James Java

• Doctor of Philosophy
• Research Associate at University of Rochester Medical Center

Objective Patients with advanced epithelial ovarian cancer (EOC) alive without progression at a landmark time-point of 10 years from diagnosis are likely cured. We report the proportion of patients with Stage III EOC who were long-term disease-free survivors (LTDFS≥10 years) following either intraperitoneal (IP) or intravenous (IV) chemotherapy as...

The female reproductive tract (FRT) microbiome plays a vital role in maintaining vaginal health. Viruses are key regulators of other microbial ecosystems, but little is known about how the FRT viruses (virome), particularly bacteriophages that comprise the phageome, impact FRT health and dysbiosis. We hypothesize that bacterial vaginosis (BV) is as...

The female reproductive tract (FRT) microbiome plays an important role in maintaining vaginal health. Viruses play a key role in regulating other microbial ecosystems, but little is known about how the FRT viruses (virome), particularly bacteriophages, impacts FRT health and dysbiosis. We hypothesize that bacterial vaginosis is associated with alte...

Background The majority of adults with persistent asthma have chronically uncontrolled disease and interventions to improve outcomes are needed. We evaluated the efficacy, feasibility, and acceptability of a multi-component smartphone-telemedicine program (TEAMS) to deliver asthma care remotely, support provider adherence to asthma management guide...

Background: Young adults (ages 18-44) have increased emergency department use for asthma and poor adherence to medications. The objective of this mixed-methods study was to understand experiences with and approaches to managing asthma, of which little is known in this age group. Methods: Surveys (Asthma Control Questionnaire, Asthma Quality of L...

Rationale: Respiratory Syncytial Virus (RSV) is a leading cause of infant respiratory disease. Infant airway microbiota has been associated with respiratory disease risk and severity. The extent to which interactions between RSV and microbiota occur in the airway, and their impact on respiratory disease susceptibility and severity, are unknown. O...

Rationale Respiratory Syncytial Virus (RSV) infection is a leading cause of infant respiratory disease and hospitalization. Infant airway microbiota occupying the nasopharynx have been associated with respiratory disease risk and severity. The extent to which interactions between RSV and microbiota occur in the airway, and their impact on respirato...

Objective: Determine the utility of a clinical calculator to predict the benefit of chemotherapy in stage IA uterine papillary serous cancer (UPSC). Patients and methods: Data were collected from NCDB from years 2010-2014. Based on demographic and surgical characteristics, a clinical score was developed using the random survival forest machine l...

Introduction: Technology-based interventions that can function within real-world practice and improve outcomes without increasing provider burden are needed, yet few successfully cross the research-to-practice divide. This paper describes the process of developing a clinically integrated smartphone-telemedicine program for adults with asthma and r...

Objective: To develop a valid research tool to measure infant respiratory illness severity using parent-reported symptoms. Study design: Nose and throat swabs were collected monthly for 1 year and during respiratory illnesses for 2 years in a prospective study of term and preterm infants in the Prematurity, Respiratory Outcomes, Immune System an...

Purpose: To compare patient/tumor characteristics and outcomes of Asians to Caucasian patients with epithelial ovarian cancer. Methods: Ancillary data were pooled and analyzed from ten prospective randomized front-line Gynecologic Oncology Group clinical trials from 1996 to 2011. Demographic, clinicopathologic features, disease-specific and all-...

Objective: To analyze clinical prognostic factors for survival after recurrence of high-grade, advanced-stage ovarian-peritoneal-tubal carcinoma and to develop a nomogram to predict individual survival after recurrence. Methods: We retrospectively analyzed patients treated in multicenter Gynecologic Oncology Group protocols for stage III and IV...

Background Accurate symptom assessment remains challenging in teen populations. Little is known of usual symptom/response patterns, and self‐reported paper diaries have traditionally low compliance rates. Therefore, we used concurrent digital voice‐diaries to capture daily asthma experiences. Objective (1) To qualitatively explore usual symptom pa...

Purpose: To determine the relationship between chemotherapy dose modification (dose adjustment or treatment delay), overall survival (OS) and progression-free survival (PFS) for women with advanced-stage epithelial ovarian carcinoma (EOC) and primary peritoneal carcinoma (PPC) who receive carboplatin and paclitaxel. Methods: Women with stages II...

Introduction: Pneumococcus is a commensal of the upper respiratory tract and colonization is common in young children. Carriage studies have provided insights on vaccine effects in children and may also be useful for assessing vaccines in adults. However, culture based prevalence studies in older adults describe low colonization rates. Therefore,...

Background: Postnatal development of the microbiota in early life influences immunity, metabolism, neurodevelopment and long-term infant health. Microbiome development occurs at multiple body sites, each with distinct community compositions and functions. Associations between microbiota at multiple sites represent an unexplored influence on the inf...

Background: Based primarily on studies concerning early-stage tumours (treated surgically), and locally advanced disease (treated with chemoradiation), the prognosis for women with adenocarcinoma (AC) or adenosquamous (AS) carcinoma has been reported to be poorer than those with squamous cell carcinoma (SCCA) of the cervix. It is unclear whether d...

Objective: Microscopic residual disease following complete cytoreduction (R0) is associated with a significant survival benefit for patients with advanced epithelial ovarian cancer (EOC). Our objective was to develop a prediction model for R0 to support surgeons in their clinical care decisions. Methods: Demographic, pathologic, surgical, and CA...

Objective: Tolerance of and complications due to minimally invasive hysterectomy and staging in the older endometrial cancer population is largely unknown despite the fact that this is the most rapidly growing age group in the United States. The objective of this retrospective review is to compare operative morbidity by age in patients on the Gyne...

Materials and methods: Qualitative survey data were collected from patients and physicians during a 12-month randomized controlled trial of virtual house calls for Parkinson's disease. Data from 149 cases were analyzed using case-based qualitative content analysis and quantitative sentiment analysis techniques. Results: Positive and negative per...

Objectives: Elderly endometrial cancer patients have worse disease-specific survival than their younger counterparts, but the cause for this discrepancy is unknown. The goal of this analysis is to compare outcomes by age in a fully staged elderly endometrial cancer population. Methods/materials: This is an analysis of patients on Gynecologic Onc...

Objectives: To determine the association between timing of adjuvant therapy initiation and survival of early stage ovarian cancer patients. Methods: Data were obtained from women who underwent primary surgical staging followed by adjuvant therapy from two Gynecologic Oncology Group trials (protocols # 95 and 157). Kaplan-Meier estimates and Cox...

Objectives: To determine the relationship of the time from surgery to intraperitoneal (IP) chemotherapy (TSIC) initiation with survival of patients with stage III epithelial ovarian cancer (EOC) patients using ancillary data from cooperative group clinical trials. Methods: Data from 420 patients with stage III EOC treated with IP chemotherapy un...

Objectives: We sought to analyze the clinicopathologic features, recurrence patterns and survival outcomes of women with high-grade uterine cancer (UC) enrolled on The Gynecologic Oncology Group (GOG) LAP2 trial. Methods: This is a post-hoc analysis of LAP-2 patients with grade 3 endometrioid adenocarcinoma (ENDO), uterine serous (USC), clear ce...

Purpose: GOG 152 was a randomized trial of secondary cytoreductive surgery (SCS) in patients with suboptimal residual disease (residual tumor nodule >1cm in greatest diameter) following primary cytoreductive surgery for advanced stage ovarian cancer. The current analysis was undertaken to evaluate the impact of disease findings at SCS on progressi...

Background: To determine whether time from surgery to initiation of chemotherapy impacts survival in advanced ovarian carcinoma. Patients and methods: This is a post-trial ad hoc analysis of Gynecologic Oncology Group protocol 218, a phase III randomized, double-blind, placebo-controlled trial designed to study the anti-angiogenesis agent, bevac...

Readmission within 30days is a measure of care quality. Ovarian cancer patients are at high risk for readmission, but specific risk factors are not defined. This study was designed to determine risk factors in patients with ovarian cancer receiving upfront surgery and chemotherapy. The study population was enrolled to GOG 0218. Factors predictive o...

Predictive factors for efficacy of bevacizumab in advanced ovarian cancer have remained elusive. We investigated ascites both as a prognostic factor and as a predictor of efficacy for bevacizumab. Using data from GOG 0218, patients receiving cytotoxic therapy plus concurrent and maintenance bevacizumab were compared to those receiving cytotoxic the...

To determine long-term survival and associated prognostic factors after intraperitoneal (IP) chemotherapy in patients with advanced ovarian cancer. Data from Gynecologic Oncology Group protocols 114 and 172 were retrospectively analyzed. Cox proportional hazards regression models were used for statistical analyses. In 876 patients, median follow-up...

To evaluate the prognostic factors in locally advanced cervical cancer limited to the pelvis and develop nomograms for 2-year progression-free survival (PFS), 5-year overall survival (OS), and pelvic recurrence. We retrospectively reviewed 2,042 patients with locally advanced cervical carcinoma enrolled onto Gynecologic Oncology Group clinical tria...

Objective: Conflicting results have been reported for adeno- and adenosquamous carcinomas of the cervix with respect to their response to therapy and prognosis. The current study sought to evaluate impact of adeno- and adenosquamous histology in the randomized trials of primary cisplatin-based chemoradiation for locally advanced cervical cancer....

Objective To determine whether chemotherapy-induced neutropenia (C-iN) is associated with improved survival in a population of primary advanced ovarian cancer and peritoneal carcinoma patients treated with a carboplatin plus paclitaxel chemotherapy backbone. Methods A post-hoc exploratory analysis of Gynecologic Oncology Group (GOG) protocol 182 w...

Objective To determine the association of body mass index (BMI) on complications, recurrence, and survival in GOG LAP2, a randomized comparison of laparoscopic versus open staging in clinically early stage uterine cancer (EC). Methods An ancillary data analysis of GOG LAP2 was performed. Categorical variables were compared using Pearson chi-square...

To develop a nomogram to predict overall survival (OS) in women with recurrent ovarian cancer treated with bevacizumab and chemotherapy. A multicenter retrospective study was conducted. Potential prognostic variables included age; stage; grade; histology; performance status; residual disease; presence of ascites and/or pleural effusions; number of...

The study objective was to determine the prognostic significance of serum CA-125 levels in patients with grade 1 serous ovarian carcinoma (SOC) enrolled in a Phase III study. An ancillary analysis of a phase III study of women with advanced epithelial ovarian cancer treated with carboplatin/paclitaxel versus triplet or sequential doublet regimens....

To examine clinicopathologic variables associated with survival among women with low-grade (grade 1) serous ovarian carcinoma enrolled in a phase III study. This was an ancillary data analysis of Gynecologic Oncology Group protocol 182, a phase III study of women with stage III-IV epithelial ovarian carcinoma treated with carboplatin and paclitaxel...

5530 Background: Conflicting results have been reported for adeno- and adenosquamous carcinomas the cervix with respect to their response to therapy and prognosis. Adeno- and adenosquamous carcinoma comprise the majority of non-squamous carcinomas of the cervix enrolled in GOG trials of chemoradiation. Methods: Adeno- and adenosquamous cervical car...

Objectives: To determine prognostic factors for survival in ovarian cancer patients treated with intraperitoneal (IP) chemotherapy using ancillary data from cooperative group clinical trials. Methods: Data were collected from 428 patients with stage III ovarian cancer who underwent optimal surgical cytoreduction (<1 cm) followed by IP paclitaxel...

5057 Background: To determine if an age group exists for which the interval from surgery to the initiation of chemotherapy influences progression free survival (PFS) and overall survival (OS) among women with advanced ovarian cancer treated on GOG 182. Methods: GOG 182 was a prospective, randomized trial of first-line chemotherapy in patients with...

5056 Background: To determine if an age group exists for which interval cytoreductive surgery (ICS) in patients with suboptimal residual disease at primary surgery influences progression free survival (PFS) and overall survival (OS) among women with advanced ovarian cancer treated on GOG 182. Methods: GOG 182 was a prospective, randomized trial of...

To estimate the risk for nodal metastasis in women with endometrial cancer based on uterine characteristics on pathology. From a study of staging for uterine cancer, women were identified as being at low risk for nodal metastasis based on three specific criteria on final pathology reports: 1) less than 50% invasion, 2) tumor size less than 2 cm, an...

For a general class of microarray data sets, the sample specific centering errors can constitute correlated measurement errors. These errors are perfectly correlated within samples in the sense that all spot assays within a given sample are centered with the same error. Under certain biological conditions, the centering errors can also be correlate...

Array Comparative Genomic Hybridization (aCGH) is an array-based technology which provides simultaneous spot assays of relative genetic abundance (RGA) levels at multiple sites across the genome. These spot assays are spatially correlated with respect to genomic location and, as a result, the univariate tests conducted using data generated from the...

The R statistical environment provides a very utile programming language, some of whose utility derives from the implementation of R as an interpreted language. However, simulation or analysis can sometimes benefit from manipulating R data in an existing library or in optimized code written in a compiled programming language. Through the mechanism...