Reproducible and clinically translatable deep neural networks for cervical screening

Cervical cancer is a leading cause of cancer mortality, with approximately 90% of the 250,000 deaths per year occurring in low- and middle-income countries (LMIC). Secondary prevention with cervical screening involves detecting and treating precursor lesions; however, scaling screening efforts in LMIC has been hampered by infrastructure and cost constraints. Recent work has supported the development of an artificial intelligence (AI) pipeline on digital images of the cervix to achieve an accurate and reliable diagnosis of treatable precancerous lesions. In particular, WHO guidelines emphasize visual triage of women testing positive for human papillomavirus (HPV) as the primary screen, and AI could assist in this triage task. In this work, we implemented a comprehensive deep-learning model selection and optimization study on a large, collated, multi-geography, multi-institution, and multi-device dataset of 9462 women (17,013 images). We evaluated relative portability, repeatability, and classification performance. The top performing model, when combined with HPV type, achieved an area under the Receiver Operating Characteristics (ROC) curve (AUC) of 0.89 within our study population of interest, and a limited total extreme misclassification rate of 3.4%, on held-aside test sets. Our model also produced reliable and consistent predictions, achieving a strong quadratic weighted kappa (QWK) of 0.86 and a minimal %2-class disagreement (% 2-Cl. D.) of 0.69%, between image pairs across women. Our work is among the first efforts at designing a robust, repeatable, accurate and clinically translatable deep-learning model for cervical screening.

Examining the perceived impact of the COVID-19 pandemic on cervical cancer screening practices among clinicians practicing in Federally Qualified Health Centers: A mixed methods study

Background

The COVID-19 pandemic led to reductions in cervical cancer screening and colposcopy. Therefore, in this mixed methods study we explored perceived pandemic-related practice changes to cervical cancer screenings in federally qualified health centers (FQHCs).

Methods

Between October 2021 and June 2022, we conducted a national web survey of clinicians (physicians and advanced practice providers) who performed cervical cancer screening in FQHCs in the United States during the post-acute phase of the COVID-19 pandemic, along with a sub-set of qualitative interviews via video conference, to examine perceived changes in cervical cancer screening practices during the pandemic.

Results

A total of 148 clinicians completed surveys; a subset (n=13) completed qualitative interviews. Most (86%) reported reduced cervical cancer screening early in the pandemic, and 28% reported continued reduction in services at the time of survey completion (October 2021- July 2022). Nearly half (45%) reported staff shortages impacting their ability to screen or track patients. Compared to clinicians in Obstetrics/Gynecology/Women's health, those in family medicine and other specialties more often reported reduced screening compared to pre-pandemic. Most (92%) felt that screening using HPV self-sampling would be very or somewhat helpful to address screening backlogs. Qualitative interviews highlighted the impacts of staff shortages and strategies for improvement.

Conclusions

Findings highlight that in late 2021 and early 2022, many clinicians in FQHCs reported reduced cervical cancer screening and of pandemic-related staffing shortages impacting screening and follow-up. If not addressed, reduced screenings among underserved populations could worsen cervical cancer disparities in the future.

Funding

This study was funded by the American Cancer Society, who had no role in the study's design, conduct, or reporting.

Online songwriting reduces loneliness and postnatal depression and enhances social connectedness in women with young babies: randomised controlled trial

OBJECTIVE

Loneliness is a public health challenge associated with postnatal depression (PND). This study developed and tested an online songwriting intervention, with the aim of reducing loneliness and symptoms of PND and enhancing social connectedness among women with young babies.

STUDY DESIGN

This was a two-armed non-blinded randomised controlled trial (RCT, ISRCTN17647261).

METHODS

Randomisation was conducted in Excel using a 1:1 allocation, with participants (N = 89) allocated to an online 6-week songwriting intervention (Songs from Home) or to waitlist control. Inclusion criteria were women aged ≥18 years, with a baby ≤9 months old, reporting loneliness (4+ on UCLA 3-Item Loneliness Scale) and symptoms of PND (10+ on Edinburgh Postnatal Depression Scale [EPDS]). Loneliness (UCLA-3) was measured at baseline, after each intervention session and at 4-week follow-up. The secondary measures of PND (EPDS) and social connectedness (Social Connectedness Revised 15-item Scale [SC-15]) were measured at baseline, postintervention and at 4-week follow-up (Week 10). Factorial mixed analyses of variance with planned custom contrasts were conducted for each outcome variable comparing the intervention and control groups over time and across baseline, Weeks 1-6 and the follow-up at Week 10 for each outcome variable.

RESULTS

Compared with waitlist control, the intervention group reported significantly lower scores postintervention and at follow-up for loneliness (P < 0.001, η²_P = 0.098) and PND (P < 0.001, η²_P = 0.174) and significantly higher scores at follow-up for social connectedness (P < 0.001, η²_P = 0.173).

CONCLUSIONS

A 6-week online songwriting intervention for women with young babies can reduce loneliness and symptoms of PND and increase social connectedness.

General and reproductive healthcare experiences of formerly incarcerated women in the United States: a qualitative study

PURPOSE

The US prison population has recently reached an all-time high, with women representing the fastest growing subpopulation. Correctional health-care system in the USA remains fragmented and nonuniform in practice, particularly in women's health care, with poor transitions between incarceration and release. This study aims to examine the qualitative health-care experiences of women while incarcerated and their transition into the community health-care setting. Additionally, this study also examined the experiences of a subset of women who were pregnant while incarcerated.

DESIGN/METHODOLOGY/APPROACH

After obtaining institutional review board approval, adult, English-speaking women with a history of incarceration within the past 10 years were interviewed using a semi-structured interview tool. Interview transcripts were analyzed using inductive content analysis.

FINDINGS

The authors completed 21 full interviews and identified six themes that were both the most significant and most novel: "feeling stigmatized and insignificant," "care as punishment," "delay in care," "exceptions to the rule," "fragmentation of care" and "obstetric trauma and resilience."

ORIGINALITY/VALUE

Women face numerous barriers and hardships when accessing basic and reproductive health-care services while incarcerated. This hardship is particularly challenging for women with substance use disorders. The authors were able to describe for the first time, partially through their own words, novel challenges described by women interacting with incarceration health care. Community providers should understand these barriers and challenges so as to effectively reengage women in care upon release and improve the health-care status of this historically marginalized group.

REPRODUCIBLE AND CLINICALLY TRANSLATABLE DEEP NEURAL NETWORKS FOR CANCER SCREENING

Cervical cancer is a leading cause of cancer mortality, with approximately 90% of the 250,000 deaths per year occurring in low- and middle-income countries (LMIC). Secondary prevention with cervical screening involves detecting and treating precursor lesions; however, scaling screening efforts in LMIC has been hampered by infrastructure and cost constraints. Recent work has supported the development of an artificial intelligence (AI) pipeline on digital images of the cervix to achieve an accurate and reliable diagnosis of treatable precancerous lesions. In particular, WHO guidelines emphasize visual triage of women testing positive for human papillomavirus (HPV) as the primary screen, and AI could assist in this triage task. Published AI reports have exhibited overfitting, lack of portability, and unrealistic, near-perfect performance estimates. To surmount recognized issues, we implemented a comprehensive deep-learning model selection and optimization study on a large, collated, multi-institutional dataset of 9,462 women (17,013 images). We evaluated relative portability, repeatability, and classification performance. The top performing model, when combined with HPV type, achieved an area under the Receiver Operating Characteristics (ROC) curve (AUC) of 0.89 within our study population of interest, and a limited total extreme misclassification rate of 3.4%, on held-aside test sets. Our work is among the first efforts at designing a robust, repeatable, accurate and clinically translatable deep-learning model for cervical screening.

Comparison of accuracy and reproducibility of colposcopic impression based on a single image versus a two-minute time series of colposcopic images

OBJECTIVE

Colposcopy is an important part of cervical screening/management programs. Colposcopic appearance is often classified, for teaching and telemedicine, based on static images that do not reveal the dynamics of acetowhitening. We compared the accuracy and reproducibility of colposcopic impression based on a single image at one minute after application of acetic acid versus a time-series of 17 sequential images over two minutes.

METHODS

Approximately 5000 colposcopic examinations conducted with the DYSIS colposcopic system were divided into 10 random sets, each assigned to a separate expert colposcopist. Colposcopists first classified single two-dimensional images at one minute and then a time-series of 17 sequential images as 'normal,' 'indeterminate,' 'high grade,' or 'cancer'. Ratings were compared to histologic diagnoses. Additionally, 5 colposcopists reviewed a subset of 200 single images and 200 time series to estimate intra- and inter-rater reliability.

RESULTS

Of 4640 patients with adequate images, only 24.4% were correctly categorized by single image visual assessment (11% of 64 cancers; 31% of 605 CIN3; 22.4% of 558 CIN2; 23.9% of 3412 < CIN2). Individual colposcopist accuracy was low; Youden indices (sensitivity plus specificity minus one) ranged from 0.07 to 0.24. Use of the time-series increased the proportion of images classified as normal, regardless of histology. Intra-rater reliability was substantial (weighted kappa = 0.64); inter-rater reliability was fair ( weighted kappa = 0.26).

CONCLUSION

Substantial variation exists in visual assessment of colposcopic images, even when a 17-image time series showing the two-minute process of acetowhitening is presented. We are currently evaluating whether deep-learning image evaluation can assist classification.

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

Gaps and Opportunities to Improve Prevention of Human Papillomavirus-Related Cancers

Human papillomavirus (HPV) infections cause more than 35,900 cancers annually in the United States. Although cervical cancer is the most prevalent HPV-related malignancy in women, the virus is also responsible for a significant percentage of anal, vaginal, and vulvar cancers. A comprehensive approach to mitigating cervical cancer includes HPV vaccination (primary prevention), screening and treatment of precancerous lesions (secondary prevention), and diagnosis and treatment of invasive cancer (tertiary prevention). Although a successful strategy, there are opportunities to innovate and increase access that can also be adapted to address the unique clinical care gaps that exist with the other anogenital cancers. The Society for Women's Health Research held a series of interdisciplinary meetings and events, during which expert researchers, clinicians, patient advocates, and health care policy leaders evaluated the current landscape of HPV-related cancers and their effects on women's health. This report summarizes the discussions of this working group and areas it identified in which to address gaps in primary and secondary prevention approaches to improve access and health outcomes for women with HPV-related anogenital cancers.

Creative interventions for symptoms of postnatal depression: A process evaluation of implementation

BACKGROUND

This article is a process evaluation of a three-arm randomised controlled trial (RCT) comparing the effects of creative interventions on symptoms of postnatal depression (PND) in new mothers.

METHODS

Analyses of quantitative evaluation data from 91 participants and qualitative interviews and focus groups with 80 participants and 3 members of staff.

RESULTS

Key assumptions of the RCT, including how the delivery of the intervention was achieved and what the intervention involved, are explored. Data suggest that the intervention was delivered as planned with a high level of fidelity. Key uncertainties surrounding the project, in particular unanticipated challenges that had to be overcome during the RCT, are also discussed and simple recommendations for improvement are made.

CONCLUSION

This process evaluation aims to illuminate the outcome and mechanisms data from the RCT and enable organisations or individuals to ascertain the feasibility of establishing their own creative classes for women with symptoms of PND.

Multidisciplinary guidelines for the management of paediatric tracheostomy emergencies

Temporary and permanent tracheostomies are required in children to manage actual or anticipated long-term ventilatory support, to aid secretion management or to manage fixed upper airway obstruction. Tracheostomies may be required from the first few moments of life, with the majority performed in children < 4 years of age. Although similarities with adult tracheostomies are apparent, there are key differences when managing the routine and emergency care of children with tracheostomies. The National Tracheostomy Safety Project identified the need for structured guidelines to aid multidisciplinary clinical decision making during paediatric tracheostomy emergencies. These guidelines describe the development of a bespoke emergency management algorithm and supporting resources. Our aim is to reduce the frequency, nature and severity of paediatric tracheostomy emergencies through preparation and education of staff, parents, carers and patients.

Time-dependent upregulation of electron transport with concomitant induction of regulated excitation dissipation in Haslea diatoms

Photoacclimation by strains of Haslea "blue" diatom species H. ostrearia and H. silbo sp. nov. ined. was investigated with rapid light curves and induction-recovery curves using fast repetition rate fluorescence. Cultures were grown to exponential phase under 50 µmol m^-2 s^-1 photosynthetic available radiation (PAR) and then exposed to non-sequential rapid light curves where, once electron transport rate (ETR) had reached saturation, light intensity was decreased and then further increased prior to returning to near growth light intensity. The non-sequential rapid light curve revealed that ETR was not proportional to the instantaneously applied light intensity, due to rapid photoacclimation. Changes in the effective absorption cross sections for open PSII reaction centres (σ_PSII') or reaction centre connectivity (ρ) did not account for the observed increases in ETR under extended high light. σ_PSII' in fact decreased as a function of a time-dependent induction of regulated excitation dissipation Y(NPQ), once cells were at or above a PAR coinciding with saturation of ETR. Instead, the observed increases in ETR under extended high light were explained by an increase in the rate of PSII reopening, i.e. Q_A^- oxidation. This acceleration of electron transport was strictly light dependent and relaxed within seconds after a return to low light or darkness. The time-dependent nature of ETR upregulation and regulated NPQ induction was verified using induction-recovery curves. Our findings show a time-dependent induction of excitation dissipation, in parallel with very rapid photoacclimation of electron transport, which combine to make ETR independent of short-term changes in PAR. This supports a selective advantage for these diatoms when exposed to fluctuating light in their environment.

Effect of singing interventions on symptoms of postnatal depression: three-arm randomised controlled trial

This study assessed whether a novel psychosocial intervention could reduce symptoms of postnatal depression (PND) in the first 40 weeks post-birth. Analyses were carried out of 134 mothers with symptoms of PND randomised into 10 weeks of group singing workshops or group play workshops for them and their babies, or usual care (trial registration: NCT02526407). Overall, among all mothers with symptoms of PND, there was a non-significant faster improvement in symptoms in the singing group (F 4,262 = 1.66, P = 0.16, η 2 = 0.012). When isolating mothers with moderate-severe symptoms of PND, this result became significant, with a faster improvement in symptoms in the singing group (F 3.9,139.8 = 2.74, P = 0.033, η 2 = 0.028). Declaration of interest None.

Factors Associated With Excessive Gestational Weight Gain: Review of Current Literature

Background:

Excessive gestational weight gain (EGWG) places women at increased risk for complications during pregnancy and also increases the likelihood that they will remain overweight after pregnancy. The Institute of Medicine (IOM) has recommended weight gain guidelines based on pre-pregnancy body mass index (BMI), but evidence-based strategies to achieve these goals are limited.

Objective:

This review discusses factors associated with EGWG with the goal of identifying targets for future intervention.

Methods:

A search was performed using the PubMed database to identify all English-language papers published between 1995 and 2014 related to excessive weight gain in pregnancy. Papers were grouped by theme: preconception BMI, sociodemographics, diet and exercise, psychosocial characteristics, and type of prenatal care.

Results:

Studies found that women who were overweight or obese at the time of conception were at higher risk of EGWG and that increased physical activity protected against EGWG. Studies on diet and sociodemographic characteristics were inconclusive. Psychological factors, specifically accurate perceptions of BMI, also appear to play a role in EGWG. Limited studies on methods of prenatal care delivery did not show improvement of weight parameters with group compared to one-on-one visits.

Conclusion:

Pre-pregnancy BMI is most strongly associated with EGWG, indicating that healthy weight habits throughout adult life may be especially important in periods of expected weight change, such as pregnancy. To decrease EGWG, providers should focus on improving pre-conception BMI through appropriate counseling on healthy eating and increased physical activity as well as encouraging pregnant women to continue moderate exercise during pregnancy when appropriate.

Factors Associated with Human Papillomavirus Vaccine Acceptance Among Haitian and African-American parents of Adolescent Sons

ACKNOWLEDGEMENTS

The authors would like to thank Cecilia Marquez, Justine Lavoye, Elaine Shu and Hailey Tipton for their efforts with participant recruitment and data collection.

OBJECTIVE

To assess knowledge, attitudes, beliefs and practices related to HPV vaccination among African-Americans and Haitian immigrant parents, and to compare vaccination rates of their sons.

STUDY DESIGN

We performed semi-structured interviews with parents of boys aged 11-17 who had not yet received the HPV vaccine. We used validated surveys of HPV knowledge, trust in physicians, and intention to vaccinate. We probed participants' thought processes about HPV vaccination, and examined parental attitudes, beliefs, and practices toward HPV vaccination using open-ended questions. We then reviewed medical records to determine whether sons were subsequently vaccinated.

RESULTS

25 African-American and 30 Haitian immigrant parents and legal guardians participated in the study. Haitian immigrants were more likely to be married and to practice a religion than African-Americans. Both groups had limited knowledge of HPV (32% of questions were answered correctly by Haitian immigrants vs. 31% by African-Americans). Sixty-four percent of African-Americans and 79% of Haitians intended to vaccinate their sons, however only 24% of African-American and 20% of Haitian sons received vaccination within 12 months of the interview. Open-ended questions revealed that most African-Americans felt that vaccination fell within the parental role, while some Haitian immigrants felt uncomfortable vaccinating against sexually transmitted infections because they felt children should not be having sex. Both groups wanted more information about HPV vaccines.

CONCLUSIONS

Improving HPV vaccine rates in Haitian and African-American boys may require culturally competent approaches that address ethnic-specific barriers among their parents.

Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing

Although many quality control (QC) methods have been developed to improve the quality of single-nucleotide variants (SNVs) in SNV-calling, QC methods for use subsequent to single-nucleotide polymorphism-calling have not been reported. We developed five QC metrics to improve the quality of SNVs using the whole-genome-sequencing data of a monozygotic twin pair from the Korean Personal Genome Project. The QC metrics improved both repeatability between the monozygotic twin pair and reproducibility between SNV-calling pipelines. We demonstrated the QC metrics improve reproducibility of SNVs derived from not only whole-genome-sequencing data but also whole-exome-sequencing data. The QC metrics are calculated based on the reference genome used in the alignment without accessing the raw and intermediate data or knowing the SNV-calling details. Therefore, the QC metrics can be easily adopted in downstream association analysis.

Using X-mode L, R and O-mode reflectometry cutoffs to measure scrape-off-layer density profiles for upgraded ORNL reflectometer on NSTX-U

The pre-existing ORNL scrape-off-layer (SOL) reflectometer that operated with the X-mode R-cutoff at 6-27 GHz to measure SOL density profiles on NSTX is being upgraded to be functional at the increased magnetic fields on NSTX-U spherical tokamak. Rather than increasing the operating frequencies to measure the higher X-mode R-cutoff frequencies on NSTX-U, it will be shown that the combined use of the X-mode R, L and O-mode cutoffs at 6-27 GHz can obtain the desired SOL density profiles. The potential capabilities and obstacles of this technique to measure SOL density profiles and possibly SOL magnetic field profiles on NSTX-U will be discussed.

Racial and ethnic differences in HPV knowledge, attitudes, and vaccination rates among low-income African-American, Haitian, Latina, and Caucasian young adult women

OBJECTIVE

To examine facilitators and barriers to HPV vaccine uptake in African-American, Haitian, Latina, and White women aged 18-22 and to determine vaccination completion rates among participants over 5 years.

DESIGN

Using semi-structured interviews and medical record review, we assessed HPV knowledge and attitudes towards HPV vaccination among young women. We then determined their subsequent HPV vaccination initiation and completion rates. We used constructs from the Health Belief Model and methods based in grounded theory and content analysis to identify attitudes towards HPV vaccination cues to initiate vaccination, perception of HPV, and how communication about issues of sexuality may impact vaccine uptake.

PARTICIPANTS

We enrolled 132 African-American, Haitian, Latina, and White women aged 18-22 years who visited an urban academic medical center and 2 affiliated community health centers between the years 2007 and 2012.

MAIN OUTCOME MEASURES

Intent to vaccinate and actual vaccination rates.

RESULTS

Of 132 participants, 116 (90%) stated that they were somewhat or very likely to accept HPV vaccination if offered by their physician, but only 51% initiated the vaccination over the next 5 years. Seventy-eight percent of those who initiated vaccination completed the 3 doses of the HPV vaccine series. Forty-five percent (45%, n = 50) of the adolescents who started the series completed 3 doses over a 5-year period: 42% of African-American (n = 16), 33% of Haitian (n = 13), 63% of Latina (n = 10), and 65% of White young women (n = 11) completed the 3-dose series. Despite low knowledge, they reported high levels of trust in physicians and were willing to vaccinate if recommended by their physicians.

CONCLUSION

Desire for HPV vaccination is high among older adolescents, physician recommendation, and use of every clinic visit opportunity may improve vaccine uptake in young women. More White young women completed the HPV vaccine series compared with other race and ethnic young women.

Corallina and Ellisolandia (Corallinales, Rhodophyta) photophysiology over daylight tidal emersion: interactions with irradiance, temperature and carbonate chemistry

The photophysiology of three geniculate coralline algal species (Corallina officinalis, C. caespitosa and Ellisolandia elongata) was determined in intertidal rock pools in the south-west UK at Combe Martin (51°12'31N 4°2'19W) and Heybrook Bay (50°31'66N 4°11'41W), at the start, middle and end of summer (September 1 and 2) and winter (February 9 and 10) daylight tidal emersion periods, in relation to prevailing irradiance, temperature and carbonate chemistry conditions. Algal photophysiology was assessed from rapid light curves performed using pulse amplitude modulation fluorometry. Corallina and Ellisolandia experienced significant fluctuations in irradiance, temperature and carbonate chemistry over seasonal and tidal cycles. Rock pool carbonate chemistry was predictable (R² = 0.82, P < 0.0001) by photodose (summed irradiance) plus water temperature, but not significantly related to photophysiology. In contrast, Corallina and Ellisolandia relative maximum electron transfer rate showed a significant negative relationship (R² = 0.65, P < 0.0001) with irradiance plus water temperature. At a seasonal resolution, photoacclimation to maximize both light harvesting during winter months and photoprotection during summer months was observed for all species. Dynamic photoinhibition was apparent over both summer and winter tidal emersion, in relation to irradiance fluctuations. More effective photoinhibition was apparent during summer months, with greater sensitivity to irradiance and slower recovery in F_v/F_m, observed during winter. With sustained high irradiance over tidal emersion, the establishment of high pH/low inorganic carbon conditions may impact photochemistry. This study represents the first assessment of C. officinalis, C. caespitosa and E. elongata photophysiology underpinned by clear species concepts and highlights their ability to adapt to the dramatically fluctuating conditions experienced in intertidal rock pools.

Efficacy of intravascular catheter lock solutions containing preservatives in the prevention of microbial colonization

There is little published evidence regarding whether heparin lock solutions containing preservatives prevent catheter-related infections. However, adverse effects from preservative-containing flushes have been documented in neonates, leading many hospitals to avoid their use altogether. Infection control records from 1982 to 2008 at St. Jude Children's Research Hospital (SJCRH) were reviewed regarding the incidence of catheter-related infections and the use of preservative-containing intravenous locks. In addition, the antimicrobial activities of heparin lock solution containing the preservatives parabens (0.165%) or benzyl alcohol (0.9%), and 70% ethanol were examined against Staphylococcus epidermidis, Staphylococcus aureus, Escherichia coli, Bacillus cereus, Pseudomonas aeruginosa and Candida albicans, and compared with preservative-free saline with and without heparin. Growth was assessed after exposure to test solutions for 0, 2, 4 and 24h at 35 °C. The activities of preservatives were assessed against both planktonic (free-floating) and sessile (biofilm-embedded) micro-organisms using the MBEC Assay. Infection control records revealed two periods of increased catheter-related infections, corresponding with two intervals when preservative-free heparin was used at SJCRH. Heparin solution containing preservatives demonstrated significant antimicrobial activity against both planktonic and sessile forms of all six microbial species. Ethanol demonstrated the greatest antimicrobial activity, especially following short incubation periods. Heparin lock solutions containing the preservatives parabens or benzyl alcohol, and 70% ethanol demonstrated significant antimicrobial activity against both planktonic and sessile micro-organisms commonly responsible for catheter-related infections. These findings, together with the authors' historical infection control experience, support the use of preservatives in intravenous lock solutions to reduce catheter related infections in patients beyond the neonatal period.

Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples

The discordance in results of independent genome-wide association studies (GWAS) indicates the potential for Type I and Type II errors. We assessed the repeatibility of current Affymetrix technologies that support GWAS. Reasonable reproducibility was observed for both raw intensity and the genotypes/copy number variants. We also assessed consistencies between different SNP arrays and between genotype calling algorithms. We observed that the inconsistency in genotypes was generally small at the specimen level. To further examine whether the differences from genotyping and genotype calling are possible sources of variation in GWAS results, an association analysis was applied to compare the associated SNPs. We observed that the inconsistency in genotypes not only propagated to the association analysis, but was amplified in the associated SNPs. Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results.

Medium to long term results of the Exeter bipolar hemiarthroplasty for femoral neck fractures in active, independent patients. 5-13 year follow-up

We present the clinical and radiographic outcome of 49 Exeter bipolar hemiarthroplasties for femoral neck fractures in 49 patients with a median age of 71 years at the time of operation. Median length of follow-up was 7.1 years (5 to 13). There was one dislocation, and one peri-prosthetic fracture. There were no revisions for infection, acetabular erosion or stem loosening. Twenty-six patients had died by the time of final follow-up with an overall 5 year cumulative survival of 60.2%. Thirty day mortality was 36% in patients with an ASA score of 3. We present excellent clinical and radiological medium to long term results with no evidence of acetabular erosion. However, careful patient selection is necessary to avoid high early mortality rates.

Cement venogram: as a result of high femoral cement pressurisation. A report of 3 cases

Current femoral cementing techniques for total hip arthroplasty (THA) have improved over recent years. High pressurisation is achieved using a cement gun with a proximal seal and a cement restrictor, maximising the microinterlock at the bone cement interface. However, there are concerns regarding over pressurisation of the femoral canal resulting in an increased risk of cardiorespiratory collapse secondary to embolic phenomena. We report on three cases over a one year period of cement within a vein (cement venogram) on a post-operative radiograph following THA. We feel that the cement venogram is an important indicator of high pressurisation and that its incidence may be on the increase with improved cementing techniques.

The functional importance of the N-terminal region of human prolylcarboxypeptidase

The renin-angiotensin-system cascade pathway generates the vasopressor and prothrombotic hormones, angiotensin II (Ang II) and angiotensin III (Ang III) from angiotensinogen. One of the key enzymes for the generation of angiotensin 1-7 (Ang 1-7) and angiotensin 2-7 (Ang 2-7) from Ang II and III, respectively, is prolylcarboxypeptidase (PRCP). To understand the contribution of the N-terminal region to catalysis, an N-terminal truncated form, lacking 179 N-terminal residues of PRCP (rPRCP(40)) was constructed. The circular dichroism (CD) spectrum of rPRCP(40) illustrated that it was structured with significant helical content as indicated by local minima at approximately 220 and 208nm. The main products of Ang III metabolized by rPRCP(40) were Ang 2-7 plus phenylalanine as determined by LC-MS. Angiotensin I (Ang I) blocked the metabolism of Ang III by rPRCP(40). These investigations showed that the C-terminal region of the rPRCP(40) contributes to PRCP's catalytic function, and provided additional experimental evidence for this suggestion.

An in silico ensemble method for lead discovery: decision forest

Recent progress in combinatorial chemistry and parallel synthesis has radically changed the approach to drug discovery in the pharmaceutical industry. At present, thousands of compounds can be made in a short period, creating a need for fast and effective in silico methods to select the most promising lead candidates. Decision forest is a novel pattern recognition method, which combines the results of multiple distinct but comparable decision tree models to reach a consensus prediction. In this article, a decision forest model was developed using a structurally diverse training data set containing 232 compounds whose estrogen receptor binding activity was tested at the U.S. Food and Drug Administration (FDA)'s National Center for Toxicological Research (NCTR). The model was subsequently validated using a test data set of 463 compounds selected from the literature, and then applied to a large data set with 57,145 compounds as a screening example. The results show that the decision forest method is a fast, reliable and effective in silico approach, which could be useful in drug discovery.

Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling

Background

The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer.

Results

In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism.

Conclusion

The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation.