Citations

Background: Corticosteroid therapy is a well-recognized risk factor for Pneumocystis pneumonia (PCP); however, it has also been proposed as an adjunct to decrease inflammation and respiratory failure. Objective: To determine the association between preadmission corticosteroid use and risk of moderate-to-severe respiratory failure at the time of PCP presentation. Methods: This retrospective cohort study evaluated HIV-negative immunosuppressed adults diagnosed with PCP at Mayo Clinic from 2006 to 2016. Multivariable regression models were used to evaluate the association between preadmission corticosteroid exposure and moderate-to-severe respiratory failure at presentation. Results: Of the 323 patients included, 174 (54%) used preadmission corticosteroids with a median daily dosage of 20 (interquartile range: 10-40) mg of prednisone or equivalent. After adjustment for baseline demographics, preadmission corticosteroid therapy did not decrease respiratory failure at the time of PCP presentation (odds ratio: 1.23, 95% confidence interval: 0.73-2.09, P = .38). Additionally, after adjusting for inpatient corticosteroid administration, preadmission corticosteroid use did not impact the need for intensive care unit admission ( P = .98), mechanical ventilation ( P = .92), or 30-day mortality ( P = .11). Conclusions: Corticosteroid exposure before PCP presentation in immunosuppressed HIV-negative adults was not associated with a reduced risk of moderate-to-severe respiratory failure.

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.

Summary Background Sarcopenia is associated with both increased wait‐list mortality and mortality following liver transplantation. Aims To determine the course of sarcopenia from transplant evaluation until 1 year post‐transplant, and its implications on hospitalisation and mortality following liver transplantation. Methods Two hundred and ninety‐three transplant recipients from 2002 to 2006 had pre‐transplant CT scans analysed at the third lumbar region for sarcopenia, myosteatosis and abdominal visceral fat content. Half the recipients had post‐transplant CT scan for interpretation (161/293). Results Sarcopenia was present in 146/293 (50%) of the patients pre‐transplant. There was a significant decrease in muscle mass (loss 2.0 ± 4.9 cm 2 /m 2 ; P < 0.001), and an increase in myosteatosis while awaiting liver transplantation. There was no significant change in abdominal visceral fat. For every 1 cm 2 /m 2 decrease in muscle mass there was an increase in post‐transplant length of stay by 0.36 days ( P = 0.005). Post‐transplant, 98/161 (61%) of patients with CT imaging had sarcopenia (25 de novo and 73 persistent), with continued increase in myosteatosis, lower Hounsfield units (−5.0 [IQR −8.6 to 0.1]; P < 0.001) and an increase in abdominal visceral fat (4.9 [IQR −4.4 to 15.6] cm 2 /m 2 ; P < 0.001). There was no statistically significant difference in 1‐year mortality in patients with de novo sarcopenia compared to patients with sarcopenia both pre‐ and post‐transplant (HR 1.88; P = 0.088). Conclusions Sarcopenia progresses up to 1 year following liver transplantation and is associated with an increase in post‐transplant length of stay.

Background. Acute kidney injury (AKI) is a common complication of treatment with liposomal amphotericin B (LAmB). The trajectory of renal recovery after LAmB-associated AKI has not been well described, nor has effect of LAmB dose on recovery of renal function been explored. Objective. Characterize the pattern of renal recovery after incident AKI during LAmB and determine potential influencing factors. Methods. This retrospective cohort study analyzed patients who developed a ≥50% increase in serum creatinine while on LAmB. Patients were followed up until complete renal recovery or death or for 30 days, whichever occurred first. The primary outcome was complete renal recovery, defined as serum creatinine convalescence to within 10% of the patient’s pretreatment baseline. Multivariable modeling was used to identify independent predictors of renal recovery. Results. Ninety-eight patients experienced nephrotoxicity during LAmB, 94% of which received doses <7 mg/kg/day. Fifty-one patients at least partially recovered renal function and, of these, 32 exhibited complete recovery after a mean 9.8 ± 7.8 days. No statistical relationship was found between LAmB dose at the time of AKI or cumulative exposure to LAmB and the likelihood of renal recovery. Concomitant nephrotoxins, age, and pretreatment renal function did not modify this effect in multivariable analysis. Conclusion and Relevance. Our data suggests that LAmB dose did not impact the likelihood of renal recovery. Additional investigation is needed to confirm these findings when aggressive dosing strategies are employe. Additional research is also warranted to further characterize the course of recovery after LAmB-associated nephrotoxicity and comprehensive spectrum of renal outcomes.

Objective Among neonates of 22 to 29 weeks' gestational age (GA) who required mechanical ventilation for the treatment of respiratory distress syndrome (RDS) and clinically diagnosed pulmonary hypertension (PH), we tested our hypothesis that the association between early treatment with inhaled nitric oxide (iNO) and survival would vary according to birth size and GA. Study Design Because iNO was not randomly prescribed to patients in this cohort, we used propensity score matching to pair a neonate who received iNO at a chronological age of ≤7 days with an unexposed neonate with similar baseline characteristics. The primary outcome was inhospital mortality, which we evaluated based on size for GA and GA strata using the Cox proportional hazards regression model. Results Among 1,531 neonates who met study criteria, we created a propensity score matched cohort of 615 pairs of neonates (iNO-exposed and unexposed). The risk of inhospital mortality for iNO-exposed neonates was observed only in the minority (<10%) who were large for GA, though this finding did not persist when matching for illness severity. Conclusion Early treatment with iNO is not associated with survival in most extremely premature neonates with RDS and clinically diagnosed PH when stratified for birth size or GA.

Abstract Introduction Sexual dysfunction is a common problem in women and the nature of its association with alcohol use remains unclear. Aim To explore the association between alcohol use and female sexual dysfunction (FSD). Methods Associations between self-reported drinking and sexual function were evaluated in 2,253 women presenting for consultation to a women’s health specialty clinic. A short version of the Alcohol Use Disorders Identification Test (AUDIT-C) was used to evaluate alcohol use. Women with an AUDIT-C ≥3 were considered at risk for hazardous drinking. Multivariable regression, controlling for depression, anxiety, and abuse (childhood and recent), was used to assess the association between alcohol consumption and FSD (defined as a Female Sexual Function Index [FSFI] ≤26.55 and Female Sexual Distress Scale [FSDS] ≥11) in sexually active women. Main Outcome Measure The main study outcome measure was the presence of FSD as defined by a score ≤26.55 on the FSFI and ≥11 on the FSDS. Results 57% of the 1,649 sexually active women were classified as having FSD; 80% reported any alcohol use and 38% reported drinking patterns with the potential to be hazardous. The women at risk for hazardous drinking had significantly higher FSFI domain scores indicating better sexual function (P ≤ .001). However, in multivariable analyses, there was no significant difference in the rates of FSD across alcohol use categories in women. Conclusion In women presenting for consultation to a women’s health specialty clinic, an association between alcohol use and FSFI scores was seen, in which greater risk of hazardous drinking was associated with better sexual function scores. However, when sexual distress was included to define sexual dysfunction, those with FSD were not at higher risk of hazardous drinking. Given the complex nature of FSD, additional study is needed to further clarify these relationships.

Study Design. This study retrospectively analyzes prospectively collected data. Objective. Here in this study we aim to determine the factors which impact a patient's ability to return to work (RTW) in the setting of cervical spine surgery in patients without worker's compensation status. Summary of Background Data. Surgical management of degenerative cervical disease has proven cost-effectiveness and shown significant improvement in quality of life. However, the ability to RTW is an important clinical outcome for preoperatively employed patients. Methods. All adult patients undergoing elective surgery for cervical degenerative disease at our institution are enrolled in a prospective, web-based registry. A multivariable Cox proportional hazards regression model was built for time to RTW. The variables included in the model were age, sex, smoking status, occupation type, number of levels operated on, ASA grade, body mass index, history of diabetes, history of coronary artery disease (CAD), history of chronic obstructive pulmonary disease (COPD), anxiety, depression, myelopathy at presentation, duration of symptoms more than 12 months, diagnosis, type of surgery performed, and preoperative Neck Disability Index, EuroQol Five Dimensions, and Numeric Rating Scale pain scores for neck pain and arm pain scores. Results. Of the total 324 patients with complete 3-month follow-up data 83% (n = 269) returned to work following surgery. The median time to RTW was 35 days (range, 2–90 d). Patients with a labor-intensive occupation, higher ASA grade, history of CAD, and history of COPD were less likely to RTW. The likelihood of RTW was lower in patients with a diagnosis of disc herniation compared with cervical stenosis, patients undergoing cervical corpectomy compared laminectomy and fusion and patient with longer operative time. Conclusion. Our study identifies the various factors associated with a lower likelihood of RTW at 3 months after cervical spine surgery in the non-worker's compensation setting. This information provides expectations for the patient and employer when undergoing cervical spine surgery. Level of Evidence: 3