Electrophysiological Characterization of Cardiac Cells Differentiated from Embryonic, Induced Pluripotent and Adipose-Derived Stem Cells for Translational Tissue Engineering Applications

Heart disease includes an array of cardiovascular diseases causing 25% of all deaths annually in the United States. Patients who live with heart disease experience significantly decreased quality of life. While current treatments on the market aim at improving heart function and cardiovascular efficiency, none are able to restore functionality to native levels. Tissue engineered approaches are becoming increasingly viewed as the definitive treatment to increasing longevity and quality of life of patients affected by heart disease. While stem cell therapies have immense potential, clinical application is still largely unsuccessful in generating healthy myocardium in patients. This study aims to differentiate and characterize human embryonic, induced pluripotent, and adipose derived stem cells into cardiomyocytes to engineer an electrically conductive construct for heart disease patients. Action potentials of embryonic, and induced pluripotent derived cardiomyocytes were measured using Nanion’s automated patch clamp system in order to attain baseline measurements. Current and voltage clamp configurations were used under physiological conditions and electrical signals were sampled every 15 seconds. In addition, two and three dimensional co-culture studies were performed using adipose-derived and embryonic-derived cardiomyocytes. The cells were seeded within an agarose gel and on 6-well plates at a 2:1 ratio. Samples were then measured using the automated patch clamp system after seven days of culture and stained for connexin-43 and desmin using immunofluorescence. Lastly, multielectrode array measurements readings were performed using embryonic derived cardiomyocytes to verify the patch clamp data. Results showed differentiated induced pluripotent stem cells produced action potentials almost identical to ventricular cardiomyocytes. No action potential readings were able to be recorded for the three dimensional cultures, however physiologically relevant action potentials were measured in the 2D co-culture groups. Additionally, the 3D co-culture samples all stained positive for connexin-43 and desmin verifying that the differentiated cells possessed unique cardiomyocyte markers. Future studies should devote more effort into differentiating successful cardiac pacemaker cells from adipose derived stem cells

An NMR Study of CO2 Dynamics and Structural Characterization of Porous Materials

Nuclear magnetic resonance (NMR) has proven to be a versatile and powerful analytical tool to study many areas of interest to the scientific community, such as molecular dynamics and structural characterization. In this dissertation, NMR was used as a probe for CO2 dynamics in metal-organic frameworks. Variable temperature (VT) NMR was used to determine molecular dynamics of CO2, going as low as 8 K. In the fast motion regime, where the CO2 hopping rate is fast compared to the NMR experiment time, 13CO2 inside of Mg-MOF-74 still exhibits a chemical shift anisotropy (CSA) powder pattern. However, there is a certain loading of CO2 inside the framework (~ 1 CO2 molecule per 1 open metal site) the results in a symmetric Gaussian lineshape where it appears that the CSA is motionally averaged. This is not the case though, the CO2 molecules adopt an average orientation inside the channels of the framework as a function of CO2 loading. This average orientation manifests itself in the CSA lineshape and can be explained using the Legendre polynomial, P2. Additionally, 27Al magic-angle spinning (MAS) NMR was performed to characterize aluminum carbide (Al4C3) and its related derivatives. Multiple-quantum magic-angle spinning of Al4C3 revealed accurate values for the quadrupolar tensor, and elucidated the presence of additional sites likely to be from an oxycarbide unit (Al4(C,O)3). Extracting accurate values for the quadrupolar tensor was critical in the understanding and deconvolution of MIL-53(Al) derived from aluminum carbide. 27Al NMR is uniquely qualified to identify the presence of [4]-, [5]-, and [6]-coordinate amorphous aluminum oxide species that would otherwise be unseen in techniques such as powder X-ray diffraction (PXRD). The formation of this aluminum oxide layer appears to be a necessary step to the formation of MIL-53(Al)

Relative pleopod length as an indicator of size at sexual maturity in slipper (Scyllarides squammosus) and spiny Hawaiian (Panulirus marginatus) lobsters

Body size at gonadal maturity is described for females of the slipper lobster (Scyllarides squammosus) (Scyllaridae) and the endemic Hawaiian spiny lobster (Panulirus marginatus) (Palinuridae) based on microscopic examination of histological preparations of ovaries. These data are used to validate several morphological metrics (relative exopodite length, ovigerous condition) of functional sexual maturity. Relative exopodite length (“pleopod length”) produced consistent estimates of size at maturity when evaluated with a newly derived statistical application for estimating size at the morphometric maturation point (MMP) for the population, identified as the midpoint of a sigmoid function spanning the estimated boundaries of overlap between the largest immature and smallest adult animals. Estimates of the MMP were related to matched (same-year) characterizations of sexual maturity based on ovigerous condition — a more conventional measure of functional maturity previously used to characterize maturity for the two lobster species. Both measures of functional maturity were similar for the respective species and were within 5% and 2% of one another for slipper and spiny lobster, respectively. The precision observed for two shipboard collection series of pleopod-length data indicated that the method is reliable and not dependent on specialized expertise. Precision of maturity estimates for S. squammosus with the pleopod-length metric was similar to that for P. marginatus with any of the other measures (including conventional evidence of ovigerous condition) and greatly exceeded the precision of estimates for S. squammosus based on ovigerous condition alone. The two measures of functional maturity averaged within 8% of the estimated size at gonadal maturity for the respective species. Appendage-to-body size proportions, such as the pleopod length metric, hold great promise, particularly for species of slipper lobsters like S. squammosus for which there exist no other reliable conventional morphological measures of sexual maturity. Morphometric proportions also should be included among the factors evaluated when assessing size at sexual maturity in spiny lobster stocks; previously, these proportions have been obtained routinely only for brachyuran crabs within the Crustacea

The Impact of Lateral Gene Transfer in Chlamydia

Lateral gene transfer (LGT) facilitates many processes in bacterial ecology and pathogenesis, especially regarding pathogen evolution and the spread of antibiotic resistance across species. The obligate intracellular chlamydiae, which cause a range of diseases in humans and animals, were historically thought to be highly deficient in this process. However, research over the past few decades has demonstrated that this was not the case. The first reports of homologous recombination in the Chlamydiaceae family were published in the early 1990s. Later, the advent of whole-genome sequencing uncovered clear evidence for LGT in the evolution of the Chlamydiaceae, although the acquisition of tetracycline resistance in Chlamydia (C.) suis is the only recent instance of interphylum LGT. In contrast, genome and in vitro studies have shown that intraspecies DNA exchange occurs frequently and can even cross species barriers between closely related chlamydiae, such as between C. trachomatis, C. muridarum, and C. suis. Additionally, whole-genome analysis led to the identification of various DNA repair and recombination systems in C. trachomatis, but the exact machinery of DNA uptake and homologous recombination in the chlamydiae has yet to be fully elucidated. Here, we reviewed the current state of knowledge concerning LGT in Chlamydia by focusing on the effect of homologous recombination on the chlamydial genome, the recombination machinery, and its potential as a genetic tool for Chlamydia

BUS-Set:A benchmark for quantitative evaluation of breast ultrasound segmentation networks with public datasets

Purpose: BUS-Set is a reproducible benchmark for breast ultrasound (BUS) lesion segmentation, comprising of publicly available images with the aim of improving future comparisons between machine learning models within the field of BUS. Method: Four publicly available datasets were compiled creating an overall set of 1154 BUS images, from five different scanner types. Full dataset details have been provided, which include clinical labels and detailed annotations. Furthermore, nine state-of-the-art deep learning architectures were selected to form the initial benchmark segmentation result, tested using five-fold cross-validation and MANOVA/ANOVA with Tukey statistical significance test with a threshold of 0.01. Additional evaluation of these architectures was conducted, exploring possible training bias, and lesion size and type effects. Results: Of the nine state-of-the-art benchmarked architectures, Mask R-CNN obtained the highest overall results, with the following mean metric scores: Dice score of 0.851, intersection over union of 0.786 and pixel accuracy of 0.975. MANOVA/ANOVA and Tukey test results showed Mask R-CNN to be statistically significant better compared to all other benchmarked models with a p-value >0.01. Moreover, Mask R-CNN achieved the highest mean Dice score of 0.839 on an additional 16 image dataset, that contained multiple lesions per image. Further analysis on regions of interest was conducted, assessing Hamming distance, depth-to-width ratio (DWR), circularity, and elongation, which showed that the Mask R-CNN's segmentations maintained the most morphological features with correlation coefficients of 0.888, 0.532, 0.876 for DWR, circularity, and elongation, respectively. Based on the correlation coefficients, statistical test indicated that Mask R-CNN was only significantly different to Sk-U-Net. Conclusions: BUS-Set is a fully reproducible benchmark for BUS lesion segmentation obtained through the use of public datasets and GitHub. Of the state-of-the-art convolution neural network (CNN)-based architectures, Mask R-CNN achieved the highest performance overall, further analysis indicated that a training bias may have occurred due to the lesion size variation in the dataset. All dataset and architecture details are available at GitHub: https://github.com/corcor27/BUS-Set, which allows for a fully reproducible benchmark

Full Text and Figure Display Improves Bioscience Literature Search

When reading bioscience journal articles, many researchers focus attention on the figures and their captions. This observation led to the development of the BioText literature search engine [1], a freely available Web-based application that allows biologists to search over the contents of Open Access Journals, and see figures from the articles displayed directly in the search results. This article presents a qualitative assessment of this system in the form of a usability study with 20 biologist participants using and commenting on the system. 19 out of 20 participants expressed a desire to use a bioscience literature search engine that displays articles' figures alongside the full text search results. 15 out of 20 participants said they would use a caption search and figure display interface either frequently or sometimes, while 4 said rarely and 1 said undecided. 10 out of 20 participants said they would use a tool for searching the text of tables and their captions either frequently or sometimes, while 7 said they would use it rarely if at all, 2 said they would never use it, and 1 was undecided. This study found evidence, supporting results of an earlier study, that bioscience literature search systems such as PubMed should show figures from articles alongside search results. It also found evidence that full text and captions should be searched along with the article title, metadata, and abstract. Finally, for a subset of users and information needs, allowing for explicit search within captions for figures and tables is a useful function, but it is not entirely clear how to cleanly integrate this within a more general literature search interface. Such a facility supports Open Access publishing efforts, as it requires access to full text of documents and the lifting of restrictions in order to show figures in the search interface

The impact of immunotherapies on COVID-19 case fatality rates during the US vaccination campaign: a multidisciplinary open data analysis using FDA Adverse Event Reporting System and Our World in Data.

Introduction: Patients under immunotherapies were excluded from the pivotal trials of vaccinations against the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), and no population-level data on disease outcomes such as case fatality rates in relation to vaccination coverage exist. Our study aims to fill this gap by investigating whether CFRs in patients with immunotherapies decrease with increasing vaccination coverage in the total population. Methods: We combined aggregated open source data on COVID-19 vaccination coverage from "Our World in Data" with publicly available anonymized COVID-19 case reports from the FDA Adverse Event Reporting System to compute COVID-19 CFRs for patients under immunotherapy at different vaccination coverage levels in the total population. CFRs at different vaccination coverage levels were then compared to CFRs before vaccination campaign start. Results: While we found an overall decrease in CFRs on population level with increasing vaccination coverage, we found no decrease in people using anti-CD20 or glucocorticoids. Discussion: Risk-mitigation strategies on an individual- and population-level are thus still needed to lower the probability of fatal SARS-CoV2 infection for these vulnerable populations