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"Fischer, C."
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Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri
Background
Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180
Arabidopsis halleri
individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for
Arabidopsis thaliana
(cross-species markers) and eight for
A. halleri
(species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq).
Results
Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-
H
e
) was not significantly correlated with genome-wide SNP diversity estimates (SNP-
H
e
and
θ
Watterson
) in
A. halleri
. Instead, microsatellite allelic richness (
A
r
) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (
F
ST
) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genome-wide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation.
Conclusions
We recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to
A. halleri
, a few thousand SNPs are sufficient to achieve this goal.
Journal Article
Effects of ethics communication in health care: a cluster randomised controlled trial
Background
Studies show that healthcare professionals encounter ethically difficult situations in everyday clinical practice, and there is a need for interprofessional communication in organised forms. Ethics communication in groups (ECG), based on Habermas’s theory of communicative actions, is a form of support for interprofessional communications about ethical issues. The ‘one to five method’ is a practical tool for healthcare professionals with education in ethics to facilitate ECG in everyday clinical practice.
Research aim
To evaluate the effects of organised ECG using the ‘one to five’ method for health care professionals concerning moral distress and ethical climate at wards with round-the-clock care compared with a control group.
Research design
This was a prospective cluster randomised study with an open, non-blinded design.
Methods
Nine wards with different medical specialisations at one university hospital were purposefully and then randomly allocated to an intervention group (IG) (
n
= 5) and a control group (CG) (
n
= 4). An ECG was performed monthly for six months in the intervention group. Prospective assessments were made at 3 and 6 months using the Measure of Moral Distress-Healthcare Professionals (MMD-HP), Moral Distress Thermometer (MDT), and the Swedish Ethical Climate Questionnaire (SwECQ).
Result
Between-group analyses showed no significant differences in moral distress over time. Within-group analysis revealed that the intervention group scored lower moral distress concerning clinical causes at the patient level at the 3-month measurement point but returned to the same level as the control group at six months. The ethical climate was rated higher in the intervention group at 3 and 6 months.
Conclusion
Participation in ECG likely fosters shared values and an enhanced ethical climate, though no significant differences in moral distress were observed. Moral distress may persist despite interventions, but open dialogue and professional growth can foster moral resilience. This study found a positive relationship between an ethical climate and participation in ethics communication groups (ECG) using the ‘one to five method.’ However, the small sample size limited statistical power. Future research should include larger-scale, multicentre studies and qualitative research to explore experiences with ECG.
Trial registration
ClinicalTrials.gov
: NCT05146102 (2021-11-05).
Journal Article
Seismic performance of non-structural elements during the 2016 Central Italy earthquake
Non-structural elements represent most of the total construction cost of typical buildings. A significant portion of the total losses in recent earthquakes worldwide, has been attributed to damage to non-structural elements. Damage to non-structural elements occurs at low levels of ground shaking, and can significantly affect the post-earthquake functionality of buildings. However, in Europe, limited prescriptions are provided in the codes for seismic design of non-structural elements and this may partially explain why it is so common for these elements to perform poorly during earthquakes. This paper describes the observed damage to non-structural elements following the 2016 Central Italy earthquake. The most commonly damaged elements were partition walls, ceiling systems, non-structural vaults, chimneys, and storage racks. As a result, it was highlighted the need to introduce seismic regulations devoted to improving the seismic performance of non-structural elements and to reduce the associated economic losses, loss of functionality, and potential threats to life safety.
Journal Article
Patient-specific musculoskeletal modeling of the hip joint for preoperative planning of total hip arthroplasty: A validation study based on in vivo measurements
Validation of musculoskeletal models for application in preoperative planning is still a challenging task. Ideally, the simulation results of a patient-specific musculoskeletal model are compared to corresponding in vivo measurements. Currently, the only possibility to measure in vivo joint forces is to implant an instrumented prosthesis in patients undergoing a total joint replacement. In this study, a musculoskeletal model of the AnyBody Modeling System was adapted patient-specifically and validated against the in vivo hip joint force measurements of ten subjects performing one-leg stance and level walking. The impact of four model parameters was evaluated; hip joint width, muscle strength, muscle recruitment, and type of muscle model. The smallest difference between simulated and in vivo hip joint force was achieved by using the hip joint width measured in computed tomography images, a muscle strength of 90 N/cm2, a third order polynomial muscle recruitment, and a simple muscle model. This parameter combination reached mean deviations between simulation and in vivo measurement during the peak force phase of 12% ± 14% in magnitude and 11° ± 5° in orientation for one-leg stance and 8% ± 6% in magnitude and 10° ± 5° in orientation for level walking.
Journal Article
Global and regional child mortality and burden of disease attributable to zinc deficiency
Background/Objectives: Zinc is an essential micronutrient and deficiency can lead to an increased risk for infectious diseases and growth retardation among children under 5 years of age. We aimed to estimate disease-specific and all-cause mortality attributable to zinc deficiency. Subject/Methods: We estimated the prevalence of zinc deficiency in Latin America, Africa and Asia, where based on zinc availability in the diet and childhood stunting rates, zinc deficiency is widespread. The relative risks of death among zinc-deficient children for diarrhea, malaria and pneumonia were estimated from randomized controlled trials. We used the comparative risk assessment methods to calculate deaths and burden of disease (measured in disability-adjusted life years, DALYs) from each of these three diseases attributable to zinc deficiency in these regions. Results: Zinc deficiency was responsible for 453 207 deaths (4.4% of childhood deaths), and 1.2% of the burden of disease (3.8% among children between 6 months and 5 years) in these three regions in 2004. Of these deaths, 260 502 were in Africa, 182 546 in Asia and 10 159 in Latin America. Zinc deficiency accounted for 14.4% of diarrhea deaths, 10.4% of malaria deaths and 6.7% of pneumonia deaths among children between 6 months and 5 years of age. Conclusions: Zinc deficiency contributes to substantial morbidity and mortality, especially from diarrhea. Zinc supplementation provided as an adjunct treatment for diarrhea may be the best way to target children most at risk of deficiency.
Journal Article
Recognition and reconstruction of cell differentiation patterns with deep learning
Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell communication to replicate common spatial arrangements like checkerboard and engulfing patterns. In this model, the cell-cell communication has been implemented as a signal that disperses throughout the tissue. On the other hand, machine learning models have been developed for pattern recognition and pattern reconstruction tasks. We combined synthetic data generated by the mathematical model with spatial summary statistics and deep learning algorithms to recognize and reconstruct cell fate patterns in organoids of mouse embryonic stem cells. Application of Moran’s index and pair correlation functions for in vitro and synthetic data from the model showed local clustering and radial segregation. To assess the patterns as a whole, a graph neural network was developed and trained on synthetic data from the model. Application to in vitro data predicted a low signal dispersion value. To test this result, we implemented a multilayer perceptron for the prediction of a given cell fate based on the fates of the neighboring cells. The results show a 70% accuracy of cell fate imputation based on the nine nearest neighbors of a cell. Overall, our approach combines deep learning with mathematical modeling to link cell fate patterns with potential underlying mechanisms.
Journal Article
Database of segmentations and surface models of bones of the entire lower body created from cadaver CT scans
The range of applications of digital surface models of the bones in science and industry is wide. Three-dimensional reconstructions of bones are used in biomechanics, biomedical engineering, medical image processing, orthopedics, traumatology, radiology, patient education, anatomy, anthropometry, forensic anthropology, ergonomics, usability and human factors engineering, or accident and injury analysis and prevention. No open access database or repository of skeletal surface models of the full lower extremities exists. Therefore, the objective of this publication was to provide access to consistent complete bone models of the pelvis and lower limbs of multiple subjects, including biometric data. Segmentations and surface models of the bones of the lower extremities of more than twenty subjects were created from open access postmortem whole-body computed tomography scans. The database provides a broad range of applications by giving access to the data of the complete process chain, from the raw medical imaging data through the segmentations to the surface models.
Journal Article