Implementation of a Molecular Tumor Registry to Support the Adoption of Precision Oncology Within an Academic Medical Center: The Duke University Experience.

Comprehensive genomic profiling to inform targeted therapy selection is a central part of oncology care. However, the volume and complexity of alterations uncovered through genomic profiling make it difficult for oncologists to choose the most appropriate therapy for their patients. Here, we present a solution to this problem, The Molecular Registry of Tumors (MRT) and our Molecular Tumor Board (MTB). PATIENTS AND METHODS: MRT is an internally developed system that aggregates and normalizes genomic profiling results from multiple sources. MRT serves as the foundation for our MTB, a team that reviews genomic results for all Duke University Health System cancer patients, provides notifications for targeted therapies, matches patients to biomarker-driven trials, and monitors the molecular landscape of tumors at our institution. RESULTS: Among 215 patients reviewed by our MTB over a 6-month period, we identified 176 alterations associated with therapeutic sensitivity, 15 resistance alterations, and 51 alterations with potential germline implications. Of reviewed patients, 17% were subsequently treated with a targeted therapy. For 12 molecular therapies approved during the course of this work, we identified between two and 71 patients who could qualify for treatment based on retrospective MRT data. An analysis of 14 biomarker-driven clinical trials found that MRT successfully identified 42% of patients who ultimately enrolled. Finally, an analysis of 4,130 comprehensive genomic profiles from 3,771 patients revealed that the frequency of clinically significant therapeutic alterations varied from approximately 20% to 70% depending on the tumor type and sequencing test used. CONCLUSION: With robust informatics tools, such as MRT, and the right MTB structure, a precision cancer medicine program can be developed, which provides great benefit to providers and patients with cancer.

Stress Fractures of the Fifth Metatarsal in Athletes.

Stress fractures of the fifth metatarsal (zones 2 and 3) remain a challenging clinical problem. It has been well established that nonsurgical treatment has unacceptably high nonunion and refracture rates. Surgical fixation remains the treatment of choice in the athletic cohort, and intramedullary screw fixation with a solid screw has been established as the most predictable means of achieving a successful outcome. Recently, the use of a plantar plate has also been advocated as has been shown in some studies to be more biomechanically advantageous. The use of bone grafting at the primary surgery and morphology and screw type are also important decisions to be made when treating these patients. This review will discuss our management of both primary fractures and refractures of the fifth metatarsal in athletes.

Results and Clinical Utilization of Foundation Medicine Molecular Tumor Profiling in Uterine and Ovarian Cancers.

BACKGROUND: Recent advances in next-generation sequencing have allowed for an increase in molecular tumor profiling. OBJECTIVE: We sought to assess the actionability and clinical utilization of molecular tumor profiling results obtained via Foundation Medicine tumor sequencing tests in uterine and ovarian cancers. PATIENTS AND METHODS: We performed a single-institution retrospective chart review to obtain demographic and clinical information in patients with uterine and ovarian cancer whose tumors were submitted to Foundation Medicine for molecular tumor profiling over a 7-year period. Alterations identified on testing were stratified according to the OncoKB database actionability algorithm. Descriptive statistics were primarily used to analyze the data. RESULTS: Tumors from 185 women with gynecologic cancer were submitted for molecular tumor profiling between 2013 and 2019. The majority of tests (144/185; 78%) were ordered after a diagnosis of recurrence. In 60 (32%), no actionable molecular alteration was identified. Thirteen (7%) identified an alteration that directed to a US Food and Drug Administration-approved therapy in that tumor type, while 112 (61%) had alterations with investigational or hypothetical treatment implications. In patients with any actionable finding, treatment was initiated in 27 (15%) based on these results. CONCLUSIONS: The majority of uterine and ovarian cancers (93%) did not have molecular alterations with corresponding Food and Drug Administration-approved treatments. Even in patients with a potentially actionable alteration, gynecologic oncologists were more likely to choose an alternative therapy. Further investigation is warranted to determine which patients with uterine and ovarian cancer are most likely to benefit from molecular tumor profiling and the ideal timing of testing. The potential to identify effective therapeutic options in a minority of patients needs to be balanced with the current limited clinical applicability of these results in most cases.

Attenuating Sulfidogenesis in a Soured Continuous Flow Column System With Perchlorate Treatment.

Hydrogen sulfide production by sulfate reducing bacteria (SRB) is the primary cause of oil reservoir souring. Amending environments with chlorate or perchlorate [collectively denoted (per)chlorate] represents an emerging technology to prevent the onset of souring. Recent studies with perchlorate reducing bacteria (PRB) monocultures demonstrated that they have the innate capability to enzymatically oxidize sulfide, thus PRB may offer an effective means of reversing souring. (Per)chlorate may be effective by (i) direct toxicity to SRB; (ii) competitive exclusion of SRB by PRB; or (iii) reversal of souring through re-oxidation of sulfide by PRB. To determine if (per)chlorate could sweeten a soured column system and assign a quantitative value to each of the mechanisms we treated columns flooded with San Francisco bay water with temporally decreasing amounts (50, 25, and 12.5 mM) of (per)chlorate. Geochemistry and the microbial community structure were monitored and a reactive transport model was developed, Results were compared to columns treated with nitrate or untreated. Souring was reversed by all treatments at 50 mM but nitrate-treated columns began to re-sour when treatment concentrations decreased (25 mM). Re-souring was only observed in (per)chlorate-treated columns when concentrations were decreased to 12.5 mM and the extent of re-souring was less than the control columns. Microbial community analyses indicated treatment-specific community shifts. Nitrate treatment resulted in a distinct community enriched in genera known to perform sulfur cycling metabolisms and genera capable of nitrate reduction. (Per)chlorate treatment enriched for (per)chlorate reducing bacteria. (Per)chlorate treatments only enriched for sulfate reducing organisms when treatment levels were decreased. A reactive transport model of perchlorate treatment was developed and a baseline case simulation demonstrated that the model provided a good fit to the effluent geochemical data. Subsequent simulations teased out the relative role that each of the three perchlorate inhibition mechanisms played during different phases of the experiment. These results indicate that perchlorate addition is an effective strategy for both souring prevention and souring reversal. It provides insight into which organisms are involved, and illuminates the interactive effects of the inhibition mechanisms, further highlighting the versatility of perchlorate as a sweetening agent.

Mechanism of H2S Oxidation by the Dissimilatory Perchlorate-Reducing Microorganism Azospira suillum PS.

The genetic and biochemical basis of perchlorate-dependent H2S oxidation (PSOX) was investigated in the dissimilatory perchlorate-reducing microorganism (DPRM) Azospira suillum PS (PS). Previously, it was shown that all known DPRMs innately oxidize H2S, producing elemental sulfur (So). Although the process involving PSOX is thermodynamically favorable (ΔG°' = -206 kJ â‹… mol-1 H2S), the underlying biochemical and genetic mechanisms are currently unknown. Interestingly, H2S is preferentially utilized over physiological electron donors such as lactate or acetate although no growth benefit is obtained from the metabolism. Here, we determined that PSOX is due to a combination of enzymatic and abiotic interactions involving reactive intermediates of perchlorate respiration. Using various approaches, including barcode analysis by sequencing (Bar-seq), transcriptome sequencing (RNA-seq), and proteomics, along with targeted mutagenesis and biochemical characterization, we identified all facets of PSOX in PS. In support of our proposed model, deletion of identified upregulated PS genes traditionally known to be involved in sulfur redox cycling (e.g., Sox, sulfide:quinone reductase [SQR]) showed no defect in PSOX activity. Proteomic analysis revealed differential abundances of a variety of stress response metal efflux pumps and divalent heavy-metal transporter proteins, suggesting a general toxicity response. Furthermore, in vitro biochemical studies demonstrated direct PSOX mediated by purified perchlorate reductase (PcrAB) in the absence of other electron transfer proteins. The results of these studies support a model in which H2S oxidation is mediated by electron transport chain short-circuiting in the periplasmic space where the PcrAB directly oxidizes H2S to So The biogenically formed reactive intermediates (ClO2- and O2) subsequently react with additional H2S, producing polysulfide and So as end products.IMPORTANCE Inorganic sulfur compounds are widespread in nature, and microorganisms are central to their transformation, thereby playing a key role in the global sulfur cycle. Sulfur oxidation is mediated by a broad phylogenetic diversity of microorganisms, including anoxygenic phototrophs and either aerobic or anaerobic chemotrophs coupled to oxygen or nitrate respiration, respectively. Recently, perchlorate-respiring microorganisms were demonstrated to be innately capable of sulfur oxidation regardless of their phylogenetic affiliation. As recognition of the prevalence of these organisms intensifies, their role in global geochemical cycles is being queried. This is further highlighted by the recently recognized environmental pervasiveness of perchlorate not only across Earth but also throughout our solar system. The inferred importance of this metabolism not only is that it is a novel and previously unrecognized component of the global sulfur redox cycle but also is because of the recently demonstrated applicability of perchlorate respiration in the control of biogenic sulfide production in engineered environments such as oil reservoirs and wastewater treatment facilities, where excess H2S represents a significant environmental, process, and health risk, with associated costs approximating $90 billion annually.

Reactive Transport Model of Sulfur Cycling as Impacted by Perchlorate and Nitrate Treatments.

Microbial souring in oil reservoirs produces toxic, corrosive hydrogen sulfide through microbial sulfate reduction, often accompanying (sea)water flooding during secondary oil recovery. With data from column experiments as constraints, we developed the first reactive-transport model of a new candidate inhibitor, perchlorate, and compared it with the commonly used inhibitor, nitrate. Our model provided a good fit to the data, which suggest that perchlorate is more effective than nitrate on a per mole of inhibitor basis. Critically, we used our model to gain insight into the underlying competing mechanisms controlling the action of each inhibitor. This analysis suggested that competition by heterotrophic perchlorate reducers and direct inhibition by nitrite produced from heterotrophic nitrate reduction were the most important mechanisms for the perchlorate and nitrate treatments, respectively, in the modeled column experiments. This work demonstrates modeling to be a powerful tool for increasing and testing our understanding of reservoir-souring generation, prevention, and remediation processes, allowing us to incorporate insights derived from laboratory experiments into a framework that can potentially be used to assess risk and design optimal treatment schemes.

Percutaneous Retrieval of Implanted Leadless Pacemakers: Feasibility at 2.5 Years Post-Implantation in an In Vivo Ovine Model.

OBJECTIVES: This in vivo ovine study describes the feasibility and safety of retrieving implanted leadless pacemakers (LPs). BACKGROUND: Although LPs have been shown to be removable soon after implantation, there are no data on the feasibility of removing chronically implanted LPs. METHODS: This study was performed in 2 phases. In the mid-term cohort, 10 chronically (5.3 months) implanted animals underwent retrieval, followed by: 1) immediate necropsy in 5; and 2) in the remaining 5, reimplantation of a new LP followed by necropsy at 6 weeks. In the long-term cohort, 8 additional sheep underwent retrieval at 2.3 ± 0.1 years followed by necropsy. Retrieval was performed using either a single or triple loop snare. All 18 LPs (100%) were successfully retrieved. The time from retrieval catheter insertion to retrieval was 2:35 ± 01:11 and 3:04 ± 01:13 minutes in the mid-term and long-term study groups, respectively. RESULTS: There were no significant differences in retrieval times using either snare. Intracardiac echocardiography was used pre- and post-retrieval to confirm the absence of pericardial effusion in all 8 sheep. On necropsy, there was no evidence of pericardial bleeding or perforation. Only minor tissue disruption and hemorrhage was noted at the implant site after retrieval. Histology demonstrated fibrous connective tissue at the contact sites of endocardium and LP can and at the helix. There was no evidence of pulmonary thromboembolism. CONCLUSIONS: We demonstrate the feasibility and safety of percutaneous, catheter-based retrieval in chronic LP implants of a maximum duration of approximately 2.5 years.

Feasibility and efficacy of percutaneously delivered leadless cardiac pacing in an in vivo ovine model.

INTRODUCTION: In this in vivo ovine study, we describe the course of pacing and sensing parameters during follow-up as well as the gross and histopathological features at the implant site of the recently described leadless cardiac pacemaker (LCP). METHODS AND RESULTS: All sheep underwent LCP implantation in the right ventricular (RV) apex. Serial pacing/sensing thresholds were assessed. In the first cohort, 11 animals were followed up for a period of 3 months, followed by necropsy. In the second cohort, 7 additional sheep were followed for a period of up to 18 months. Mean pacing and sensing thresholds in the 3-month cohort were 1.0 ± 0.5 V and 9.0 ± 3.7 mV at implant, and 0.7 ± 0.2 V and 8.1 ± 3.9 mV at 90 days, respectively. At necropsy at 3 months, all devices were securely implanted at the RV apex without extrusion of helix beyond the RV wall. Besides endocardial reactive changes in the RV apex surrounding the distal portion of the LCP, there were no other grossly visible abnormalities. In the second cohort (7 sheep), mean pacing and sensing thresholds were 1.0 ± 0.5 V and 9.9 ± 3.8 mV at implant, and 0.86 ± 0.4 V and 4.25 ± 1 mV, respectively, at 18 months of follow-up. CONCLUSION: We demonstrate that after implantation of the LCP, pacing/sensing parameters remain adequate up to 18 months in follow-up. In addition, pathological changes at the implant site and within the RV are limited in severity at 90 days, supporting the efficacy and safety of this novel approach to pacing.

Isotopic insights into microbial sulfur cycling in oil reservoirs.

Microbial sulfate reduction in oil reservoirs (biosouring) is often associated with secondary oil production where seawater containing high sulfate concentrations (~28 mM) is injected into a reservoir to maintain pressure and displace oil. The sulfide generated from biosouring can cause corrosion of infrastructure, health exposure risks, and higher production costs. Isotope monitoring is a promising approach for understanding microbial sulfur cycling in reservoirs, enabling early detection of biosouring, and understanding the impact of souring. Microbial sulfate reduction is known to result in large shifts in the sulfur and oxygen isotope compositions of the residual sulfate, which can be distinguished from other processes that may be occurring in oil reservoirs, such as precipitation of sulfate and sulfide minerals. Key to the success of this method is using the appropriate isotopic fractionation factors for the conditions and processes being monitored. For a set of batch incubation experiments using a mixed microbial culture with crude oil as the electron donor, we measured a sulfur fractionation factor for sulfate reduction of -30‰. We have incorporated this result into a simplified 1D reservoir reactive transport model to highlight how isotopes can help discriminate between biotic and abiotic processes affecting sulfate and sulfide concentrations. Modeling results suggest that monitoring sulfate isotopes can provide an early indication of souring for reservoirs with reactive iron minerals that can remove the produced sulfide, especially when sulfate reduction occurs in the mixing zone between formation waters (FW) containing elevated concentrations of volatile fatty acids (VFAs) and injection water (IW) containing elevated sulfate. In addition, we examine the role of reservoir thermal, geochemical, hydrological, operational and microbiological conditions in determining microbial souring dynamics and hence the anticipated isotopic signatures.

Temperature and injection water source influence microbial community structure in four Alaskan North Slope hydrocarbon reservoirs.

A fundamental knowledge of microbial community structure in petroleum reservoirs can improve predictive modeling of these environments. We used hydrocarbon profiles, stable isotopes, and high-density DNA microarray analysis to characterize microbial communities in produced water from four Alaskan North Slope hydrocarbon reservoirs. Produced fluids from Schrader Bluff (24-27°C), Kuparuk (47-70°C), Sag River (80°C), and Ivishak (80-83°C) reservoirs were collected, with paired soured/non-soured wells sampled from Kuparuk and Ivishak. Chemical and stable isotope data suggested Schrader Bluff had substantial biogenic methane, whereas methane was mostly thermogenic in deeper reservoirs. Acetoclastic methanogens (Methanosaeta) were most prominent in Schrader Bluff samples, and the combined δD and δ(13)C values of methane also indicated acetoclastic methanogenesis could be a primary route for biogenic methane. Conversely, hydrogenotrophic methanogens (e.g., Methanobacteriaceae) and sulfide-producing Archaeoglobus and Thermococcus were more prominent in Kuparuk samples. Sulfide-producing microbes were detected in all reservoirs, uncoupled from souring status (e.g., the non-soured Kuparuk samples had higher relative abundances of many sulfate-reducers compared to the soured sample, suggesting sulfate-reducers may be living fermentatively/syntrophically when sulfate is limited). Sulfate abundance via long-term seawater injection resulted in greater relative abundances of Desulfonauticus, Desulfomicrobium, and Desulfuromonas in the soured Ivishak well compared to the non-soured well. In the non-soured Ivishak sample, several taxa affiliated with Thermoanaerobacter and Halomonas predominated. Archaea were not detected in the deepest reservoirs. Functional group taxa differed in relative abundance among reservoirs, likely reflecting differing thermal and/or geochemical influences.

Inhibition of microbial sulfate reduction in a flow-through column system by (per)chlorate treatment.

Microbial sulfate reduction is a primary cause of oil reservoir souring. Here we show that amendment with chlorate or perchlorate [collectively (per)chlorate] potentially resolves this issue. Triplicate packed columns inoculated with marine sediment were flushed with coastal water amended with yeast extract and one of nitrate, chlorate, or perchlorate. Results showed that although sulfide production was dramatically reduced by all treatments, effluent sulfide was observed in the nitrate (10 mM) treatment after an initial inhibition period. In contrast, no effluent sulfide was observed with (per)chlorate (10 mM). Microbial community analyses indicated temporal community shifts and phylogenetic clustering by treatment. Nitrate addition stimulated Xanthomonadaceae and Rhizobiaceae growth, supporting their role in nitrate metabolism. (Per)chlorate showed distinct effects on microbial community structure compared with nitrate and resulted in a general suppression of the community relative to the untreated control combined with a significant decrease in sulfate reducing species abundance indicating specific toxicity. Furthermore, chlorate stimulated Pseudomonadaceae and Pseudoalteromonadaceae, members of which are known chlorate respirers, suggesting that chlorate may also control sulfidogenesis by biocompetitive exclusion of sulfate-reduction. Perchlorate addition stimulated Desulfobulbaceae and Desulfomonadaceae, which contain sulfide oxidizing and elemental sulfur-reducing species respectively, suggesting that effluent sulfide concentrations may be controlled through sulfur redox cycling in addition to toxicity and biocompetitive exclusion. Sulfur isotope analyses further support sulfur cycling in the columns, even when sulfide is not detected. This study indicates that (per)chlorate show great promise as inhibitors of sulfidogenesis in natural communities and provides insight into which organisms and respiratory processes are involved.

Control of sulfidogenesis through bio-oxidation of H2S coupled to (per)chlorate reduction.

We investigated H2S attenuation by dissimilatory perchlorate-reducing bacteria (DPRB). All DPRB tested oxidized H2S coupled to (per)chlorate reduction without sustaining growth. H2S was preferentially utilized over organic electron donors resulting in an enriched (34S)-elemental sulfur product. Electron microscopy revealed elemental sulfur production in the cytoplasm and on the cell surface of the DPRB Azospira suillum. Based on our results, we propose a novel hybrid enzymatic-abiotic mechanism for H2S oxidation similar to that recently proposed for nitrate-dependent Fe(II) oxidation. The results of this study have implications for the control of biosouring and biocorrosion in a range of industrial environments.

The power of the claw.

Scratches on bones have routinely been attributed to tooth marks (a predominantly untested speculation), ignoring the effects of claws, perhaps because of the general assumption that claws are too soft to damage bone. However, some pathologies appears to be more compatible with claw rather than tooth impacts. Therefore, it is critical to determine if the claws of any animal are capable of scratching into the surface of any bone--a test and proof of concept. A tiger enrichment program was used to document actual bone damage unequivocally caused by claws, by assuring that the tiger had access to bones only by using its paws (claws). The spectrum of mechanisms causing bone damage was expanded by evidentiary analysis of claw-induced pathology. While static studies suggested that nails/claws could not disrupt bone, specific tiger enrichment activities documented that bones were susceptible to damage from the kinetic energy effect of the striking claw. This documents an expanded differential consideration for scratch marks on bone and evidences the power of the claw.

Septic arthritis and osteomyelitis due to the chromoblastomycosis agent Fonsecaea pedrosoi.

Fonsecaea pedrosoi is the most common agent of chromoblastomycosis, a chronic localized fungal infection of the skin and subcutaneous tissues mainly involving the lower extremities. We report a rare case of septic arthritis and osteomyelitis due to the chromoblastomycosis agent F pedrosoi, which was successfully treated with arthrotomy and debridement, followed by a long course of oral antifungal therapy. To our knowledge, this is the second case of F pedrosoi osteomyelitis treated successfully to be ever reported.

A new way to teach an old topic: the cadaver-based anatomy short course for high school students.

An outreach program has been developed at the Department of Biological Sciences, Northern Illinois University (NIU), that offers an intensive short course in human gross anatomy to high school students and their teachers. Prior to the short course, the high school teachers attend a laboratory orientation, view the facilities, and then develop a syllabus suitable for the class needs. When the students arrive, they spend between 1 and 2 days rotating through five different work stations. Using their syllabus, they identify and learn the function of various structures on human cadavers and models. Evaluation and content testing of 143 students demonstrated a significant degree of enthusiasm and retention of the syllabus material at the end of the course. All teachers who participated in the program indicated that they wish to return the following year and new groups have already applied to attend. The results of the program demonstrate ways that universities can generate excitement about science and learning at the high school level.