Prospective ECG-gated High-Pitch Photon-Counting CT Angiography: Evaluation of measurement accuracy for aortic annulus sizing in TAVR planning.

PURPOSE: In planning transcatheter aortic valve replacement (TAVR), retrospective cardiac spiral-CT is recommended to measure aortic annulus with subsequent CT-angiography (CTA) to evaluate access routes. Photon-counting detector (PCD)-CT enables to assess the aortic annulus in desired cardiac phases, using prospective ECG-gated high-pitch CTA. The aim of this study was to evaluate the measurement accuracy of aortic annulus using prospective ECG-gated high-pitch CTA against retrospective spiral-CT reference. METHOD: Thirty patients underwent cardiac spiral-CT and prospective ECG-gated (30% R-R on aortic valve level) high-pitch CTA. Using propensity score matching, another 30 patients were identified whose CTA was performed using high-pitch mode without ECG-synchronization. Two investigators measured annular diameter, perimeter, and area on cardiac spiral-CT and high-pitch CTA. RESULTS: The aortic valve was imaged in systole in 90 % of prospective ECG-gated CTA cases but only 50 % of non-ECG-gated CTA cases (p = 0.002). There was a strong correlation (r ≥ 0.94) without significant differences (p ≥ 0.09) between cardiac spiral-CT and prospective ECG-gated high-pitch CTA for all annulus measurements. In contrast, significant differences were found in annular short-axis diameter and area between cardiac spiral-CT and non-ECG-gated high-pitch CTA (p ≤ 0.03). Furthermore, prospective ECG-gated high-pitch CTA showed significantly reduced radiation exposure compared with cardiac spiral-CT (CTDI 4.52 vs. 24.10 mGy; p < 0.001). CONCLUSION: PCD-CT-based prospective ECG-gated high-pitch scans with targeted systolic acquisition at the level of the aortic valve can simultaneously visualize TAVR access routes and accurately measure systolic annulus size. This approach could aid in optimizing protocols to achieve lower radiation doses in the growing population of younger, low-risk TAVR patients.

Transcriptome analysis of CpGV in midguts of type II resistant codling moth larvae and identification of contaminant infections by SNP mapping of RNA-Seq data.

Various isolates of the Cydia pomonella granulovirus (CpGV) are used as insect pest control agents against codling moth (CM, Cydia pomonella L.), a predominant pest in apple orchards. Three different types (I-III) of dominantly inherited field resistance of CM larvae to CpGV have been recently identified. In this study, transcription of virus genes in midgut cells of type II-resistant CM larvae infected with different CpGV isolates, i.e., CpGV-M and CpGV-S (both prone to type II resistance) as well as CpGV-E2 (breaking type II resistance) was determined by strand-specific RNA sequencing (RNA-Seq) at an early infection stage (72 h post infection). Based on principal component analysis of read counts and the quantitative distribution of single nucleotide polymorphisms (SNPs) in the RNA-Seq data, a bioinformatics analysis pipeline was developed for an a posteriori identification of the infective agents. We report that (i) identification of infective agent is crucial, especially in in vivo infection experiments, when activation of covert virus infections is a possibility, (ii) no substantial difference between CpGV-M and CpGV-S transcription was found in type II-resistant CM larvae despite a different resistance mechanism, (iii) the transcription level of CpGV-M and CpGV-S was much lower than that of CpGV-E2, and (iv) orf59 (sod), orf89 (pif-6), orf92 (p18), and orf137 (lef-10) were identified as significantly downregulated genes in resistance-prone isolates CpGV-M and CpGV-S. For type II resistance of CM larvae, we conclude that CpGV-M and CpGV-S are both able to enter midgut cells, but viral transcription is significantly impaired at an early stage of infection compared to the resistance-breaking isolate CpGV-E2. IMPORTANCE: CpGV is a highly virulent pathogen of codling moth, and it has been developed into one of the most successful commercial baculovirus biocontrol agents for pome fruit production worldwide. The emergence of field resistance in codling moth to commercial CpGV products is a threat toward the sustainable use of CpGV. In recent years, different types of resistance (type I-III) were identified. For type II resistance, very little is known regarding the infection process. By studying the virus gene expression patterns of different CpGV isolates in midguts of type II-resistant codling moth larvae, we found that the type II resistance mechanism is most likely based on intracellular factors rather than a receptor component. By applying SNP mapping of the RNA-Seq data, we further emphasize the importance of identifying the infective agents in in vivo experiments when activation of a covert infection cannot be excluded.

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants.

Naturally occurring isolates of baculoviruses, such as the Bombyx mori nucleopolyhedrovirus (BmNPV), usually consist of numerous genetically different haplotypes. Deciphering the different haplotypes of such isolates is hampered by the large size of the dsDNA genome, as well as the short read length of next generation sequencing (NGS) techniques that are widely applied for baculovirus isolate characterization. In this study, we addressed this challenge by combining the accuracy of NGS to determine single nucleotide variants (SNVs) as genetic markers with the long read length of Nanopore sequencing technique. This hybrid approach allowed the comprehensive analysis of genetically homogeneous and heterogeneous isolates of BmNPV. Specifically, this allowed the identification of two putative major haplotypes in the heterogeneous isolate BmNPV-Ja by SNV position linkage. SNV positions, which were determined based on NGS data, were linked by the long Nanopore reads in a Position Weight Matrix. Using a modified Expectation-Maximization algorithm, the Nanopore reads were assigned according to the occurrence of variable SNV positions by machine learning. The cohorts of reads were de novo assembled, which led to the identification of BmNPV haplotypes. The method demonstrated the strength of the combined approach of short- and long-read sequencing techniques to decipher the genetic diversity of baculovirus isolates.

Pathogens of the oak processionary moth Thaumetopoea processionea: Developing a user-friendly bioassay system and metagenome analyses for microorganisms.

The oak processionary moth (OPM) Thaumetopoea processionea is a pest of oak trees and poses health risks to humans due to the urticating setae of later instar larvae. For this reason, it is difficult to rear OPM under laboratory conditions, carry out bioassays or examine larvae for pathogens. Biological control targets the early larval instars and is based primarily on commercial preparations of Bacillus thuringiensis ssp. kurstaki (Btk). To test the entomopathogenic potential of other spore-forming bacteria, a user-friendly bioassay system was developed that (i) applies bacterial spore suspensions by oak bud dipping, (ii) targets first instar larvae through feeding exposure and (iii) takes into account their group-feeding behavior. A negligible mortality in the untreated control proved the functionality of the newly established bioassay system. Whereas the commercial Btk HD-1 strain was used as a bioassay standard and confirmed as being highly efficient, a Bacillus wiedmannii strain was ineffective in killing OPM larvae. Larvae, which died during the infection experiment, were further subjected to Nanopore sequencing for a metagenomic approach for entomopathogen detection. It further corroborated that B.wiedmannii was not able to infect and establish in OPM, but identified potential insect pathogenic species from the genera Serratia and Pseudomonas.

Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets.

Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.

A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler's hybrid assemblies.

Generating complete, high-quality genome assemblies is key for any downstream analysis, such as comparative genomics. For bacterial genome assembly, various algorithms and fully automated pipelines exist, which are free-of-charge and easily accessible. However, these assembly tools often cannot unambiguously resolve a bacterial genome, for example due to the presence of sequence repeat structures on the chromosome or on plasmids. Then, a more sophisticated approach and/or manual curation is needed. Such modifications can be challenging, especially for non-bioinformaticians, because they are generally not considered as a straightforward process. In this study, we propose a standardized approach for manual genome completion focusing on the popular hybrid assembly pipeline Unicycler. The provided Galaxy workflow addresses two weaknesses in Unicycler's hybrid assemblies: (i) collapse of inter-plasmidic repeats and (ii) false loss of single-copy sequences. To demonstrate and validate how to detect and resolve these assembly errors, we use two genomes from the Bacillus cereus group. By applying the proposed pipeline following an automated assembly, the genome sequence quality can be significantly improved.

Discovery and development of BI 1265162, an ENaC inhibitor for the treatment of cystic fibrosis.

Lung selective inhibition of the endothelial sodium channel (ENaC) is a potential mutation agnostic treatment of Cystic Fibrosis (CF). We describe the discovery and development of BI 1265162, the first ENaC inhibitor devoid of the amiloride structural motif that entered clinical trials. The design of BI 1265162 focused on its suitability for inhalation via the Respimat® Soft Mist™ Inhaler and a long duration of action. A convergent and scalable route for the synthesis of BI 1265162 as dihydrogen phosphate salt is presented, that was applied to support clinical trials. A phase 2 study with BI 1265162 did not provide a clear sign of clinical benefit. Whether ENaC inhibition will be able to hold its promise for CF patients remains an open question.

Parameters influencing the fracture of Mo films and their wider significance.

Fragmentation testing has been used for decades to assess thin film fracture and delamination. Hooke's law is generally used to determine a film fracture stress from the crack onset strain observed in micrographs or measured as an electrical resistance increase. While this method is in theory suitable in the elastic regime, it neglects important film characteristics, such as residual stress, microstructure, or film architecture. Thus, there is a need to improve fracture analysis using fragmentation to avoid significant errors in measuring fracture stress or apparent fracture toughness of thin films. In-situ X-ray diffraction fragmentation experiments can measure the film fracture stress even for individual layers being part of a multilayer. Which characteristics influence the apparent fracture behavior will be demonstrated on Mo thin films on polyimide.

[Report template from the German Society of Urology and the German Radiological Society for standardized, structured reporting of native computed tomography scans in the diagnosis of urinary stones]. / Befundvorlage der Deutschen Gesellschaft für Urologie e. V. und der Deutschen Röntgengesellschaft zur standardisierten strukturierten Befundung von nativen Computertomographien in der Harnsteindiagnostik.

Standardized structured radiological reporting (SSRB) has been promoted in recent years. The aims of SSRB include that reports be complete, clear, understandable, and stringent. Repetitions or superfluous content should be avoided. In addition, there are advantages in the presentation of chronological sequences, tracking and correlations with structured findings from other disciplines and also the use of artificial intelligence (AI)-based methods. The development of the presented template for SSRB of native computed tomography for urinary stones followed the "process for the creation of quality-assured and consensus-based report templates as well as subsequent continuous quality control and updating" proposed by the German Radiological Society (DRG). This includes several stages of drafts, consensus meetings and further developments. The final version was published on the DRG website ( www.befundung.drg.de ). The template will be checked annually by the steering group and adjusted as necessary. The template contains 6 organ domains (e.g., right kidney) for which entries can be made for a total of 21 different items, mostly with selection windows. If "no evidence of stones" is selected for an organ in the first query, the query automatically jumps to the next organ, so that the processing can be processed very quickly despite the potentially high total number of individual queries for all organs. The German, European, and North American Radiological Societies perceive the establishment of a standardized structured diagnosis of tomographic imaging methods not only in oncological radiology as one of the current central tasks. With the present template for the description of computed tomographic findings for urinary stone diagnostics, we are presenting the first version of a urological template. Further templates for urological diseases are to follow.

Elucidating the genomic history of commercially used Bacillus thuringiensis subsp. tenebrionis strain NB176.

Bacillus thuringiensis subsp. tenebrionis (Btt) produces a coleopteran-specific crystal protoxin protein (Cry3Aa δ-endotoxin). After its discovery in 1982, the strain NB125 (DSM 5526) was eventually registered in 1990 to control the Colorado potato beetle (Leptinotarsa decemlineata). Gamma-irradiation of NB125 resulted in strain NB176-1 (DSM 5480) that exhibited higher cry3Aa production and became the active ingredient of the plant protection product Novodor® FC. Here, we report a comparative genome analysis of the parental strain NB125, its derivative NB176-1 and the current commercial production strain NB176. The entire genome sequences of the parental and derivative strains were deciphered by a hybrid de novo approach using short (Illumina) and long (Nanopore) read sequencing techniques. Genome assembly revealed a chromosome of 5.4 to 5.6 Mbp and six plasmids with a size range from 14.9 to 250.5 kbp for each strain. The major differences among the original NB125 and the derivative strains NB176-1 and NB176 were an additional copy of the cry3Aa gene, which translocated to another plasmid as well as a chromosomal deletion (~ 178 kbp) in NB176. The assembled genome sequences were further analyzed in silico for the presence of virulence and antimicrobial resistance (AMR) genes.

Endocannabinergic modulation of central serotonergic activity in healthy human volunteers.

BACKGROUND: The serotonergic and the endocannabinoid system are involved in the etiology of depression. Depressive patients exhibit low serotonergic activity and decreased level of the endocannabinoids anandamide (AEA) and 2-arachidonylglycerol (2AG). Since the cannabinoid (CB) 1 receptor is activated by endogenous ligands such as AEA and 2AG, whose concentration are controlled by the fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase, respectively, we investigated the effects on serotonergic utilization. In this study, we investigated the impact of the rs1049353 single-nucleotide polymorphism (SNP) of the cannabinoid receptor 1 (CNR1) gene, which codes the endocannabinoid CB1 receptor, and the rs324420 SNP of the FAAH gene on the serotonergic and endocannabinoid system in 59 healthy volunteers. METHODS: Serotonergic activity was measured by loudness dependence of auditory-evoked potentials (LDAEP). Plasma concentrations of AEA, 2AG and its inactive isomer 1AG were determined by mass spectrometry. Genotyping of two SNPs (rs1049353, rs344420) was conducted by polymerase chain reaction (PCR) and differential enzymatic analysis with the PCR restriction fragment length polymorphism method. RESULTS: Genotype distributions by serotonergic activity or endocannabinoid concentration showed no differences. However, after detailed consideration of the CNR1-A-allele-carriers, a reduced AEA (A-allele-carrier M = 0.66, SD = 0.24; GG genotype M = 0.72, SD = 0.24) and 2AG (A-allele-carriers M = 0.70, SD = 0.33; GG genotype M = 1.03, SD = 0.83) plasma concentration and an association between the serotonergic activity and the concentrations of AEA and 2AG has been observed. CONCLUSIONS: Our results suggest that carriers of the CNR1-A allele may be more susceptible to developing depression.

The distribution and characteristic of two transposable elements in the genome of Cydia pomonella granulovirus and codling moth.

Baculoviruses are capable to acquire insect host transposable elements (TEs) in their genomes and are hypothesized as possible vectors of insect transposons between Lepidopteran species. Here, we investigated the host origin of two TEs, namely the Tc1/mariner-like element TCp3.2 and a 0.7 kbp insertion sequence (IS07), found in the genome of different isolates of Cydia pomonella granulovirus (CpGV), a member of the Betabaculovirus genus. The sequences of both TEs were searched for in the full genome sequence database of codling moth (CM, Cydia pomonella L.). A total of eleven TCp3.2 TE copies and 76 copies of the IS07 fragments were identified in the CM genome. These TEs were distributed over the 22 autosomes and the Z chromosome (chr1) of CM, except chr6, chr12, chr16, chr23, chr27 and the W chromosome (chr29). TCp3.2 copies with two transposase genes in opposite direction, representing a novel feature, were identified on chr10 and chr18. The TCp3.2 transposase was characterized by DD41D motif of classic Tc1/mariner transposons, consisting of DNA-binding domain, catalytic domain and nuclear localization signal (NLS). Transcription analyses of uninfected and CpGV-infected CM larvae suggested a doubling of the TCp3.2 transposase transcription rate in virus infected larvae. Furthermore, IS07 insertion into the CpGV genome apparently added new transcription initiation sites to the viral genome. The global analysis of the distribution of two TEs in the genome of CM addressed the influx of mobile TEs from CM to CpGV, a genetic process that contributes to the population diversity of baculoviruses.

Identification of a new nucleopolyhedrovirus isolated from the olive leaf moth, Palpita vitrealis, from two locations in Egypt.

The olive leaf moth (jasmine moth), Palpita vitrealis (Lepidoptera: Crambidae), is an important insect pest of olives in several Mediterranean countries. A new alphabaculovirus was isolated from diseased larvae of P. vitrealis in Egypt, first in Giza in spring 2005 and again in Marsa Matrouh in 2019.The larvae exhibited typical symptoms of a baculovirus infection. Light and scanning electron microscopy studies revealed polyhedral occlusion bodies. Transmission electron microscopy of ultrathin sections of purified OBs revealed virions with multiple embedded nucleocapsids. The identity of the two virus isolates was confirmed by sequencing the partial polyhedrin and lef-8 genes, and sequence comparison suggested a relationship to group I alphabaculoviruses. Therefore, this virus was termed Palpita vitrealis nucleopolyhedrovirus (PaviNPV). Whole genome sequencing of the PaviNPV isolate from Giza (Gz05) revealed a genome of 117,533 bp, 131 open reading frames (ORFs) and four homologous repeat (hr) regions. Phylogenetic reconstruction and genetic distance analyses using 38 core genes indicated that PaviNPV should be considered to belong to a novel species within the genus Alphabaculovirus. In bioassays, PaviNPV was highly virulent against second-instar larvae of P. vitrealis. The study reports a novel baculovirus that might have potential as a biological control agent of the olive leaf moth.

PanelDesign: Integrating Epidemiological Information into the Design of Diagnostic NGS Gene Panels.

We report upon PanelDesign, a framework to support the design of diagnostic next generation DNA sequencing panels with epidemiological information. Two publicly available resources, namely Genomics England PanelApp and Orphadata, were combined into a single data set to allow genes in a given NGS panel to be ranked according to the frequency of the associated diseases, thereby highlighting potential core genes as defined by the Eurogenetest/ESHG guidelines for diagnostic next generation DNA sequencing. In addition, PanelDesign can be used to evaluate the contribution of different genes to a given disease following ACMG (American College of Medical Genetics) technical standards.

The azulene scaffold from a medicinal chemist's perspective: Physicochemical and in vitro parameters relevant for drug discovery.

Azulene is a bicyclic scaffold rarely applied in medicinal chemistry. Here we report physicochemical and in vitro parameters relevant for drug discovery for a series of diversely substituted azulenes. We synthesized and characterized several scaffold hopping series of analogously substituted azulenes, indoles and naphthalenes. This enabled a comparison of azulene with the more common scaffolds indole and naphthalene. Our data indicates that undesirably low photostability of azulenes is restricted to certain substitution patterns. Generally, we conclude that azulene is an underused lipophilic bicycle and should be considered as a valuable complement to the collection of medicinal chemistry scaffolds.

Viruses of the Fall Armyworm Spodoptera frugiperda: A Review with Prospects for Biological Control.

The fall armyworm (FAW), Spodoptera frugiperda, is a native pest species in the Western hemisphere. Since it was first reported in Africa in 2016, FAW has spread throughout the African continent and is now also present in several countries in Asia as well as Australia. The invasion of FAW in these areas has led to a high yield reduction in crops, leading to huge economic losses. FAW management options in the newly invaded areas are limited and mainly rely on the use of synthetic pesticides. Since there is a risk of resistance development against pesticides in addition to the negative environmental and human health impacts, other effective, sustainable, and cost-efficient control alternatives are desired. Insect pathogenic viruses fulfil these criteria as they are usually effective and highly host-specific with no significant harmful effect on beneficial insects and non-target organisms. In this review, we discuss all viruses known from FAW and their potential to be used for biological control. We specifically focus on baculoviruses and describe the recent advancements in the use of baculoviruses for biological control in the native geographic origin of FAW, and their potential use in the newly invaded areas. Finally, we identify current knowledge gaps and suggest new avenues for productive research on the use of viruses as a biopesticide against FAW.

Genome Sequence of a Spodoptera frugiperda Multiple Nucleopolyhedrovirus Isolated from Fall Armyworm (Spodoptera frugiperda) in Nigeria, West Africa.

We report the entire genome sequence of an isolate of Spodoptera frugiperda multiple nucleopolyhedrovirus from Nigeria, West Africa. The genome is 132,710 bp long and contains 144 open reading frames. The GC content is 40.3% and, based on baculovirus species demarcation criteria, the isolate belongs to the species Spodoptera frugiperda multiple nucleopolyhedrovirus.

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus.

The mulberry silkworm, Bombyx mori (L.), is a model organism of lepidopteran insects with high economic importance. The viral diseases of the silkworm caused by Bombyx mori nucleopolyhedrovirus (BmNPV) and Bombyx mori bidensovirus (BmBDV) inflict huge economic losses and significantly impact the sericulture industry of India and other countries. To understand the distribution of Indian isolates of the BmNPV and to investigate their genetic composition, an in-depth population structure analysis was conducted using comprehensive and newly developed genomic analysis methods. The seven new Indian BmNPV isolates from Anantapur, Dehradun, Ghumarwin, Jammu, Kashmir, Mysore and Salem grouped in the BmNPV clade, and are most closely related to Autographa californica multiple nucleopolyhedrovirus and Rachiplusia ou multiple nucleopolyhedrovirus on the basis of gene sequencing and phylogenetic analyses of the partial polh, lef-8 and lef-9 gene fragments. The whole genome sequencing of three Indian BmNPV isolates from Mysore (-My), Jammu (-Ja) and Dehradun (-De) was conducted, and intra-isolate genetic variability was analyzed on the basis of variable SNP positions and the frequencies of alternative nucleotides. The results revealed that the BmNPV-De and BmNPV-Ja isolates are highly similar in their genotypic composition, whereas the population structure of BmNPV-My appeared rather pure and homogenous, with almost no or few genetic variations. The BmNPV-De and BmNPV-Ja samples further contained a significant amount of BmBDV belonging to the Bidnaviridae family. We elucidated the genotype composition within Indian BmNPV and BmBDV isolates, and the results presented have broad implications for our understanding of the genetic diversity and evolution of BmNPV and co-occurring BmBDV isolates.

Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition.

The mechanisms by which transposable elements (TEs) can be horizontally transferred between animals are unknown, but viruses are possible candidate vectors. Here, we surveyed the presence of host-derived TEs in viral genomes in 35 deep sequencing data sets produced from 11 host-virus systems, encompassing nine arthropod host species (five lepidopterans, two dipterans, and two crustaceans) and six different double-stranded (ds) DNA viruses (four baculoviruses and two iridoviruses). We found evidence of viral-borne TEs in 14 data sets, with frequencies of viral genomes carrying a TE ranging from 0.01% to 26.33% for baculoviruses and from 0.45% to 7.36% for iridoviruses. The analysis of viral populations separated by a single replication cycle revealed that viral-borne TEs originating from an initial host species can be retrieved after viral replication in another host species, sometimes at higher frequencies. Furthermore, we detected a strong increase in the number of integrations in a viral population for a TE absent from the hosts' genomes, indicating that this TE has undergone intense transposition within the viral population. Finally, we provide evidence that many TEs found integrated in viral genomes (15/41) have been horizontally transferred in insects. Altogether, our results indicate that multiple large dsDNA viruses have the capacity to shuttle TEs in insects and they underline the potential of viruses to act as vectors of horizontal transfer of TEs. Furthermore, the finding that TEs can transpose between viral genomes of a viral species sets viruses as possible new niches in which TEs can persist and evolve.