Early Breast Cancer Evolution by Autosomal Broad Copy Number Alterations.

The availability of comprehensive genomic datasets across patient populations enables the application of novel methods for reconstructing tumor evolution within individual patients. To this end, we propose studying autosomal broad copy number alterations (CNAs) as a framework to better understand early tumor evolution. We compared the broad CNAs and somatic mutations of patients with 1 to 10 autosomal broad CNAs against the full set of patients, using data from The Cancer Genome Atlas breast cancer project. We reveal here that the frequency of a chromosome arm obtaining a broad CNA and a genome acquiring somatic mutations changes as autosomal broad CNAs accumulate. Therefore, we propose that the number of autosomal broad CNAs is an important characteristic of breast tumors that needs to be taken into consideration when studying breast tumors. To investigate this idea more in-depth, we next studied the frequency that specific chromosome arms acquire broad CNAs in patients with 1 to 10 broad CNAs. With this process, we identified the broad CNAs that exhibit the fastest rates of accumulation across all patients. This finding suggests a likely order of occurrence of these alterations in patients, which is apparent when we consider a subset of patients with few broad CNAs. Here, we lay the foundation for future studies to build upon our findings and use autosomal broad CNAs as a method to monitor breast tumor progression in vivo to further our understanding of how early tumor evolution unfolds.

Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant.

Identifying order of symptom onset of infectious diseases might aid in differentiating symptomatic infections earlier in a population thereby enabling non-pharmaceutical interventions and reducing disease spread. Previously, we developed a mathematical model predicting the order of symptoms based on data from the initial outbreak of SARS-CoV-2 in China using symptom occurrence at diagnosis and found that the order of COVID-19 symptoms differed from that of other infectious diseases including influenza. Whether this order of COVID-19 symptoms holds in the USA under changing conditions is unclear. Here, we use modeling to predict the order of symptoms using data from both the initial outbreaks in China and in the USA. Whereas patients in China were more likely to have fever before cough and then nausea/vomiting before diarrhea, patients in the USA were more likely to have cough before fever and then diarrhea before nausea/vomiting. Given that the D614G SARS-CoV-2 variant that rapidly spread from Europe to predominate in the USA during the first wave of the outbreak was not present in the initial China outbreak, we hypothesized that this mutation might affect symptom order. Supporting this notion, we found that as SARS-CoV-2 in Japan shifted from the original Wuhan reference strain to the D614G variant, symptom order shifted to the USA pattern. Google Trends analyses supported these findings, while weather, age, and comorbidities did not affect our model's predictions of symptom order. These findings indicate that symptom order can change with mutation in viral disease and raise the possibility that D614G variant is more transmissible because infected people are more likely to cough in public before being incapacitated with fever.

Modeling the Onset of Symptoms of COVID-19.

COVID-19 is a pandemic viral disease with catastrophic global impact. This disease is more contagious than influenza such that cluster outbreaks occur frequently. If patients with symptoms quickly underwent testing and contact tracing, these outbreaks could be contained. Unfortunately, COVID-19 patients have symptoms similar to other common illnesses. Here, we hypothesize the order of symptom occurrence could help patients and medical professionals more quickly distinguish COVID-19 from other respiratory diseases, yet such essential information is largely unavailable. To this end, we apply a Markov Process to a graded partially ordered set based on clinical observations of COVID-19 cases to ascertain the most likely order of discernible symptoms (i.e., fever, cough, nausea/vomiting, and diarrhea) in COVID-19 patients. We then compared the progression of these symptoms in COVID-19 to other respiratory diseases, such as influenza, SARS, and MERS, to observe if the diseases present differently. Our model predicts that influenza initiates with cough, whereas COVID-19 like other coronavirus-related diseases initiates with fever. However, COVID-19 differs from SARS and MERS in the order of gastrointestinal symptoms. Our results support the notion that fever should be used to screen for entry into facilities as regions begin to reopen after the outbreak of Spring 2020. Additionally, our findings suggest that good clinical practice should involve recording the order of symptom occurrence in COVID-19 and other diseases. If such a systemic clinical practice had been standard since ancient diseases, perhaps the transition from local outbreak to pandemic could have been avoided.

Surgical Management of Lower Extremity Pyoderma Gangrenosum With Viable Cryopreserved Umbilical Tissue: A Case Series.

INTRODUCTION: Pyoderma gangrenosum (PG) is a rare skin disease that often presents as a uniquely painful and necrotic ulceration of the lower extremity. Pyoderma gangrenosum is often misdiagnosed and can have deleterious consequences to the patient, as there is no gold standard treatment and it can be difficult to manage. Surgery for these wounds is controversial, as pathergy can develop, worsening the ulceration. Advanced wound care products such as cellular- and/or tissue-based products (CTPs) are effective in helping stagnant chronic wounds reach full closure. Amnion/chorion-based skin substitutes that have been cryopreserved and contain viable cells have been shown to promote more cell recruitment and reduce inflammation. OBJECTIVE: This case series presents evidence of using a cryopreserved umbilical cord tissue with living cells in adjunctive treatment of wounds associated with PG. MATERIALS AND METHODS: This report presents 3 different clinical scenarios of lower extremity PG treated surgically with viable cryopreserved umbilical tissue (vCUT). RESULTS: All 3 patients were successfully treated with vCUT and resulted in complete healing. CONCLUSIONS: To the best of the authors' knowledge, this is the first case series demonstrating the ability of vCUT to heal these difficult-to-treat ulcers. In addition, it may be an effective modality to adjunctive management of PG.

Uncovering the Genomic Origins of Life.

The Origin of Life Domain (OLD) is the period during which life on Earth began. Here, we derive and use a new phylogenetic algorithm to analyze Protein Families in order to reconstruct the chronological steps by which the OLD evolved. During this period, life began with the appearance of the fundamental components of life such as RNAs, DNAs, amino acids, and membranes. Chronologically, the Origin of Life preceded the Last Universal Common Ancestor, which then subsequently engendered modern life on Earth. Our phylogenetic algorithm allows us to explicitly answer previously unknown origin of life questions. Specifically, we explain and illustrate our computational methods by reconstructing the rings describing the evolution of the RNA and DNA worlds. We phylogenetically reconstruct how the RNA and DNA worlds evolved, infer the origins and chronological order of appearance of the first genetic codes, test whether the Ribosomal RNA world preceded the Membrane world, and interpret these new findings with respect to the experimental and theoretical origin of life studies by others.

Pull Incentives for Antibacterial Drug Development: An Analysis by the Transatlantic Task Force on Antimicrobial Resistance.

New alternative market models are needed to incentivize companies to invest in developing new antibacterial drugs. In a previous publication, the Transatlantic Task Force on Antimicrobial Resistance (TATFAR) summarized the key areas of consensus for economic incentives for antibacterial drug development. That work determined that there was substantial agreement on the need for a mixture of push and pull incentives and particularly those that served to delink the revenues from the volumes sold. Pull incentives reward successful development by increasing or ensuring future revenue. Several pull incentives have been proposed that could substantially reward the development of new antibacterial drugs. In this second article authored by representatives of TATFAR, we examine the advantages and disadvantages of different pull incentives for antibacterial drug development. It is TATFAR's hope that this analysis, combined with other related analyses, will provide actionable information that will shape policy makers' thinking on this important issue.

Challenges and Opportunities of Nontraditional Approaches to Treating Bacterial Infections.

Due to increasing rates of antimicrobial-resistant infections and the current inadequacy of the antibiotic pipeline, there is increasing interest in nontraditional approaches to antibacterial therapies. We define "traditional" agents as small-molecule agents that directly target bacterial components to exert a bacteriostatic or bactericidal effect, and "nontraditional approaches" as antimicrobial therapeutics that work through other means (ie, not a small molecule and/or utilizes a nontraditional target). Due to their atypical features, such therapies may be less susceptible to the emergence of resistance than traditional antibiotics. They include approaches such as monoclonal antibodies, virulence disruptors, immunomodulators, phage therapies, microbiome-based therapies, antibiotic potentiators, and antisense approaches. This article discusses both the developmental and regulatory advantages and challenges associated with each of these technologies. By identifying existing regulatory and developmental gaps, we hope to provide a sense of where focusing resources may provide the greatest impact on successful product development.

Economic Incentives for Antibacterial Drug Development: Literature Review and Considerations From the Transatlantic Task Force on Antimicrobial Resistance.

The Trans-Atlantic Task Force on Antimicrobial Resistance (TATFAR) in 2015 was tasked with exploring economic incentives for antibacterial drug development and providing recommendations for potential global implementation. Due to the continual decline of pharmaceutical companies investing in new antibiotic development and the rise in antimicrobial resistance, there is an urgent need to examine market mechanisms that are appropriate to encourage small, medium, and large companies to reinvest in this space. This review provides a summary of the various models that have been proposed and highlights positions posed by several policy documents, peer-reviewed publications, organization proposals, and government-sponsored reviews. The findings support a form of a de-linkage model and a combination of push and pull incentive mechanisms. This level of consensus could culminate in global coordination of incentives that strike a balance of rewarding innovation and ensuring appropriate antibiotic use.

Use of administrative data to increase the practicality of clinical trials: Insights from the Women's Health Initiative.

BACKGROUND: To reduce research costs in the context of pragmatic trials, consideration is given to using administrative data (Medicare claims) to ascertain clinical outcomes. METHODS: In the historical context of the Women's Health Initiative, the correspondence between selected cardiovascular events derived from Medicare claims was compared to those documented and adjudicated in this large-scale prevention trial. RESULTS: Classification performance varies somewhat by type of outcome, but hazard ratios and confidence intervals derived from the two data sources were quite comparable. CONCLUSION: These encouraging results provided the needed support to launch a new embedded pragmatic trial of physical activity that will rely heavily on Medicare claims to ascertain cardiovascular disease incidence in the majority of those randomized.

Accelerating global innovation to address antibacterial resistance: introducing CARB-X.

A global response to the chronic shortfall in antibiotic innovation is urgently needed to combat antimicrobial resistance. Here, we introduce CARB-X, a new global public-private partnership that will invest more than US$350 million in the next 5 years to accelerate the progression of a diverse portfolio of innovative antibacterial products into clinical trials.

Rings Reconcile Genotypic and Phenotypic Evolution within the Proteobacteria.

Although prokaryotes are usually classified using molecular phylogenies instead of phenotypes after the advent of gene sequencing, neither of these methods is satisfactory because the phenotypes cannot explain the molecular trees and the trees do not fit the phenotypes. This scientific crisis still exists and the profound disconnection between these two pillars of evolutionary biology--genotypes and phenotypes--grows larger. We use rings and a genomic form of goods thinking to resolve this conundrum (McInerney JO, Cummins C, Haggerty L. 2011. Goods thinking vs. tree thinking. Mobile Genet Elements. 1:304-308; Nelson-Sathi S, et al. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517:77-80). The Proteobacteria is the most speciose prokaryotic phylum known. It is an ideal phylogenetic model for reconstructing Earth's evolutionary history. It contains diverse free living, pathogenic, photosynthetic, sulfur metabolizing, and symbiotic species. Due to its large number of species (Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc Nat Acad Sci U S A. 95:6578-6583) it was initially expected to provide strong phylogenetic support for a proteobacterial tree of life. But despite its many species, sequence-based tree analyses are unable to resolve its topology. Here we develop new rooted ring analyses and study proteobacterial evolution. Using protein family data and new genome-based outgroup rooting procedures, we reconstruct the complex evolutionary history of the proteobacterial rings (combinations of tree-like divergences and endosymbiotic-like convergences). We identify and map the origins of major gene flows within the rooted proteobacterial rings (P < 3.6 × 10(-6)) and find that the evolution of the "Alpha-," "Beta-," and "Gammaproteobacteria" is represented by a unique set of rings. Using new techniques presented here we also root these rings using outgroups. We also map the independent flows of genes involved in DNA-, RNA-, ATP-, and membrane- related processes within the Proteobacteria and thereby demonstrate that these large gene flows are consistent with endosymbioses (P < 3.6 × 10(-9)). Our analyses illustrate what it means to find that a gene is present, or absent, within a gene flow, and thereby clarify the origin of the apparent conflicts between genotypes and phenotypes. Here we identify the gene flows that introduced photosynthesis into the Alpha-, Beta-, and Gammaproteobacteria from the common ancestor of the Actinobacteria and the Firmicutes. Our results also explain why rooted rings, unlike trees, are consistent with the observed genotypic and phenotypic relationships observed among the various proteobacterial classes. We find that ring phylogenies can explain the genotypes and the phenotypes of biological processes within large and complex groups like the Proteobacteria.

Workshop on treatment of and postexposure prophylaxis for Burkholderia pseudomallei and B. mallei Infection, 2010.

The US Public Health Emergency Medical Countermeasures Enterprise convened subject matter experts at the 2010 HHS Burkholderia Workshop to develop consensus recommendations for postexposure prophylaxis against and treatment for Burkholderia pseudomallei and B. mallei infections, which cause melioidosis and glanders, respectively. Drugs recommended by consensus of the participants are ceftazidime or meropenem for initial intensive therapy, and trimethoprim/sulfamethoxazole or amoxicillin/clavulanic acid for eradication therapy. For postexposure prophylaxis, recommended drugs are trimethoprim/sulfamethoxazole or co-amoxiclav. To improve the timely diagnosis of melioidosis and glanders, further development and wide distribution of rapid diagnostic assays were also recommended. Standardized animal models and B. pseudomallei strains are needed for further development of therapeutic options. Training for laboratory technicians and physicians would facilitate better diagnosis and treatment options.

State-of-the-art therapeutic medical countermeasures for viral threat agents.

In recent years, there has been an increase in the perceived threat of biological agents being used against civilian populations. This has prompted an urgent need for the development and procurement of medical countermeasures (MCMs) against highly pathogenic viruses that can prevent morbidity and mortality from infections caused by these agents. To date, antiviral drug development has been largely focused on clinically prevalent chronic infections due to their commercial viability. This has left a huge gap in the drug development path for acute infections of biodefense importance. In this review, we discuss the antiviral research and development initiatives focusing specifically on poxviruses, filoviruses, and equine encephalitis viruses (EEV). We discuss the benefits and technical challenges in the current development strategies and the hurdles in the licensure path for MCMs against these highly pathogenic viruses under the FDA Animal Rule, and we provide recommendations for the path forward.

Alphavirus antiviral drug development: scientific gap analysis and prospective research areas.

The New World alphaviruses Venezuelan equine encephalitis virus (VEEV), eastern equine encephalitis virus (EEEV), and western equine encephalitis virus (WEEV) pose a significant threat to human health as the etiological agents of serious viral encephalitis through natural infection as well as through their potential use as a biological weapon. At present, there is no FDA-approved medical treatment for infection with these viruses. The Defense Threat Reduction Agency, Joint Science and Technology Office for Chemical and Biological Defense (DTRA/JSTO), is currently funding research aimed at developing antiviral drugs and vaccines against VEEV, EEEV, and WEEV. A review of antiviral drug discovery efforts for these viruses revealed significant gaps in the data, assays, and models required for successful drug development. This review provides a description of these gaps and highlights specific critical research areas for the development of a target-based drug discovery program for the VEEV, EEEV, and WEEV nonstructural proteins. These efforts will increase the probability of the successful development of a pharmaceutical intervention against these viral threat agents.

Pathogenesis of Burkholderia pseudomallei and Burkholderia mallei.

Burkholderia pseudomallei and mallei are biological agents of military significance. There has been significant research in recent years to develop medical countermeasures for these organisms. This review summarizes work which details aspects of the pathogenesis of B. pseudomallei and mallei and discusses key scientific questions and directions for future research.

N-linked protein glycosylation is required for full competence in Campylobacter jejuni 81-176.

The recent sequencing of the virulence plasmid of Campylobacter jejuni 81-176 revealed the presence of genes homologous to type IV secretion systems (TFSS) that have subsequently been found in Helicobacter pylori and Wolinella succinogenes. Mutational analyses of some of these genes have implicated their involvement in intestinal epithelial cell invasion and natural competence. In this report, we demonstrate that one of these type IV secretion homologs, Cjp3/VirB10, is a glycoprotein. Treatment with various glycosidases and binding to soybean agglutinin indicated that the structure of the glycan present on VirB10 contains a terminal GalNAc, consistent with previous reports of N-linked glycans in C. jejuni. Site-directed mutagenesis of five putative N-linked glycosylation sites indicated that VirB10 is glycosylated at two sites, N32 and N97. Mutants in the N-linked general protein glycosylation (pgl) system of C. jejuni are significantly reduced in natural transformation, which is likely due, in part, to lack of glycosylation of VirB10. The natural transformation defect in a virB10 mutant can be complemented in trans by using a plasmid expressing wild-type VirB10 or an N32A substitution but not by using a mutant expressing VirB10 with an N97A substitution. Taken together, these results suggest that glycosylation of VirB10 specifically at N97 is required for the function of the TFSS and for full competence in C. jejuni 81-176.