FAIR data pipeline: provenance-driven data management for traceable scientific workflows.

Modern epidemiological analyses to understand and combat the spread of disease depend critically on access to, and use of, data. Rapidly evolving data, such as data streams changing during a disease outbreak, are particularly challenging. Data management is further complicated by data being imprecisely identified when used. Public trust in policy decisions resulting from such analyses is easily damaged and is often low, with cynicism arising where claims of 'following the science' are made without accompanying evidence. Tracing the provenance of such decisions back through open software to primary data would clarify this evidence, enhancing the transparency of the decision-making process. Here, we demonstrate a Findable, Accessible, Interoperable and Reusable (FAIR) data pipeline. Although developed during the COVID-19 pandemic, it allows easy annotation of any data as they are consumed by analyses, or conversely traces the provenance of scientific outputs back through the analytical or modelling source code to primary data. Such a tool provides a mechanism for the public, and fellow scientists, to better assess scientific evidence by inspecting its provenance, while allowing scientists to support policymakers in openly justifying their decisions. We believe that such tools should be promoted for use across all areas of policy-facing research. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Improving the uptake of cervical screening in pregnant and recently postnatal women: a quality improvement project.

BACKGROUND: In 2018, cervical screening uptake was at its lowest level since screening began, particularly in those aged 25-35, coinciding with the peak incidence of cervical cancer and average age at first delivery. PROBLEM: Retrospective baseline data of pregnant women found 47.3% (n=123/260) were overdue for screening by delivery, of whom 74% (n=91/123) remained overdue by 6 months postnatal. METHODS: We undertook a quality improvement project from April 2018 to April 2019 to improve cervical screening uptake in pregnant and postnatal women. We mapped out the screening process and canvassed stakeholders. The main theme was inconsistency of advice received by women. From February 2018 to May 2020, we undertook a prospective audit of 10 women per week who gave birth in our maternity department, recording screening status at delivery and 6 months postnatal.Interventions included introducing evidence-based guidelines about cervical screening in pregnancy and the postnatal period, flow charts for maternity staff, multiprofessional teaching for all maternity staff and information dissemination to women (via the HANDiApp platform, a social media campaign and adapting results letters following colposcopy, highlighting dates when screening would be due). Primary care opening hours were extended for screening and women received a letter from their midwives, if they required cervical screening in pregnancy. RESULTS: Locally, the percentage of women overdue for cervical screening by 6 months postnatal improved by 8.0% during this project, compared with a 1.6% change in national screening rates in women aged 25-49. CONCLUSIONS: We increased the percentage of local pregnant and postnatal women attending cervical screening by introduction of a package of information, targeted education and widening access to screening appointments.

Involving community pharmacists in transfer of care from hospital: Indications of reduced 30-day hospital readmission rates for patients in Cornwall.

OBJECTIVES: The purpose of this study was to determine any benefit from a discharge transfer of care service from hospital to community pharmacy. METHOD: A cross-sectional cohort design was used to compare actioned and non-actioned transfers of care. KEY FINDINGS: Of the 1130 transfers of care referrals to pharmacies in 2017, 365 patients received an actioned community pharmacy service after discharge. The 30-day readmission rate was 8.5% (31/365) in those who received an actioned community pharmacist service compared to 23.3% (178/765) in those who did not. Odds ratio for readmission at 30 days was 3.26 (95% CI 2.04 to 4.59, P < 0.0001), significantly higher in those not receiving an actioned transfer of care service. CONCLUSION: Involving community pharmacy at patient discharge appears to contribute to lower rates of readmission.

Longitudinal evaluation of a countywide alternative to the Quality and Outcomes Framework in UK General Practice aimed at improving Person Centred Coordinated Care.

OBJECTIVES: To evaluate a county-wide deincentivisation of the Quality and Outcomes Framework (QOF) payment scheme for UK General Practice (GP). SETTING: In 2014, National Health Service England signalled a move towards devolution of QOF to Clinical Commissioning Groups. Fifty-five GPs in Somerset established the Somerset Practice Quality Scheme (SPQS)-a deincentivisation of QOF-with the goal of redirecting resources towards Person Centred Coordinated Care (P3C), especially for those with long-term conditions (LTCs). We evaluated the impact on processes and outcomes of care from April 2016 to March 2017. PARTICIPANTS AND DESIGN: The evaluation used data from 55 SPQS practices and 17 regional control practices for three survey instruments. We collected patient experiences ('P3C-EQ'; 2363 returns from patients with 1+LTC; 36% response rate), staff experiences ('P3C-practitioner'; 127 professionals) and organisational data ('P3C-OCT'; 36 of 55 practices at two time points, 65% response rate; 17 control practices). Hospital Episode Statistics emergency admission data were analysed for 2014-2017 for ambulatory-sensitive conditions across Somerset using interrupted time series. RESULTS: Patient and practitioner experiences were similar in SPQS versus control practices. However, discretion from QOF incentives resulted in time savings in the majority of practices, and SPQS practice data showed a significant increase in P3C oriented organisational processes, with a moderate effect size (Wilcoxon signed rank test; p=0.01; r=0.42). Analysis of transformation plans and organisational data suggested stronger federation-level agreements and informal networks, increased multidisciplinary working, reallocation of resources for other healthcare professionals and changes to the structure and timings of GP appointments. No disbenefits were detected in admission data. CONCLUSION: The SPQS scheme leveraged time savings and reduced administrative burden via discretionary removal of QOF incentives, enabling practices to engage actively in a number of schemes aimed at improving care for people with LTCs. We found no differences in the experiences of patients or healthcare professionals between SPQS and control practices.

Risk factors of patients with and without postoperative nausea (PON).

This purpose of this analysis was to study risk factors of postoperative nausea (PON) and their strength. Data were obtained during the screening phase of a controlled clinical trial of aromatherapy for PON. In a sample of 1151 postsurgical subjects, 301 (26.2%) reported PON. Significant risk factors identified in the order of odds ratios for nausea were female gender, gastrointestinal surgery, use of volatile anesthesia gases, history of PON, history of motion sickness, and use of opioids after surgery. Although still over 1.0, the risk factors of length of surgery over 1 hour and gynecologic surgery had the lowest odds ratios. Likelihood of nausea increased significantly with the number of significant risk factors (P<.0001). Administration of preventive antiemetic medication also increased with the number of significant risk factors (P<.0001). Among 301 subjects reporting nausea, 49 (16.28%) received preventive medication. Despite prevention efforts, PON remains a substantial side effect for many surgical patients.

Femtosecond laser micromachining of waveguides in silicone-based hydrogel polymers.

By tightly focusing 27 fs laser pulses from a Ti:sapphire oscillator with 1.3 nJ pulse energy at 93 MHz repetition rate, we are able to fabricate optical waveguides inside hydrogel polymers containing approximately 36% water by weight. A tapered lensed fiber is used to couple laser light at a wavelength of 632.8 nm into these waveguides within a water environment. Strong waveguiding is observed due to large refractive index changes. A large waveguide propagation loss is found, and we show that this is caused by surface roughness which can be reduced by optimizing the waveguides.

Efficacy of the male latex condom and of the female polyurethane condom as barriers to semen during intercourse: a randomized clinical trial.

In this 2000-2001 study, the authors compared the effectiveness of the male latex condom and the female polyurethane condom by assessing frequency and types of mechanical failure and by evaluating semen exposure during use. Eligible women from Birmingham, Alabama, were randomly assigned to begin the study with 10 male condoms and then switch to 10 female condoms (n = 55), or vice versa (n = 53), and were trained to use both types. Data collection included questionnaires for each condom use and measurement of prostate-specific antigen in specimens of vaginal fluid taken before and after intercourse. Participants returned 700 male condoms and 678 female condoms, and they reported mechanical problems for 9% and 34%, respectively. Moderate-high postcoital prostate-specific antigen levels (> or = 22 ng/ml) were detected in 3.5% of male condom uses and 4.5% of female condom uses (difference = 1%, 95% confidence interval: -1.6, 3.7). Moderate-high prostate-specific antigen values (> or = 22 ng/ml) were more frequent with mechanical problems (male condom, 9.6%; female condom, 9.4%) but less frequent with other problems (3.0% and 0.9%) or correct use with no problems (2.7% and 2.5%). This study indicates that although mechanical problems are more common with the female condom than with the male condom, these devices may involve a similar risk of semen exposure. Objectively assessed semen exposure is associated with self-reported mechanical problems.

Self-reported mechanical problems during condom use and semen exposure. Comparison of two randomized trials in the United States of America and Brazil.

OBJECTIVES/GOAL: To compare self-reported condom use problems and objectively determined semen exposure in 2 populations. STUDY DESIGN: Two randomized crossover trials in the United States and Brazil compared the failure rates of the female condom (FC) and male condom (MC). Participants used both condom types, completed condom-specific questionnaires to report problems, and collected precoital and postcoital samples of vaginal fluid. Prostate-specific antigen (PSA) was detected by immunoassay. RESULTS: Problems with condom use were reported less frequently in the Brazilian study (rate difference: FC = 24%, P <0.0001, MC = 5%, P = 0.003). By contrast, the PSA detection rates were similar for both the FC and the MC (rate difference: FC = 2%, MC = 1%, not significant). These results suggest that the PSA detection rate was similar in the 2 study groups and that self-reported problems may be a less reliable measure of condom failure. CONCLUSIONS: Use of biomarkers of condom failure like PSA may help to strengthen the validity of studies promoting behavior change for the prevention of sexually transmitted diseases.

A case of infertility in a patient with a ventriculoperitoneal shunt.

OBJECTIVE AND IMPORTANCE: Complications arising from the placement of ventriculoperitoneal (VP) shunts are well documented. A case of infertility is presented that was thought to result from factors related to the distal end of a VP shunt residing within a patient's abdomen. CLINICAL PRESENTATION: A 30-year-old female with a 3-year history of infertility was referred for fallopian tube blockage. An exploratory laparoscopy revealed multiple adhesions adjoining the distal end of her fallopian tubes. The distal portion of a VP shunt placed at childhood (with subsequent revisions) was found entangled among grossly inflamed and densely adhesive pelvic viscera. INTERVENTION: Laparoscopic adhesiolysis was performed and the patient's fallopian tubes were reconstituted. The distal portion of the VP shunt was freed from the surrounding viscera and was not revised. CONCLUSION: VP shunts may produce adhesive disease and complicate fertility via mechanical, chemical, and/or infectious processes.

Large refractive index change in silicone-based and non-silicone-based hydrogel polymers induced by femtosecond laser micro-machining.

A Ti:Sapphire femtosecond laser with a pulse energy of 1.3 nJ at a 93 MHz repetition rate has been used to micro-machine optical gratings inside several silicone-based and non-silicone-based hydrogel polymers. By measuring the diffraction efficiency of the gratings at 632.8 nm, we find as large as 0.06+/- 0.005 average refractive index change within the irradiated area.

Acceptability of five nonoxynol-9 spermicides.

OBJECTIVE: To examine the acceptability of five nonoxynol-9 (N-9) spermicides. METHODS: We analyzed data from a randomized trial of five products, including three gels containing different amounts of N-9 per dose, a film and a suppository. In the trial, 1536 participants were asked to use the assigned spermicide for 7 months and to complete questionnaires 4 weeks after admission and at discontinuation. RESULTS: Overall, 43% of participants liked their spermicide "very much." This proportion was higher in the three gel groups than in the suppository and film groups. Difficulty with insertion, messiness and discontent with timing of insertion were common complaints in all groups. After adjustment for selected baseline factors, acceptability on the first questionnaire was not related to duration or consistency of subsequent spermicide use or to subsequent time to pregnancy. CONCLUSIONS: In this study, all five spermicides were considered acceptable by most users. Acceptability did not appear to influence spermicide use or pregnancy risk.

Participant characteristics associated with withdrawal from a large randomized trial of spermicide effectiveness.

BACKGROUND: In most recent large efficacy trials of barrier contraceptive methods, a high proportion of participants withdrew before the intended end of follow-up. The objective of this analysis was to explore characteristics of participants who failed to complete seven months of planned participation in a trial of spermicide efficacy. METHODS: Trial participants were expected to use the assigned spermicide for contraception for 7 months or until pregnancy occurred. In bivariable and multivariable analyses, we assessed the associations between failure to complete the trial and 17 pre-specified baseline characteristics. In addition, among women who participated for at least 6 weeks, we evaluated the relationships between failure to complete, various features of their first 6 weeks of experience with the spermicide, and characteristics of the study centers and population. RESULTS: Of the 1514 participants in this analysis, 635 (42%) failed to complete the study for reasons other than pregnancy. Women were significantly less likely to complete if they were younger or unmarried, had intercourse at least 8 times per month, or were enrolled at a university center or at a center that enrolled fewer than 4 participants per month. Noncompliance with study procedures in the first 6 weeks was also associated with subsequent early withdrawal, but dissatisfaction with the spermicide was not. However, many participants without these risk factors withdrew early. CONCLUSIONS: Failure to complete is a major problem in barrier method trials that seriously compromises the interpretation of results. Targeting retention efforts at women at high risk for early withdrawal is not likely to address the problem sufficiently.

Partner characteristics, intensity of the intercourse, and semen exposure during use of the female condom.

The objective of this study was to assess how characteristics of the intercourse and the couple relate to semen exposure during use of the female condom. From 1996 to 1998, 210 women in Birmingham, Alabama, were trained to use the female condom and follow study procedures during a group session and individually practiced inserting the device. The outcome was semen exposure as defined by comparing pre- and postcoital prostate-specific antigen levels in vaginal fluid. Women who had high income levels had lower rates of semen exposure (odds ratio (OR) = 0.3, 95% confidence interval (CI): 0.2, 0.7), while those in a relationship of less than 2 years were at greater risk (OR = 2.4, 95% CI: 1.3, 4.1). Couples with a large disparity in vaginal fundus size and penis size were at increased risk of semen exposure (OR = 2.7, 95% CI: 1.2, 6.0). Engaging in very active intercourse also increased the risk (OR = 1.7, 95% CI: 1.1, 2.6). Thus, the protective effect of the female condom appears to be a function of user- and intercourse-specific characteristics. Future studies of male condom efficacy should focus on collecting detailed data about the users and characteristics of intercourse to predict failure accurately.

Efficacy of the female condom as a barrier to semen during intercourse.

In 1996-1998, the authors measured prostate-specific antigen (PSA) in vaginal fluid to assess the frequency of female condom failure and to evaluate the association of self-reported failure with semen exposure. Women at low risk of sexually transmitted diseases (n = 210) were recruited in Birmingham, Alabama. They were trained to use the female condom, sample vaginal fluid before and after condom use, and complete forms to report problems during each use. Semen exposure was assessed by comparing pre- and postcoital PSA levels in vaginal fluid. A total of 175 women used 2,232 condoms. The rate of semen exposure ranged from 7% to 21% of condom uses, depending on the exposure criterion. Exposure was more likely (21-34%) and more intense (mean postcoital PSA, 24.7 ng/ml) if participants reported a mechanical problem versus other problems or no problems (exposure rate, 5-20% in both instances; mean postcoital PSA, 9.6 and 7.8 ng/ml, respectively). In logistic regression analyses for repeated measurements, user-reported problems accounted for less than 59% of the instances of semen exposure. The female condom prevented semen exposure in 79-93% of condom uses. Exposure was associated with user-reported problems but also occurred in their absence. Reported problems and semen exposure decreased with user experience.