Citations

Abstract Summary We present MetaMarker, a pipeline for discovering metagenomic biomarkers from whole-metagenome sequencing samples. Different from existing methods, MetaMarker is based on a de novo approach that does not require mapping raw reads to a reference database. We applied MetaMarker on whole-metagenome sequencing of colorectal cancer (CRC) stool samples from France to discover CRC specific metagenomic biomarkers. We showed robustness of the discovered biomarkers by validating in independent samples from Hong Kong, Austria, Germany and Denmark. We further demonstrated these biomarkers could be used to build a machine learning classifier for CRC prediction. Availability and implementation MetaMarker is freely available at https://bitbucket.org/mkoohim/metamarker under GPLv3 license. Supplementary information Supplementary data are available at Bioinformatics online.

Tumor recurrence in glioblastoma multiforme (GBM) is often attributed to acquired resistance to the standard chemotherapeutic agent, temozolomide (TMZ). Promoter methylation of the DNA repair gene MGMT (O6-methylguanine–DNA methyltransferase) has been associated with sensitivity to TMZ, whereas increased expression of MGMT has been associated with TMZ resistance. Clinical studies have observed a downward shift in MGMT methylation percentage from primary to recurrent stage tumors; however, the evolutionary processes that drive this shift and more generally the emergence and growth of TMZ-resistant tumor subpopulations are still poorly understood. Here, we develop a mathematical model, parameterized using clinical and experimental data, to investigate the role of MGMT methylation in TMZ resistance during the standard treatment regimen for GBM—surgery, chemotherapy, and radiation. We first found that the observed downward shift in MGMT promoter methylation status between detection and recurrence cannot be explained solely by evolutionary selection. Next, our model suggests that TMZ has an inhibitory effect on maintenance methylation of MGMT after cell division. Finally, incorporating this inhibitory effect, we study the optimal number of TMZ doses per adjuvant cycle for patients with GBM with high and low levels of MGMT methylation at diagnosis.

Purpose Glioblastomas, lethal primary brain tumors, are known for their heterogeneity and invasiveness. A growing body of literature has been developed demonstrating the clinical relevance of a biomathematical model, the proliferation-invasion model, of glioblastoma growth. Of interest here is the development of a treatment response metric, days gained (DG). This metric is based on individual tumor kinetics estimated through segmented volumes of hyperintense regions on T1-weighted gadolinium-enhanced and T2-weighted magnetic resonance images. This metric was shown to be prognostic of time to progression. Furthermore, it was shown to be more prognostic of outcome than standard response metrics. Although promising, the original article did not account for uncertainty in the calculation of the DG metric, leaving the robustness of this cutoff in question. Methods We harnessed the Bayesian framework to consider the impact of two sources of uncertainty: (1) image acquisition and (2) interobserver error in image segmentation. We first used synthetic data to characterize what nonerror variants are influencing the final uncertainty in the DG metric. We then considered the original patient cohort to investigate clinical patterns of uncertainty and to determine how robust this metric is for predicting time to progression and overall survival. Results Our results indicate that the key clinical variants are the time between pretreatment images and the underlying tumor growth kinetics, matching our observations in the clinical cohort. Finally, we demonstrated that for this cohort, there was a continuous range of cutoffs between 94 and 105 for which the prediction of the time to progression was over 80% reliable. Conclusion Although additional validation must be performed, this work represents a key step in ascertaining the clinical utility of this metric.

Background: Interest in facial masculinization surgery is expected to increase as gender-affirming surgery becomes more widely accepted and available. The purpose of this study is to summarize the current literature describing operative techniques in facial masculinization surgery and provide an algorithmic approach to treating this patient population. Methods: PubMed, EMBASE, and Medline databases were queried for literature on operative techniques and outcomes of facial masculinization surgery in transgender and cisgender patients, published through July 2018. Data on patient demographics, follow-up, operative techniques, complications, and outcomes were collected. Results: Fifteen of the 24 identified studies met inclusion criteria. Two studies discussed the outcomes of 7 subjects (6 trans-male and 1 cis-male) who underwent facial masculinization procedures. No objective outcomes were reported in either study; however, subjects were generally satisfied and there were no complications. The remaining studies reviewed operative techniques utilized in the cisgender population. Conclusion: A summary of considerations for each facial anatomic subunit and respective operative techniques for facial masculinization is presented. Current facial masculinization procedures in cisgender patients may be considered in the transgender patient population with favorable outcomes. However, further research is needed on techniques and objective outcome measures of facial masculinization procedures in the transgender population.

BackgroundClinician preferences and practices regarding appropriate vasopressin use in light of its increased acquisition cost secondary to rebranding has not been evaluated or described since the most recent iteration of the Surviving Sepsis Campaign Guideline was published.ObjectiveTo assess vasopressin cost containment initiatives and pharmacists' opinions regarding appropriate vasopressin use.MethodsA scenario‐based survey was distributed to critical care and emergency medicine pharmacists. Responses were characterized using frequency and descriptive statistics. Categorical variables between those who implemented changes (Vasopressin Cost Consideration) and those who did not (Usual Care) were compared using chi‐square or Fisher's exact tests. McNemar's test was used to compare responses in clinical scenarios between Vasopressin Cost Consideration and Usual Care groups.ResultsAmong 1757 pharmacists surveyed, 200 (11.3%) responded. When respondents considered vasopressin cost and evidence (vs evidence alone), fewer respondents would use vasopressin adjunctively with norepinephrine (21% vs 26.6%, P = 0.031), to raise mean arterial pressure compared with epinephrine (65.2% vs 72.3%, P = 0.012), or to reduce norepinephrine infusion rates (71.4% vs 81.4%, P < 0.001), but would use with steroids (62.4% vs 28.3%, P < 0.001). Most (72%) respondents had implemented vasopressin cost containment and/or education initiatives. The Vasopressin Cost Consideration group respondents were more likely to initiate vasopressin at 0.03 units/minute without titrating (47.9% vs 33.9%, P = 0.045).ConclusionSince vasopressin was generically rebranded, most institutions have implemented at least one initiative to reduce vasopressin use and/or educate clinicians about its appropriate use. When vasopressin acquisition costs were considered, pharmacists recommended its use less frequently, particularly in clinical scenarios where its use is controversial.

Male and female glioblastomas are biologically distinct, and improving outcomes may require sex-specific approaches to treatment.