SifiNet: a robust and accurate method to identify feature gene sets and annotate cells.

SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multi-omic cellular profiles. It is conveniently available as an open-source R package.

DYNATE: Localizing rare-variant association regions via multiple testing embedded in an aggregation tree.

Rare-variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggregate the effects of RVs across genomic regions to study their collective impact. Some existing methods utilize a static delineation of genomic regions, often resulting in suboptimal effect aggregation, as neutral subregions within the test region will result in an attenuation of signal. Other methods use varying windows to search for signals but often result in long regions containing many neutral RVs. To pinpoint short genomic regions enriched for disease-associated RVs, we developed a novel method, DYNamic Aggregation TEsting (DYNATE). DYNATE dynamically and hierarchically aggregates smaller genomic regions into larger ones and performs multiple testing for disease associations with a controlled weighted false discovery rate. DYNATE's main advantage lies in its strong ability to identify short genomic regions highly enriched for disease-associated RVs. Extensive numerical simulations demonstrate the superior performance of DYNATE under various scenarios compared with existing methods. We applied DYNATE to an amyotrophic lateral sclerosis study and identified a new gene, EPG5, harboring possibly pathogenic mutations.

Immune Phenotype and Postoperative Complications After Elective Surgery.

OBJECTIVES: To characterize and quantify accumulating immunologic alterations, pre and postoperatively in patients undergoing elective surgical procedures. BACKGROUND: Elective surgery is an anticipatable, controlled human injury. Although the human response to injury is generally stereotyped, individual variability exists. This makes surgical outcomes less predictable, even after standardized procedures, and may provoke complications in patients unable to compensate for their injury. One potential source of variation is found in immune cell maturation, with phenotypic changes dependent on an individual's unique, lifelong response to environmental antigens. METHODS: We enrolled 248 patients in a prospective trial facilitating comprehensive biospecimen and clinical data collection in patients scheduled to undergo elective surgery. Peripheral blood was collected preoperatively, and immediately on return to the postanesthesia care unit. Postoperative complications that occurred within 30 days after surgery were captured. RESULTS: As this was an elective surgical cohort, outcomes were generally favorable. With a median follow-up of 6 months, the overall survival at 30 days was 100%. However, 20.5% of the cohort experienced a postoperative complication (infection, readmission, or system dysfunction). We identified substantial heterogeneity of immune senescence and terminal differentiation phenotypes in surgical patients. More importantly, phenotypes indicating increased T-cell maturation and senescence were associated with postoperative complications and were evident preoperatively. CONCLUSIONS: The baseline immune repertoire may define an immune signature of resilience to surgical injury and help predict risk for surgical complications.

Neuroimaging and immunological features of neurocognitive function related to substance use in people with HIV.

This study sought to identify neuroimaging and immunological factors associated with substance use and that contribute to neurocognitive impairment (NCI) in people with HIV (PWH). We performed cross-sectional immunological phenotyping, neuroimaging, and neurocognitive testing on virally suppressed PWH in four substance groups: cocaine only users (COC), marijuana only users (MJ), dual users (Dual), and Non-users. Participants completed substance use assessments, multimodal MRI brain scan, neuropsychological testing, and blood and CSF sampling. We employed a two-stage analysis of 305 possible biomarkers of cognitive function associated with substance use. Feature reduction (Kruskal Wallis p-value < 0.05) identified 53 biomarkers associated with substance use (22 MRI and 31 immunological) for model inclusion along with clinical and demographic variables. We employed eXtreme Gradient Boosting (XGBoost) with these markers to predict cognitive function (global T-score). SHapley Additive exPlanations (SHAP) values were calculated to rank features for impact on model output and NCI. Participants were 110 PWH with sustained HIV viral suppression (33 MJ, 12 COC, 22 Dual, and 43 Non-users). The ten highest ranking biomarkers for predicting global T-score were 4 neuroimaging biomarkers including functional connectivity, gray matter volume, and white matter integrity; 5 soluble biomarkers (plasma glycine, alanine, lyso-phosphatidylcholine (lysoPC) aC17.0, hydroxy-sphingomyelin (SM.OH) C14.1, and phosphatidylcholinediacyl (PC aa) C28.1); and 1 clinical variable (nadir CD4 count). The results of our machine learning model suggest that substance use may indirectly contribute to NCI in PWH through both metabolomic and neuropathological mechanisms.

Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects.

Older AML patients have low remission rates and poor survival outcomes with standard chemotherapy. Microtransplantation (MST) refers to infusion of allogeneic hematopoietic stem cells without substantial engraftment. MST has been shown to improve clinical outcomes compared with chemotherapy alone. This is the first trial reporting on broad correlative studies to define immunologic mechanisms of action of MST in older AML patients. Older patients with newly diagnosed AML were eligible for enrollment, receiving induction chemotherapy with cytarabine (100 mg/m2) on days 1-7 and idarubicin (12 mg/m2) on days 1-3 (7 + 3). MST was administered 24 hours later. Patients with complete response (CR) were eligible for consolidation with high dose cytarabine (HiDAC) and a second cycle of MST. Responses were evaluated according to standard criteria per NCCN. Immune correlative studies were performed. Sixteen patients were enrolled and received 7 + 3 and MST (median age 73 years). Nine (56%) had high-risk and seven (44%) had standard-risk cytogenetics. Ten episodes of CRS were observed. No cases of GVHD or treatment-related mortality were reported. Event-free survival (EFS) was 50% at 6 months and 19% at 1 year. Overall survival (OS) was 63% at 6 months and 44% at 1 year. Donor microchimerism was not detected. Longitudinal changes were noted in NGS, TCR sequencing, and cytokine assays. Addition of MST to induction and consolidation chemotherapy was well tolerated in older AML patients. Inferior survival outcomes in our study may be attributed to a higher proportion of very elderly patients with high-risk features. Potential immunologic mechanisms of activity of MST include attenuation of inflammatory cytokines and emergence of tumor-specific T cell clones.

Genetic variants in the calcium signaling pathway genes are associated with cutaneous melanoma-specific survival.

Remodeling or deregulation of the calcium signaling pathway is a relevant hallmark of cancer including cutaneous melanoma (CM). In this study, using data from a published genome-wide association study (GWAS) from The University of Texas M.D. Anderson Cancer Center, we assessed the role of 41,377 common single-nucleotide polymorphisms (SNPs) of 167 calcium signaling pathway genes in CM survival. We used another GWAS from Harvard University as the validation dataset. In the single-locus analysis, 1830 SNPs were found to be significantly associated with CM-specific survival (CMSS; P ≤ 0.050 and false-positive report probability ≤ 0.2), of which 9 SNPs were validated in the Harvard study (P ≤ 0.050). Among these, three independent SNPs (i.e. PDE1A rs6750552 T>C, ITPR1 rs6785564 A>G and RYR3 rs2596191 C>A) had a predictive role in CMSS, with a meta-analysis-derived hazards ratio of 1.52 (95% confidence interval = 1.19-1.94, P = 7.21 × 10-4), 0.49 (0.33-0.73, 3.94 × 10-4) and 0.67 (0.53-0.86, 0.0017), respectively. Patients with an increasing number of protective genotypes had remarkably improved CMSS. Additional expression quantitative trait loci analysis showed that these genotypes were also significantly associated with mRNA expression levels of the genes. Taken together, these results may help us to identify prospective biomarkers in the calcium signaling pathway for CM prognosis.

bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.

Summary: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error. The algorithm uses a Trie data structure for speed and resolves ambiguous mappings by using a statistical sequencing error model based on Phred scores for each read. Availability and implementation: The package source code and an accompanying tutorial are available at http://bioconductor.org/packages/bcSeq/. Supplementary information: Supplementary data are available at Bioinformatics online.

Prevalence and Cost Analysis of Chronic Pain After Hernia Repair: A Potential Alternative Approach With Neurostimulation.

OBJECTIVES: Chronic pain (CP) affects a significant number of patients following hernia repair, ranging from 11 to 54% in the literature. The aim of this study was to assess the prevalence, overall costs, and health care utilization associated with CP after hernia repair. MATERIALS AND METHODS: A retrospective longitudinal study was performed using the Truven MarketScan® data base to identify patients who develop chronic neuropathic posthernia repair pain from 2001 to 2012. Patients were grouped into CP and No Chronic Pain (No CP) cohorts. Patients were excluded if they 1) were under 18 years of age; 2) had a previous pain diagnosis; 3) had CP diagnosed <90 days after the index hernia repair; 4) had less than one year of follow-up; or 5) had less than one-year baseline record before hernia repair. Patients were grouped into the CP cohort if their CP diagnosis was made within the two years following index hernia repair. Total, outpatient, and pain prescription costs were collected in the period of five years prehernia to nine years posthernia repair. A longitudinal multivariate analysis was used to model the effects of chronic neuropathic posthernia repair pain on total inpatient/outpatient and pain prescription costs. RESULTS: We identified 76,173 patients who underwent hernia repair and met inclusion criteria (CP: n = 14,919, No CP: n = 61,254). There was a trend for increased total inpatient/outpatient and pain prescription costs one-year posthernia repair, when compared to baseline costs for both cohorts. In both cohorts, total inpatient/outpatient costs remained elevated from baseline through nine years posthernia repair, with the CP cohort experiencing significantly higher cumulative median costs (CP: $51,334, No CP: $37,388). The CP diagnosis year was associated with a 1.75-fold increase (p < 0.001) in total inpatient/outpatient costs and a 2.26-fold increase (p < 0.001) in pain prescription costs versus all other years. In the longitudinal analysis, the CP cohort had a 1.14-fold increase (p < 0.001) in total inpatient/outpatient costs and 2.00-fold increase (p < 0.001) in pain prescription costs. CONCLUSIONS: Our study demonstrates the prevalence of CP after hernia surgery to be nearly 20%, with significantly increased costs and healthcare resource utilization. While current treatment paradigms are effective for many, there remains a large number of patients that could benefit from an overall approach that includes nonopioid treatments, such as potentially incorporating neurostimulation, for CP that presents posthernia repair.

Genetic variants in the platelet-derived growth factor subunit B gene associated with pancreatic cancer risk.

The platelet-derived growth factor (PDGF) signaling pathway plays important roles in development and progression of human cancers. In our study, we aimed to identify genetic variants of the PDGF pathway genes associated with pancreatic cancer (PC) risk in European populations using three published genome-wide association study datasets, which consisted of 9,381 cases and 7,719 controls. The expression quantitative trait loci (eQTL) analysis was also performed using data from the 1000 Genomes, TCGA and GTEx projects. As a result, we identified two potential susceptibility loci (rs5757573 and rs6001516) of PDGFB associated with PC risk [odds ratio (OR) = 1.10, 95% confidence interval (CI) = 1.05-1.16, and p = 4.70 × 10-5 for the rs5757573 C allele and 1.21, 1.11-1.32, and 2.01 × 10-5 for the rs6001516 T allele]. Haplotype analysis revealed that the C-T haplotype carriers had a significantly increased risk of PC than those carrying the T-C haplotype (OR = 1.23, 95% CI = 1.12-1.34, p =5.00 × 10-6 ). The multivariate regression model incorporating the number of unfavorable genotypes (NUGs) with age and sex showed that carriers with 1-2 NUGs, particularly among 60-70 age group or males, had an increased risk of PC, compared to those without NUG. Furthermore, the eQTL analysis revealed that both loci were correlated with a decreased mRNA expression level of PDGFB in lymphoblastoid cell lines and pancreatic tumor tissues (p = 0.015 and 0.071, respectively). Our results suggest that genetic variants in PDGFB may play a role in susceptibility to PC. Further population and functional validations of our findings are warranted.

Genetic variant of IRAK2 in the toll-like receptor signaling pathway and survival of non-small cell lung cancer.

The toll-like receptor (TLR) signaling pathway plays an important role in the innate immune responses and antigen-specific acquired immunity. Aberrant activation of the TLR pathway has a significant impact on carcinogenesis or tumor progression. Therefore, we hypothesize that genetic variants in the TLR signaling pathway genes are associated with overall survival (OS) of patients with non-small cell lung cancer (NSCLC). To test this hypothesis, we first performed Cox proportional hazards regression analysis to evaluate associations between genetic variants of 165 TLR signaling pathway genes and NSCLC OS using the genome-wide association study (GWAS) dataset from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). The results were further validated by the Harvard Lung Cancer Susceptibility GWAS dataset. Specifically, we identified IRAK2 rs779901 C > T as a predictor of NSCLC OS, with a variant-allele (T) attributed hazards ratio (HR) of 0.78 [95% confidence interval (CI) = 0.67-0.91, P = 0.001] in the PLCO dataset, 0.84 (0.72-0.98, 0.031) in the Harvard dataset, and 0.81 (0.73-0.90, 1.08x10-4 ) in the meta-analysis of these two GWAS datasets. In addition, the T allele was significantly associated with an increased mRNA expression level of IRAK2. Our findings suggest that IRAK2 rs779901 C > T may be a promising prognostic biomarker for NSCLC OS.

Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer.

The P38MAPK pathway participates in regulating cell cycle, inflammation, development, cell death, cell differentiation, and tumorigenesis. Genetic variants of some genes in the P38MAPK pathway are reportedly associated with lung cancer risk. To substantiate this finding, we used six genome-wide association studies (GWASs) to comprehensively investigate the associations of 14 904 single nucleotide polymorphisms (SNPs) in 108 genes of this pathway with lung cancer risk. We identified six significant lung cancer risk-associated SNPs in two genes (CSNK2B and ZAK) after correction for multiple comparisons by a false discovery rate (FDR) <0.20. After removal of three CSNK2B SNPs that are located in the same locus previously reported by GWAS, we performed the LD analysis and found that rs3769201 and rs7604288 were in high LD. We then chose two independent representative SNPs of rs3769201 and rs722864 in ZAK for further analysis. We also expanded the analysis by including these two SNPs from additional GWAS datasets of Harvard University (984 cases and 970 controls) and deCODE (1319 cases and 26 380 controls). The overall effects of these two SNPs were assessed using all eight GWAS datasets (OR = 0.92, 95%CI = 0.89-0.95, and P = 1.03 × 10-5 for rs3769201; OR = 0.91, 95%CI = 0.88-0.95, and P = 2.03 × 10-6 for rs722864). Finally, we performed an expression quantitative trait loci (eQTL) analysis and found that these two SNPs were significantly associated with ZAK mRNA expression levels in lymphoblastoid cell lines. In conclusion, the ZAK rs3769201 and rs722864 may be functional susceptibility loci for lung cancer risk.

Prevalence and Cost Analysis of Complex Regional Pain Syndrome (CRPS): A Role for Neuromodulation.

OBJECTIVE: The diagnosis and treatment of complex regional pain syndrome (CRPS) is challenging and there is a paucity of data describing its overall cost burden and quantifying its impact on the US healthcare system. The aim of this study was to assess the prevalence and healthcare utilization costs associated with CRPS. MATERIALS AND METHODS: A retrospective longitudinal study was performed using the Truven MarketScan® database to identify patients with a new indexed diagnosis of CRPS (Type I, II, or both) from 2001 to 2012. We collected total, outpatient, and pain prescription costs three years prior to CRPS diagnosis (baseline), at year of CRPS diagnosis, and eight-year post-CRPS diagnosis. A longitudinal multivariate analysis was used to model the estimated total and pain prescription cost ratios comparing patients diagnosed before and after CRPS. RESULTS: We included 35,316 patients with a newly indexed diagnosis of CRPS (Type I: n = 18,703, Type II: n = 14,599, Unspecified: n = 2014). Baseline characteristics were similar between the CRPS cohorts. Compared to two- and three-year baseline costs, one-year prior to diagnosis for all CRPS patients yielded the highest interquartile median [IQR] costs: total costs $7904[$3469, $16,084]; outpatient costs $6706[$3119, $12,715]; and pain prescription costs $1862[$147, $7649]. At the year of CRPS diagnosis, the median [IQR] costs were significantly higher than baseline costs: total costs $8508[$3943, $16,666]; outpatient costs $7251[$3527, $13,568]; and pain prescription costs $2077[$140, $8856]. Over the eight-year period after CRPS diagnosis, costs between all the years were similar, ranging from the highest (one-year) to lowest (seven-years), $4845 to $3888. The median total cumulative cost 8-years after CRPS diagnosis was $43,026 and $12,037 for pain prescription costs. [Correction added on 06 November 2017 after first online publication: the preceding sentence has been updated to demonstrate the median cumulative cost in replacement of the additive cumulative mean costs.]. During the CRPS diagnosis period, patients are expected to have a total cost 2.17-fold and prescription cost 2.56-fold of their baseline cost annually. CONCLUSIONS: Our study demonstrates that there is a significant increase in cost and healthcare resource utilization one-year prior to and around the time of CRPS diagnosis. Furthermore, there is an increased annual cost post-diagnosis compared to baseline costs prior to CRPS diagnosis.

Drivers and Risk Factors of Unplanned 30-Day Readmission Following Spinal Cord Stimulator Implantation.

OBJECTIVES: Unplanned 30-day readmission rates contribute significantly to growing national healthcare expenditures. Drivers of unplanned 30-day readmission after spinal cord stimulator (SCS) implantation are relatively unknown. The aim of this study was to determine drivers of 30-day unplanned readmission following SCS implantation. METHODS: The National Readmission Database was queried to identify all patients who underwent SCS implantation for the 2013 calendar year. Patients were grouped by readmission status, "No Readmission" and "Unplanned 30-day Readmission." Patient demographics and comorbidities were collected for each patient. The primary outcome of interest was the rate of unplanned 30-day readmissions and associated driving factors. A multivariate analysis was used to determine independent predictors of unplanned 30-day readmission after SCS implantation. RESULTS: We identified 1521 patients who underwent SCS implantation, with 113 (7.4%) experiencing an unplanned readmission within 30 days. Baseline patient demographics, comorbidities, and hospital characteristics were similar between both cohorts. The three main drivers for 30-day readmission after SCS implantation include: 1) infection (not related to SCS device), 2) infection due to device (limited to only hardware infection), and 3) mechanical complication of SCS device. Furthermore, obesity was found to be an independent predictor of 30-day readmission (OR: 1.86, p = 0.008). CONCLUSION: Our study suggests that infectious and mechanical complications are the primary drivers of unplanned 30-day readmission after SCS implantation, with obesity as an independent predictor of unplanned readmission. Given the technological advancements in SCS, repeated studies are necessary to identify factors associated with unplanned 30-day readmission rates after SCS implantation to improve patient outcomes and reduce associated costs.

The Volume-Outcome Effect: Impact on Trial-to-Permanent Conversion Rates in Spinal Cord Stimulation.

OBJECTIVES: Conversion rates from trial leads to permanent spinal cord stimulation (SCS) systems have important implications for healthcare resource utilization (HCRU) and pain management. We hypothesized that there is a volume-outcome effect, with chronic pain patients who visit high volume SCS implanters will have higher trial-to-permanent conversion rates. MATERIALS AND METHODS: We designed a large, retrospective analysis using the Truven MarketScan database analyzing adult SCS patients with provider information available, with or without IPG implantation from the years 2007 to 2012 was designed. Patients were divided into three provider-based groups: high (>25), medium (9-24), and low (3-8) volume providers. Univariate and multivariate models identified factors associated with successful conversion. RESULTS: A total of 17,850 unique trial implants were performed by 3028 providers. Of 13,879 patients with baseline data available, 8981 (64.7%) progressed to permanent SCS. Higher volume providers were associated with slightly higher conversion rates (65.9% vs. 63.3% low volume, p = 0.029), explant rates (9.2% vs. 7.7% medium volume, p = 0.026), younger age (52.0 ± 13.4 years vs. 53.0 ± 13.4 years, p = 0.0026), Medicare/Medicaid (47.8% vs. 35.0% low volume, p < 0.0001), Southern region (53.5% vs. 38.9% low volume, p < 0.0001), and higher Charlson comorbidity scores (1.0 [SD = 1.4], p = 0.0002). Multivariate regression results showed female gender (1.13 [95% CI: 1.05-1.22], p < 0.001) and high volume providers associated with higher odds of successful trial conversion (1.12 [95% CI: 1.02-1.22], p = 0.014). CONCLUSIONS: In this nationwide analysis, high volume providers achieved higher trial-to-permanent SCS conversion rates than lower volume providers. The study has implications for both training requirements and referral patterns to delineate minimum implant experience necessary for provider proficiency. Future studies may be useful to understand HCRU differences.

Explantation Rates and Healthcare Resource Utilization in Spinal Cord Stimulation.

OBJECTIVES: Certain patients ultimately undergo explantation of their spinal cord stimulation (SCS) devices. Understanding the predictors and rates of SCS explantation has important implications for healthcare resource utilization (HCRU) and pain management. The present study identifies explant predictors and discerns differences in HCRU for at-risk populations. METHODS: We designed a large, retrospective analysis using the Truven MarketScan Database. We included all adult patients who underwent a SCS trial from 2007 to 2012. Patients were grouped into cohorts that remained explant-free or underwent explantation over a three-year period, and multivariate models evaluated differences in healthcare resource utilization. RESULTS: A total of 8727 unique instances of trial implants between 2007 and 2012 were identified. Overall, 805 (9.2%) patients underwent device explantation. One year prior to SCS implantation, the explant cohort had significantly higher median baseline costs ($42,140.3 explant vs. $27,821.7 in non-explant groups; p < 0.0001), total number of pain encounters (180 vs. 103 p < 0.0001), and associated costs ($15,446.9 vs. $9,227.9; p < 0.0001). The explant cohort demonstrated increased use of procedures (19.0 vs. 9.0; p < 0.0001) compared to non-explanted patients. For each month after initial SCS implantation, explanted patients had a slower decrease in total costs (4% vs. 6% in non-explant; p < 0.01). At the month of explant, explant patients were expected to have incurred 2.65 times the total cost compared to the non-explant cohort (CR 2.65, 95% CI [1.83, 3.84]; p < 0.001). Medium volume providers had lower rates of explantation at one-year and three-years compared to low volume providers (p = 0.042). Increased age and Charlson index were independent predictors of explantation during the same periods. CONCLUSIONS: In this nationwide analysis, we identified that SCS device explantation is correlated with patients who have higher baseline costs, higher total cost post-SCS implantation, and increased use of procedures to control pain. The higher rates of explantation at three-years postimplant among low volume providers suggest that variations in provider experience and approach also contributes to differences in explantation rates.

Specialty-Based Variations in Spinal Cord Stimulation Success Rates for Treatment of Chronic Pain.

OBJECTIVES: Spinal cord stimulation (SCS) has emerged as an appropriate modality of treatment for intractable chronic pain. The present study examines variations in SCS trial-to-permanent conversion rates based on provider types performing the procedure. MATERIALS AND METHODS: We designed a large, retrospective analysis using the Truven MarketScan data base analyzing adult SCS patients with provider information available, with or without IPG implantation from the years 2007-2012. Patients were categorized based on provider type performing the implantation including anesthesiologists, neurosurgeons, orthopedic surgeons, and physical medicine and rehabilitation (PM&R). Univariate and multivariate models identified factors associated with successful conversion. RESULTS: A total of 7667 unique instances of SCS implants were identified across five providers. Overall, 4842 (63.2%) of those receiving trials underwent permanent SCS system implantation. Anesthesiology performed the majority of implants (62.8%), followed by neurosurgery (22.0%), orthopedic surgery (10.2%), and PM&R (5.3%). Compared to anesthesiologists, both neurosurgeons (OR 10.99, 95% CI [9.11, 13.25]; p < 0.001) and orthopedic surgeons (OR 4.64, 95% CI [3.81, 5.65]; p < 0.001) had significantly higher conversion rates, while PM&R (OR 0.71, 95% CI [0.58, 0.87]; p = 0.001) had significantly lower. Percutaneous implants comprised 5473 (71.4%) of all implants. Neurosurgeons and orthopedic surgeons performed a significantly greater number of paddle implants among the different providers (p < 0.0001). Explant rates were similar across all cohorts analyzed (average 11.6%; p = 0.546). CONCLUSIONS: In this nationwide analysis, our results suggest that over a recent five-year period, conversion rates are highest when SCS trials are performed by neurosurgeons and orthopedic surgeons. The study has important implications for establishing uniform guidelines for training, patient selection, and education of physicians across multiple disciplines.

Impact of Insurance Provider on Overall Costs in Failed Back Surgery Syndrome: A Cost Study of 122,827 Patients.

OBJECTIVES: Failed back surgery syndrome (FBSS) affects 40% of patients following spine surgery with estimated costs of $20 billion to the US health care system. The aim of this study was to assess the cost differences across the different insurance providers for FBSS patients. METHODS: A retrospective longitudinal study was performed using the Truven MarketScan® database to identify FBSS patients from 2001 to 2012. Patients were grouped into Commercial, Medicaid, or Medicare cohorts. We collected one-year prior to FBSS diagnosis (baseline), then at year of spinal cord stimulation (SCS)-implantation and nine-year post-SCS implantation cost outcomes. RESULTS: We identified 122,827 FBSS patients, with 117,499 patients who did not undergo an SCS-implantation (Commercial: n = 49,075, Medicaid: n = 23,180, Medicare: n = 45,244) and 5328 who did undergo an SCS implantation (Commercial: n = 2279, Medicaid: n = 1003, Medicare: n = 2046). Baseline characteristics were similar between the cohorts, with the Medicare-cohort being significantly older. Over the study period, there were significant differences in overall cost metrics between the cohorts who did not undergo SCS implantation with the Medicaid-cohort had the lowest annual median (interquartile range) total cost (Medicaid: $4530.4 [$1440.6, $11,973.5], Medicare: $7292.0 [$3371.4, $13,989.4], Commercial: $4944.3 [$363.8, $13,294.0], p < 0.0001). However, when comparing the patients who underwent SCS implantation, the commercial-cohort had the lowest annual median (interquartile range) total costs (Medicaid: $4045.6 [$1146.9, $11,533.9], Medicare: $7158.1 [$3160.4, $13,916.6], Commercial: $2098.1 [$0.0, $8919.6], p < 0.0001). CONCLUSIONS: Our study demonstrates a significant difference in overall costs between various insurance providers in the management of FBSS, with Medicaid-insured patients having lower overall costs compared to Commercial- and Medicare-patients. SCS is cost-effective across all insurance groups (Commercial > Medicaid > Medicare) beginning at two years and continuing through nine-year follow-up. Further studies are necessary to understand the cost differences between these insurance providers, in hopes of reducing unnecessary health care expenditures for patients with FBSS.

PenPC: A two-step approach to estimate the skeletons of high-dimensional directed acyclic graphs.

Estimation of the skeleton of a directed acyclic graph (DAG) is of great importance for understanding the underlying DAG and causal effects can be assessed from the skeleton when the DAG is not identifiable. We propose a novel method named PenPC to estimate the skeleton of a high-dimensional DAG by a two-step approach. We first estimate the nonzero entries of a concentration matrix using penalized regression, and then fix the difference between the concentration matrix and the skeleton by evaluating a set of conditional independence hypotheses. For high-dimensional problems where the number of vertices p is in polynomial or exponential scale of sample size n, we study the asymptotic property of PenPC on two types of graphs: traditional random graphs where all the vertices have the same expected number of neighbors, and scale-free graphs where a few vertices may have a large number of neighbors. As illustrated by extensive simulations and applications on gene expression data of cancer patients, PenPC has higher sensitivity and specificity than the state-of-the-art method, the PC-stable algorithm.

Joint Estimation of Multiple High-dimensional Precision Matrices.

Motivated by analysis of gene expression data measured in different tissues or disease states, we consider joint estimation of multiple precision matrices to effectively utilize the partially shared graphical structures of the corresponding graphs. The procedure is based on a weighted constrained ℓ∞/ℓ1 minimization, which can be effectively implemented by a second-order cone programming. Compared to separate estimation methods, the proposed joint estimation method leads to estimators converging to the true precision matrices faster. Under certain regularity conditions, the proposed procedure leads to an exact graph structure recovery with a probability tending to 1. Simulation studies show that the proposed joint estimation methods outperform other methods in graph structure recovery. The method is illustrated through an analysis of an ovarian cancer gene expression data. The results indicate that the patients with poor prognostic subtype lack some important links among the genes in the apoptosis pathway.

Implantable Neurostimulation for Headache Disorders: Effect on Healthcare Utilization and Expenditures.

OBJECTIVES: Chronic daily headache is a considerable source of morbidity for patients and also carries an enormous economic burden. Patients who fail standard medication regimens lack well-defined therapies, and neurostimulation is an emerging option for these patients. The purpose of this study was to analyze the cost utility of implantable neurostimulation for treatment of headache. METHODS: We utilized the Thompson Reuters Marketscan Data base to identify individuals diagnosed with headache disorders who underwent percutaneous neurostimulation. Healthcare expenditures for individuals who subsequently received permanent, surgically implanted neurostimulatory devices were compared to those who did not. Only individuals who sought implantable neurostimulation were included to account for headache severity. The cohorts were adjusted for comorbidity and prior headache-related expenses. Costs were modeled longitudinally using a generalized estimating equation. RESULTS: A total of 579 patients who underwent percutaneous trial of neurostimulation were included, of which 324 (55.96%) converted to permanent neurostimulation within one year. Unadjusted expenditures were greater for patients who underwent conversion to the permanent neurostimulation device, as expected. Costs grew at a lower rate for patients who converted to permanent device implantation. Cost neutrality for patients receiving the permanent device was reached in less than five years after the enrollment date. The mean cost of conversion to a permanent implantation was $18,607.53 (SD $26,441.34). CONCLUSIONS: Our study suggests that implantable neurostimulation reduces healthcare expenditures within a relatively short time period in patients with severe refractory headache.