HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.

Multimodal functional and still imaging of a transplanted human heart reanimated using Visible Heart® methodologies.

BACKGROUND: Our research team obtained a human heart with the right lung attached from a recent transplantation patient via a research collaboration with LifeSource, a local organ procurement organization. The heart and lungs were not viable for transplant given the patient's medical history and were subsequently offered to the University of Minnesota for research purposes. METHODS: Using Visible Heart® methodologies, we reanimated the specimen en bloc and collected multimodal direct visualization from inside the cardiac chambers and great vessels of the functioning heart. RESULTS: Video footage, using videoscopic and fluoroscopic imaging, was captured and is presented in this report as supporting material. Multiple still images highlight the surgical suture sites of the transplantation procedures. CONCLUSIONS: This multimodal imaging offers unique educational value for medical students, clinicians, and medical device designers for improving transplantation techniques and patient outcomes.

Edge-to-edge repairs of P2 prolapsed mitral valves in isolated swine hearts.

BACKGROUND AND AIM OF THE STUDY: The study aim was to determine if mitral stenosis occurred after edge-to-edge (E2E) repair of P2 mitral valve prolapse. METHODS: Six swine hearts were reanimated and videoscopes placed to view the mitral valve from the left atrium and left ventricle. Image analyses provided measures of the valve annulus area, orifice area, and regurgitant area. Hemodynamic data were collected (heart rates, left ventricular (LV) pressures, left atrial pressures, maximal LV dP/dt, and maximal LV -dP/dt) from three groups: (i) native functioning valve (Normal); (ii) mitral valve following excision of strut chordae from the P2 region (Prolapse); and (iii) following E2E repair. RESULTS: The mitral valve annulus areas were unaffected by the creation of prolapses, or following repairs (Normal 10.50 +/- 4.22 cm2; Prolapse 9.41 +/- 3.70 cm2; E2E 9.66 +/- 3.37 cm2; p < 0.01), with similar decreases in annulus areas throughout the cardiac cycles, measured at 15 +/- 3%. The orifice areas did not change with the creation of prolapses, but decreased following repairs (Normal 4.49 +/- 2.70 cm2; Prolapse 4.13 +/- 2.16 cm2; E2E 1.99 +/- 1.19 cm2; p = 0.12). The regurgitant areas increased following induced prolapse, and returned to near-normal levels upon repair (Normal 0.20 +/- 0.16 cm2; Prolapse 0.73 +/- 0.35 cm2; E2E 0.12 +/- 0.10 cm2; p < 0.01). The max LV dP/dt measures did not decrease significantly, whereas max LV -dP/dt measures were decreased. CONCLUSION: In this acute assessment of E2E repair of surgically induced mitral valve P2 prolapses, it was observed that a placed A2-P2 (Alfieri) stitch did not change the annulus area, but caused a significant decrease in the orifice area while successfully eliminating regurgitation, but without causing stenosis.

1p36 Deletion Syndrome and Left Ventricular Non-compaction Cardiomyopathy-Two Cases Report.

1p36 deletion is the most common terminal deletion syndrome in humans. Herein, we report two cases, a 5-month-old female and a 14.5-year-old female, both with 1p36 deletion and left ventricular non-compaction cardiomyopathy. They presented with severely depressed left ventricle function and underwent heart transplantation with excellent outcomes. Given the incidence of heart defects and cardiomyopathy in 1p36 deletion syndrome, it should be recommended that children with this genetic condition have screening for cardiac disease. These cases add to the current literature by demonstrating the potential therapeutic options for non-compaction in 1p36 deletion syndrome and showed the favorable outcomes.

MRI assessment of pacing induced ventricular dyssynchrony in an isolated human heart.

This study demonstrates the capabilities of MRI in the assessment of cardiac pacing induced ventricular dyssynchrony, and the findings support the need for employing more physiological pacing. A human donor heart deemed non-viable for transplantation, was reanimated using an MR compatible, four-chamber working perfusion system. The heart was imaged using a 1.5T MR scanner while being paced from the right ventricular apex (RVA) via an epicardial placed lead. Four-chamber, short-axis, and tagged short-axis cines were acquired in order to track wall motion and intramyocardial strain during pacing. The results of this study revealed that the activation patterns of the left ventricle (LV) during RVA pacing demonstrated intraventricular dyssynchrony; as the left ventricular mechanical activation proceeded from the septum and anterior wall to the lateral wall, with the posterior wall being activated last. As such, the time difference to peak contraction between the septum and lateral wall was approximately 125 msec. Likewise, interventricular dyssynchrony was demonstrated from the four-chamber cine as the time difference between the peak LV and RV free wall motion was 180 msec. With the ongoing development of MR safe and MR compatible pacing systems, we can expect MRI to be added to the list of imaging modalities used to optimize cardiac resynchronization therapy (CRT) and/or alternate site pacing.

Cardiac patient-specific three-dimensional models as surgical planning tools.

BACKGROUND: Three-dimensional printing is an additive manufacturing method that builds objects from digitally generated computational models. Core technologies behind three-dimensional printing are evolving rapidly with major advances in materials, resolution, and speed that enable greater realism and higher accuracy. These improvements have led to novel applications of these processes in the medical field. METHODS: The process of going from a medical image data set (computed tomography, magnetic resonance imaging, ultrasound) to a physical three-dimensional print includes several steps that are described. Medical images originate from Digital Imaging and Communications in Medicine files or data sets, the current standard for storing and transmitting medical images. Via Digital Imaging and Communications in Medicine manipulation software packages, a segmentation process, and manual intervention by an expert user, three-dimensional digital and printed models can be constructed in great detail. RESULTS: Cardiovascular medicine is one of the fastest growing applications for medical three-dimensional printing. The technology is more frequently being used for patient and clinician education, preprocedural planning, and medical device design and prototyping. We report on three case studies, describing how our three-dimensional printing has contributed to the care of cardiac patients at the University of Minnesota. CONCLUSION: Medical applications of computational three-dimensional modeling and printing are already extensive and growing rapidly and are routinely used for visualizing complex anatomies from patient imaging files to plan surgeries and create surgical simulators. Studies are needed to determine whether three-dimensional printed models are cost effective and can consistently improve clinical outcomes before they become part of routine clinical practice.

Strategies for Maintaining the Coach-Analyst Relationship Within Professional Football Utilizing the COMPASS Model: The Performance Analyst's Perspective.

There is a considerable body of research by that has investigated the coach-athlete relationship in sport. However, given the multi-disciplinary nature of modern elite coaching, there is a scarcity of research focusing on the relationship between coaches and other members of the coaching and support team. This study examined the perceptions of six elite professional football analyst's relationships with their respective coaches. Semi structured interviews utilizing the COMPASS Framework were conducted focusing on Conflict, Openness, Motivation, Preventative Strategies, Assurance, Support, and Social Networks. The results verified that the COMPASS Model of relationship maintenance was applicable to this dyad. Content analysis indicated that there was 215 raw data units comprising of 16 higher order themes across the model which was further broken down into 29 lower order themes. All aspects of the model were found to contribute toward a positively maintained relationship. Having an open relationship underpinned by honesty and being able to provide an opinion was seen as the highest rated attribute that was closely followed by supporting the coach by understanding their requirements for successful coaching practice. Not meeting the coach's expectations was found to cause conflict and was further highlighted by an inductive analysis that revealed the existence of a relationship that is fundamentally dictated by the coach. Implications of this investigation are that professionals which support elite performers need to set out clear expectations of working practice and hierarchies in order to minimize the chance of internal conflict that can impact on the service levels received by the performer.

Right Atrioventricular Valve Leaflet Morphology Redefined: Implications for Transcatheter Repair Procedures.

OBJECTIVES: The authors aimed to comprehensively detail the right atrioventricular valve functional leaflet anatomies. BACKGROUND: The rapid development of both surgical and percutaneous repair techniques for tricuspid regurgitation has renewed interest in variations in the morphology of the right atrioventricular valve. METHODS: The functioning right atrioventricular valves of 40 reanimated human hearts were imaged using Visible Heart methodologies. Hearts were then perfusion-fixed and dissected, uniquely allowing for the comparative assessments of functional versus fixed valve anatomies from the same set of donor hearts. RESULTS: The right atrioventricular valves have "3-leaflet" configurations in 57.5% and "4-leaflet" configurations in the remaining hearts. For 4-leaflet valves, extra leaflets were commonly observed in the most inferior regions of the annuli. No difference in valve perimeters between 2 valve types were observed (112.2 vs. 117.1 mm; p = 0.14). In 3-leaflet valves, septal, mural, and superior leaflets occupied 32.2 ± 6.5%, 15.9 ± 5.5%, and 25.5 ± 6.2% of the annulus, respectively, whereas in the 4-leaflet arrangements, these values were 27.0 ± 5.8% (septal), 12.0 ± 4.5% (inferior), 13.7 ± 9.4% (mural), and 19.8 ± 6.1% (superior). The muroseptal/inferoseptal commissures were usually located in the cavotricuspid regions, whereas the inferomural and superomural commissures were in the right atrial appendage vestibule area. CONCLUSIONS: The right atrioventricular valve has 4 functional leaflets in more than 40% of cases. The authors found that the inferomural region is the most variable area of the valve and believe that anatomic variation is an important consideration for planned interventions.

Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana.

Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp., urging the need for the magnitude of Campylobacter-associated diarrhoea to be established. In this survey, we have characterised the genomic diversity of Campylobacter spp. circulating in Botswana isolated from cases of diarrhoeal disease in humans (n = 20) and from those that colonised commercial broiler (n = 35) and free-range (n = 35) chickens. Phylogeny showed that the Campylobacter spp. isolated from the different poultry and human sources were highly related, suggesting that zoonotic transmission has likely occurred. We found that for Campylobacter spp. isolated from humans, broilers and free-range chickens, 52% was positive for tetO, 47% for gyrA-T86I, 72% for blaOXA-61, with 27% carrying all three resistance determinants. No 23S mutations conferring macrolide resistance were detected in this survey. In summary, our study provides insight into Campylobacter spp. in poultry reservoirs and in diarrhoeal patients, and the relevance for treatment regimens in Botswana.

Genome and Plasmid Sequences of Escherichia coli KV7, an Extended-Spectrum ß-Lactamase Isolate Derived from Feces of a Healthy Pig.

We present single-contig assemblies for Escherichia coli strain KV7 (serotype O27, phylogenetic group D) and its six plasmids, isolated from a healthy pig, as determined by PacBio RS II and Illumina MiSeq sequencing. The chromosome of 4,997,475 bp and G+C content of 50.75% harbored 4,540 protein-encoding genes.

Hepatoblastoma: A Need for Cell Lines and Tissue Banks to Develop Targeted Drug Therapies.

Limited research exists regarding the most aggressive forms of hepatoblastoma. Cell lines of the rare subtypes of hepatoblastoma with poor prognosis are not only difficult to attain but also challenging to characterize histologically. A community-driven approach to educating parents and families, regarding the need for donated tissue, is necessary for scientists to have access to resources for murine models and drug discovery. Herein, we describe the currently available resources, existing gaps in research, and the path to move forward for uniform cure of hepatoblastoma.

3D anatomical reconstruction of human cardiac conduction system and simulation of bundle branch block after TAVI procedure.

The cardiac conduction system (CCS) is responsible for the initiation and propagation of action potentials through the heart ensuring efficient pumping of blood. Understanding the anatomy of the CCS and its relationship with other major cardiac components is important to help understand arrhythmias and how certain procedures may increase the incidence of arrhythmias developing. We sectioned a whole human heart and performed Masson's trichrome histology in order to identify the components of the CCS. The histology images were used to construct a 3D anatomical model. We have shown that it is possible to create a 3D anatomical model of the human heart incorporating the CCS based on histological images, and that this model can be used to perform computer simulations of cardiac excitation. From the reconstruction we have been able to show the relative positions of the CCS components to each other. We have also shown how the close proximity of the CCS to the aortic valve can explain some of the conduction complications, such as left bundle branch block, that arise after aortic valve replacement procedures.

The clinical anatomy and pathology of the human atrioventricular valves: implications for repair or replacement.

A critical understanding of cardiac anatomy is essential for design engineers and clinicians with the intent of developing and/or employing improved or novel technologies or therapies for treating an impaired atrioventricular valve. Likewise, such knowledge is required for directing translational research, including initiating preclinical research, assessing the feasibility of clinical trials, and performing first-in-man procedures. There are two atrioventricular valves in the human heart, namely the tricuspid and mitral valves. Both are complex structures whose normal anatomies can vary greatly amongst individuals, and also become modified by disease processes. In this review, we discuss the anatomy, pathology, and issues related to surgical and transcatheter repair of the atrioventricular valves in a translational manner. This article is part of a JCTR special issue on Cardiac Anatomy.

The clinical anatomy and pathology of the human arterial valves: implications for repair or replacement.

A thorough understanding of valvar anatomy is essential for design engineers and clinicians in the development and/or employment of improved technologies or therapies for treating valvar pathologies. There are two arterial valves in the human heart--pulmonary and aortic valves. Both are complex structures whose normal anatomical components can vary greatly between individuals. We discuss the anatomy, pathology, and challenges relating to transcatheter and surgical repair/replacement of the arterial valves in a translational manner. The high prevalence of aortic valvar pathologies in the burgeoning elderly population, coupled with poor clinical outcomes for patients who go untreated, has resulted in prolific spending in the research and development of more effective and less traumatic therapies. The accelerated development of therapies for treating arterial valves has been guided by anatomical information gathered from high-resolution imaging technologies, which have focused attention on the need for complete understanding of arterial valvar clinical anatomies. This article is part of a JCTR special issue on Cardiac Anatomy.

The benefits of the Atlas of Human Cardiac Anatomy website for the design of cardiac devices.

This paper describes how the Atlas of Human Cardiac Anatomy website can be used to improve cardiac device design throughout the process of development. The Atlas is a free-access website featuring novel images of both functional and fixed human cardiac anatomy from over 250 human heart specimens. This website provides numerous educational tutorials on anatomy, physiology and various imaging modalities. For instance, the 'device tutorial' provides examples of devices that were either present at the time of in vitro reanimation or were subsequently delivered, including leads, catheters, valves, annuloplasty rings and stents. Another section of the website displays 3D models of the vasculature, blood volumes and/or tissue volumes reconstructed from computed tomography and magnetic resonance images of various heart specimens. The website shares library images, video clips and computed tomography and MRI DICOM files in honor of the generous gifts received from donors and their families.

Imaging in the context of replacement heart valve development: use of the Visible Heart(®) methodologies.

In recent years huge strides have been made in the fields of interventional cardiology and cardiac surgery which now allow physicians and surgeons to repair or replace cardiac valves with greater success in a larger demographic of patients. Pivotal to these advances has been significant improvements in cardiac imaging and improved fundamental understanding of valvular anatomies and morphologies. We describe here a novel series of techniques utilized within the Visible Heart(®) laboratory by engineers, scientists, and/or anatomists to visualize and analyze the form and function of the four cardiac valves and to assess potential repair or replacement therapies. The study of reanimated large mammalian hearts (including human hearts) using various imaging modalities, as well as specially prepared anatomical specimens, has enhanced the design, development, and testing of novel cardiac therapies.

Accuracy of aortic annular measurements obtained from three-dimensional echocardiography, CT and MRI: human in vitro and in vivo studies.

OBJECTIVES: To determine the accuracy of calcium-containing rings measurements imaged by three-dimensional echocardiography (3DE), multi-slice CT (MSCT) and cardiac magnetic resonance (CMR) under ideal conditions against the true ring dimensions. To compare the accuracy of aortic annulus (AoA) measurements in ex vivo human hearts using 3DE, MSCT and CMR. To determine the accuracy of AoA measurements in an in vivo human model. DESIGN: 3DE, MSCT and CMR imaging were performed on 30 calcium-containing rings and 28 explanted human hearts. Additionally, 15 human subjects with clinical indication for MSCT underwent 3DE. Two experts in each modality measured the images. MAIN OUTCOME MEASURES: Bias and intraclass correlation coefficient for accuracy of imaging measurements when compared with actual ring dimensions. Bias, intraclass correlation coefficient and variability were obtained: (1) when comparing explanted human heart AoA measurements from the two remaining imaging modalities with the most accurate one as determined from the ring measurements and (2) in in vivo human AoA measurements. Analysis was repeated on explanted heart subgroups divided by aortic valve Agatston score. RESULTS: Against the known ring dimensions, CMR had the highest accuracy and the lowest variability. MSCT measurements had high accuracy but wider variability and 3DE had the lowest accuracy with the largest variability. When 3DE and MSCT were compared with CMR, 3DE underestimated and MSCT overestimated AoA dimensions, but inter-measurement variability of 3DE and MSCT were similar. When divided by Agatston score, both 3DE and MSCT measurements were larger and showed greater variability with increasing calcium burden. The in vivo study showed that the correlation between 3DE and MSCT measurements was high; however, 3DE measurements were smaller than those measured with MSCT. CONCLUSIONS: In the in vitro model, CMR measurements were the most accurate for assessing the actual dimensions suggesting that further investigations on its role in AoA measurement in TAVR are needed. However from the in vivo model, MSCT and 3DE are reasonable alternatives with the understanding that they can slightly overestimate and underestimate annular dimensions, respectively.

Comparative imaging of cardiac structures and function for the optimization of transcatheter approaches for valvular and structural heart disease.

The detailed assessment of cardiac anatomy using multiple imaging modalities is essential to understand the high degree of variations that exist in human hearts (i.e., with and without pathologies). Additionally, such information should provide one with important insights regarding which imaging modality will best provide the required visualization of device placement via a given transcatheter approach. We describe here an unique set of such studies performed on either preserved heart specimens or within reanimated large mammalian hearts, including human (using Visible Heart(®) methodologies). Such anatomical and device-tissue interface knowledge is critical for both design engineers and clinicians that seek to develop and/or employ less invasive cardiac repair approaches for patients with acquired or congenital structural heart defects.