Exploring genetic influences on adverse outcome pathways using heuristic simulation and graph data science.

Adverse outcome pathways provide a powerful tool for understanding the biological signaling cascades that lead to disease outcomes following toxicity. The framework outlines downstream responses known as key events, culminating in a clinically significant adverse outcome as a final result of the toxic exposure. Here we use the AOP framework combined with artificial intelligence methods to gain novel insights into genetic mechanisms that underlie toxicity-mediated adverse health outcomes. Specifically, we focus on liver cancer as a case study with diverse underlying mechanisms that are clinically significant. Our approach uses two complementary AI techniques: Generative modeling via automated machine learning and genetic algorithms, and graph machine learning. We used data from the US Environmental Protection Agency's Adverse Outcome Pathway Database (AOP-DB; aopdb.epa.gov) and the UK Biobank's genetic data repository. We use the AOP-DB to extract disease-specific AOPs and build graph neural networks used in our final analyses. We use the UK Biobank to retrieve real-world genotype and phenotype data, where genotypes are based on single nucleotide polymorphism data extracted from the AOP-DB, and phenotypes are case/control cohorts for the disease of interest (liver cancer) corresponding to those adverse outcome pathways. We also use propensity score matching to appropriately sample based on important covariates (demographics, comorbidities, and social deprivation indices) and to balance the case and control populations in our machine language training/testing datasets. Finally, we describe a novel putative risk factor for LC that depends on genetic variation in both the aryl-hydrocarbon receptor (AHR) and ATP binding cassette subfamily B member 11 (ABCB11) genes.

Discovering Venom-Derived Drug Candidates Using Differential Gene Expression.

Venoms are a diverse and complex group of natural toxins that have been adapted to treat many types of human disease, but rigorous computational approaches for discovering new therapeutic activities are scarce. We have designed and validated a new platform-named VenomSeq-to systematically identify putative associations between venoms and drugs/diseases via high-throughput transcriptomics and perturbational differential gene expression analysis. In this study, we describe the architecture of VenomSeq and its evaluation using the crude venoms from 25 diverse animal species and 9 purified teretoxin peptides. By integrating comparisons to public repositories of differential expression, associations between regulatory networks and disease, and existing knowledge of venom activity, we provide a number of new therapeutic hypotheses linking venoms to human diseases supported by multiple layers of preliminary evidence.

A clinical model to predict postoperative improvement in sub-domains of the modified Japanese Orthopedic Association score for degenerative cervical myelopathy.

PURPOSE: The modified Japanese Orthopedic Association (mJOA) score consists of six sub-domains and is used to quantify the severity of cervical myelopathy. The current study aimed to assess for predictors of postoperative mJOA sub-domains scores following elective surgical management for patients with cervical myelopathy and develop the first clinical prediction model for 12-month mJOA sub-domain scores.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [Byron F.] Last name [Stephens], Author 2 Given name: [Lydia J.] Last name [McKeithan], Author 3 Given name: [W. Hunter] Last name [Waddell], Author 4 Given name: [Anthony M.] Last name [Steinle], Author 5 Given name: [Wilson E.] Last name [Vaughan], Author 6 Given name: [Jacquelyn S.] Last name [Pennings], Author 7 Given name: [Jacquelyn S.] Last name [Pennings], Author 8 Given name: [Scott L.] Last name [Zuckerman], Author 9 Given name: [Kristin R.] Last name [Archer], Author 10 Given name: [Amir M.] Last name [Abtahi] Also, kindly confirm the details in the metadata are correct.Last Author listed should be Kristin R. Archer METHODS: A multivariable proportional odds ordinal regression model was developed for patients with cervical myelopathy. The model included patient demographic, clinical, and surgery covariates along with baseline sub-domain scores. The model was internally validated using bootstrap resampling to estimate the likely performance on a new sample of patients. RESULTS: The model identified mJOA baseline sub-domains to be the strongest predictors of 12-month scores, with numbness in legs and ability to walk predicting five of the six mJOA items. Additional covariates predicting three or more items included age, preoperative anxiety/depression, gender, race, employment status, duration of symptoms, smoking status, and radiographic presence of listhesis. Surgical approach, presence of motor deficits, number of surgical levels involved, history of diabetes mellitus, workers' compensation claim, and patient insurance had no impact on 12-month mJOA scores. CONCLUSION: Our study developed and validated a clinical prediction model for improvement in mJOA scores at 12 months following surgery. The results highlight the importance of assessing preoperative numbness, walking ability, modifiable variables of anxiety/depression, and smoking status. This model has the potential to assist surgeons, patients, and families when considering surgery for cervical myelopathy. LEVEL OF EVIDENCE: Level III.

Outcomes Following Direct Versus Indirect Decompression Techniques for Lumbar Spondylolisthesis: A Propensity-Matched Analysis.

STUDY DESIGN: Retrospective review. OBJECTIVE: The aim was to compare outcomes at 3 and 12 months for patients with lumbar spondylolisthesis treated with direct decompression (DD) versus indirect decompression (ID) techniques. SUMMARY OF BACKGROUND DATA: Debate persists regarding the optimal surgical strategy to treat lumbar spondylolisthesis. Novel techniques relying on ID have shown superior radiographic outcomes compared to DD, however, doubt remains regarding their effectiveness in achieving adequate decompression. Currently, there is a paucity of data comparing the clinical efficacy of DD to ID. METHODS: The Quality Outcomes Database (QOD), a national, multicenter prospective spine registry, was queried for patients who underwent DD and ID between April 2013 and January 2019. Propensity scores for each treatment were estimated using logistic regression dependent on baseline covariates potentially associated with outcomes. The propensity scores were used to exclude nonsimilar patients. Multivariable regression analysis was performed with the treatment and covariate as independent variables and outcomes as dependent variables. RESULTS: A total of 4163 patients were included in the DD group and 86 in the ID group. The ID group had significantly lower odds of having a longer hospital stay and for achieving 30% improvement in back and leg pain at 3 months. These trends were not statistically significant at 12 months. There were no differences in ED5D scores or Oswestry disability index 30% improvement scores at 3 or 12 months. ID patient had a significantly higher rate of undergoing a repeat operation at 3 months (4.9% vs. 1.5%, P =0.015). CONCLUSION: Our study suggests that both DD and ID for the treatment of lumbar spondylolisthesis result in similar clinical outcomes, with the exception that those treated with ID experienced a lower reduction in back and leg pain at 3 months and a higher 3-month reoperation rate. This data can provide surgeons with additional information when counseling patients on the pros and cons of ID versus DD surgery.

The Impact of Antibiotic-Loaded Bone Cement on Antibiotic Resistance in Periprosthetic Knee Infections.

BACKGROUD: Antibiotic-loaded bone cement (ALBC) is commonly used in total knee arthroplasty (TKA), especially among high-risk patients. While previous studies have reported on the efficacy of ALBC in reducing the rate of periprosthetic joint infection (PJI), its impact on antibiotic resistance has not been determined. The purpose of this study was to investigate antibiotic resistance among organisms causing PJIs after TKA in which ALBC was utilized. METHODS: A retrospective review from December 1998 through December 2017 identified 36 PJIs that met inclusion criteria. Patients with culture-negative infection and unknown cement type were excluded. Patient characteristics, infecting organism, and antibiotic susceptibilities were recorded. ABLC included an aminoglycoside in all cases. RESULTS: There was no difference in the type of PJI between the 2 groups. Staphylococcus species was the most commonly isolated, with 9 of 16 cases (56.3%) using non-ALBC and 14 of 20 (65.0%) cases using ALBC. Of those infected with Staphylococcus, there was no significant difference in antibiotic susceptibilities between groups. Overall, there were only 3 cases where the infecting organism was aminoglycoside resistant (standard cement, 1; ALBC, 2). CONCLUSIONS: These results suggest that the use of ALBC does not increase the risk of antibiotic resistance or affect the pattern of infection, even as the use of ALBC continues to increase, particularly among high-risk patients.

Gender Differences in Program Factors Important to Applicants When Evaluating Orthopaedic Surgery Residency Programs.

BACKGROUND: Despite specialty-driven efforts to improve diversity in the field, few women apply to orthopaedic residency, and women are unevenly distributed among programs. There is little evidence-based information on factors that may attract female applicants. OBJECTIVE: This study aims to identify factors important to applicants when evaluating orthopaedic residency programs and to identify gender-specific differences. METHODS: All applicants to a single orthopaedic surgery residency program in the 2017 Match were asked to fill out an anonymous survey. Respondents rated the importance of 35 factors when evaluating orthopaedic residency programs. The percentage of highly rated factors was calculated. Statistical analysis was performed for each factor to assess differences by gender. RESULTS: Of 1013 applicants who applied to orthopaedic surgery residency in 2017, 815 (80%) applied to our program, and 218 (27%) completed the survey. The most important factors when evaluating a residency program for both genders were (1) perceptions of current residents; (2) interactions with members of the program; (3) program reputation and fellowship placement; (4) geographic location; and (5) impressions after rotation at a program. Female applicants rated the presence of female and minority residents and faculty and program reputation for gender and racial/ethnic diversity higher than male applicants. CONCLUSIONS: When choosing an orthopaedic surgery residency program, women more often reported the presence of female residents and faculty, program reputation for gender diversity, reputation for racial/ethnic diversity, presence of minority residents and faculty, and their personal interactions with members of the program as important factors.

Design of amidobenzimidazole STING receptor agonists with systemic activity.

Stimulator of interferon genes (STING) is a receptor in the endoplasmic reticulum that propagates innate immune sensing of cytosolic pathogen-derived and self DNA1. The development of compounds that modulate STING has recently been the focus of intense research for the treatment of cancer and infectious diseases and as vaccine adjuvants2. To our knowledge, current efforts are focused on the development of modified cyclic dinucleotides that mimic the endogenous STING ligand cGAMP; these have progressed into clinical trials in patients with solid accessible tumours amenable to intratumoral delivery3. Here we report the discovery of a small molecule STING agonist that is not a cyclic dinucleotide and is systemically efficacious for treating tumours in mice. We developed a linking strategy to synergize the effect of two symmetry-related amidobenzimidazole (ABZI)-based compounds to create linked ABZIs (diABZIs) with enhanced binding to STING and cellular function. Intravenous administration of a diABZI STING agonist to immunocompetent mice with established syngeneic colon tumours elicited strong anti-tumour activity, with complete and lasting regression of tumours. Our findings represent a milestone in the rapidly growing field of immune-modifying cancer therapies.

A strategic action framework for multipurpose prevention technologies combining contraceptive hormones and antiretroviral drugs to prevent pregnancy and HIV.

OBJECTIVE: Multipurpose prevention technologies (MPTs) are an innovative class of products that deliver varied combinations of human immunodeficiency virus (HIV) prevention, other sexually transmitted infection (STI) prevention, and contraception. Combining separate strategies for different indications into singular prevention products can reduce the stigma around HIV and STI prevention, improve acceptability of and adherence to more convenient products, and be more cost-effective by addressing overlapping risks. METHODS: This article outlines a strategic action framework developed as an outcome of a series of expert meetings held between 2014 and 2016. The meetings focused on identifying opportunities and challenges for MPTs that combine hormonal contraception (HC) with antiretroviral drugs into single products. The framework aims to present an actionable strategy, by addressing key research gaps and outlining the key areas for progress, to guide current and future HC MPT development. RESULTS: We identified eight primary action areas for the development of impactful HC MPTs, and includes aspects from epidemiology, pharmacology, clinical trial design, regulatory requirements, manufacturing and commercialisation, behavioural science, and investment needs for research and development. CONCLUSION: Overall, the challenges involved with reconciling the critical social-behavioural context that will drive MPT product use and uptake with the complexities of research and development and regulatory approval are of paramount importance. To realise the potential of MPTs given their complexity and finite resources, researchers in the MPT field must be strategic about the way forward; increased support among policy-makers, advocates, funders and the pharmaceutical industry is critical.

Pharmacokinetics and pharmacodynamics in HIV prevention; current status and future directions: a summary of the DAIDS and BMGF sponsored think tank on pharmacokinetics (PK)/pharmacodynamics (PD) in HIV prevention.

Thirty years after its beginning, the HIV/AIDS epidemic is still raging around the world. According to UNAIDS, in 2011 alone 1.7M deaths were attributable to AIDS, and 2.5M people were newly infected by the virus. Despite the success in treating HIV-infected people with potent antiretroviral drugs, preventing HIV infection is the key to ending the epidemic. Recently, the efficacy of topical and systemic antiviral chemoprophylaxis (i.e., preexposure prophylaxis or "PrEP"), using the same drugs used for HIV treatment, has been demonstrated in a number of clinical trials. However, results from other trials have been inconsistent, especially those evaluating PrEP in women. These inconsistencies may result from our incomplete understanding of pharmacokinetics (PK)/pharmacodynamics (PD) at the mucosal sites of sexual transmission: the male and female gastrointestinal and reproductive tracts. The drug concentrations used in these trials were derived from those used for treatment; however, we still do not know the relationship between the therapeutic and the preventive dose. This article presents the first comprehensive review of the available data in the HIV pharmacology field from animal models to human studies, and outlines gaps, challenges, and future directions. Addressing these pharmacological gaps and challenges will be critical in selecting and advancing future PrEP candidates and strategies with the greatest impact on the HIV epidemic.

Pharmacokinetics of tenofovir following intravaginal and intrarectal administration of tenofovir gel to rhesus macaques.

Tenofovir gel (1%) is being developed as a microbicide for the prevention of human immunodeficiency virus (HIV) infection and has been shown to reduce transmission to women by 39%. The gel also prevents infection in macaques when applied intravaginally or intrarectally prior to challenge with simian-human immunodeficiency virus (SHIV), but very little pharmacokinetic information for macaques is available to help extrapolate the data to humans and thus inform future development activities. We have determined the pharmacokinetics of tenofovir in macaques following intravaginal and intrarectal administration of 0.2, 1, and 5% gels. Plasma and vaginal and rectal fluid samples were collected up to 24 h after dosing, and at 24 h postdosing biopsy specimens were taken from the vaginal wall, cervix, and rectum. Following vaginal and rectal administration, tenofovir rapidly distributed to the matrices distal to the site of administration. In all matrices, exposure increased with increasing dose, and with the 1% and 5% formulations, concentrations remained detectable in most animals 24 h after dosing. At all doses, concentrations at the dosing site were typically 1 to 2 log units higher than those in the opposite compartment and 4 to 5 log units higher than those in plasma. Exposure in vaginal fluid after vaginal dosing was 58 to 82% lower than that in rectal fluid after rectal dosing, but plasma exposure was 1- to 2-fold greater after vaginal dosing than after rectal dosing. These data suggest that a tenofovir-based microbicide may have the potential to protect when exposure is via vaginal or anal intercourse, regardless of whether the microbicide is applied vaginally or rectally.

Advances in microbicide vaginal rings.

Vaginal ring devices capable of providing sustained/controlled release of incorporated actives are already marketed for steroidal contraception and estrogen replacement therapy. In recent years, there has been considerable interest in developing similar ring devices for the administration of microbicidal compounds to prevent vaginal HIV transmission. Intended to be worn continuously, such coitally independent microbicide rings are being developed to maintain effective vaginal microbicide concentrations over many weeks or months, thereby overcoming issues around timing of product application, user compliance and acceptability associated with more conventional semi-solid formulations. In this article, an overview of vaginal ring technologies is presented, followed by a review of recent advances and issues pertaining to their application for the delivery of HIV microbicides. This article forms part of a special supplement on presentations covering intravaginal rings, based on the symposium "Trends in Microbicide Formulations", held on 25 and 26 January 2010, Arlington, VA.

Pharmacokinetics of 2 dapivirine vaginal microbicide gels and their safety vs. Hydroxyethyl cellulose-based universal placebo gel.

Dapivirine, a nonnucleoside reverse transcriptase inhibitor, is in development as a microbicide for the protection of women against HIV infection. A randomized, double-blind, phase 1 trial was conducted in 36 healthy HIV-negative women to compare the pharmacokinetics of 2 dapivirine vaginal gel formulations (0.05% each) and their safety with the hydroxyethyl cellulose-based universal placebo gel. Gel was self-administered once daily for a total of 11 days. Blood and vaginal fluid samples were collected sequentially over 24 days for pharmacokinetic analysis. Safety was evaluated by pelvic examination, colposcopy, adverse events, and clinical laboratory assessments. Adverse event profiles were similar for the 3 gels. Most events were mild and not related to study gel. Headache and vaginal hemorrhage (any vaginal bleeding) were most common. Plasma concentrations of dapivirine did not exceed 1.1 ng/mL. Steady-state conditions were reached within approximately 10 days. Dapivirine concentrations in vaginal fluids were slightly higher for Gel 4789, but Cmax values on days 1 and 14 were not significantly different. Terminal half-life was 72-73 hours in plasma and 15-17 hours in vaginal fluids. Both formulations of dapivirine gel were safe and well tolerated. Dapivirine was delivered to the lower genital tract at concentrations at least 5 logs greater than in vitro inhibitory concentrations.

Synthesis and evaluation of novel tricyclic benzo[4.5]cyclohepta[1.2]pyridine derivatives as NMDA/NR2B antagonists.

A novel series of annulated tricyclic compounds was synthesized and evaluated as NMDA/NR2B antagonists. Structure-activity development was directed towards in vitro optimization of NR2B activity and selectivity over the hERG K(+) channel. Preferred compounds were subsequently evaluated for selectivity in an alpha(1)-adrenergic receptor binding counter-screen and a cell-based assay of NR2B activity.

Safety and pharmacokinetics of dapivirine delivery from matrix and reservoir intravaginal rings to HIV-negative women.

Vaginal microbicides for the prevention of HIV transmission may be an important option for protecting women from infection. Incorporation of dapivirine, a lead candidate nonnucleoside reverse transcriptase inhibitor, into intravaginal rings (IVRs) for sustained mucosal delivery may increase microbicide product adherence and efficacy compared with conventional vaginal formulations. Twenty-four healthy HIV-negative women 18-35 years of age were randomly assigned (1:1:1) to dapivirine matrix IVR, dapivirine reservoir IVR, or placebo IVR. Dapivirine concentrations were measured in plasma and vaginal fluid samples collected at sequential time points over the 33-day study period (28 days of IVR use, 5 days of follow-up). Safety was assessed by pelvic/colposcopic examinations, clinical laboratory tests, and adverse events. Both IVR types were safe and well tolerated with similar adverse events observed in the placebo and dapivirine groups. Dapivirine from both IVR types was successfully distributed throughout the lower genital tract at concentrations over 4 logs greater than the EC50 against wild-type HIV-1 (LAI) in MT4 cells. Maximum concentration (Cmax) and area under the concentration-time curve (AUC) values were significantly higher with the matrix than reservoir IVR. Mean plasma concentrations of dapivirine were <2 ng/mL. These findings suggest that IVR delivery of microbicides is a viable option meriting further study.

The future of HIV microbicides: challenges and opportunities.

HIV microbicides are topical, self-administered products aimed at preventing or reducing HIV infection in women and may represent the most promising strategy for combating the HIV/AIDS epidemic at the present time. Although a safe and effective microbicide has yet to be identified, all products tested in Phase III trials to date have been vaginal gels containing non-specific compounds with modest potency that had to be applied close to the time of sexual intercourse. Issues regarding these early generation products were further complicated by widely publicized cases of halted efficacy trials. However, as a result of each of these challenges, new information and essential lessons have emerged for the field. These lessons have resulted in a meaningful increase in microbicide development efforts focusing on compounds with highly potent and HIV-specific mechanisms of action, combination products, novel formulations, and carefully designed pharmacokinetic and pharmacodynamic evaluations, all of which are reasons for renewed confidence that a safe and effective microbicide is achievable.

Characterization of vaginal transmission of a simian human immunodeficiency virus (SHIV) encoding the reverse transcriptase gene from HIV-1 in Chinese rhesus macaques.

Replication competent recombinant simian-human immunodeficiency virus encoding the reverse transcriptase gene (RT SHIV) from HIV-1 was characterized for vaginal transmission in rhesus macaques. RT SHIV was shown to transmit efficiently via the vaginal route in macaques with detectable plasma viremia persisting for a year in some animals. Analyses of virus load in tissues of infected animals revealed accumulation of viral RNA in lymph nodes and spleen with levels correlating with plasma viremia. RT-SHIV was inhibited by dapivirine, nevirapine, efavirenz and tenofovir in vitro, although the effect was less pronounced with tenofovir. Virus isolated from infected animals at early and later time points had limited changes in RT sequences and exhibited similar sensitivity to RT inhibitors as the challenge virus. The vaginal transmission of RT SHIV demonstrated here suggests this virus may possibly be used in the nonhuman primate model for limited evaluation of RT inhibitors applied vaginally.