Learning three-dimensional aortic root assessment based on sparse annotations.

Purpose: Analyzing the anatomy of the aorta and left ventricular outflow tract (LVOT) is crucial for risk assessment and planning of transcatheter aortic valve implantation (TAVI). A comprehensive analysis of the aortic root and LVOT requires the extraction of the patient-individual anatomy via segmentation. Deep learning has shown good performance on various segmentation tasks. If this is formulated as a supervised problem, large amounts of annotated data are required for training. Therefore, minimizing the annotation complexity is desirable. Approach: We propose two-dimensional (2D) cross-sectional annotation and point cloud-based surface reconstruction to train a fully automatic 3D segmentation network for the aortic root and the LVOT. Our sparse annotation scheme enables easy and fast training data generation for tubular structures such as the aortic root. From the segmentation results, we derive clinically relevant parameters for TAVI planning. Results: The proposed 2D cross-sectional annotation results in high inter-observer agreement [Dice similarity coefficient (DSC): 0.94]. The segmentation model achieves a DSC of 0.90 and an average surface distance of 0.96 mm. Our approach achieves an aortic annulus maximum diameter difference between prediction and annotation of 0.45 mm (inter-observer variance: 0.25 mm). Conclusions: The presented approach facilitates reproducible annotations. The annotations allow for training accurate segmentation models of the aortic root and LVOT. The segmentation results facilitate reproducible and quantifiable measurements for TAVI planning.

SLO-1-channels of parasitic nematodes reconstitute locomotor behaviour and emodepside sensitivity in Caenorhabditis elegans slo-1 loss of function mutants.

The calcium-gated potassium channel SLO-1 in Caenorhabditis elegans was recently identified as key component for action of emodepside, a new anthelmintic drug with broad spectrum activity. In this study we identified orthologues of slo-1 in Ancylostoma caninum, Cooperia oncophora, and Haemonchus contortus, all important parasitic nematodes in veterinary medicine. Furthermore, functional analyses of these slo-1 orthologues were performed using heterologous expression in C. elegans. We expressed A. caninum and C. oncophora slo-1 in the emodepside-resistant genetic background of the slo-1 loss-of-function mutant NM1968 slo-1(js379). Transformants expressing A. caninum slo-1 from C. elegans slo-1 promoter were highly susceptible (compared to the fully emodepside-resistant slo-1(js379)) and showed no significant difference in their emodepside susceptibility compared to wild-type C. elegans (p = 0.831). Therefore, the SLO-1 channels of A. caninum and C. elegans appear to be completely functionally interchangeable in terms of emodepside sensitivity. Furthermore, we tested the ability of the 5' flanking regions of A. caninum and C. oncophora slo-1 to drive expression of SLO-1 in C. elegans and confirmed functionality of the putative promoters in this heterologous system. For all transgenic lines tested, expression of either native C. elegans slo-1 or the parasite-derived orthologue rescued emodepside sensitivity in slo-1(js379) and the locomotor phenotype of increased reversal frequency confirming the reconstitution of SLO-1 function in the locomotor circuits. A potent mammalian SLO-1 channel inhibitor, penitrem A, showed emodepside antagonising effects in A. caninum and C. elegans. The study combined the investigation of new anthelmintic targets from parasitic nematodes and experimental use of the respective target genes in C. elegans, therefore closing the gap between research approaches using model nematodes and those using target organisms. Considering the still scarcely advanced techniques for genetic engineering of parasitic nematodes, the presented method provides an excellent opportunity for examining the pharmacofunction of anthelmintic targets derived from parasitic nematodes.

Updating International Society for Biological and Environmental Repositories Best Practices, Fifth Edition: A New Process for Relevance in an Evolving Landscape.

The recently published fifth edition of the International Society for Biological and Environmental Repositories (ISBER) Best Practices signifies a pivotal milestone in navigating the complexities of repository management. Repositories operate within a constantly evolving landscape influenced by the changing fields of biospecimen science, technology, legal requirements, and ethical considerations. This dynamic is further amplified by unprecedented local and global challenges, such as pandemics, conflicts, and supply chain disruptions. Creating this new edition required a comprehensive approach capable of delivering a focused and coherent resource reflecting the broad horizon of its diverse users. The innovative approach used the existing phased development process and integrated the canvassing of opinions, formal evaluation, and real-time collaboration platforms. Merging these techniques enabled efficient collection and effective distillation of the latest in biobanking practices, enhancing the value of the fifth edition for repositories of specimens and associated data. The expanded document is a testament to the collective efforts of many dedicated individuals who have built upon the foundations of prior editions.

mGene: accurate SVM-based gene finding with an application to nematode genomes.

We present a highly accurate gene-prediction system for eukaryotic genomes, called mGene. It combines in an unprecedented manner the flexibility of generalized hidden Markov models (gHMMs) with the predictive power of modern machine learning methods, such as Support Vector Machines (SVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. Considering the average of sensitivity and specificity, the developmental version of mGene exhibited the best prediction performance on nucleotide, exon, and transcript level for ab initio and multiple-genome gene-prediction tasks. The fully developed version shows superior performance in 10 out of 12 evaluation criteria compared with the other participating gene finders, including Fgenesh++ and Augustus. An in-depth analysis of mGene's genome-wide predictions revealed that approximately 2200 predicted genes were not contained in the current genome annotation. Testing a subset of 57 of these genes by RT-PCR and sequencing, we confirmed expression for 24 (42%) of them. mGene missed 300 annotated genes, out of which 205 were unconfirmed. RT-PCR testing of 24 of these genes resulted in a success rate of merely 8%. These findings suggest that even the gene catalog of a well-studied organism such as C. elegans can be substantially improved by mGene's predictions. We also provide gene predictions for the four nematodes C. briggsae, C. brenneri, C. japonica, and C. remanei. Comparing the resulting proteomes among these organisms and to the known protein universe, we identified many species-specific gene inventions. In a quality assessment of several available annotations for these genomes, we find that mGene's predictions are most accurate.

Investigating the Relation of Intelligence and Executive Functions in Children and Adolescents with and without Intellectual Disabilities.

Despite their separate research traditions, intelligence and executive functioning (EF) are both theoretically and empirically closely related to each other. Based on a subsample of 8- to 20-year-olds of the standardization and validation sample (N = 1540) of an internationally available instrument assessing both cognitive abilities, this study aimed at investigating a comprehensive structural model of intelligence and EF tasks and at gaining insight into whether this comprehensive model is applicable across sexes and age groups as well as to a subsample of participants with (borderline) intellectual disabilities (IQ ≤ 85, n = 255). The results of our exploratory factor analysis indicated one common EF factor that could be sufficiently integrated into the intelligence model within our confirmatory factor analyses. The results suggest that the EF factor can be added into the model as a sixth broad ability. The comprehensive model largely showed measurement invariance across sexes and age groups but did not converge within the subsample of participants with (borderline) intellectual disabilities. The results and implications are discussed in light of the current literature.

Parenting Stress in Fathers: Do We Need Father Specific Reference Samples? And Do They Differ in Regard of Taking Parental Leave?

The German version of the Parenting stress Index from Abidin, the Eltern-Belastungs-Inventar (EBI) merely provides reference samples of 538 mothers of children in toddlers and preschool age. Although meant to measure parenting stress, there are no father specific reference samples provided. The aim was to investigate differences in parenting stress between fathers and the provided reference samples of German mothers. Furthermore, the aim was to examine potential differences in the perceived stress between fathers who did and those who did not take parental leave. A total of 497 fathers living in Germany, of which more than half took parental leave, filled out the questionnaire via an online survey or the paper-pencil-version. All fathers completed the EBI and provided socio-economic data. The collected data were analyzed in terms of test quality, such as mean and standard deviation, corrected item-total correlation and reliability. Moreover, differences between the provided norm data and our sample were calculated. Analyses showed that fathers reported significantly higher levels of parenting stress than mothers. Furthermore, fathers taking parental leave did not differ significantly from those who did not, regarding their level of education or their perceived parenting stress. In conclusion, as it stands right now, the EBI does not adequately measure parenting stress in fathers, and father specific norms are needed to properly assess their levels of parenting stress. The results concerning parenting stress and parental leave were thus inconclusive. Furthermore, since reducing parenting stress in fathers is beneficial for the child's development and the welfare of the parents, further studies focusing on fathers' parenting stress are needed.

Structural Equation Modeling of Common Cognitive Abilities in Preschool-Aged Children Using WPPSI-IV and BRIEF-P.

Various studies have addressed the relationship between intelligence and executive functions (EF). There is widespread agreement that EF in preschool children is a unitary construct in which the subordinate factors of Updating, Inhibition, and Shifting are still undifferentiated and correlate moderately with a general factor of intelligence (g). The aim of this study is to investigate the common structural relationship between these two constructs using confirmatory factor analysis. Furthermore, we intend to close the gap of more daily life-associated executive functions and replicate findings in preschool-aged children. Data from a sample of N = 124 average developed children without severe impairments (aged 4 years 0 months-6 years 11 months) were analyzed using the data pool of the standardization and validation studies on the German Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition. Additionally, Executive functions were assessed using a standardized parent-completed questionnaire (BRIEF-P) on their children's everyday behavior. A second-order factor solution revealed that a model with a loading of the common factor of general intelligence (g-factor) onto the EF factor fits the data best. To specify possible method effects due to different sources of measurements, a latent method factor was generated. The results indicate a heterogeneous method effect and a decreasing factor loading from g on to EF while controlling for the method factor.

What Is Mathematical Giftedness? Associations with Intelligence, Openness, and Need for Cognition.

It is common practice in the educational system to foster high mathematical abilities in schools as well as in specific promotional programs. Still, little is known about the construct of mathematical giftedness itself. In line with intellectual investment theories, our study investigates the relationship between fluid intelligence (figural and numerical), openness, and the need for cognition with mathematical abilities. The current study is based on a sample (N = 115) of seventh graders participating in the application process for a promotion program. The results of our regression analyses show a positive link between fluid intelligence and mathematical abilities. However, neither the association with openness nor the need for cognition reached significance, emphasizing the importance of cognitive abilities for mathematical giftedness. Limitations and further directions are discussed.

Cascaded neural network-based CT image processing for aortic root analysis.

PURPOSE: Careful assessment of the aortic root is paramount to select an appropriate prosthesis for transcatheter aortic valve implantation (TAVI). Relevant information about the aortic root anatomy, such as the aortic annulus diameter, can be extracted from pre-interventional CT. In this work, we investigate a neural network-based approach for segmenting the aortic root as a basis for obtaining these parameters. METHODS: To support valve prosthesis selection, geometric measures of the aortic root are extracted from the patient's CT scan using a cascade of convolutional neural networks (CNNs). First, the image is reduced to the aortic root, valve, and left ventricular outflow tract (LVOT); within that subimage, the aortic valve and ascending aorta are segmented; and finally, the region around the aortic annulus. From the segmented annulus region, we infer the annulus orientation using principal component analysis (PCA). The area-derived diameter of the annulus is approximated based on the segmentation of the aortic root and LVOT and the plane orientation resulting from the PCA. RESULTS: The cascade of CNNs was trained using 90 expert-annotated contrast-enhanced CT scans routinely acquired for TAVI planning. Segmentation of the aorta and valve within the region of interest achieved an F1 score of 0.94 on the test set of 36 patients. The area-derived diameter within the annulus region was determined with a mean error below 2 mm between the automatic measurement and the diameter derived from annotations. The calculated diameters and resulting errors are comparable to published results of alternative approaches. CONCLUSIONS: The cascaded neural network approach enabled the assessment of the aortic root with a relatively small training set. The processing time amounts to 30 s per patient, facilitating time-efficient, reproducible measurements. An extended training data set, including different levels of calcification or special cases (e.g., pre-implanted valves), could further improve this method's applicability and robustness.

Selective toxicity of the anthelmintic emodepside revealed by heterologous expression of human KCNMA1 in Caenorhabditis elegans.

Emodepside is a resistance-breaking anthelmintic of a new chemical class, the cyclooctadepsipeptides. A major determinant of its anthelmintic effect is the calcium-activated potassium channel SLO-1. SLO-1 belongs to a family of channels that are highly conserved across the animal phyla and regulate neurosecretion, hormone release, muscle contraction, and neuronal network excitability. To investigate the selective toxicity of emodepside, we performed transgenic experiments in which the nematode SLO-1 channel was swapped for a mammalian ortholog, human KCNMA1. Expression of either the human channel or Caenorhabditis elegans slo-1 from the native slo-1 promoter in a C. elegans slo-1 functional null mutant rescued behavioral deficits that otherwise resulted from loss of slo-1 signaling. However, worms expressing the human channel were 10- to 100-fold less sensitive to emodepside than those expressing the nematode channel. Strains expressing the human KCNMA1 channel were preferentially sensitive to the mammalian channel agonists NS1619 and rottlerin. In the C. elegans pharyngeal nervous system, slo-1 is expressed in neurons, not muscle, and cell-specific rescue experiments have previously shown that emodepside inhibits serotonin-stimulated feeding by interfering with SLO-1 signaling in the nervous system. Here we show that ectopic overexpression of slo-1 in pharyngeal muscle confers sensitivity of the muscle to emodepside, consistent with a direct interaction of emodepside with the channel. Taken together, these data predict an emodepside-selective pharmacophore harbored by SLO-1. This has implications for the development of this drug/target interface for the treatment of helminth infections.

The putative cyclooctadepsipeptide receptor depsiphilin of the canine hookworm Ancylostoma caninum.

The G-Protein-coupled receptor Hc110-R of Haemonchus contortus and its orthologue in Caenorhabditis elegans, the latrophilin-like protein 1 (LAT-1), were shown to play a role in the mode of action of the new anthelmintic compound emodepside. C. elegans LAT-1 knockout mutants showed a decreased paralysing effect of emodepside on the pharyngeal muscle. In the present study, the LAT-1 orthologue in the canine hookworm Ancylostoma caninum was identified and named depsiphilin. To obtain more information about the regulation of this receptor and to facilitate phylogenetic and evolutionary analyses of parasitic nematode genes, the genomic structure of A. caninum depsiphilin was investigated. High consistency regarding the position of introns in comparison to C. elegans LAT-1 was observed, providing indication of the same origin of the genes. With a view to possible differences in efficacy of emodepside on different developmental stages, we analysed the transcript level of A. caninum depsiphilin in eggs, L1, L3, male and female adult worms using quantitative real-time PCR. Depsiphilin is transcribed in all five examined stages, but we found a significantly lower transcript level in third-stage larvae. A correlation between these findings and a reduced emodepside activity remains to be investigated.

The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue.

Netrin-1 is a guidance cue that can trigger either attraction or repulsion effects on migrating axons of neurons, depending on the repertoire of receptors available on the growth cone. How a single chemotropic molecule can act in such contradictory ways has long been a puzzle at the molecular level. Here we present the crystal structure of netrin-1 in complex with the Deleted in Colorectal Cancer (DCC) receptor. We show that one netrin-1 molecule can simultaneously bind to two DCC molecules through a DCC-specific site and through a unique generic receptor binding site, where sulfate ions staple together positively charged patches on both DCC and netrin-1. Furthermore, we demonstrate that UNC5A can replace DCC on the generic receptor binding site to switch the response from attraction to repulsion. We propose that the modularity of binding allows for the association of other netrin receptors at the generic binding site, eliciting alternative turning responses.

Phylogenetic characterization of ß-tubulins and development of pyrosequencing assays for benzimidazole resistance in cattle nematodes.

Control of helminth infections is a major task in livestock production to prevent health constraints and economic losses. However, resistance to established anthelmintic substances already impedes effective anthelmintic treatment in many regions worldwide. Thus, there is an obvious need for sensitive and reliable methods to assess the resistance status of at least the most important nematode populations. Several single nucleotide polymorphisms (SNPs) in the ß-tubulin isotype 1 gene of various nematodes correlate with resistance to benzimidazoles (BZ), a major anthelmintic class. Here we describe the full-length ß-tubulin isotype 1 and 2 and α-tubulin coding sequences of the cattle nematode Ostertagia ostertagi. Additionally, the Cooperia oncophora α-tubulin coding sequence was identified. Phylogenetic maximum-likelihood analysis revealed that both isotype 1 and 2 are orthologs to the Caenorhabditis elegans ben-1 gene which is also associated with BZ resistance upon mutation. In contrast, a Trichuris trichiura cDNA, postulated to be ß-tubulin isotype 1 involved in BZ resistance in this human parasite, turned out to be closely related to C. elegans ß-tubulins tbb-4 and mec-7 and would therefore represent the first non-ben-1-like ß-tubulin to be under selection through treatment with BZs. A pyrosequencing assay was established to detect BZ resistance associated SNPs in ß-tubulin isotype 1 codons 167, 198 and 200 of C. oncophora and O. ostertagi. PCR-fragments representing either of the two alleles were combined in defined ratios to evaluate the pyrosequencing assay. The correlation between the given and the measured allele frequencies of the respective SNPs was very high. Subsequently laboratory isolates and field populations with known resistance status were analyzed. With the exception of codon 167 in Cooperia, increases of resistance associated alleles were detected for all codons in at least one of the phenotypically resistant population. Pyrosequencing provides a fast, inexpensive and sensitive alternative to conventional resistance detection methods.

Decreased emodepside sensitivity in unc-49 γ-aminobutyric acid (GABA)-receptor-deficient Caenorhabditis elegans.

Emodepside, a semi-synthetic derivative of PF1022A, belongs to a new class of anthelmintic drugs, the cyclooctadepsipeptides, and shows good efficacy against macrocyclic lactone-, levamisole- or benzimidazole-resistant nematode populations. Although putative receptors for emodepside have already been discovered, its mode of action is still not fully understood. The involvement of the γ-aminobutyric acid (GABA)-receptor on the PF1022A mode of action has previously been postulated. Therefore, a possible role of the GABA-receptor, unc-49, in the mode of action of emodepside was investigated using two different Caenorhabditis elegans in vitro assays, a motility assay and a development assay. It was found that there is a clearly reduced sensitivity against emodepside of strains carrying a GABA-receptor, unc-49, loss of function mutation compared with N2 wild type C. elegans. To transfer these results from the model system to parasitic nematodes, the Toxocara canis unc-49B cDNA sequence was identified and used in a rescue experiment. The emodepside-susceptible phenotype could be fully rescued by injection of the T. canis unc-49B cDNA sequence. We believe that this is the first functional rescue of a C. elegans mutant strain with a gene from a clade III parasitic nematode. These findings, together with the earlier data on GABA-receptor binding of PF1022A, suggest that the GABA(A)-receptor UNC-49 is associated with the emodepside mode of action. However, the only partially resistant phenotype of the loss of function mutants indicates that other pathways play a more significant role.