Epilepsy surgery perceptions among general neurologists and epilepsy specialists: A survey.

OBJECTIVE: Surgical intervention for drug-resistant epilepsy (DRE) is a safe and efficacious evidence-based treatment. Yet, neurologists have historically revealed hesitance in referring patients for surgical evaluations. The present study surveyed general neurologists and epilepsy specialists to assess their views and process in referring patients for specialized epilepsy care and epilepsy surgery. METHODS: A 14-item survey assessing epilepsy referrals and views of epilepsy surgery was distributed to all neurologists currently practicing in a large national integrated health system using REDCap. Responses were qualitatively analyzed and differences between general neurologists and epileptologists were assessed using chi-squared tests. RESULTS: In total, 100 responses were received from 67 general neurologists and 33 epileptologists with several similarities and differences emerging between the two groups. Both groups endorsed surgery and neuromodulation as treatment options in DRE, felt that seizure frequency rather than duration was relevant in considering epilepsy surgery, and indicated patient preference as the largest barrier limiting epilepsy surgery. General neurologists were more likely to require ≥ 3 ASMs to fail to diagnose DRE compared to epileptologists (45% vs. 15%, p < 0.01) who more often required ≥ 2 ASMs to fail. Epileptologists were also more likely than neurologists to try a new ASM (75.8% vs. 53.7%, p < 0.05) or optimize the current ASM (75.8% vs. 49.3%, p < 0.05) in DRE. General neurologists were more likely to consider epilepsy surgery to be less efficacious (p = 0.001) or less safe (p < 0.05). SIGNIFICANCE: Overall, neurologists appear to have generally positive opinions of epilepsy surgery, which is a change from prior literature and represents a changing landscape of views toward this intervention. Furthermore, epileptologists and general neurologists endorsed more similarities than differences in their opinions of surgery and steps to referral, which is another encouraging finding. Those gaps that remain between epileptologists and general neurologists, particularly in standards of ASM prescription, may be addressed by more consistent education about DRE and streamlining of surgical referral procedures.

HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery.

MOTIVATION: Double minute (DM) chromosomes are acentric extrachromosomal DNA artifacts that are frequently observed in the cells of numerous cancers. They are highly amplified and contain oncogenes and drug-resistance genes, making their presence a challenge for effective cancer treatment. Algorithmic discovery of DM can potentially improve bench-derived therapies for cancer treatment. A hindrance to this task is that DMs evolve, yielding circular chromatin that shares segments from progenitor DMs. This creates DMs with overlapping amplicon coordinates. Existing DM discovery algorithms use whole genome shotgun sequencing (WGS) in isolation, which can potentially incorrectly classify DMs that share overlapping coordinates. RESULTS: In this study, we describe an algorithm called 'HolistIC' that can predict DMs in tumor genomes by integrating WGS and Hi-C sequencing data. The consolidation of these sources of information resolves ambiguity in DM amplicon prediction that exists in DM prediction with WGS data used in isolation. We implemented and tested our algorithm on the tandem Hi-C and WGS datasets of three cancer datasets and a simulated dataset. Results on the cancer datasets demonstrated HolistIC's ability to predict DMs from Hi-C and WGS data in tandem. The results on the simulated data showed the HolistIC can accurately distinguish DMs that have overlapping amplicon coordinates, an advance over methods that predict extrachromosomal amplification using WGS data in isolation. AVAILABILITY AND IMPLEMENTATION: Our software, named 'HolistIC', is available at http://www.github.com/mhayes20/HolistIC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The complex interplay of iron, biofilm formation, and mucoidy affecting antimicrobial resistance of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is a Gram-negative opportunistic bacterial pathogen that is refractory to a variety of current antimicrobial therapeutic regimens. Complicating treatment for such infections is the ability of P. aeruginosa to form biofilms, as well as several innate and acquired resistance mechanisms. Previous studies suggest iron plays a role in resistance to antimicrobial therapy, including the efficacy of an FDA-approved iron chelator, deferasirox (DSX), or Gallium, an iron analog, in potentiating antibiotic-dependent killing of P. aeruginosa biofilms. Here, we show that iron-replete conditions enhance resistance of P. aeruginosa nonbiofilm growth against tobramycin and tigecycline. Interestingly, the mechanism of iron-enhanced resistance to each of these antibiotics is distinct. Whereas pyoverdine-mediated iron uptake is important for optimal resistance to tigecycline, it does not enhance tobramycin resistance. In contrast, heme supplementation results in increased tobramycin resistance, while having no significant effect on tigecycline resistance. Thus, nonsiderophore bound iron plays an important role in resistance to tobramycin, while pyoverdine increases the ability of P. aeruginosa to resist tigecycline treatment. Lastly, we show that iron increases the minimal concentration of tobramycin, but not tigecycline, required to eradicate P. aeruginosa biofilms. Moreover, iron depletion blocks the previous observed induction of biofilm formation by subinhibitory concentrations of tobramycin, suggesting iron and tobramycin signal through overlapping regulatory pathways to affect biofilm formation. These data further support the role of iron in P. aeruginosa antibiotic resistance, providing yet another compelling case for targeting iron acquisition for future antimicrobial drug development.