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Background and Aims: Cancer and Leukemia Group B 80303 was a randomized, phase III study in patients with advanced pancreatic cancer treated with gemcitabine plus either bevacizumab or placebo. We prospectively collected germline DNA and conducted a genome-wide association study (GWAS) using overall survival (OS) as the endpoint.Experimental Design: DNA from 351 patients was genotyped for more than 550,000 single-nucleotide polymorphisms (SNP). Associations between OS and SNPs were investigated using the log-linear 2-way multiplicative Cox proportional hazards model. The subset of 294 genetically European patients was used for the primary analysis.Results: A nonsynonymous SNP in interleukin (IL)17F (rs763780, H161R) and an intronic SNP in strong linkage disequilibrium (rs7771466) were associated with OS using genome-wide criteria (P ≤ 10−7). Median OS was significantly shorter (P = 2.61 × 10−8) for the rs763780 heterozygotes [3.1 months; 95% confidence interval (CI), 2.3–4.3] than for the patients without this variant (6.8 months; 95% CI, 5.8–7.3). After adjustment by stratification factors, the P value for the association was 9.51 × 10−7.Conclusions: The variant 161R form of IL-17F is a natural antagonist of the antiangiogenic effects of wild-type 161H IL-17F, and angiogenesis may play an important role in the metastatic spread of pancreatic cancer. In this preliminary study, we hypothesize that the angiogenetic potential of pancreatic cancers in patients with variant IL-17F is higher than that of tumors in patients with wild-type IL-17F, conferring worse prognosis. This exploratory GWAS may provide the foundation for testing the biology and clinical effects of novel genes and their heritable variants through mechanistic and confirmatory studies in pancreatic cancer. Clin Cancer Res; 18(2); 577–84. ©2011 AACR.

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The efficient market hypothesis (EMH), based on rational expectations and market equilibrium, is the dominant perspective for modelling economic markets. However, the most notable critique of the EMH is the inability to model periods of out-of-equilibrium behaviour in the absence of any significant external news. When such dynamics emerge endogenously, the traditional economic frameworks provide no explanation for such behaviour and the deviation from equilibrium. This work offers an alternate perspective explaining the endogenous emergence of punctuated out-of-equilibrium dynamics based on bounded rational agents. In a concise market entrance game, we show how boundedly rational strategic reasoning can lead to endogenously emerging crises, exhibiting fat tails in "returns". We also show how other common stylised facts of economic markets, such as clustered volatility, can be explained due to agent diversity (or lack thereof) and the varying learning updates across the agents. This work explains various stylised facts and crisis emergence in economic markets, in the absence of any external news, based purely on agent interactions and bounded rational reasoning., Comment: 10 pages + 7 page appendix, 7 figures

Introduction: Blood cultures are the gold standard for identifying bloodstream infections. The Clinical and Laboratory Standards Institute recommends a blood culture contamination rate of

Introduction: The MYC gene family (MYCf), which includes MYC, MYCN, and MYCL, is deregulated in ~70% of cancers and is associated with treatment resistance. Whereas older investigational therapies for MYC amplified tumors were unsuccessful, promising novel targeted therapies are in early phase clinical trials. Unfortunately, it remains unclear how to select patients whose cancers may harbor true MYC addiction. We thus sought to characterize factors such as amplification level, focality, and clonality that may correlate with increased MYC dependence. Methods: Utilizing a center-wide next generation sequencing (NGS) program of >71,000 sequenced patients, genomic and clinical data from pediatric and adult patients with MYC, MYCN, and MYCL amplifications were identified between 2014 and 2022. Patients were characterized as harboring MYC, MYCN, and MYCL amplification based on a read-depth methodology using a DNA-based hybrid-capture NGS (MSK-IMPACT) and Fraction and Allele-Specific Copy Number Estimates from the Tumor Sequencing (FACETS). All cases underwent clinical data curation including baseline demographic, tumor characteristics, and treatment histories. Results: We identified 3911 cancers with MYCf amplification (n=3257 (82%) MYC; n=364 (9%) MYCL; n=330 (8%) MYCN) across 40 malignancies, for an overall 5.5% incidence. The most frequent tumor types with MYCf amplification were breast (22%), non-small cell lung (NSCLC) (11%), colorectal (8%), ovarian (8%), prostate (7%), brain (5%), and small cell lung cancers (SCLC) (2%). Cancers with MYC amplification had longer segment lengths than MYCL and MYCN amplification, which appeared more focal (median = 19, 4.3 and 4.5 MB, respectively, p < 0.001). MYCN amplified cancers had higher total copy number than MYC and MYCL amplified cancers (median = 19, 8, 9, respectively, p < 0.001). MYC, MYCN, and MYCL samples were predominantly clonal (median clonal fraction > 99% for all genes). Most NSCLC, squamous cell lung cancers, and pulmonary carcinoids had MYC amplifications (93%, 70%, and 67% respectively). Conversely, SCLCs most often had MYCL amplifications (49%). No concurrent targetable driver alterations were found in 33% of metastatic NSCLCs with MYC, 75% of MYCN, and 6% of MYCL amplifications. Conclusions: While MYCf amplification is observed across a broad range of cancer types, factors such as gene type (MYC, MYCN, MYCL), focality, total copy number, clonality, and concurrent oncogenic drivers vary widely. Novel MYC-directed trials may consider enrichment for a subpopulation of cancers with higher-level, focal, and clonal MYCf amplifications without concurrent other drivers. Citation Format: Monica F. Chen, Allison Richards, Patrick Evans, Patrick Lee, Adam Price, Matteo Repetto, Soo Ryum Yang, Jason Chang, Rose Brannon, Ezra Rosen, David Brown, Charles Rudin, Nitya Raj, Mark G. Kris, Jorge Reis-Filho, Mark Donoghue, Alexander E. Drilon, Noura J. Choudhury. Comprehensive clinical and genomic analysis for patients with MYC, MYCN, and MYCL amplified solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1394.

The increasing use of electronic health records (EHRs) and biobanks offers unique opportunities to study Mendelian diseases. We described a novel approach to summarize clinical manifestations from patient EHRs into phenotypic evidence for cystic fibrosis (CF) with potential to alert unrecognized patients of the disease. We estimated genetically predicted expression (GReX) of cystic fibrosis transmembrane conductance regulator (CFTR) and tested for association with clinical diagnoses in the Vanderbilt University biobank (N = 9142 persons of European descent with 71 cases of CF). The top associated EHR phenotypes were assessed in combination as a phenotype risk score (PheRS) for discriminating CF case status in an additional 2.8 million patients from Vanderbilt University Medical Center (VUMC) and 125,305 adult patients including 25,314 CF cases from MarketScan, an independent external cohort. GReX of CFTR was associated with EHR phenotypes consistent with CF. PheRS constructed using the EHR phenotypes and weights discovered by the genetic associations improved discriminative power for CF over the initially proposed PheRS in both VUMC and MarketScan. Our study demonstrates the power of EHRs for clinical description of CF and the benefits of using a genetics-informed weighing scheme in construction of a phenotype risk score. This research may find broad applications for phenomic studies of Mendelian disease genes.

OBJECTIVE To assess the safety, feasibility and treatment outcomes of holmium laser enucleation of the prostate (HoLEP) as a same day surgery (SDS). METHODS HoLEPs performed from November 2013 to December 2018 at our institution were reviewed retrospectively. Inclusion criteria for same day surgery (SDS) included living in the local metropolitan area with access to local hospital and Eastern Cooperative Oncology Group (ECOG) 0-2, regardless of prostate size and anticoagulation status. Those patients who were discharged directly from the postoperative care unit were identified as SDS cases. Patients admitted overnight after HoLEP during the same period were used as a matched cohort. Patient demographics, disease characteristics and treatment outcomes were compared. RESULTS A total of 377 patients were identified, including 199 SDS and 178 non-SDS patients. No statistical difference was present between the 2 groups regarding the post-op complication and readmission rates. The non-SDS group had a significantly higher percentage of patients with history of urinary retention, lower pre-op Qmax, and larger prostate volume. The SDS group had shorter operative time, length of stay (LOS), and catherization time (all P CONCLUSION Same day outpatient surgery for HoLEP is safe in patients who live in close proximity and have ECOG status 0-2. Our readmission rate and complication rate are comparable to those reported in the literature with markedly decreased LOS. Long-term functional outcome is not compromised by SDS.

3104 Background: First-generation TRK tyrosine kinase inhibitors (TKIs) are approved in a tumor-agnostic fashion in more than 40 countries for patients with NTRK fusion-positive adult and pediatric cancers. While resistance to these agents has previously been described, the exact frequency with which major mechanisms of resistance emerges is not clearly understood. Methods: Patients with an NTRK-fusion-positive tumor who received a first-generation TRK TKI were eligible. We retrospectively identified those patients that had post-progression tumor tissue analyzed by next-generation sequencing (NGS). The pattern of serial resistance to a second-generation TKI was analyzed when available. Results: Eighteen patients were identified. The median age was 46 years (range 2-67). Nine unique fusions were detected in ten different tumor types. NTRK1, NTRK2, and NTRK3 fusions were found in eight (44%), one (6%), and nine (50%) patients, respectively. Thirteen patients (72%) were treated with larotrectinib and five patients (28%) received entrectinib. NGS (MSK-IMPACT n = 17, Foundation One n = 1) carried out on post-progression tissue revealed the following profile of acquired resistance: on-target resistance (83%, n = 15/18), off-target resistance (11%, n = 2/18), and no identifiable mechanism (6%, n = 1/18). Among patients with on-target resistance, the most common mutation involved the solvent front (87%, n = 13/15: n = 7 NTRK3 G623R, n = 4 NTRK1 G595R, n = 1 NTRK2 G639L, n = 1 NTRK3 G623E) followed by the gatekeeper region (13%, n = 2/15: n = 1 NTRK1 F589L, n = 1 NTRK3 F617I). Two patients developed off-target alterations. One acquired BRAF V600E mutation and the other MET amplification. Interestingly, solvent front mutation loss was observed in two patients who transitioned to and progressed on a second-generation TRK TKI. One patient with a baseline NTRK1 G595R mutation developed polyclonal resistance with acquisition of KRAS G12A and NTRK1 G667A alterations as well as NTRK1 G595R loss. The other patient with NTRK3 G623R developed an NTRK3 F617I gatekeeper mutation with NTRK3 G623R loss. Conclusions: In NTRK fusion-positive cancers, on-target resistance preferentially involving the solvent front is more frequent than off-target resistance to first-generation TKI therapy. Furthermore, the sequential use of second-generation therapy appears to alter the evolutionary kinetics of mutation retention and acquisition.

Exfoliation syndrome (XFS) is an age-related systemic disorder characterized by excessive production and progressive accumulation of abnormal extracellular material, with pathognomonic ocular manifestations. It is the most common cause of secondary glaucoma, resulting in widespread global blindness. We performed Transcriptomic Wide Association Studies (TWAS) using PrediXcan models trained in 48 GTEx tissues to identify genetically- determined gene expression changes associated with XFS risk, leveraging on results from a global GWAS that included 123,457 individuals from 24 countries. We observed twenty-eight genes in a three-Megabase chr15q22-25 region that showed statistically significant associations, which were further whittled down to ten genes after additional statistical validations. In experimental analysist of these ten genes, mRNA transcript levels for ARID3B, CD276, LOXL1, NEO1, SCAMP2, and UBL7 were significantly decreased in iris tissues from XFS patients compared to control samples. Genes with genetically determined expression changes in XFS were significantly enriched for genes associated with inflammatory conditions. We further explored the health consequences of high susceptibility to XFS using a large electronic health record and observed a higher incidence of XFS comorbidity with inflammatory and connective tissue diseases. Our results implicate a role for connective tissues and inflammation in the etiology of XFS. Targeting the inflammatory pathway may be a potential therapeutic option to reduce progression in XFS.

Debugging symbols in binary executables carry the names of functions and global variables. When present, they greatly simplify the process of reverse engineering, but they are almost always removed (stripped) for deployment. We present the design and implementation of punstrip, a tool which combines a probabilistic fingerprint of binary code based on high-level features with a probabilistic graphical model to learn the relationship between function names and program structure. As there are many naming conventions and developer styles, functions from different applications do not necessarily have the exact same name, even if they implement the exact same functionality. We therefore evaluate punstrip across three levels of name matching: exact; an approach based on natural language processing of name components; and using Symbol2Vec, a new embedding of function names based on random walks of function call graphs. We show that our approach is able to recognize functions compiled across different compilers and optimization levels and then demonstrate that punstrip can predict semantically similar function names based on code structure. We evaluate our approach over open source C binaries from the Debian Linux distribution and compare against the state of the art.

Many complex human phenotypes exhibit sex-differentiated characteristics. However, the molecular mechanisms underlying these differences remain largely unknown. We generated a catalog of sex differences in gene expression and in the genetic regulation of gene expression across 44 human tissue sources surveyed by the Genotype-Tissue Expression project (GTEx, v8 release). We demonstrate that sex influences gene expression levels and cellular composition of tissue samples across the human body. A total of 37% of all genes exhibit sex-biased expression in at least one tissue. We identify cis expression quantitative trait loci (eQTLs) with sex-differentiated effects and characterize their cellular origin. By integrating sex-biased eQTLs with genome-wide association study data, we identify 58 gene-trait associations that are driven by genetic regulation of gene expression in a single sex. These findings provide an extensive characterization of sex differences in the human transcriptome and its genetic regulation. INTRODUCTION: Many complex human pheno-types, including diseases, exhibit sex-differentiated characteristics. These sex differences have been variously attributed to hormones, sex chromosomes, genotype × sex effects, differences in behavior, and differences in environmental exposures; however, their mechanisms and underlying biology remain largely unknown. The Genotype-Tissue Expression (GTEx) project provides an opportunity to investigate the prevalence and genetic mechanisms of sex differences in the human transcriptome by surveying many tissues that have not previously been characterized in this manner. RATIONALE: To characterize sex differences in the human transcriptome and its regulation, and to discover how sex and genetics interact to influence complex traits and disease, we generated a catalog of sex differences in gene expression and its genetic regulation across 44 human tissue sources surveyed by the GTEx project (v8 data release), analyzing 16,245 RNA-sequencing samples and genotypes of 838 adult individuals. We report sex differences in gene expression levels, tissue cell type composition, and cis expression quantitative trait loci (cis-eQTLs). To assess their impact, we integrated these results with gene function, transcription factor binding annotation, and genome-wide association study (GWAS) summary statistics of 87 GWASs. RESULTS: Sex effects on gene expression are ubiquitous (13,294 sex-biased genes across all tissues). However, these effects are small and largely tissue-specific. Genes with sex-differentiated expression are not primarily driven by tissue-specific gene expression and are involved in a diverse set of biological functions, such as drug and hormone response, embryonic development and tissue morphogenesis, fertilization, sexual reproduction and spermatogenesis, fat metabolism, cancer, and immune response. Whereas X-linked genes with higher expression in females suggest candidates for escape from X-chromosome inactivation, sex-biased expression of autosomal genes suggests hormone-related transcription factor regulation and a role for additional transcription factors, as well as sex-differentiated distribution of epigenetic marks, particularly histone H3 Lys(27) trimethylation (H3K27me3). Sex differences in the genetic regulation of gene expression are much less common (369 sex-biased eQTLs across all tissues) and are highly tissue-specific. We identified 58 gene-trait associations driven by genetic regulation of gene expression in a single sex. These include loci where sex-differentiated cell type abundances mediate genotype-phenotype associations, as well as loci where sex may play a more direct role in the underlying molecular mechanism of the association. For example, we identified a female-specific eQTL in liver for the hexokinase HKDC1 that influences glucose metabolism in pregnant females, which is subsequently reflected in the birth weight of the offspring. CONCLUSION: By integrating sex-aware analyses of GTEx data with gene function and transcription factor binding annotations, we describe tissue-specific and tissue-shared drivers and mechanisms contributing to sex differences in the human transcriptome and eQTLs. We discovered multiple sex-differentiated genetic effects on gene expression that colocalize with complex trait genetic associations, thereby facilitating the mechanistic interpretation of GWAS signals. Because the causative tissue is unknown for many phenotypes, analysis of the diverse GTEx tissue collection can serve as a powerful resource for investigations into the basis of sex-biased traits. This work provides an extensive characterization of sex differences in the human transcriptome and its genetic regulation. ■

Exfoliation syndrome (XFS) is an age-related systemic disorder characterized by excessive production and progressive accumulation of abnormal extracellular material, with pathognomonic ocular manifestations. It is the most common cause of secondary glaucoma, resulting in widespread global blindness. We performed Transcriptomic Wide Association Studies using PrediXcan models trained in 48 GTEx tissues to identify genetically-determined gene expression changes associated with XFS risk, leveraging on results from a global GWAS that included 123,457 individuals from 24 countries. Twenty-eight genes in the chr15q22-25 region showed statistically significant associations in both single-tissue and multi-tissue analysis. Reduced models for these genes that excluded variants in LD with the known LOXL1 signal showed genome-wide significant association signals in nine genes, independently of LOXL1. Out of these ten genes, mRNA transcript levels for ARID3B, CD276, LOXL1, NEO1, SCAMP2, and UBL7 were significantly decreased in iris tissues from XFS patients compared to control samples. Genes with genetically determined expression changes in XFS were significantly enriched for genes associated with inflammatory conditions. We further explored the health consequences of high susceptibility to XFS using a large electronic health record and observed a higher incidence of XFS comorbidity with inflammatory and connective tissue diseases. Our results implicate a role for connective tissues and inflammation in the etiology of XFS. Targeting the inflammatory pathway may be a potential therapeutic option to reduce progression in XFS.

BACKGROUND The World Health Organization’s End TB Strategy envisions a world free of tuberculosis (TB)—free of deaths, disease, and suffering due to TB—by 2035. Nonadherence reduces cure rates, prolongs infectiousness, and contributes to the emergence of multidrug-resistant TB (MDR-TB). Moreover, MDR-TB is a growing, complex, and costly problem that presents a major obstacle to TB control. Directly observed therapy (DOT) for treatment adherence monitoring is the recommended standard; however, it is challenging to implement at scale because it is labor-intensive. Mobile health interventions can facilitate remote adherence monitoring and minimize the costs and inconveniences associated with standard DOT. OBJECTIVE The study aims to evaluate the effectiveness of using video directly observed therapy (VDOT) plus incentives to improve medication adherence in TB treatment versus usual-care DOT in an African context. METHODS The DOT Selfie study is an open-label, randomized controlled trial (RCT) with 2 parallel groups, in which 144 adult patients with TB aged 18-65 years will be randomly assigned to receive the usual-care DOT monitoring or VDOT as the intervention. The intervention will consist of a smartphone app, a weekly internet subscription, translated text message reminders, and incentives for those who adhere. The participant will use a smartphone to record and send time-stamped encrypted videos showing their daily medication ingestion. This video component will directly substitute the need for daily face-to-face meetings between the health provider and patients. We hypothesize that the VDOT intervention will be more effective because it allows patients to swallow their pills anywhere, anytime. Moreover, patients will receive mobile-phone–based “social bundle” incentives to motivate adherence to continued daily submission of videos to the health system. The health providers will log into a secured computer system to verify treatment adherence, document missed doses, investigate the reasons for missed doses, and follow prespecified protocol measures to re-establish medication adherence. The primary endpoint is the adherence level as measured by the fraction of expected doses observed over the treatment period. The main secondary outcome will be time-to-treatment completion in both groups. RESULTS This study was funded in 2019. Enrollment began in July and is expected to be completed by November 2020. Data collection and follow-up are expected to be completed by June 2021. Results from the analyses based on the primary endpoint are expected to be submitted for publication by December 2021. CONCLUSIONS This random control trial will be among the first to evaluate the effectiveness of VDOT within an African setting. The results will provide robust scientific evidence on the implementation and adoption of mobile health (mHealth) tools, coupled with incentives to motivate TB medication adherence. If successful, VDOT will apply to other low-income settings and a range of chronic diseases with lifelong treatment, such as HIV/AIDs. CLINICALTRIAL ClinicalTrials.gov NCT04134689; http://clinicaltrials.gov/ct2/show/NCT04134689 INTERNATIONAL REGISTERED REPORT DERR1-10.2196/18029

A common problem machine learning developers are faced with is overfitting, that is, fitting a pipeline too closely to the training data that the performance degrades for unseen data. Automated machine learning aims to free (or at least ease) the developer from the burden of pipeline creation, but this overfitting problem can persist. In fact, this can become more of a problem as we look to iteratively optimise the performance of an internal cross-validation (most often \textit{k}-fold). While this internal cross-validation hopes to reduce this overfitting, we show we can still risk overfitting to the particular folds used. In this work, we aim to remedy this problem by introducing dynamic fitness evaluations which approximate repeated \textit{k}-fold cross-validation, at little extra cost over single \textit{k}-fold, and far lower cost than typical repeated \textit{k}-fold. The results show that when time equated, the proposed fitness function results in significant improvement over the current state-of-the-art baseline method which uses an internal single \textit{k}-fold. Furthermore, the proposed extension is very simple to implement on top of existing evolutionary computation methods, and can provide essentially a free boost in generalisation/testing performance., 19 pages, 4 figures

BackgroundCurrent practice methods are unclear as to the most safe and effective prophylactic pharmacotherapy and method of delivery to reduce postoperative endophthalmitis occurrence.MethodsA systematic review and meta-analysis using Meta-analysis of Observational Studies in Epidemiology guidelines was performed to compare the efficacy of intracameral cefuroxime, moxifloxacin and vancomycin in preventing postphacoemulsification cataract surgery endophthalmitis. A safety analysis of intracameral antibiotics was concurrently performed.Data sourcesBIOSIS Previews, CINAHL, ClinicalTrials.gov, Cochrane Library, Dissertations & Theses, EMBASE, PubMed, ScienceDirect and Scopus were searched from inception to January 2017. Data were pooled using a random effects model. All articles were individually reviewed and data were extracted by two independent reviewers. Funnel plot, risk of bias and quality of evidence analyses were performed.ResultsSeventeen studies with over 900 000 eyes were included, which favoured the use of intracameral antibiotics at the end of cataract surgery (OR 0.20; 95% CI 0.13 to 0.32; P0.3). Most studies had low to moderate risk of bias. The safety analysis showed minimal toxicity for moxifloxacin. Dosing errors led to the majority of toxicities with cefuroxime. Although rare, vancomycin was associated with toxic retinal events.ConclusionIntracameral cefuroxime and moxifloxacin reduced endophthalmitis rates compared with controls with minimal or no toxicity events at standard doses. Additionally, intracameral antibiotics alone may be as effective as intracameral plus topical antibiotics.