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The use of artificial intelligence (AI) systems in biomedical and clinical settings can disrupt the traditional doctor–patient relationship, which is based on trust and transparency in medical advice and therapeutic decisions. When the diagnosis or selection of a therapy is no longer made solely by the physician, but to a significant extent by a machine using algorithms, decisions become nontransparent. Skill learning is the most common application of machine learning algorithms in clinical decision making. These are a class of very general algorithms (artificial neural networks, classifiers, etc.), which are tuned based on examples to optimize the classification of new, unseen cases. It is pointless to ask for an explanation for a decision. A detailed understanding of the mathematical details of an AI algorithm may be possible for experts in statistics or computer science. However, when it comes to the fate of human beings, this “developer’s explanation” is not sufficient. The concept of explainable AI (XAI) as a solution to this problem is attracting increasing scientific and regulatory interest. This review focuses on the requirement that XAIs must be able to explain in detail the decisions made by the AI to the experts in the field.
Sex differences in pain perception have been extensively studied, but precision medicine applications such as sex-specific pain pharmacology have barely progressed beyond proof-of-concept. A data set of pain thresholds to mechanical (blunt and punctate pressure) and thermal (heat and cold) stimuli applied to non-sensitized and sensitized (capsaicin, menthol) forearm skin of 69 male and 56 female healthy volunteers was analyzed for data structures contingent with the prior sex structure using unsupervised and supervised approaches. A working hypothesis that the relevance of sex differences could be approached via reversibility of the association, i.e., sex should be identifiable from pain thresholds, was verified with trained machine learning algorithms that could infer a person's sex in a 20% validation sample not seen to the algorithms during training, with balanced accuracy of up to 79%. This was only possible with thresholds for mechanical stimuli, but not for thermal stimuli or sensitization responses, which were not sufficient to train an algorithm that could assign sex better than by guessing or when trained with nonsense (permuted) information. This enabled the translation to the molecular level of nociceptive targets that convert mechanical but not thermal information into signals interpreted as pain, which could eventually be used for pharmacological precision medicine approaches to pain. By exploiting a key feature of machine learning, which allows for the recognition of data structures and the reduction of information to the minimum relevant, experimental human pain data could be characterized in a way that incorporates "non" logic that could be translated directly to the molecular pharmacological level, pointing toward sex-specific precision medicine for pain.
Bacteria that are capable of organizing themselves as biofilms are an important public health issue. Knowledge discovery focusing on the ability to swarm and conquer the surroundings to form persistent colonies is therefore very important for microbiological research communities that focus on a clinical perspective. Here, we demonstrate how a machine learning workflow can be used to create useful models that are capable of discriminating distinct associated growth behaviors along distinct phenotypes. Based on basic gray-scale images, we provide a processing pipeline for binary image generation, making the workflow accessible for imaging data from a wide range of devices and conditions. The workflow includes a locally estimated regression model that easily applies to growth-related data and a shape analysis using identified principal components. Finally, we apply a density-based clustering application with noise (DBSCAN) to extract and analyze characteristic, general features explained by colony shapes and areas to discriminate distinct Bacillus subtilis phenotypes. Our results suggest that the differences regarding their ability to swarm and subsequently conquer the medium that surrounds them result in characteristic features. The differences along the time scales of the distinct latency for the colony formation give insights into the ability to invade the surroundings and therefore could serve as a useful monitoring tool.
Knowledge discovery in biomedical data using supervised methods assumes that the data contain structure relevant to the class structure if a classifier can be trained to assign a case to the correct class better than by guessing. In this setting, acceptance or rejection of a scientific hypothesis may depend critically on the ability to classify cases better than randomly, without high classification performance being the primary goal. Random forests are often chosen for knowledge-discovery tasks because they are considered a powerful classifier that does not require sophisticated data transformation or hyperparameter tuning and can be regarded as a reference classifier for tabular numerical data. Here, we report a case where the failure of random forests using the default hyperparameter settings in the standard implementations of R and Python would have led to the rejection of the hypothesis that the data contained structure relevant to the class structure. After tuning the hyperparameters, classification performance increased from 56% to 65% balanced accuracy in R, and from 55% to 67% balanced accuracy in Python. More importantly, the 95% confidence intervals in the tuned versions were to the right of the value of 50% that characterizes guessing-level classification. Thus, tuning provided the desired evidence that the data structure supported the class structure of the data set. In this case, the tuning made more than a quantitative difference in the form of slightly better classification accuracy, but significantly changed the interpretation of the data set. This is especially true when classification performance is low and a small improvement increases the balanced accuracy to over 50% when guessing.
Bayesian inference is ubiquitous in science and widely used in biomedical research such as cell sorting or “omics” approaches, as well as in machine learning (ML), artificial neural networks, and “big data” applications. However, the calculation is not robust in regions of low evidence. In cases where one group has a lower mean but a higher variance than another group, new cases with larger values are implausibly assigned to the group with typically smaller values. An approach for a robust extension of Bayesian inference is proposed that proceeds in two main steps starting from the Bayesian posterior probabilities. First, cases with low evidence are labeled as “uncertain” class membership. The boundary for low probabilities of class assignment (threshold 𝜀
) is calculated using a computed ABC analysis as a data-based technique for item categorization. This leaves a number of cases with uncertain classification (p < 𝜀
). Second, cases with uncertain class membership are relabeled based on the distance to neighboring classified cases based on Voronoi cells. The approach is demonstrated on biomedical data typically analyzed with Bayesian statistics, such as flow cytometric data sets or biomarkers used in medical diagnostics, where it increased the class assignment accuracy by 1–10% depending on the data set. The proposed extension of the Bayesian inference of class membership can be used to obtain robust and plausible class assignments even for data at the extremes of the distribution and/or for which evidence is weak.
In dengue-endemic countries such as Indonesia, Zika may be misdiagnosed as dengue, leading to underestimates of Zika disease and less foreknowledge of pregnancy-related complications such as microcephaly. Objective: To assess the attitudes of frontline physicians in a dengue-endemic country toward testing for Zika infection among patients with dengue-like illnesses. Methods: A cross-sectional online survey was conducted among general practitioners (GPs) in Indonesia. The survey assessed their attitude and also collected sociodemographic data, characteristics of their medical education, professional background, and workplace, and exposure to Zika cases. A two-step logistic regression analysis was used to assess possible variables associated with these attitudes. Results: A total of 370 GPs were included in the final analysis of which 70.8% had good attitude. Unadjusted analyses suggested that GPs who were 30 years old or older and those who had medical experience five years or longer had lower odds of having a positive attitude compared to those who aged younger than 30 years and those who had medical experience less than five years, OR: 0.58; 95%CI: 0.37, 0.91 and OR: 0.55; 95%CI: 0.35, 0.86, respectively. No explanatory variable was associated with attitude in the fully adjusted model. Conclusion: Our findings point to younger GPs with a shorter medical experience being more likely to consider testing for Zika infection among their patients presenting with dengue-like illnesses. Strategic initiatives may be needed to enhance older or longer-experienced physicians' capacity in diagnosing Zika infection.
BH3 mimetics are promising novel anticancer therapeutics. By selectively inhibiting BCL-2, BCL-xL, or MCL-1 (i.e. ABT-199, A-1331852, S63845) they shift the balance of pro- and anti-apoptotic proteins in favor of apoptosis. As Bromodomain and Extra Terminal (BET) protein inhibitors promote pro-apoptotic rebalancing, we evaluated the potential of the BET inhibitor JQ1 in combination with ABT-199, A-1331852 or S63845 in rhabdomyosarcoma (RMS) cells. The strongest synergistic interaction was identified for JQ1/A-1331852 and JQ1/S63845 co-treatment, which reduced cell viability and long-term clonogenic survival. Mechanistic studies revealed that JQ1 upregulated BIM and NOXA accompanied by downregulation of BCL-xL, promoting pro-apoptotic rebalancing of BCL-2 proteins. JQ1/A-1331852 and JQ1/S63845 co-treatment enhanced this pro-apoptotic rebalancing and triggered BAK- and BAX-dependent apoptosis since a) genetic silencing of BIM, BAK or BAX, b) inhibition of caspase activity with zVAD.fmk and c) overexpression of BCL-2 all rescued JQ1/A-1331852- and JQ1/S63845-induced cell death. Interestingly, NOXA played a different role in both treatments, as genetic silencing of NOXA significantly rescued from JQ1/A-1331852-mediated apoptosis but not from JQ1/S63845-mediated apoptosis. In summary, JQ1/A-1331852 and JQ1/S63845 co-treatment represent new promising therapeutic strategies to synergistically trigger mitochondrial apoptosis in RMS.
Burkitt's lymphoma (BL) is a highly aggressive form of B-cell non-Hodgkin's lymphoma. The clinical outcome in children with BL has improved over the last years but the prognosis for adults is still poor, highlighting the need for novel treatment strategies. Here, we report that the combinational treatment with the Smac mimetic BV6 and TRAIL triggers necroptosis in BL when caspases are blocked by zVAD.fmk (TBZ treatment). The sensitivity of BL cells to TBZ correlates with MLKL expression. We demonstrate that necroptotic signaling critically depends on MLKL, since siRNA-induced knockdown and CRISPR/Cas9-mediated knockout of MLKL profoundly protect BL cells from TBZ-induced necroptosis. Conversely, MLKL overexpression in cell lines expressing low levels of MLKL leads to necroptosis induction, which can be rescued by pharmacological inhibitors, highlighting the important role of MLKL for necroptosis execution. Importantly, the methylation status analysis of the MLKL promoter reveals a correlation between methylation and MLKL expression. Thus, MLKL is epigenetically regulated in BL and might serve as a prognostic marker for treatment success of necroptosis-based therapies. These findings have crucial implications for the development of new treatment options for BL.
The evaluation of pharmacological data using machine learning requires high data quality. Therefore, data preprocessing, that is, cleaning analytical laboratory errors, replacing missing values or outliers, and transforming data adequately before actual data analysis, is crucial. Because current tools available for this purpose often require programming skills, preprocessing tools with graphical user interfaces that can be used interactively are needed. In collaboration between data scientists and experts in bioanalytical diagnostics, a graphical software package for data preprocessing called pguIMP is proposed, which contains a fixed sequence of preprocessing steps to enable reproducible interactive data preprocessing. As an R-based package, it also allows direct integration into this data science environment without requiring any programming knowledge. The implementation of contemporary data processing methods, including machine-learning-based imputation techniques, ensures the generation of corrected and cleaned bioanalytical data sets that preserve data structures such as clusters better than is possible with classical methods. This was evaluated on bioanalytical data sets from lipidomics and drug research using k-nearest-neighbors-based imputation followed by k-means clustering and density-based spatial clustering of applications with noise. The R package provides a Shiny-based web interface designed to be easy to use for non–data analysis experts. It is demonstrated that the spectrum of methods provided is suitable as a standard pipeline for preprocessing bioanalytical data in biomedical research domains. The R package pguIMP is freely available at the comprehensive R archive network (https://cran.r-project.org/web/packages/pguIMP/index.html).
Background: Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound by transcription factors (TFs). Differential expression of TFs and their binding affinity at putative CREs determine tissue- and developmental-specific transcriptional activity. Consolidating genomic data sets can offer further insights into the accessibility of CREs, TF activity, and, thus, gene regulation. However, the integration and analysis of multi-modal data sets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined chromatin state data (e.g., ChIP-seq, ATAC-seq, or DNase-seq) and RNA-seq data exist, they do not offer convenient usability, have limited support for large-scale data processing, and provide only minimal functionality for visually interpreting results.
Results: We developed TF-Prioritizer, an automated pipeline that prioritizes condition-specific TFs from multi-modal data and generates an interactive web report. We demonstrated its potential by identifying known TFs along with their target genes, as well as previously unreported TFs active in lactating mouse mammary glands. Additionally, we studied a variety of ENCODE data sets for cell lines K562 and MCF-7, including twelve histone modification ChIP-seq as well as ATAC-seq and DNase-seq datasets, where we observe and discuss assay-specific differences.
Conclusion: TF-Prioritizer accepts ATAC-seq, DNase-seq, or ChIP-seq and RNA-seq data as input and identifies TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.
Background Eukaryotic gene expression is controlled by cis-regulatory elements (CREs) including promoters and enhancers which are bound by transcription factors (TFs). Differential expression of TFs and their putative binding sites on CREs cause tissue and developmental-specific transcriptional activity. Consolidating genomic data sets can offer further insights into the accessibility of CREs, TF activity, and thus gene regulation. However, the integration and analysis of multi-modal data sets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined ChIP-seq and RNA-seq data exist, they do not offer good usability, have limited support for large-scale data processing, and provide only minimal functionality for visual result interpretation.
Results We developed TF-Prioritizer, an automated java pipeline to prioritize condition-specific TFs derived from multi-modal data. TF-Prioritizer creates an interactive, feature-rich, and user-friendly web report of its results. To showcase the potential of TF-Prioritizer, we identified known active TFs (e.g., Stat5, Elf5, Nfib, Esr1), their target genes (e.g., milk proteins and cell-cycle genes), and newly classified lactating mammary gland TFs (e.g., Creb1, Arnt).
Conclusion TF-Prioritizer accepts ChIP-seq and RNA-seq data, as input and suggests TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.
Co-targeting MCL-1 and ERK1/2 kinase induces mitochondrial apoptosis in rhabdomyosarcoma cells
(2021)
The RAS/MEK/ERK genetic axis is commonly altered in rhabdomyosarcoma (RMS), indicating high activity of downstream effector ERK1/2 kinase. Previously, we have demonstrated that inhibition of the RAS/MEK/ERK signaling pathway in RMS is insufficient to induce cell death due to residual pro-survival MCL-1 activity. Here, we show that the combination of ERK1/2 inhibitor Ulixertinib and MCL-1 inhibitor S63845 is highly synergistic and induces apoptotic cell death in RMS in vitro and in vivo. Importantly, Ulixertinib/S63845 co-treatment suppresses long-term survival of RMS cells, induces rapid caspase activation and caspase-dependent apoptosis. Mechanistically, Ulixertinib-mediated upregulation of BIM and BMF in combination with MCL-1 inhibition by S63845 shifts the balance of BCL-2 proteins towards a pro-apoptotic state resulting in apoptosis induction. A genetic silencing approach reveals that BIM, BMF, BAK and BAX are all required for Ulixertinib/S63845-induced apoptosis. Overexpression of BCL-2 rescues cell death triggered by Ulixertinib/S63845 co-treatment, confirming that combined inhibition of ERK1/2 and MCL-1 effectively induces cell death of RMS cells via the intrinsic mitochondrial apoptotic pathway. Thus, this study is the first to demonstrate the cytotoxic potency of co-inhibition of ERK1/2 and MCL-1 for RMS treatment.
This survey reports on the DNA identification and occurrence of Culex torrentium and Cx. pipiens s.s. in Belgium. These native disease-vector mosquito species are morphologically difficult to separate, and the biotypes of Cx. pipiens s.s. are morphologically indistinguishable. Culex torrentium and Cx. pipiens s.s. were identified using the COI and ACE2 loci. We recorded 1248 Cx. pipiens s.s. and 401 Cx. torrentium specimens from 24 locations in Belgium (collected between 2017 and 2019). Culex pipiens biotypes pipiens and molestus, and their hybrids, were differentiated using fragment-size analysis of the CQ11 locus (956 pipiens and 227 molestus biotype specimens, 29 hybrids). Hybrids were observed at 13 out of 16 sympatric sites. These results confirm that both species are widespread in Belgium, but while Cx. torrentium revealed many COI haplotypes, Cx. pipiens s.s. showed only one abundant haplotype. This latter observation may either reflect a recent population-wide demographic or range expansion, or a recent bottleneck, possibly linked to a Wolbachia infection. Finally, new evidence is provided for the asymmetric but limited introgression of the molestus biotype into the pipiens biotype.
Most sRNA biogenesis mechanisms involve either RNAseIII cleavage or ping-pong amplification by different Piwi proteins harboring slicer activity. Here, we follow the question why the mechanism of transgene-induced silencing in the ciliate Paramecium needs both Dicer activity and two Ptiwi proteins. This pathway involves primary siRNAs produced from non-translatable transgenes and secondary siRNAs from endogenous remote loci. Our data does not indicate any signatures from ping-pong amplification but Dicer cleavage of long dsRNA. We show that Ptiwi13 and 14 have different preferences for primary and secondary siRNAs but do not load them mutually exclusive. Both Piwis enrich for antisense RNAs and Ptiwi14 loaded siRNAs show a 5′-U signature. Both Ptiwis show in addition a general preference for Uridine-rich sRNAs along the entire sRNA length. Our data indicates both Ptiwis and 2’-O-methylation to contribute to strand selection of Dicer cleaved siRNAs. This unexpected function of two distinct vegetative Piwis extends the increasing knowledge of the diversity of Piwi functions in diverse silencing pathways. As both Ptiwis show differential subcellular localisation, Ptiwi13 in the cytoplasm and Ptiwi14 in the vegetative macronucleus, we conclude that cytosolic and nuclear silencing factors are necessary for efficient chromatin silencing.
The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics, including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin, our study characterizes the functional epigenomic organization necessary for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) reveal no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicate H3K4me3 levels inside ORFs to be the main factor associated with gene expression, and H3K27me3 appears in association with H3K4me3 in plastic genes. Silent and lowly expressed genes show low nucleosome occupancy, suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Because of a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different from that of other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data imply that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. In summary, gene activation and silencing in Paramecium run counter to the current understanding of chromatin biology.
Background: Blood donation saves lives. Provided they are in good health, male volunteers can donate as often as six times per year from the age of 18 into their late sixties. The burden of blood donation is very unevenly distributed, with a small minority of altruistic individuals providing this critical resource. While the consequences of persistent iron depletion in blood donors have been studied in the context of cancer and coronary heart disease, potential effects of the erythropoietic stress from repetitive large-volume phlebotomy remain unexplored. We sought to investigate if and how repeated blood donations affect the clonal composition of the hematopoietic stem and progenitor cell (HSPC) compartment.
Methods: 105 healthy, male individuals with an extensive blood donation history (median of 120 donations per donor; median age of 66 yrs.) were screened for the presence of clonal hematopoiesis (CH) using a sequencing panel covering 141 genes commonly mutated in human myeloid neoplasms. The control cohort consisted of 103 healthy, male donors with a median of 5 donations per donor and a median age of 63. Donors positive for CH were subsequently studied longitudinally. The pathogenicity of detected variants was compared using established scoring systems. Finally, to assess the functional consequences of blood-donation induced CH, selected CH mutations were introduced by CRISPR-mediated editing into HSPCs from human cord blood (CB) or bone marrow (BM). The effect of these mutations was tested under different stress stimuli using functional ex vivo long-term culture initiating cells (LTC-IC) assays.
Results: Compared to the control cohort, frequent donors were significantly more likely to have mutations in genes encoding for epigenetic modifiers (44.7 vs. 22.3 %), most specifically in the two genes most commonly mutated in CH, DNMT3A and TET2 (35.2 vs. 20.3 %). However, no difference in the variant allele frequency (VAF) of detected mutations was found between the groups. Longitudinal analysis revealed that the majority of the mutations remained at a stable VAF over an observation period of approximately one year. Three DNMT3A variants from the frequent donor cohort were introduced into healthy HSPCs and functionally analyzed: All expanded in response to EPO, but none responded to LPS or IFNγ stimulation. This contrasted with the leukemogenic DNMT3A R882H mutation, which did not expand in the presence of EPO but instead responded strongly to inflammatory stimuli.
Conclusions: Frequent whole blood donation is associated with a higher prevalence of CH driven by mutations in genes encoding for epigenetic modifiers, with DNMT3A and TET2 being the most common. This increased CH prevalence is not associated with a higher pathogenicity of the associated variants and is likely a result of the selection of clones with improved responsiveness to EPO under the condition of bleeding stress. Our data show that even highly frequent blood donations over many years is not increasing the risk for malignant clones further underscoring the safety of repetitive blood donations. To our knowledge, this is the first CH study analyzing a cohort of individuals known for their superior health and survival, able to donate blood until advanced age. Thus, our analysis possibly identified mutations associated with beneficial outcomes, rather than a disease condition, such as mutations in DNMT3A that mediated the improved expansion of HSPCs in EPO enriched environments. Our data support the notion of ongoing Darwinian evolution in humans at the somatic stem cell level and present EPO as one of the environmental factors to which HSPCs with specific mutations may respond with superior fitness.
Objective: This paper presents a novel digital workflow that expedites and facilitates the manufacturing of high-end full-ceramic restorations based on “Print and Press”-Technology combined with 3D-printed colored 3D-models.
Clinical considerations: Despite ongoing innovations and developments in the digital workflow, the precision, and the final esthetic outcome is still limited compared with conventional press ceramics. The proposed method combines the advantages of digital scan- and design technologies with the proven conventional press-technology to accomplish high-end full-ceramic restorations. The restoration is digitally designed, the data set is 3D-printed in resin that can be burned out, subsequently conventionally embedded and pressed. Final esthetic finishing of the partial restorations is done on a 3D-printed physical colored 3D-model.
Conclusion: The report describes synergetic effects of digital and analog procedures. 3D-printed colored 3D-models can positively support the manufacturing of full ceramic restorations regarding their optical integration. Therefore, the use of 3D-printed colored 3D-models signifies a new innovative technique with many promising application areas.
Clinical significance: The combination of excellent clinical long-term data for pressed ceramic restorations and proven digital processes, like intraoral scanning, design, and additive manufacturing, in the dental field promise an individual workflow for predictability and excellent esthetics.
Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease of the hair follicles leading to painful lesions, associated with increased levels of pro-inflammatory cytokines. Numerous guidelines recommend antibiotics like clindamycin and rifampicin in combination, as first-line systemic therapy in moderate-to-severe forms of inflammation. HS has been proposed to be mainly an auto-inflammatory disease associated with but not initially provoked by bacteria. Therefore, it has to be assumed that the pro-inflammatory milieu previously observed in HS skin is not solely dampened by the bacteriostatic inhibition of DNA-dependent RNA polymerase. To further clarify the mechanism of anti-inflammatory effects of rifampicin, ex vivo explants of lesional HS from 8 HS patients were treated with rifampicin, and its effect on cytokine production, immune cells as well as the expression of Toll-like receptor 2 (TLR2) were investigated. Analysis of cell culture medium of rifampicin-treated HS explants revealed an anti-inflammatory effect of rifampicin that significantly inhibiting interleukin (IL)-1β, IL-6, IL-8, IL-10 and tumour necrosis factor (TNF)-α production. Immunohistochemistry of the rifampicin-treated explants suggested a tendency for it to reduce the expression of TLR2 while not affecting the number of immune cells.
In gastric cancer (GC), there are four molecular subclasses that indicate whether patients respond to chemotherapy or immunotherapy, according to the TCGA. In clinical practice, however, not every patient undergoes molecular testing. Many laboratories have used well-implemented in situ techniques (IHC and EBER-ISH) to determine the subclasses in their cohorts. Although multiple stains are used, we show that a staining approach is unable to correctly discriminate all subclasses. As an alternative, we trained an ensemble convolutional neuronal network using bagging that can predict the molecular subclass directly from hematoxylin–eosin histology. We also identified patients with predicted intra-tumoral heterogeneity or with features from multiple subclasses, which challenges the postulated TCGA-based decision tree for GC subtyping. In the future, deep learning may enable targeted testing for molecular subtypes and targeted therapy for a broader group of GC patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Non-organ confined stage and upgrading rates in exclusive PSA high-risk prostate cancer patients
(2022)
Background: The pathological stage of prostate cancer with high-risk prostate-specific antigen (PSA) levels, but otherwise favorable and/or intermediate risk characteristics (clinical T-stage, Gleason Grade group at biopsy [B-GGG]) is unknown. We hypothesized that a considerable proportion of such patients will exhibit clinically meaningful GGG upgrading or non-organ confined (NOC) stage at radical prostatectomy (RP).
Materials and methods: Within the Surveillance, Epidemiology, and End Results database (2010–2015) we identified RP-patients with cT1c-stage and B-GGG1, B-GGG2, or B-GGG3 and PSA 20–50 ng/ml. Rates of GGG4 or GGG5 and/or rates of NOC stage (≥ pT3 and/or pN1) were analyzed. Subsequently, separate univariable and multivariable logistic regression models tested for predictors of NOC stage and upgrading at RP.
Results: Of 486 assessable patients, 134 (28%) exhibited B-GGG1, 209 (43%) B-GGG2, and 143 (29%) B-GGG3, respectively. The overall upgrading and NOC rates were 11% and 51% for a combined rate of upgrading and/or NOC stage of 53%. In multivariable logistic regression models predicting upgrading, only B-GGG3 was an independent predictor (odds ratio [OR]: 5.29; 95% confidence interval [CI]: 2.21–14.19; p < 0.001). Conversely, 33%–66% (OR: 2.36; 95% CI: 1.42–3.95; p = 0.001) and >66% of positive biopsy cores (OR: 4.85; 95% CI: 2.84–8.42; p < 0.001), as well as B-GGG2 and B-GGG3 were independent predictors for NOC stage (all p ≤ 0.001).
Conclusions: In cT1c-stage patients with high-risk PSA baseline, but low- to intermediate risk B-GGG, the rate of upgrading to GGG4 or GGG5 is low (11%). However, NOC stage is found in the majority (51%) and can be independently predicted with percentage of positive cores at biopsy and B-GGG.
Background: No North-American study tested the survival benefit of chemotherapy in de novo metastatic prostate cancer according to race/ethnicity. We addressed this void.
Methods: We identified de novo metastatic prostate cancer patients within the Surveillance, Epidemiology, and End Results database (2014–2015). Separate and specific Kaplan–Meier plots and Cox regression models tested for overall survival differences between chemotherapy-exposed versus chemotherapy-naïve patients in four race/ethnicity groups: Caucasian versus African-American versus Hispanic/Latino vs Asian. Race/ethnicity specific propensity score matching was applied. Here, additional landmark analysis was performed.
Results: Of 4232 de novo metastatic prostate cancer patients, 2690 (63.3%) were Caucasian versus 783 (18.5%) African-American versus 504 (11.8%) Hispanic/Latino versus 257 (6.1%) Asian. Chemotherapy rates were: 21.3% versus 20.8% versus 21.0% versus 20.2% for Caucasians versus African-Americans versus Hispanic/Latinos versus Asians, respectively. At 30 months of follow-up, overall survival rates between chemotherapy-exposed versus chemotherapy-naïve patients were 61.5 versus 53.2% (multivariable hazard ratio [mHR]: 0.76, 95 confidence interval [CI]: 0.63–0.92, p = 0.004) in Caucasians, 55.2 versus 51.6% (mHR: 0.76, 95 CI: 0.54–1.07, p = 0.11) in African-Americans, 62.8 versus 57.0% (mHR: 1.11, 95 CI: 0.73–1.71, p = 0.61) in Hispanic/Latinos and 77.7 versus 65.0% (mHR: 0.31, 95 CI: 0.11–0.89, p = 0.03) in Asians. Virtually the same findings were recorded after propensity score matching within each race/ethnicity group.
Conclusions: Caucasian and Asian de novo metastatic prostate cancer patients exhibit the greatest overall survival benefit from chemotherapy exposure. Conversely, no overall survival benefit from chemotherapy exposure could be identified in either African-Americans or Hispanic/Latinos. Further studies are clearly needed to address these race/ethnicity specific disparities.
Long non-coding RNAs were once considered as “junk” RNA produced by aberrant DNA transcription. They are now understood to play central roles in diverse cellular processes from proliferation and migration to differentiation, senescence and DNA damage control. LncRNAs are classed as transcripts longer than 200 nucleotides that do not encode a peptide. They are relevant to many physiological and pathophysiological processes through their control of fundamental molecular functions. This review summarises the recent progress in lncRNA research and highlights the far-reaching physiological relevance of lncRNAs. The main areas of lncRNA research encompassing their characterisation, classification and mechanisms of action will be discussed. In particular, the regulation of gene expression and chromatin landscape through lncRNA control of proteins, DNA and other RNAs will be introduced. This will be exemplified with a selected number of lncRNAs that have been described in numerous physiological contexts and that should be largely representative of the tens-of-thousands of mammalian lncRNAs. To some extent, these lncRNAs have inspired the current thinking on the central dogmas of epigenetics, RNA and DNA mechanisms.
Polo-like kinase 1 (PLK1) is a crucial regulator of cell cycle progression. It is established that the activation of PLK1 depends on the coordinated action of Aurora-A and Bora. Nevertheless, very little is known about the spatiotemporal regulation of PLK1 during G2, specifically, the mechanisms that keep cytoplasmic PLK1 inactive until shortly before mitosis onset. Here, we describe PLK1 dimerization as a new mechanism that controls PLK1 activation. During the early G2 phase, Bora supports transient PLK1 dimerization, thus fine-tuning the timely regulated activation of PLK1 and modulating its nuclear entry. At late G2, the phosphorylation of T210 by Aurora-A triggers dimer dissociation and generates active PLK1 monomers that support entry into mitosis. Interfering with this critical PLK1 dimer/monomer switch prevents the association of PLK1 with importins, limiting its nuclear shuttling, and causes nuclear PLK1 mislocalization during the G2-M transition. Our results suggest a novel conformational space for the design of a new generation of PLK1 inhibitors.
Nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) can show variable histological growth patterns and present remarkable overlap with T-cell/histiocyte-rich large B-cell lymphoma (THRLBCL). Previous studies suggest that NLPHL histological variants represent progression forms of NLPHL and THRLBCL transformation in aggressive disease. Since molecular studies of both lymphomas are limited due to the low number of tumor cells, the present study aimed to learn if a better understanding of these lymphomas is possible via detailed measurements of nuclear and cell size features in 2D and 3D sections. Whereas no significant differences were visible in 2D analyses, a slightly increased nuclear volume and a significantly enlarged cell size were noted in 3D measurements of the tumor cells of THRLBCL in comparison to typical NLPHL cases. Interestingly, not only was the size of the tumor cells increased in THRLBCL but also the nuclear volume of concomitant T cells in the reactive infiltrate when compared with typical NLPHL. Particularly CD8+ T cells had frequent contacts to tumor cells of THRLBCL. However, the nuclear volume of B cells was comparable in all cases. These results clearly demonstrate that 3D tissue analyses are superior to conventional 2D analyses of histological sections. Furthermore, the results point to a strong activation of T cells in THRLBCL, representing a cytotoxic response against the tumor cells with unclear effectiveness, resulting in enhanced swelling of the tumor cell bodies and limiting proliferative potential. Further molecular studies combining 3D tissue analyses and molecular data will help to gain profound insight into these ill-defined cellular processes.
Hepatocellular carcinoma (HCC) is one of the most difficult cancer types to treat. Liver cancer is often diagnosed at late stages and therapeutic treatment is frequently accompanied by development of multidrug resistance. This leads to poor outcomes for cancer patients. Understanding the fundamental molecular mechanisms leading to liver cancer development is crucial for developing new therapeutic approaches, which are more efficient in treating cancer. Mice with a liver specific UDP-glucose ceramide glucosyltransferase (UGCG) knockout (KO) show delayed diethylnitrosamine (DEN)-induced liver tumor growth. Accordingly, the rationale for our study was to determine whether UGCG overexpression is sufficient to drive cancer phenotypes in liver cells. We investigated the effect of UGCG overexpression (OE) on normal murine liver (NMuLi) cells. Increased UGCG expression results in decreased mitochondrial respiration and glycolysis, which is reversible by treatment with EtDO-P4, an UGCG inhibitor. Furthermore, tumor markers such as FGF21 and EPCAM are lowered following UGCG OE, which could be related to glucosylceramide (GlcCer) and lactosylceramide (LacCer) accumulation in glycosphingolipid-enriched microdomains (GEMs) and subsequently altered signaling protein phosphorylation. These cellular processes lead to decreased proliferation in NMuLi/UGCG OE cells. Our data show that increased UGCG expression itself does not induce pro-cancerous processes in normal liver cells, which indicates that increased GlcCer expression leads to different outcomes in different cancer types.
The impact of GABAergic transmission on neuronal excitability depends on the Cl--gradient across membranes. However, the Cl--fluxes through GABAA receptors alter the intracellular Cl- concentration ([Cl-]i) and in turn attenuate GABAergic responses, a process termed ionic plasticity. Recently it has been shown that coincident glutamatergic inputs significantly affect ionic plasticity. Yet how the [Cl-]i changes depend on the properties of glutamatergic inputs and their spatiotemporal relation to GABAergic stimuli is unknown. To investigate this issue, we used compartmental biophysical models of Cl- dynamics simulating either a simple ball-and-stick topology or a reconstructed CA3 neuron. These computational experiments demonstrated that glutamatergic co-stimulation enhances GABA receptor-mediated Cl- influx at low and attenuates or reverses the Cl- efflux at high initial [Cl-]i. The size of glutamatergic influence on GABAergic Cl--fluxes depends on the conductance, decay kinetics, and localization of glutamatergic inputs. Surprisingly, the glutamatergic shift in GABAergic Cl--fluxes is invariant to latencies between GABAergic and glutamatergic inputs over a substantial interval. In agreement with experimental data, simulations in a reconstructed CA3 pyramidal neuron with physiological patterns of correlated activity revealed that coincident glutamatergic synaptic inputs contribute significantly to the activity-dependent [Cl-]i changes. Whereas the influence of spatial correlation between distributed glutamatergic and GABAergic inputs was negligible, their temporal correlation played a significant role. In summary, our results demonstrate that glutamatergic co-stimulation had a substantial impact on ionic plasticity of GABAergic responses, enhancing the attenuation of GABAergic inhibition in the mature nervous systems, but suppressing GABAergic [Cl-]i changes in the immature brain. Therefore, glutamatergic shift in GABAergic Cl--fluxes should be considered as a relevant factor of short-term plasticity.
Purpose: To compare the effective lens position (ELP), anterior chamber depth (ACD) changes, and visual outcomes in patients with and without pseudoexfoliation syndrome (PEX) after cataract surgery.
Design: Prospective, randomized, fellow-eye controlled clinical case series.
Methods: This prospective comparative case series enrolled 56 eyes of 56 consecutive patients with (n = 28) or without PEX (n = 28) and clinically significant cataract who underwent standard phacoemulsification and were implanted with single-piece acrylic posterior chamber intraocular lenses (IOLs). The primary outcome parameters were the ACD referring to the distance between the corneal anterior surface and the lens anterior surface, which is an indicator of the postoperative axial position of the IOL (the so-called ELP) and distance corrected visual acuity (DCVA).
Results: Before surgery, the ACD was 2.54 ± 0.42 mm in the PEX group and 2.53 ± 0.38 mm in the control group (p = 0.941). Postoperatively, the ACD was 4.29 ± 0.71 mm in the PEX group and 4.33 ± 0.72 mm in the normal group, respectively (p = 0.533). There was no significant difference in ACD changes between groups (PEX group: 1.75 ± 0.74 mm, control group: 1.81 ± 0.61 mm, p = 0.806) and DCVA pre- (p = 0.469) and postoperatively (PEX group: 0.11 ± 0.13 logMAR, control group: 0.09 ± 0.17 logMAR, p = 0.245) between groups.
Conclusion: Preoperative and postoperative ACD, as an indicator of ELP, between PEX eyes and healthy eyes after cataract surgery showed no significant difference. Phacoemulsification induced similar changes in eyes with PEX compared to healthy eyes.
Background: Sodium bituminosulfonate is derived from naturally occurring sulphur-rich oil shale and is used for the treatment of the inflammatory skin disease rosacea. Major molecular players in the development of rosacea include the release of enzymes that process antimicrobial peptides which, together with reactive oxygen species (ROS) and vascular endothelial growth factor (VEGF), promote pro-inflammatory processes and angiogenesis. The aim of this study was to address the molecular mechanism(s) underlying the therapeutic benefit of the formulation sodium bituminosulfonate dry substance (SBDS), which is indicated for the treatment of skin inflammation, including rosacea.
Methods: We investigated whether SBDS regulates the expression of cytokines, the release of the antimicrobial peptide LL-37, calcium mobilization, proteases (matrix metalloproteinase, elastase, kallikrein (KLK)5), VEGF or ROS in primary human neutrophils. In addition, activity assays with 5-lipoxygenase (5-LO) and recombinant human MMP9 and KLK5 were performed.
Results: We observed that SBDS reduces the release of the antimicrobial peptide LL-37, calcium, elastase, ROS and VEGF from neutrophils. Moreover, KLK5, the enzyme that converts cathelicidin to LL-37, and 5-LO that produces leukotriene (LT)A4, the precursor of LTB4, were both inhibited by SBDS with an IC50 of 7.6 μg/mL and 33 μg/mL, respectively.
Conclusion: Since LTB4 induces LL-37 which, in turn, promotes increased intracellular calcium levels and thereby, ROS/VEGF/elastase release, SBDS possibly regulates the LTB4/LL-37/calcium – ROS/VEGF/elastase axis by inhibiting 5-LO and KLK5. Additional direct effects on other pro-inflammatory pathways such as ROS generation cannot be ruled out. In summary, SBDS reduces the generation of inflammatory mediators from human neutrophils possibly accounting for its anti-inflammatory effects in rosacea.
Effects of foam rolling duration on tissue stiffness and perfusion: a randomized cross-over trial
(2021)
Despite its beneficial effects on flexibility and muscle soreness, there is still conflicting evidence regarding dose-response relationships and underlying mechanisms of foam rolling (FR). This study aimed to investigate the impact of different FR protocols on tissue perfusion and tissue stiffness. In a randomized crossover trial, two FR protocols (2x1 min, 2x3 min) were applied to the right anterior thigh of twenty healthy volunteers (11 females, 25 ± 4 years). Tissue perfusion (near infrared spectroscopy, NIRS) and stiffness (Tensiomyography, TMG and Myotonometry, MMT) were assessed before and after FR application. Variance analyses revealed a significant interaction of FR duration and tissue perfusion (F[1,19] = 7.098, p = 0.015). Local blood flow increased significantly from pre to post test (F[1,19] = 7.589, p = 0.013), being higher (Δ +9.7%) in the long-FR condition than in the short-FR condition (Δ +2.8%). Tissue stiffness (MMT) showed significant main effects for time (F[1,19] = 12.074, p = 0.003) and condition (F[1,19] = 7.165, p = 0.015) with decreases after short-FR (Δ -1.6%) and long-FR condition (Δ -1.9%). However, there was no time*dose-interaction (F[1,19] = 0.018, p = 0.895). No differences were found for TMG (p > 0.05). FR-induced changes failed to exceed the minimal detectable change threshold (MDC). Our data suggest that increased blood flow and altered tissue stiffness may mediate the effects of FR although statistical MDC thresholds were not achieved. Longer FR durations seem to be more beneficial for perfusion which is of interest for exercise professionals designing warm-up and cool-down regimes. Further research is needed to understand probable effects on parasympathetic outcomes representing systemic physiological responses to locally applied FR stimulations.
Introduction and hypothesis: We conducted a systematic review of the effectiveness of local preemptive analgesia for postoperative pain control in women undergoing vaginal hysterectomy.
Methods: MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials and the Cochrane Database of Systematic Reviews were searched systematically to identify eligible studies published through September 25, 2019. Only randomized controlled trials and systematic reviews addressing local preemptive analgesia compared to placebo at vaginal hysterectomy were considered. Data were extracted by two independent reviewers. Results were compared, and disagreement was resolved by discussion. Forty-seven studies met inclusion criteria for full-text review. Four RCTs, including a total of 197 patients, and two SRs were included in the review.
Results: Preemptive local analgesia reduced postoperative pain scores up to 6 h and postoperative opioid requirements in the first 24 h after surgery.
Conclusion: Preemptive local analgesia at vaginal hysterectomy results in less postoperative pain and less postoperative opioid consumption.
Background: Iron deficiency anemia is common in pregnancy with a prevalence of approximately 16% in Austria; however, international guideline recommendations on screening and subsequent treatment with iron preparations are inconsistent. The aim of this study was to find out how often pregnant women take iron-containing supplements, and who recommended them. As hemoglobin data were available for a sub-group of women, hemoglobin status during pregnancy and associated consumption of iron-containing medications were also recorded.
Methods: This cross-sectional study was conducted at the Mother-Child-Booklet service center of the Styrian Health Insurance Fund in Graz, Austria. A questionnaire containing seven questions was developed. Absolute and relative numbers were determined, and corresponding 95% confidence intervals calculated using bootstrapping techniques.
Results: A total of 325 women completed the questionnaire, 11% had been diagnosed with anemia before becoming pregnant, 67% reported taking iron-containing compounds. The women reported taking 45 different products but 61% took 1 of 3 different supplements. Overall, 185 (57%) women had not been diagnosed with anemia before becoming pregnant but reported taking an iron-containing supplement and 89% of the women took supplements on the recommendation of their physician. Of the 202 women whose hemoglobin status was assessed, 92% were found not to be anemic.
Conclusion: Overall, 67% of pregnant women took iron-containing compounds, irrespective of whether they were deficient in iron. Physicians were generally responsible for advising them to take them. No standardized procedure is available on which to base the decision whether to take iron during pregnancy, even in guidelines. As most guidelines only recommend taking iron supplements in cases of anemia, the high percentage of women taking them in Austria is incomprehensible.e
Background Coronavirus disease 2019 (COVID-19) represents a significant challenge to health care systems around the world. A well-functioning primary care system is crucial in epidemic situations as it plays an important role in the development of a system-wide response.
Methods 2,187 Austrian and German GPs answered an internet suvey on preparedness, testing, staff protection, perception of risk, self-confidence, a decrease in the number of patient contacts, and efforts to control the spread of the virus in the practice during the early phase of the COVID-pandemic (3rd to 30th April).
Results The completion rate of the questionnaire was high (90.9%). GPs gave low ratings to their preparedness for a pandemic, testing of suspected cases and efforts to protect staff. The provision of information to GPs and the perception of risk were rated as moderate. On the other hand, the participants rated their self-confidence, a decrease in patient contacts and their efforts to control the spread of the disease highly.
Conclusion Primary care is an important resource for dealing with a pandemic like COVID-19. The workforce is confident and willing to take an active role, but needs to be provided with the appropriate surrounding conditions. This will require that certain conditions are met.
Registration Trial registration at the German Clinical Trials Register: DRKS00021231
Background: Coronavirus disease 2019 (COVID-19) represents a significant challenge to health care systems around the world. A well-functioning primary care system is crucial in epidemic situations as it plays an important role in the development of a system-wide response.
Methods: 2,187 Austrian and German GPs answered an internet survey on preparedness, testing, staff protection, perception of risk, self-confidence, a decrease in the number of patient contacts, and efforts to control the spread of the virus in the practice during the early phase of the COVID-pandemic (3rd to 30th April).
Results: The completion rate of the questionnaire was high (90.9%). GPs gave low ratings to their preparedness for a pandemic, testing of suspected cases and efforts to protect staff. The provision of information to GPs and the perception of risk were rated as moderate. On the other hand, the participants rated their self-confidence, a decrease in patient contacts and their efforts to control the spread of the disease highly.
Conclusion: Primary care is an important resource for dealing with a pandemic like COVID-19. The workforce is confident and willing to take an active role, but needs to be provided with the appropriate surrounding conditions. This will require that certain conditions are met.
Registration: Trial registration at the German Clinical Trials Register: DRKS00021231.
The MICOS complex subunit MIC13 is essential for mitochondrial cristae organization. Mutations in MIC13 cause severe mitochondrial hepato-encephalopathy displaying defective cristae morphology and loss of the MIC10-subcomplex. Here we identified SLP2 as a novel interacting partner of MIC13 and decipher a critical role of SLP2 for MICOS assembly at distinct steps. SLP2 provides a large interaction hub for MICOS subunits and loss of SLP2 imparted YME1L-mediated proteolysis of MIC26 and drastic alterations in cristae morphology. We further identified a MIC13-specific role in stabilizing the MIC10-subcomplex via a MIC13-YME1L axis. SLP2 together with the stabilized MIC10-subcomplex promotes efficient assembly of the MIC60-subcomplex forming the MICOS-MIB complex. Consistently, super-resolution nanoscopy showed a dispersed distribution of the MIC60 in cells lacking SLP2 and MIC13. Our study reveals converging and interdependent assembly pathways for the MIC10- and MIC60-subcomplexes which are controlled in two ways, the MIC13-YME1L and the SLP2-YME1L axes, revealing mechanistic insights of these factors in cristae morphogenesis. These results will be helpful in understanding the human pathophysiology linked to mutations in MIC13 or its interaction partners.
The new variant of concern (VOC) of SARS-CoV-2, Omicron (B.1.1.529), is genetically very different from other VOCs. We compared Omicron with the preceding VOC Delta (B.1.617.2) and the wildtype (wt) strain (B.1) with respect to their interactions with the antiviral interferon (IFN-alpha/beta) response in infected cells. Our data indicate that IFN induction by Omicron is low and comparable to the wt, whereas Delta showed an increased IFN induction. However, Omicron exceeded both the wt and the Delta strain with respect to the ability to withstand the antiviral state imposed by IFN-alpha.
Oral swabs, sputum and blood samples from 18 patients with SARS-CoV-2 infection were examined using real-time reverse transcription polymerase chain reaction (RT-PCR) testing. Whereas oral swabs or sputum from the lower respiratory tract were tested RT-PCR positive in all patients, RNAemia was neither detected in 3 patients without symptoms nor in 14 patients with flu-like symptoms, fever or pneumonia. The only patient with RNAemia suffered from acute respiratory distress syndrome (ARDS) and was artificially ventilated in an intensive care unit. Risk for SARS-CoV-2 transmission through blood components in asymptomatic SARS-CoV-2 infected individuals therefore seems negligible but further studies are needed.
Graph data is an omnipresent way to represent information in machine learning. Especially, in neuroscience research, data from Diffusion-Tensor Imaging (DTI) and functional Magnetic Resonance Imaging (fMRI) is commonly represented as graphs. Exploiting the graph structure of these modalities using graph-specific machine learning applications is currently hampered by the lack of easy-to-use software. PHOTONAI Graph aims to close the gap between domain experts of machine learning, graph experts and neuroscientists. Leveraging the rapid machine learning model development features of the Python machine learning API PHOTONAI, PHOTONAI Graph enables the design, optimization, and evaluation of reliable graph machine learning models for practitioners. As such, it provides easy access to custom graph machine learning pipelines including, hyperparameter optimization and algorithm evaluation ensuring reproducibility and valid performance estimates. Integrating established algorithms such as graph neural networks, graph embeddings and graph kernels, it allows researchers without significant coding experience to build and optimize complex graph machine learning models within a few lines of code. We showcase the versatility of this toolbox by building pipelines for both resting–state fMRI and DTI data in the hope that it will increase the adoption of graph-specific machine learning algorithms in neuroscience research.
Context information supports serial dependence of multiple visual objects across memory episodes
(2019)
Visual perception operates in an object-based manner, by integrating associated features via attention. Working memory allows a flexible access to a limited number of currently relevant objects, even when they are occluded or physically no longer present. Recently, it has been shown that we compensate for small changes of an object’s feature over memory episodes, which can support its perceptual stability. This phenomenon was termed ‘serial dependence’ and has mostly been studied in situations that comprised only a single relevant object. However, since we are typically confronted with situations where several objects have to be perceived and held in working memory, the central question of how we selectively create temporal stability of several objects has remained unsolved. As different objects can be distinguished by their accompanying context features, like their color or temporal position, we tested whether serial dependence is supported by the congruence of context features across memory episodes. Specifically, we asked participants to remember the motion directions of two sequentially presented colored dot fields per trial. At the end of a trial one motion direction was cued for continuous report either by its color (Experiment 1) or serial position (Experiment 2). We observed serial dependence, i.e., an attractive bias of currently toward previously memorized objects, between current and past motion directions that was clearly enhanced when items had the same color or serial position across trials. This bias was particularly pronounced for the context feature that was used for cueing and for the target of the previous trial. Together, these findings demonstrate that coding of current object representations depends on previous representations, especially when they share similar content and context features. Apparently the binding of content and context features is not completely erased after a memory episode, but it is carried over to subsequent episodes. As this reflects temporal dependencies in natural settings, the present findings reveal a mechanism that integrates corresponding bundles of content and context features to support stable representations of individualized objects over time.
As the current SARS-CoV-2 pandemic continues, serological assays are urgently needed for rapid diagnosis, contact tracing and for epidemiological studies. So far, there is little data on how commercially available tests perform with real patient samples and if detected IgG antibodies provide protective immunity. Focusing on IgG antibodies, we demonstrate the performance of two ELISA assays (Euroimmun SARS-CoV-2 IgG & Vircell COVID-19 ELISA IgG) in comparison to one lateral flow assay ((LFA) FaStep COVID-19 IgG/IgM Rapid Test Device) and two in-house developed assays (immunofluorescence assay (IFA) and plaque reduction neutralization test (PRNT)). We tested follow up serum/plasma samples of individuals PCR-diagnosed with COVID-19. Most of the SARS-CoV-2 samples were from individuals with moderate to severe clinical course, who required an in-patient hospital stay.
For all examined assays, the sensitivity ranged from 58.8 to 76.5% for the early phase of infection (days 5-9) and from 93.8 to 100% for the later period (days 10-18) after PCR-diagnosed with COVID-19. With exception of one sample, all positive tested samples in the analysed cohort, using the commercially available assays examined (including the in-house developed IFA), demonstrated neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-CoV-2. Regarding specificity, there was evidence that samples of endemic coronavirus (HCoV-OC43, HCoV-229E) and Epstein Barr virus (EBV) infected individuals cross-reacted in the ELISA assays and IFA, in one case generating a false positive result (may giving a false sense of security). This need to be further investigated.
In natural environments, background noise can degrade the integrity of acoustic signals, posing a problem for animals that rely on their vocalizations for communication and navigation. A simple behavioral strategy to combat acoustic interference would be to restrict call emissions to periods of low-amplitude or no noise. Using audio playback and computational tools for the automated detection of over 2.5 million vocalizations from groups of freely vocalizing bats, we show that bats (Carollia perspicillata) can dynamically adapt the timing of their calls to avoid acoustic jamming in both predictably and unpredictably patterned noise. This study demonstrates that bats spontaneously seek out temporal windows of opportunity for vocalizing in acoustically crowded environments, providing a mechanism for efficient echolocation and communication in cluttered acoustic landscapes.
Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ~70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated trans-membrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ∼70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated transmembrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
Endothelial tip cells are essential for VEGF-induced angiogenesis, but underlying mechanisms are elusive. Endothelial-specific deletion of EVL, a member of the mammalian Ena/VASP protein family, reduced the expression of the tip cell marker protein endothelial cell specific molecule-1 (Esm1) and compromised the radial sprouting of the vascular plexus in the postnatal mouse retina. The latter effects could at least partly be attributed to reduced VEGF receptor 2 (VEGFR2) internalization and signaling but the underlying mechanisms(s) are not fully understood. In the present study, we revealed that the expression of the long non-coding RNA H19 was significantly reduced in endothelial cells from postnatal EVL-/- mice and in siRNA-transfected human endothelial cells under hypoxic conditions. H19 was recently shown to promote VEGF expression and bioavailability via Esm1 and hypoxia inducible factor 1α (HIF-1α). Similar to EVL-/- mice, the radial outgrowth of the vascular plexus was significantly delayed in the postnatal retina of H19-/- mice. In summary, our data suggests that loss of EVL not only impairs VEGFR2 internalition and downstream signaling, but also impairs VEGF expression and bioavailability in the hypoxic retina via downregulation of lncRNA H19.
The antiviral drugs tecovirimat, brincidofovir, and cidofovir are considered for mpox (monkeypox) treatment despite a lack of clinical evidence. Moreover, their use is affected by toxic side-effects (brincidofovir, cidofovir), limited availability (tecovirimat), and potentially by resistance formation. Hence, additional, readily available drugs are needed. Here, therapeutic concentrations of nitroxoline, a hydroxyquinoline antibiotic with a favourable safety profile in humans, inhibited the replication of 12 mpox virus isolates from the current outbreak in primary cultures of human keratinocytes and fibroblasts and a skin explant model by interference with host cell signalling. Tecovirimat, but not nitroxoline, treatment resulted in rapid resistance development. Nitroxoline remained effective against the tecovirimat-resistant strain and increased the anti-mpox virus activity of tecovirimat and brincidofovir. Moreover, nitroxoline inhibited bacterial and viral pathogens that are often co-transmitted with mpox. In conclusion, nitroxoline is a repurposing candidate for the treatment of mpox due to both antiviral and antimicrobial activity.
Background and Aim: Genome-wide association studies revealed a strong association between cardiovascular diseases (CVD) and clonal hematopoiesis of indeterminate potential (CHIP), highlighting one of its most common CHIP-driving mutations-TET2 (ten-eleven translocation 2), as a target for CHIP related CVD research. Our lab has established the generation of self-organizing cardiac organoids (SCO), which demonstrate the cellular composition and organization of the native human heart, and mimics human myocardial responses to stress stimulation. This project aims to examine whether SCOs would be an appropriate CHIP model and decipher promising drugs for cardiovascular CHIP treatment.
Methods: To study TET2-mutant cardiovascular CHIP, we set up the TET2 cardiac-CHIP model through a knockdown (KD) of TET2 in myeloid cells that infiltrated our lab-made SCO. Immunofluorescence and qPCR were performed to ascertain TET2-KD myeloid cell infiltration, SCO fibrosis, and apoptosis assessments. SCO fibrosis was further analyzed by immunofluorescence staining, and cardiac contractile frequency and amplitude were determined by calcium flux analysis. Finally, RNAseq was performed to analyze transcriptomic changes in drug/vehicle-treated TET2-KD myeloid cells and the TET2 cardiac-CHIP model.
Results: The TET2 cardiac-CHIP model resulted in significantly increased inflammation in SCO, accompanied by fibrosis and more cleaved Caspase-3, causing cardiomyocytes apoptosis and promoting the release of cTNT. The shortlisted drugs revealed a reduction of proliferation in TET2-KD myeloid cells, decreased pro-inflammatory cytokines, and a higher apoptosis level. Furthermore, the TET2 cardiac-CHIP model treated with selected drugs showed a remarkable decline in TET2-KD myeloid cell infiltration and pro-inflammation cytokines, cardiomyocyte apoptosis, fibrosis, and lowered cTNT levels, while drug control groups were not affected. Moreover, the drug treatment groups improved the heartbeat frequency and amplitude accessed by the calcium transient assay. RNAseq data also validated the above findings.
Conclusions & Discussion: Our results indicate that SCOs are an efficient pre-clinical model for studying and validating CHIP genes and drug interactions. Our data revealed that TET2-KD myeloid cells invade SCO and secrete pro-inflammatory cytokines, which promote apoptosis of cardiomyocytes and the release of cTNT. In this regard, our TET2 cardiac-CHIP model matches the inflammatory phenotype previously characterized in CHIP patients. Nevertheless, this phenotype could be rescued using positive drug candidates (Clopidogrel, R406, and Lanatoside C) selected by this project, emphasizing the significant value of our TET2 cardiac-CHIP model for drug screens and pre-clinical validation studies. Furthermore, among these three drug candidates, we found Lancatoside C, as proved by FDA/EMA, showed an unmet possibility for clinical therapeutic demand, insinuating potential benefit in repurposing Lanatoside C for the treatment of TET2-mutant cardiovascular CHIP.
Objective: This study was undertaken to quantify epilepsy-related costs of illness (COI) in Germany and identify cost-driving factors.
Methods: COI were calculated among adults with epilepsy of different etiologies and severities. Multiple regression analysis was applied to determine any epilepsy-related and sociodemographic factors that serve as cost-driving factors.
Results: In total, 486 patients were included, with a mean age of 40.5 ± 15.5 years (range = 18–83 years, 58.2% women). Mean 3-month COI were estimated at €4911, €2782, and €2598 for focal, genetic generalized, and unclassified epilepsy, respectively. The mean COI for patients with drug-refractory epilepsy (DRE; €7850) were higher than those for patients with non-DRE (€4720), patients with occasional seizures (€3596), or patients with seizures in remission for >1 year (€2409). Identified cost-driving factors for total COI included relevant disability (unstandardized regression coefficient b = €2218), poorer education (b = €2114), living alone (b = €2612), DRE (b = €1831), and frequent seizures (b = €2385). Younger age groups of 18–24 years (b = −€2945) and 25–34 years (b = −€1418) were found to have lower overall expenditures. A relevant disability (b = €441), DRE (b = €1253), frequent seizures (b = €735), and the need for specialized daycare (b = €749) were associated with higher direct COI, and poorer education (b = €1969), living alone (b = €2612), the presence of a relevant disability (b = €1809), DRE (b = €1831), and frequent seizures (b = €2385) were associated with higher indirect COI.
Significance: This analysis provides up-to-date COI data for use in further health economics analyses, highlighting the high economic impacts associated with disease severity, disability, and disease-related loss of productivity among adult patients with epilepsy. The identified cost drivers could be used as therapeutic and socioeconomic targets for future cost-containment strategies.
1. Locating an optimal oviposition site can be a challenging task for female insects, especially when dealing with a patchy, unpredictable and ephemeral food source such as carrion. Understanding the biotic and abiotic parameters that influence the oviposition behaviour of necrophagous flies is not just of great biological importance but also essential for their application in legal investigations.
2. In this study, we monitored the oviposition activity of necrophagous flies (Calliphoridae, Sarcophagidae) using mouse carcasses in an urban (city) and a rural (mixed forest) habitat in Frankfurt/Germany over a 2-year period.
3. Over 240 sampling days, 220,963 larvae of 4 blow fly species and 1 flesh fly were sampled. The most abundant species was the blow fly Lucilia ampullacea, followed by its family members Calliphora vicina and Lucilia caesar, the flesh fly Sarcophaga caerulescens and Lucilia sericata. Up to seven environmental parameters were statistically significant predictors for a colonisation of the carcasses, leading to unique patterns of seasonal and daily oviposition activity for all five species.
4. Overall, the analysis showed that the seasonal adaption (the phenology of each species), the habitat (rural vs. urban) as well as temperature are the most important factors influencing the oviposition behaviour and activity of necrophagous blow flies and flesh flies.
Introduction: The treatment of carious lesions is one of the most fundamental competencies in daily dental practice. However, many commercially available training models lack in reality regarding the simulation of pathologies such as carious lesions. 3D printed models could provide a more realistic simulation. This study provides an exemplary description of the fabrication of 3D printed dental models with carious lesions and assesses their educational value compared to commercially available models in conservative dentistry.
Materials and Methods: A single-stage, controlled cohort study was conducted within the context of a curricular course. A stereolithographic model was obtained from an intraoral scan and then printed using fused deposition modelling. These models were first piloted by experts and then implemented and compared against commercial models in a conservative dentistry course. Experts and students evaluated both models using a validated questionnaire. Additionally, a cost analysis for both models was carried out.
Results: Thirteen dentists and twenty-seven 5th year dental students participated in the study. The 3D printed models were rated significantly more realistic in many test areas. In particular, the different tactility and the distinction in colour was rated positively in the 3D printed models. At 28.29€ (compared to 112.36€), the 3D printed models were exceptionally cost-efficient.
Conclusions: 3D printed dental models present a more realistic and cost-efficient alternative to commercial models in the undergraduate training of conservative dentistry.
Background and purpose: The transition from relapsing–remitting to secondary progressive multiple sclerosis (SPMS) is not well defined. Different definitions and tools to identify SPMS have been proposed. Meanwhile, early diagnosis of “active” SPMS is getting progressively more important as pharmaceutical treatment options are developed. In this study, we compared different classification methods regarding their accuracy to reliably identify “active SPMS.”
Methods: Independent from previous diagnostic classification, we descriptively analyzed the disease course (regarding relapses, progression, and magnetic resonance imaging activity) in 208 consecutive multiple sclerosis (MS) patients treated in our MS outpatient clinic in 2018. Patients were reclassified according to different SPMS criteria and tools. Diagnostic accuracy in identifying patients with “active SPMS” was determined.
Results: Comparing the tools to each other, significant variability in the number of patients identified as having SPMS as well as in the proportion of these patients having “active SPMS” was noted. Applying both diagnostic criteria “SPMS” and “active disease” reduced the sensitivity in identifying patients with active progressive disease in all approaches.
Conclusions: We propose lessening the emphasis on the label “SPMS” in favor of the more open term “active progressive disease” to simplify the process of identifying patients who may benefit from immune therapy.