earlier, malaria was considered and he was transferred to the department of tropical medicine and infectious diseases of the University of Rostock., Investigations: The patient was somnolent, his speech was slurred, and he had amnesic aphasia, as well as impaired fine motor control, but no meningism, focal signs, pyramidal tract or sensory impairment. Cerebrospinal fluid (CSF) showed mild lymphocytosis (9,400 leukocytes per microL; 89% lymphocytes) and elevated protein concentration (1322 mg/L) with blood brain barrier impairment and intrathecal IgM synthesis. Anti-tick-bite encephalitis (TBE) antibodies (ELISA: IgG and IgM) were present in serum and CSF, and serum immunofluorescence showed an eight-fold titer increase within two weeks. These findings confirm the diagnosis of TBE. Other infections (including those with cross-reacting flaviviruses) were excluded by appropriate antibody testing., Therapy and Clinical Course: There is no specific antiviral treatment for TBE, but on symptomatic therapy the patient recovered fully within four weeks., Conclusion: The site of the patient's infection is located 10 km to the west of an old TBE focus, but no TBE virus had been detected there after 1975. The case demonstrates that TBE should be included in the differential diagnosis of meningoencephalitis, even if the patient has not been in an acknowledged TBE endemic area.