Faculty and Resident Perspectives of the Complexity of Wellness Program Implementation: A Qualitative Exploration.

Introduction: Developing and implementing a wellness curriculum in a family medicine residency program is a complex process. We developed and implemented a new wellness curriculum in line with the national wellness conversation with a focus on the allocation of dedicated resources, the use of evidence-informed interventions, and the goal to be responsive to the feedback of both residents and residency leadership. Our research aim was to better understand the complexity of wellness curriculum implementation with a focus on identification of challenges to implementation. Methods: We developed a wellness program with structured curricular elements initially focused on evidence-informed skill development that iterated after year 1 to include more process-oriented elements. For the years 2016-2019 we collected and analyzed qualitative, open-ended survey questions, anonymous resident curriculum feedback, and faculty observation forms to assess resident and faculty perspectives on the new curriculum. Results: One hundred eighty-three survey invitations were sent with 122 total responses (66.7% response rate). Forty-eight of 56 residents responded to at least one survey. We analyzed responses along with the additional qualitative data that revealed several themes impacting the work of residency wellness curriculum implementation. These included how to manage curricular time, where the locus of control for the curricular content resides, and how residents and faculty differ in their definitions of wellness. Conclusions: We believe programs will be well positioned if they further investigate the complex structures at play that influence residency wellness, including both systemic factors and individual and community level interventions, and design curriculum that is well-defined, includes essential elements, and is informed by resident participation.

A collaborative approach to improving representation in viral genomic surveillance.

The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and racial inequities have contributed to a greater burden of cases and deaths among minority groups. To begin to address these problems, we developed a new variant surveillance model geared toward building 'next generation' genome sequencing capacity at universities in or near rural areas and engaging the participation of their local communities. The resulting genomic surveillance network has generated more than 1,000 SARS-CoV-2 genomes to date, including the first confirmed case in northeast Louisiana of Omicron, and the first and sixth confirmed cases in Georgia of the emergent BA.2.75 and BQ.1.1 variants, respectively. In agreement with other studies, significantly higher viral gene copy numbers were observed in Delta variant samples compared to those from Omicron BA.1 variant infections, and lower copy numbers were seen in asymptomatic infections relative to symptomatic ones. Collectively, the results and outcomes from our collaborative work demonstrate that establishing genomic surveillance capacity at smaller academic institutions in rural areas and fostering relationships between academic teams and local health clinics represent a robust pathway to improve pandemic readiness.

The Impact of Virtual Interviews on the Resident Candidate: A Before-and-After Comparison.

BACKGROUND AND OBJECTIVES: A significant impact of the COVID-19 pandemic on family medicine residency recruitment has been a requested transition to virtual interviewing by the Association of American Medical Colleges and the academic family medicine community. This has led to creative and adaptive approaches to virtual interviewing with little previous knowledge, experience, or processes. This work describes the impact of transitioning to virtual recruitment on applicants' reported experiences and factors influencing decision-making with family medicine at a large research university. METHODS: We made a comparison of 2 years of in-person interview day surveys with 2 years of virtual interview surveys following transition to virtual recruitment. We tested differences between in-person and virtual interviews for significance using χ2 tests. RESULTS: There were significant differences in factors influencing a candidate's decision to apply. Candidates who participated in virtual interviews were more interested in urban training settings, a community setting, and obstetrical training compared with the in-person interview cohort. Nearly 50% of virtual candidates reported preferring virtual interviews in the future. There were no significant differences in how candidates rated their experience of the interview process and they indicated adequate contact with resident personnel despite a transition to virtual interviews. CONCLUSIONS: The transition to virtual recruitment has been well received by candidates, as indicated by the high positive ratings of the cohorts. The transition has not resulted in a negative impact on the recruitment experience or the ability to meet with resident leadership.

A collaborative approach to improve representation in viral genomic surveillance.

The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and racial inequities have contributed to a greater burden of cases and deaths among minority groups. To begin to address these problems, we developed a new variant surveillance model geared toward building microbial genome sequencing capacity at universities in or near rural areas and engaging the participation of their local communities. The resulting genomic surveillance network has generated more than 1,000 SARS-CoV-2 genomes to date, including the first confirmed case in northeast Louisiana of Omicron, and the first and sixth confirmed cases in Georgia of the emergent BA.2.75 and BQ.1.1 variants, respectively. In agreement with other studies, significantly higher viral gene copy numbers were observed in Delta variant samples compared to those from Omicron BA.1 variant infections, and lower copy numbers were seen in asymptomatic infections relative to symptomatic ones. Collectively, the results and outcomes from our collaborative work demonstrate that establishing genomic surveillance capacity at smaller academic institutions in rural areas and fostering relationships between academic teams and local health clinics represent a robust pathway to improve pandemic readiness. Author summary: Genomic surveillance involves decoding a pathogen’s genetic code to track its spread and evolution. During the pandemic, genomic surveillance programs around the world provided valuable data to scientists, doctors, and public health officials. Knowing the complete SARS-CoV-2 genome has helped detect the emergence of new variants, including ones that are more transmissible or cause more severe disease, and has supported the development of diagnostics, vaccines, and therapeutics. The impact of genomic surveillance on public health depends on representative sampling that accurately reflects the diversity and distribution of populations, as well as rapid turnaround time from sampling to data sharing. After a slow start, SARS-CoV-2 genomic surveillance in the United States grew exponentially. Despite this, many rural regions and ethnic minorities remain poorly represented, leaving significant gaps in the data that informs public health responses. To address this problem, we formed a network of universities and clinics in Louisiana, Georgia, and Mississippi with the goal of increasing SARS-CoV-2 sequencing volume, representation, and equity. Our results demonstrate the advantages of rapidly sequencing pathogens in the same communities where the cases occur and present a model that leverages existing academic and clinical infrastructure for a powerful decentralized genomic surveillance system.

Obstructive sleep apnoea and perioperative medicine: a growing concern.

Obstructive sleep apnoea represents a sizable public health and economic burden. Owing to rising obesity rates, the prevalence of obstructive sleep apnoea is increasing, and it is a condition that is significantly underdiagnosed. Exacerbated by the COVID-19 pandemic, the backlog of elective surgeries is also sizable and growing. A combination of these factors means that many patients due to have surgery will have obstructive sleep apnoea, either diagnosed or otherwise. Patients with obstructive sleep apnoea have a significantly increased risk of operative complications, but the evidence base for optimum perioperative management of these patients is limited. This article reviews sleep apnoea, its prevalence and its impact on operative management and perioperative outcomes for patients. The evidence base for screening and treating undiagnosed obstructive sleep apnoea is also comprehensively assessed. Finally, a pathway to manage patients with possible undiagnosed obstructive sleep apnoea is proposed, and areas for further research identified.

Large volume paracentesis of 39.5 liters chylous ascites in the setting of high-grade follicular lymphoma.

The American Association for the Study of Liver Diseases recognizes large volume paracentesis as draining greater than 5 liters of ascites and states there is no limit in the amount of ascites drained with appropriate replacement of albumin. For many practitioners performing safe large volume paracentesis between 5 and 10 liters or even 20 liters is not an uncommon practice. However, drainage of higher volumes outside common practice may raise concerns of patient intolerance and complication. The largest volume paracentesis reported in the literature to date is 41 liters. However, few other reports approach this volume. This case report demonstrates patient tolerance of a 39.5-liter paracentesis performed with close monitoring and hypertonic albumin replacement in a patient with chylous ascites due to high-grade follicular lymphoma.

When worlds collide: Socio-political conflict in patient care.

The country as a whole has been on high alert since early 2020. That year began with the SARS-CoV-2 pandemic, then moved through the largest single day drop of the Dow Jones industrial average, the murders of Breonna Taylor and George Floyd and subsequent Black Lives Matter protests, murder hornets, the election of Joe Biden, alleged voter fraud, and then culminated on January 6, 2021, with the assault on the United States Capital Building. Societal issues including racism, discrimination, and distrust of leaders have been themes in the news and social media. It should come as no surprise that we may be called upon to provide treatment to patients with whom we have significantly different belief systems, which could result in conflict. The emotional rawness that pervades much of society lays emotions bare for many. Our ethical responsibilities as healthcare providers compel us to think about these complex relationships intentionally, and with compassion. In an interactive workshop conducted at the 42nd Forum for Behavioral Science in Family Medicine, participants were led through scenarios in which conflict could enter the exam room, discussion of the potential consequences, and consideration of ways to respond ethically in those situations. The discussions were couched in the codes of ethics of the American Psychological Association, the National Association of Social Workers, and the American Medical Association. The interactive session was designed to encourage participants to (1) consider potentialities of patient-provider conflict, (2) consider ethical, compassionate responses, and (3) be mindful of social media.

Assessment of the Effect of Soil Sample Preparation, Water Content and Excitation Time on Proximal X-ray Fluorescence Sensing.

X-ray fluorescence (XRF) spectroscopy offers a fast and efficient method for analysing soil elemental composition, both in the laboratory and the field. However, the technique is sensitive to spectral interference as well as physical and chemical matrix effects, which can reduce the precision of the measurements. We systematically assessed the XRF technique under different sample preparations, water contents, and excitation times. Four different soil samples were used as blocks in a three-way factorial experiment, with three sample preparations (natural aggregates, ground to ≤2 mm and ≤1 mm), three gravimetric water contents (air-dry, 10% and 20%), and three excitation times (15, 30 and 60 s). The XRF spectra were recorded and gave 540 spectra in all. Elemental peaks for Si, K, Ca, Ti, Fe and Cu were identified for analysis. We used analysis of variance (anova) with post hoc tests to identify significant differences between our factors and used the intensity and area of the elemental peaks as the response. Our results indicate that all of these factors significantly affect the XRF spectrum, but longer excitation times appear to be more defined. In most cases, no significant difference was found between air-dry and 10% water content. Moisture has no apparent effect on coarse samples unless ground to 1 mm. We suggested that the XRF measurements that take 60 s from dry samples or only slightly moist ones might be an optimum option under field conditions.

Bacterial lipopolysaccharides can initiate regeneration of the Xenopus tadpole tail.

Tadpoles of the frog Xenopus laevis can regenerate tails except for a short "refractory" period in which they heal rather than regenerate. Rapid and sustained production of ROS by NADPH oxidase (Nox) is critical for regeneration. Here, we show that tail amputation results in rapid, transient activation of the ROS-activated transcription factor NF-κB and expression of its direct target cox2 in the wound epithelium. Activation of NF-κB is also sufficient to rescue refractory tail regeneration. We propose that bacteria on the tadpole's skin could influence tail regenerative outcomes, possibly via LPS-TLR4-NF-κB signaling. When raised in antibiotics, fewer tadpoles in the refractory stage attempted regeneration, whereas addition of LPS rescued regeneration. Short-term activation of NF-κB using small molecules enhanced regeneration of tadpole hindlimbs, but not froglet forelimbs. We propose a model in which host microbiome contributes to creating optimal conditions for regeneration, via regulation of NF-κB by the innate immune system.

Space-time modelling of groundwater level and salinity.

Soil salinization resulting from shallow saline groundwater is a major global environmental issue causing land degradation, especially in semi-arid regions such as Australia. The adverse impact of shallow saline groundwater on soil salinization varies in space and time due to the variation in groundwater levels and salt concentration. Understanding the spatio-temporal variation is therefore vital to develop an effective salinity management strategy. In New South Wales, Australia, a hydrogeological landscape unit approach is generally applied, based on spatial information and expert operators, classifying the landscape in relation to landscape and climate. In this paper, a data science approach (random forest model) is introduced, based on historical groundwater quality and quantity data providing predictions in a 4-dimensional space. As a case study, we demonstrate the spatio-temporal factors impacting standing water levels (SWL) and associated salinity and predict the spatial and temporal variability in the Muttama catchment (1059 km2), in NSW, south eastern Australia. The random forest model explains 77% of the variance in the groundwater salinity (electrical conductivity) and 65% of the SWL. Spatial factors were the most significant variables determining the space-time variation in groundwater salinity and the occurrence of groundwater at the surface. Drilled piezometer depth and elevation are dominant factors controlling SWL, while salinity is mainly determined by underlying geology. The methodology in this study predicts salinity and SWL in the landscape at fine scales, through time, improving options for salinity management.

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA to recognize ligands and consequently on its functionality. In this sense, the knowledge obtained from the sequence-dependent structural properties of B-DNA has always been thought crucial to rationalize how ligands and, most notably, proteins recognize B-DNA and modulate its activity, i.e. the structural basis of gene regulation. Honouring the anniversary of the first high-resolution X-ray structure of a B-DNA molecule, in this contribution, we present the most important discoveries of the last 40 years on the sequence-dependent structural and dynamical properties of B-DNA, from the early beginnings to the current frontiers in the field.

Genome Dashboards: Framework and Examples.

Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics- and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.

Genome editing approaches to augment livestock breeding programs.

The prospect of genome editing offers a number of promising opportunities for livestock breeders. Firstly, these tools can be used in functional genomics to elucidate gene function, and identify causal variants underlying monogenic traits. Secondly, they can be used to precisely introduce useful genetic variation into structured livestock breeding programs. Such variation may include repair of genetic defects, the inactivation of undesired genes, and the moving of useful alleles and haplotypes between breeds in the absence of linkage drag. Editing could also be used to accelerate the rate of genetic progress by enabling the replacement of the germ cell lineage of commercial breeding animals with cells derived from genetically elite lines. In the future, editing may also provide a useful complement to evolving approaches to decrease the length of the generation interval through in vitro generation of gametes. For editing to be adopted, it will need to seamlessly integrate with livestock breeding schemes. This will likely involve introducing edits into multiple elite animals to avoid genetic bottlenecks. It will also require editing of different breeds and lines to maintain genetic diversity, and enable structured cross-breeding. This requirement is at odds with the process-based trigger and event-based regulatory approach that has been proposed for the products of genome editing by several countries. In the absence of regulatory harmony, researchers in some countries will have the ability to use genome editing in food animals, while others will not, resulting in disparate access to these tools, and ultimately the potential for global trade disruptions.

Computational Design and Analysis of a Magic Snake.

The Magic Snake (Rubik's Snake) is a toy that was invented decades ago. It draws much less attention than Rubik's Cube, which was invented by the same professor, Erno Rubik. The number of configurations of a Magic Snake, determined by the number of discrete rotations about the elementary wedges in a typical snake, is far less than the possible configurations of a typical cube. However, a cube has only a single three-dimensional (3D) structure while the number of sterically allowed 3D conformations of the snake is unknown. Here, we demonstrate how to represent a Magic Snake as a one-dimensional (1D) sequence that can be converted into a 3D structure. We then provide two strategies for designing Magic Snakes to have specified 3D structures. The first enables the folding of a Magic Snake onto any 3D space curve. The second introduces the idea of "embedding" to expand an existing Magic Snake into a longer, more complex, self-similar Magic Snake. Collectively, these ideas allow us to rapidly list and then compute all possible 3D conformations of a Magic Snake. They also form the basis for multidimensional, multi-scale representations of chain-like structures and other slender bodies including certain types of robots, polymers, proteins, and DNA.

TMB Library of Nucleosome Simulations.

Nucleosomes are the fundamental building blocks of chromatin, the biomaterial that houses the genome in all higher organisms. A nucleosome consists of 145-147 base pairs of DNA wrapped 1.7 times around eight histones. Given a four-letter code (A, C, G, T), there are approximately 4147 or 1088 oligonucleotides that can form a nucleosome. Comparative, rather than comprehensive, studies are required. Here we introduce the TMB Library of nucleosome simulations and present a meta-analysis of over 20 µs of all atom molecular dynamics simulations representing 518 different realizations of the nucleosome. The TMB Library serves as a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES Lite as a tool for managing a laboratory's simulation library. For every simulation, dewatered trajectories, RMSD, and DNA helical parameter data are provided through iBIOMES Lite in a Web browser and a file browser format. A novel view of nucleosomal DNA emerges from our meta-analysis of the TMB Library. DNA conformation is restricted to a specific left-handed superhelix, but the range of conformations observed for individual bases and base pairs is not more restricted nor more highly deformed than DNA free in solution. With the exception of Roll, mean DNA helical parameter values obtained from simulations of nucleosomes are largely within the range of thermal motion of DNA free in solution. The library provides evidence of DNA kinking in the nucleosome and clearly demonstrates the effects of DNA sequence on the gross structure and dynamics of nucleosomes. These effects and mispositioning of the 601 super strong nucleosome positioning sequence can be detected in short simulations (10 ns). Collectively, the results provide a basis for comparative simulation studies of nucleosomes and extend our understanding of the binding of proteins and drugs to nucleosomal DNA. The TMB Library can be found at http://dna.engr.latech.edu/~tmbshare/ .

Mental Disorders and Learning Disabilities in Children and Adolescents: Learning Disabilities.

Learning disabilities are estimated to affect 5% to 9% of US children. Risk factors include a family history of learning disabilities, environmental factors during gestation or birth, and social adversity. Individuals with learning disabilities may experience social exclusion and bullying, poor self-image, or underachievement. They may struggle with tasks and in settings that depend on reading, mathematical skills and reasoning, or written and verbal communication. The family physician often is the first to be approached by parents regarding learning delays in children. The initial evaluation should include a thorough history and physical examination for medical conditions and mental disorders that may manifest as or coexist with learning disabilities. Physicians should advise parents to request that the child's school administer tests for learning disabilities. Physicians should be aware of common tests used to assess for learning disabilities, understand the laws that support provision of special education, and recognize the main categories of learning disabilities. Interventions provided through an Individualized Education Program or Section 504 plan may include educational strategies, accommodations in test taking time or setting, speech or occupational therapy, and adaptive tools. Physicians should help connect families with children with learning disabilities with services and resources.

Combining ancillary soil data with VisNIR spectra to improve predictions of organic and inorganic carbon content of soils.

While traditional laboratory methods of determining soil organic carbon (SOC) content are generally simple, this becomes more challenging when carbonates are present in the soil; such is commonly found in semi-arid areas. Additionally, soil inorganic carbon (SIC) content itself is difficult to determine. This study uses visible near infrared (VisNIR) spectra to predict SOC and SIC contents of samples, and the impact of including soil pH and soil total carbon (STC) data as predictor variables was evaluated. The results indicated that combining available soil pH and STC content data with VisNIR spectra dramatically improved prediction accuracy of the Cubist models. Using the full suite of predictor variables, Cubist models trained on the calibration dataset (75%) could predict the validation dataset (25%) for SOC content with a Lin's concordance correlation coefficient (LCCC) of 0.94, and an LCCC of 0.83 for SIC content. This is compared to an LCCC of 0.81 and 0.35 for SOC and SIC content, respectively, when no ancillary soil data was included with VisNIR spectra as predictor variables. These results suggest that there may be promise for using other readily available soil data in combination with VisNIR spectra to improve the predictions of different soil properties. •It can be laborious and expensive to measure soil organic and inorganic carbon content with traditional laboratory methods, and there has been recent focus on using spectroscopic techniques to overcome this.•This study demonstrates that combining ancillary soil data (pH and total carbon content) with these spectroscopic techniques can considerably improve predictions of SOC and SIC content.

Breaking bad news to patients with cancer: A randomized control trial of a brief communication skills training module incorporating the stories and preferences of actual patients.

OBJECTIVE: This study tested the effectiveness of a brief, learner-centered, breaking bad news (BBN) communication skills training module using objective evaluation measures. METHODS: This randomized control study (N=66) compared intervention and control groups of students (n=28) and residents' (n=38) objective structured clinical examination (OSCE) performance of communication skills using Common Ground Assessment and Breaking Bad News measures. RESULTS: Follow-up performance scores of intervention group students improved significantly regarding BBN (colon cancer (CC), p=0.007, r=-0.47; breast cancer (BC), p=0.003, r=-0.53), attention to patient responses after BBN (CC, p<0.001, r=-0.74; BC, p=0.001, r=-0.65), and addressing feelings (BC, p=0.006, r=-0.48). At CC follow-up assessment, performance scores of intervention group residents improved significantly regarding BBN (p=0.004, r=-0.43), communication related to emotions (p=0.034, r=-0.30), determining patient's readiness to proceed after BBN and communication preferences (p=0.041, r=-0.28), active listening (p=0.011, r=-0.37), addressing feelings (p<0.001, r=-0.65), and global interview performance (p=0.001, r=-0.51). CONCLUSION: This brief BBN training module is an effective method of improving BBN communication skills among medical students and residents. PRACTICE IMPLICATIONS: Implementation of this brief individualized training module within health education programs could lead to improved communication skills and patient care.