Workload characterization of the shared/buy-in computing cluster at Boston University

Computing clusters provide a complete environment for computational research, including bio-informatics, machine learning, and image processing. The Shared Computing Cluster (SCC) at Boston University is based on a shared/buy-in architecture that combines shared computers, which are free to be used by all users, and buy-in computers, which are computers purchased by users for semi-exclusive use. Although there exists significant work on characterizing the performance of computing clusters, little is known about shared/buy-in architectures. Using data traces, we statistically analyze the performance of the SCC. Our results show that the average waiting time of a buy-in job is 16.1% shorter than that of a shared job. Furthermore, we identify parameters that have a major impact on the performance experienced by shared and buy-in jobs. These parameters include the type of parallel environment and the run time limit (i.e., the maximum time during which a job can use a resource). Finally, we show that the semi-exclusive paradigm, which allows any SCC user to use idle buy-in resources for a limited time, increases the utilization of buy-in resources by 17.4%, thus significantly improving the performance of the system as a whole.http://people.bu.edu/staro/MIT_Conference_Yoni.pdfAccepted manuscrip

Implementation of a Large System-Wide Hepatitis C Virus Screening and Linkage to Care Program for Baby Boomers.

BackgroundWe implemented and evaluated a large health system-wide hepatitis C virus (HCV) screening and linkage to care program for persons born between 1945 and 1965 ("baby boomers").MethodsAn electronic health record (EHR) clinical decision support (CDS) tool for HCV screening for baby boomers was introduced in August 2015 for patients seen in the outpatient University of California, Los Angeles healthcare system setting. An HCV care coordinator was introduced in January 2016 to facilitate linkage to HCV care. We compared HCV testing in the year prior (August 2014-July 2015) to the year after (August 2015-July 2016) implementation of the CDS tool. Among patients with reactive HCV antibody testing, we compared outcomes related to the care cascade including HCV ribonucleic acid (RNA) testing, HCV RNA positivity, and linkage to HCV specialty care.ResultsDuring the study period, 19606 participants were screened for HCV antibody. Hepatitis C virus antibody screening increased 145% (from 5676 patients tested to 13930 tested) after introduction of the CDS intervention. Screening increased across all demographic groups including age, sex, and race/ethnicity, with the greatest increases among those in the older age groups. The addition of an HCV care coordinator increased follow-up HCV RNA testing for HCV antibody positive patients from 83% to 95%. Ninety-four percent of HCV RNA positive patients were linked to care postimplementation.ConclusionsIntroduction of an EHR CDS tool and care coordination markedly increased the number of baby boomers screened for HCV, rates of follow-up HCV RNA testing, and linkage to specialty HCV care for patients with chronic HCV infection

Predictors of incident herpes simplex virus type 2 infections in young women at risk for unintended pregnancy in San Francisco.

BackgroundYoung women receiving family planning services are at risk for both unintended pregnancy and herpes simplex virus type 2 (HSV-2) infection.MethodsWe performed a secondary analysis using data from a previously published randomized controlled trial evaluating access to emergency contraception on reproductive health outcomes. Women aged 15 to 24 years were recruited from two Planned Parenthood clinics and two community health clinics in San Francisco. Demographic information and sexual history were obtained by interview. HSV-2 seropositivity was determined by fingerstick blood test. New pregnancies were measured by self-report, urine testing and medical chart review. Subjects were evaluated for incident HSV-2 infection and pregnancy at a 6-month follow-up appointment. Women who were pregnant or intending to become pregnant at enrolment were excluded.ResultsAt enrolment 2,104 women were screened for HSV-2 and 170 (8.1%) were seropositive. Eighty-seven percent of initially seronegative women completed the study (n = 1,672) and 73 (4.4%) became HSV-2 seropositive. HSV-2 seroincidence was 7.8 cases per 100 person-years. One hundred and seventeen women (7%) became pregnant and 7 (6%) of these had a seroincident HSV-2 infection during the study. After adjustment for confounders, predictors of incident HSV-2 infection were African American race and having multiple partners in the last six months. Condom use at last sexual encounter was protective.ConclusionHSV-2 seroincidence and the unintended pregnancy rate in young women were high. Providers who counsel women on contraceptive services and sexually transmitted infection prevention could play an expanded role in counselling women about HSV-2 prevention given the potential sequelae in pregnancy. The potential benefit of targeted screening and future vaccination against HSV-2 needs to be assessed in this population

Sentinel surveillance of HIV-1 transmitted drug resistance, acute infection and recent infection.

BackgroundHIV-1 acute infection, recent infection and transmitted drug resistance screening was integrated into voluntary HIV counseling and testing (VCT) services to enhance the existing surveillance program in San Francisco. This study describes newly-diagnosed HIV cases and characterizes correlates associated with infection.Methodology/principal findingsA consecutive sample of persons presenting for HIV VCT at the municipal sexually transmitted infections (STI) clinic from 2004 to 2006 (N = 9,868) were evaluated by standard enzyme-linked immunoassays (EIA). HIV antibody-positive specimens were characterized as recent infections using a less-sensitive EIA. HIV-RNA pooled testing was performed on HIV antibody-negative specimens to identify acute infections. HIV antibody-positive and acute infection specimens were evaluated for drug resistance by sequence analysis. Multivariable logistic regression was performed to evaluate associations. The 380 newly-diagnosed HIV cases included 29 acute infections, 128 recent infections, and 47 drug-resistant cases, with no significant increases or decreases in prevalence over the three years studied. HIV-1 transmitted drug resistance prevalence was 11.0% in 2004, 13.4% in 2005 and 14.9% in 2006 (p = 0.36). Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI) was the most common pattern detected, present in 28 cases of resistance (59.6%). Among MSM, recent infection was associated with amphetamine use (AOR = 2.67; p<0.001), unprotected anal intercourse (AOR = 2.27; p<0.001), sex with a known HIV-infected partner (AOR = 1.64; p = 0.02), and history of gonorrhea (AOR = 1.62; p = 0.03).ConclusionsNew HIV diagnoses, recent infections, acute infections and transmitted drug resistance prevalence remained stable between 2004 and 2006. Resistance to NNRTI comprised more than half of the drug-resistant cases, a worrisome finding given its role as the backbone of first-line antiretroviral therapy in San Francisco as well as worldwide. The integration of HIV-1 drug resistance, recent infection, and acute infection testing should be considered for existing HIV/STI surveillance and prevention activities, particularly in an era of enhanced efforts for early diagnosis and treatment

Meta-analysis of the Cepheid Xpert® CT/NG assay for extragenital detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections.

Background Most studies evaluating extragenital testing performance for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) detection by the Xpert® CT/NG show high per cent agreement with comparison assays; however, the precision around positive per cent agreement is low and thus the values that have been reported are not highly informative. Therefore, a systematic review was conducted and data from five studies were combined to better assess positive per cent agreement.MethodsThe literature indexed on PubMed.gov was searched. Included studies were those that were an evaluation of the Xpert CT/NG assay with rectal and/or pharyngeal specimen types compared with another nucleic acid amplification test (NAAT), the Aptima transcription mediated amplification assay. A full Bayesian method was used for bivariate fixed-effect meta-analysis of positive and negative per cent agreement and pooled estimates (and 95% confidence intervals (CI)) were presented for each.ResultsThe pooled positive and negative per cent agreement for detection of CT in rectal specimens was 89.72% (95% CI: 84.97%, 93.64%) and 99.23% (95% CI: 98.74%, 99.60%), and in pharyngeal specimens, they were 89.96% (95% CI: 66.38%, 99.72%) and 99.62% (95% CI: 98.95%, 99.95%) respectively. For NG detection in rectal specimens, the pooled positive and negative per cent agreement was 92.75% (95% CI: 87.91%, 96.46%) and 99.75% (95% CI: 99.46%, 99.93%), and in pharyngeal specimens, they were 92.51% (95% CI: 85.84%, 97.18%) and 98.56% (95% CI: 97.69%, 99.23%) respectively.ConclusionsIt was found that the Xpert CT/NG assay performed similarly to the Aptima transcription mediated amplification assay for the detection of CT and NG in extragenital specimens. The Xpert assay has the benefit of providing faster results at the point-of-care, thus reducing the turnaround time for results, potentially enabling same-day treatment

Sociodemographic and clinical characteristics of persons who experienced spontaneous hepatitis C viral clearance.

BackgroundIn the United States Hepatitis C virus (HCV) viral clearance is estimated to range between 20 and 30%. The objective of this study was to estimate the frequency of HCV clearance and identify correlates of viral clearance among patients newly identified as HCV antibody positive in a large urban health system in Los Angeles, California.MethodsWe identified patients between November 2015 and September 2017 as part of a newly implemented HCV screening and linkage-to-care program at University of California Los Angeles (UCLA) Health System. All patients were eligible for screening, though there were additional efforts to screen patients born between 1945 and 1965. We reviewed Medical records to categorize anti-HCV antibody positive patients as having spontaneously cleared HCV infection (HCV RNA not detected) or not (HCV RNA detected). We excluded those with a prior history of anti-HCV positivity or history of HCV treatment. We compared differences between those with and without detectable HCV RNA using chi-square test, Fisher's exact test, and t-test as appropriate. We assessed factors associated with HCV clearance using logistic regression analysis.ResultsAmong the 320 patients included in this study, 56% were male. Baby boomers (52-72 years of age) comprised the single largest age group (62%). We found spontaneous HCV clearance in 58% (n = 185). HCV viral clearance was slightly higher among women as compared to men (63% vs. 53%; p value = 0.07) and varied by race/ethnicity: clearance among Blacks/African Americans was 37% vs. 58% among whites (p value = 0.02). After adjusting for age, race/ethnicity, and sex we found that those diagnosed with chronic kidney disease had a tendency of decreased HCV viral clearance (adjusted OR = 0.34; 95% CI 0.14-1.03).ConclusionOf those patients newly identified as anti-HCV positive, 58% had cleared HCV virus, while the rest showed evidence of active infection. In addition, we found that clearance varied by race/ethnicity and clinical characteristics

Antimicrobial Resistance in Neisseria gonorrhoeae: Proceedings of the STAR Sexually Transmitted Infection-Clinical Trial Group Programmatic Meeting.

The goal of the Sexually Transmitted Infection Clinical Trial Group's Antimicrobial Resistance (AMR) in Neisseria gonorrhoeae (NG) meeting was to assemble experts from academia, government, nonprofit and industry to discuss the current state of research, gaps and challenges in research and technology and priorities and new directions to address the continued emergence of multidrug-resistant NG infections. Topics discussed at the meeting, which will be the focus of this article, include AMR NG global surveillance initiatives, the use of whole genome sequencing and bioinformatics to understand mutations associated with AMR, mechanisms of AMR, and novel antibiotics, vaccines and other methods to treat AMR NG. Key points highlighted during the meeting include: (i) US and International surveillance programs to understand AMR in NG; (ii) the US National Strategy for combating antimicrobial-resistant bacteria; (iii) surveillance needs, challenges, and novel technologies; (iv) plasmid-mediated and chromosomally mediated mechanisms of AMR in NG; (v) novel therapeutic (eg, sialic acid analogs, factor H [FH]/Fc fusion molecule, monoclonal antibodies, topoisomerase inhibitors, fluoroketolides, LpxC inhibitors) and preventative (eg, peptide mimic) strategies to combat infection. The way forward will require renewed political will, new funding initiatives, and collaborations across academic and commercial research and public health programs

Prevalence and Correlates of Primary Infertility in Mysore, India

Background & objectives: There are sparse data on the prevalence of primary infertility in India and almost none from Southern India. This study describes the correlates and prevalence of primary infertility among young women in Mysore, India. Methods: The baseline data were collected between November 2005 through March 2006, among 897 sexually active women, aged 15-30 yr, for a study investigating the relationship of bacterial vaginosis and acquisition of herpes simplex virus type-2 (HSV-2) infection. A secondary data analysis of the baseline data was undertaken. Primary infertility was defined as having been married for longer than two years, not using contraception and without a child. Logistic regression was used to examine factors associated with primary infertility. Results: The mean age of the women was 25.9 yr (range: 16-30 yr) and the prevalence of primary infertility was 12.6 per cent [95% Confidence Interval (CI): 10.5-15.0%]. The main factor associated with primary infertility was HSV-2 seropositivity (adjusted odds ratio: 3.41; CI: 1.86, 6.26). Interpretation & conclusions: The estimated prevalence of primary infertility among women in the study was within the range reported by the WHO and similar to other estimates from India. Further research is needed to examine the role of HSV-2 in primary infertility