CRISPR single base-editing: in silico predictions to variant clonal cell lines

Engineering single base edits using CRISPR technology including specific deaminases and single-guide RNA (sgRNA) is a rapidly evolving field. Different types of base edits can be constructed, with cytidine base editors (CBEs) facilitating transition of C-to-T variants, adenine base editors (ABEs) enabling transition of A-to-G variants, C-to-G transversion base editors (CGBEs) and recently adenine transversion editors (AYBE) that create A-to-C and A-to-T variants. The base-editing machine learning algorithm BE-Hive predicts which sgRNA and base editor combinations have the strongest likelihood of achieving desired base edits. We have used BE-Hive and TP53 mutation data from The Cancer Genome Atlas (TCGA) ovarian cancer cohort to predict which mutations can be engineered, or reverted to wild-type (WT) sequence, using CBEs, ABEs or CGBEs. We have developed and automated a ranking system to assist in selecting optimally designed sgRNA that considers the presence of a suitable protospacer adjacent motif (PAM), the frequency of predicted bystander edits, editing efficiency and target base change. We have generated single constructs containing ABE or CBE editing machinery, an sgRNA cloning backbone and an enhanced green fluorescent protein tag (EGFP), removing the need for co-transfection of multiple plasmids. We have tested our ranking system and new plasmid constructs to engineer the p53 mutants Y220C, R282W and R248Q into WT p53 cells and shown that these mutants cannot activate four p53 target genes, mimicking the behaviour of endogenous p53 mutations. This field will continue to rapidly progress, requiring new strategies such as we propose to ensure desired base-editing outcomes.

Use of gender distribution in routine surveillance data to detect potential transmission of gastrointestinal infections among men who have sex with men in England

Detecting gastrointestinal (GI) infection transmission among men who have sex with men (MSM) in England is complicated by a lack of routine sexual behavioural data. We investigated whether gender distributions might generate signals for increased transmission of GI pathogens among MSM. We examined the percentage male of laboratory-confirmed patient-episodes for patients with no known travel history for 10 GI infections of public health interest in England between 2003 and 2013, stratified by age and region. An adult male excess was observed for Shigella spp. (annual maximum 71% male); most pronounced for those aged 25-49 years and living in London, Brighton and Manchester. An adult male excess was observed every year for Entamoeba histolytica (range 59.8-76.1% male), Giardia (53.1-57.6%) and Campylobacter (52.1-53.5%) and for a minority of years for hepatitis A (max. 69.8%) and typhoidal salmonella (max. 65.7%). This approach generated a signal for excess male episodes for six GI pathogens, including a characterised outbreak of Shigella among MSM. Stratified analyses by geography and age group were consistent with MSM transmission for Shigella. Optimisation and routine application of this technique by public health authorities elsewhere might help identify potential GI infection outbreaks due to sexual transmission among MSM, for further investigation.

Painful sex (dyspareunia) in women: prevalence and associated factors in a British population probability survey

Objective

To estimate the prevalence of painful sex among women in Britain, and to explore associated sexual, relationship and health factors that should be considered in assessment.

Design

Multi‐stage, clustered and stratified population probability sample survey, using computer‐assisted self‐interview. Sample frame was the British Postcode Address File.

Setting

Participants interviewed at home between 2010 and 2012.

Sample

A total of 15 162 adults aged 16–74 years (8869 women). Data reported from 6669 sexually active women.

Methods

Age‐adjusted logistic regressions to examine associations between painful sex and indicators of sexual, relational, mental and physical health.

Main outcome measure

Physical pain as a result of sex for ≥3 months in the past year, plus measures of symptom severity.

Results

Painful sex was reported by 7.5% (95% CI 6.7–8.3) of sexually active women, of whom one‐quarter experienced symptoms very often or always, for ≥6 months, and causing distress. Reporting painful sex was strongly associated with other sexual function problems, notably vaginal dryness (age adjusted odds ratio 7.9; 6.17–10.12), anxiety about sex (6.34; 4.76–8.46) and lacking enjoyment in sex (6.12; 4.81–7.79). It was associated with sexual relationship factors [such as not sharing same level of interest in sex (2.56; 1.97–3.33)], as well as with adverse experiences such as non‐volitional sex (2.17; 1.68–2.80). Associations were also found with measures of psychological and physical health, including depressive symptoms (1.68; 1.28–2.21).

Conclusion

Painful sex is reported by a sizeable minority of women in Britain. Health professionals should be supported to undertake holistic assessment and treatment which takes account of the sexual, relationship and health context of symptoms.

Tweetable abstract

Painful sex—reported by 7.5% of women in Britain—is linked to poorer sexual, physical, relational and mental health.

Painful sex–reported by 7.5% of women in Britain–is linked to poorer sexual, physical, relational and mental health.

This article includes Author Insights, a video abstract available at https://vimeo.com/rcog/authorinsights14518.

Salivary Testosterone Levels and Health Status in Men and Women in the British General Population: Findings from the Third National Survey of Sexual Attitudes and Lifestyles (Natsal-3)

CONTEXT

Salivary T (Sal-T) measurement by liquid chromatography-tandem mass spectroscopy resents the opportunity to examine health correlates of Sal-T in a large-scale population survey.

OBJECTIVE

This study sought to examine associations between Sal-T and health-related factors in men and women age 18-74 years.

DESIGN AND SETTING

Morning saliva samples were obtained from participants in a cross-sectional probability-sample survey of the general British population (Natsal-3). Self-reported health and lifestyle questions were administered as part of a wider sexual health interview.

PARTICIPANTS

Study participants included 1599 men and 2123 women.

METHODS

Sal-T was measured using liquid chromatography-tandem mass spectroscopy. Linear regression was used to examine associations between health factors and mean Sal-T.

RESULTS

In men, mean Sal-T was associated with a range of health factors after age adjustment, and showed a strong independent negative association with body mass index (BMI) in multivariable analysis. Men reporting cardiovascular disease or currently taking medication for depression had lower age-adjusted Sal-T, although there was no association with cardiovascular disease after adjustment for BMI. The decline in Sal-T with increasing age remained after adjustment for health-related factors. In women, Sal-T declined with increasing age; however, there were no age-independent associations with health-related factors or specific heath conditions with the exception of higher Sal-T in smokers.

CONCLUSIONS

Sal-T levels were associated, independently of age, with a range of self-reported health markers, particularly BMI, in men but not women. The findings support the view that there is an age-related decline in Sal-T in men and women, which cannot be explained by an increase in ill health. Our results demonstrate the potential of Sal-T as a convenient measure of tissue androgen exposure for population research.

Prevalence of infertility and help seeking among 15 000 women and men

STUDY QUESTION

What is the prevalence of infertility and of help seeking among women and men in Britain?

SUMMARY ANSWER

One in eight women and one in ten men aged 16–74 years had experienced infertility, defined by unsuccessfully attempting pregnancy for a year or longer, and little more than half of these people sought medical or professional help.

WHAT IS KNOWN ALREADY

Estimates of infertility and help seeking in Britain vary widely and are not easily comparable because of different definitions and study populations.

STUDY DESIGN, SIZE, DURATION

A cross-sectional population survey was conducted between 2010 and 2012 with a sample of 15 162 women and men aged 16–74 years.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Participants completed the Natsal-3 questionnaire, using computer-assisted personal interviewing (CAPI) and computer-assisted self-interview (CASI).

MAIN RESULTS AND THE ROLE OF CHANCE

The reported prevalence of infertility was 12.5% (CI 95% 11.7–13.3) among women and 10.1% (CI 95% 9.2–11.1) among men. Increased prevalence was associated with later cohabitation with a partner, higher socio-economic status and, for those who had a child, becoming parents at older ages. The reported prevalence of help seeking was 57.3% (CI 95% 53.6–61.0) among women and 53.2% (CI 95% 48.1–58.1) among men. Help seekers were more likely to be better educated and in higher status occupations and, among those who had a child, to have become parents later in life.

LIMITATIONS, REASONS FOR CAUTION

These data are cross-sectional so it is not possible to establish temporality or infer causality. Self-reported data may be subject to recall bias.

WIDER IMPLICATIONS OF THE FINDINGS

The study provides estimates of infertility and help seeking in Britain and the results indicate that the prevalence of infertility is higher among those delaying parenthood. Those with higher educational qualifications and occupational status are more likely to consult with medical professionals for fertility problems than others and these inequalities in help seeking should be considered by clinical practice and public health.

STUDY FUNDING/COMPETING INTEREST(S)

Funding was provided by grants from the Medical Research Council and the Wellcome Trust, with support from the Economic and Social Research Council and the Department of Health. AMJ is a Governor of the Wellcome Trust. Other authors have no competing interests.

Intensified shigellosis epidemic associated with sexual transmission in men who have sex with men--Shigella flexneri and S. sonnei in England, 2004 to end of February 2015

Surveillance data suggest an intensification of the shigellosis epidemic associated with sexual transmissionin men who have sex with men (MSM) in England with separate introductions into the population. In 2014, sexual transmission between MSM might have accounted for 97%, 89%, and 43% of non-travel associated Shigella flexneri 3a and S. flexneri 2a, andS. sonnei diagnoses. Clinicians should sensitively ascertain sexual history for men with enteric infections to facilitate prompt diagnosis and appropriate management.

The impact of Prader-Willi syndrome on the family's quality of life and caregiving, and the unaffected siblings' psychosocial adjustment

BACKGROUND

Prader-Willi syndrome (PWS), a complex multisystem genetic disorder, is characterised by developmental abnormalities leading to somatic and psychological symptoms. Symptoms of PWS include infantile hypotonia and failure-to-thrive, followed by life-long hyperphagia, developmental delays and moderate-to-severe behavioural problems and several physical problems that impact health. This study examined the effects of caring for a child diagnosed with PWS on the mothers and unaffected siblings. We assessed overall family functioning, the mothers' psychological health, the psychosocial and behavioural functioning of siblings, and the quality of life of siblings.

METHODS

Participants included 12 mothers and 13 siblings of a child with genetically confirmed PWS. Self-report measures administered to the mothers evaluated overall family functioning (PedsQL - Family Impact Module), the mothers' psychological health (Brief Symptom Inventory), and the mothers' perception of the sibling's quality of life (PedsQL - Parent Proxy). Self-report measures administered to the siblings evaluated their perceived quality of life (PedsQL) and symptoms of post-traumatic stress disorder (PTSD) (UCLA PTSD Index).

RESULTS

Families/mothers/siblings with children with PWS showed poorer perceived quality of life compared with general inpatient and outpatient samples of children with complex health conditions. Families/mothers/siblings with children with PWS reported difficulties in family functioning, communication problems, and an increased number of conflicts. They appeared to be experiencing significant behavioural distress symptoms, with higher than average levels of depression and feelings of isolation, anger and worry. Ninety-two per cent of the siblings indicated moderate-to-severe symptoms of PTSD. Compared with normative populations, siblings demonstrated poorer quality of life, with mothers perceiving more significant deficits in the sibling.

CONCLUSION

This study reaffirms that PWS affects the entire family system. Mothers and siblings would benefit from psychosocial support due to the multiple challenges of living with and caring for a child/young adult with PWS.

Quantifying errors in the estimation of tuberculosis mortality in a population of South African miners

BACKGROUND

All-cause mortality, based on national tuberculosis programme (NTP) register deaths, may under- or overestimate tuberculosis (TB) specific mortality in the population.

OBJECTIVE

To assess the factors influencing this measurement in a single large population with high TB prevalence and mortality.

METHODS

Routinely collected data on TB cases and treatment outcomes were linked to population data from a cohort of South African miners from 1995 to 2008. Vital status and cause of death were determined from multiple sources, including the TB programme, death register and autopsy.

RESULTS

The TB mortality rate, based on 430 deaths on the TB register, was 192/100,000 person-years (py). Many of these deaths (57%) were not caused by TB, and 483 TB deaths were identified outside the programme. Overall, there were 674 TB-specific deaths; the TB-specific mortality rate was 302/100,000 py. These deaths included 191 (28%) on the TB register, 23 (3%) among defaulters/transfers, 153 (23%) after anti-tuberculosis treatment and 307 (46%) in men who had never been on the programme.

CONCLUSIONS

This study highlights methodological issues in estimating TB mortality. In this population, a method using the product of TB incidence and case fatality consistently underestimated TB mortality. Accurate estimates of TB-specific mortality are crucial for the proper evaluation of TB control programmes.

Fulminant hepatitis following primary herpes simplex virus infection

Fulminant hepatic failure (FHF) is a rare but well-recognized complication of primary herpes simplex virus (HSV) infection in immunocompromised patients. Here, we report two cases of acute hepatitis and FHF secondary to primary HSV type 1 infection following renal transplantation in the absence of any mucocutaneous manifestation. High levels of HSV type-1 DNA were detected in the blood. Both patients were seronegative for HSV 1 and HSV 2 immunoglobulin G (IgG) before transplantation, whereas the donor of patient 1 was HSV 1 IgG-positive but had no viremia and the donor of patient 2 was HSV-seronegative. Patient 1 recovered with acyclovir and immunoglobulin whereas patient 2 did not respond and succumbed to death. HSV-seronegative patients are potentially at risk of developing severe primary HSV disease following transplantation, particularly in the absence of routine anti-viral prophylaxis. HSV infection should always be excluded in transplant patients with hepatic dysfunction.

The relation of self-esteem variability to emotion variability, mood, personality traits, and depressive tendencies

The relation of self-esteem variability to personality, mood, and behavior was investigated. Self-esteem variability was measured by calculating the standard deviation of self-ratings made during a week of experience-sampling. Participants high in self-esteem variability were self-conscious, socially anxious, and avoidant of social contexts. Self-esteem variability was partially independent of the conceptually similar trait of affect-intensity. The contributions of the study to work on self-esteem stability are discussed.

Relationships of perceived stress to coping, attachment and social support among HIV-positive persons

The purpose of this study was to examine the relationships of coping, attachment style and perceived social support to perceived stress within a sample of HIV-positive persons. Participants were 147 HIV-positive persons (80 men and 67 women). Multiple regression analysis was used to examine the relationships of the demographic variables, AIDS status, three coping styles, three attachment styles and perceived quality of general social support with total score on the Perceived Stress Scale (PSS). PSS score was significantly associated with less income, greater use of behavioural and emotional disengagement in coping with HIV/AIDS, and less secure and more anxious attachment styles. These results indicate that HIV-positive persons who experience the greatest stress in their daily lives are those with lower incomes, those who disengage behaviourally/emotionally in coping with their illness, and those who approach their interpersonal relationships in a less secure or more anxious style.

Preeclampsia: is induction of labor more successful?

OBJECTIVE

To test the hypothesis that preeclamptic women are more readily inducible than are nonpreeclamptic women, regardless of cervical condition.

METHODS

One hundred eighty-three preeclamptic women and 461 nonpreeclamptic women requiring labor induction were studied prospectively. Patients were categorized by Bishop score, parity, gestational age, and method of induction. Outcome variables were success of induction and cesarean delivery rates.

RESULTS

Failed induction was significantly more common in the preeclamptic group (8.2% versus 1.7%; odds ratio [OR] 5.06; 95% confidence interval [CI] 1.97, 13.28), as was cesarean delivery (28% versus 16%; OR 2.09; 95% CI 1.36, 3.18). When controlled by logistic regression for Bishop score, parity, method of induction, epidural anesthesia, macrosomia, and gestational age, a fourfold higher risk of failed induction and a twofold higher risk of cesarean delivery were found in the preeclamptic group.

CONCLUSIONS

Induction of labor in preeclamptic women has a higher risk of failure and consequently of cesarean delivery than in nonpreeclamptic women. The vast majority of patients achieve vaginal delivery.

Is fetal heart rate variability a good predictor of fetal outcome?

OBJECTIVE

The purpose of this study was to investigate, in a prospective manner, whether fetal heart rate (FHR) variability serves as a reliable single predictor of fetal outcome.

METHODS

We undertook a prospective study of 2,200 consecutive deliveries. Preterms < 37 weeks, twins, stillbirths and fetal malformations were excluded from the study. FHR tracings were analyzed for variability in every delivery. Three windows were evaluated: 1) early in labor (30 min); 2) in the active phase of labor - 1 h prior to complete cervical dilatation (30 min); and 3) throughout the second stage of delivery, in segments of 30 min. Using the tracings taken at admission and prior to delivery, FHR variability was scored according to five previously used evaluative methods, and was correlated to the following three fetal outcome parameters: a) arterial cord blood pH < 7.2, > 7.2; b) 5-min Apgar >6, < 7; and c) immediate outcome ('good' defined as newborn going home after 2-5 days, with no neonatal intensive care unit (NICU) admission).

RESULTS

1. The majority of cases with adverse fetal outcome exhibited good FHR variability (mean, 80%). 2. Low FHR variability is not common in newborns with adverse general outcome (mean, 11.5%). 3. The predictability of FHR variability (using the five most common scoring methods) for evaluating adverse fetal outcome revealed low sensitivity (mean, 20.3%) and low predictive value (mean, 11.6%).

CONCLUSION

FHR variability by itself cannot serve as the only indicator of fetal wellbeing. The presence of low variability should alert the physician; however, good FHR variability should not be interpreted as reassuring.

The assessment of ego development in borderline personality disorders

The purpose of the study was to assess levels of ego functioning in a cohort of patients who met the criteria for borderline personality disorder. The Sentence Completion Test (SCT) and the Descriptions of Significant Others (DSO) test were used to measure dimensions of ego maturity. The borderline patients' responses on the SCT were compared with the responses of an outpatient sample of psychiatric patients and with general population norms established for the test. The scores on the SCT for a selected subgroup of five subjects were compared with their scores on the DSO. Contrary to expectation, the responses on the SCT by those with borderline personality disorder did not differ from those for the psychiatric outpatient sample or the general population norms. However the within-group comparisons between the SCT and the DSO for the subgroup of five subjects showed comparable trends between tests. Discussion of the results focuses on the interpretations of the borderline patients' responses to the two tests. Emphasis is placed on the need to distinguish subsets of ego functions, which can be assessed separately using a variety of measurement strategies.

Neurofibromatosis and other disorders among children with CNS tumors and their families

We conducted a population-based case-control study with 338 patients, less than 15 years of age, diagnosed with a primary tumor of the central nervous system from January 1968 through December 1977 in 53 New York State counties. The study also included 676 controls selected from the birth certificate files of the New York State Department of Health. We collected information on neurofibromatosis and congenital anomalies in study subjects, their siblings and parents by telephone interview with the mother of each case and control. We obtained supplemental information on neurofibromatosis in the patients and their families from hospital medical records. This study confirmed the strong association of neurofibromatosis with risk of CNS tumors. Thirteen cases and no controls had neurofibromatosis. Two fathers and 3 mothers of cases had neurofibromatosis. Five cases had siblings with neurofibromatosis. None of the first-degree relatives of controls had neurofibromatosis. We observed a relative risk of 4.49 for history of seizures. Seizures are often among the presenting symptoms for CNS tumors. We observed no difference between cases and controls in the occurrence of congenital anomalies. There was a nonsignificant excess of congenital anomalies among siblings of cases compared with controls. This decreased to 1.13 when adjusted for number of siblings.

Fractured anterior calcaneal process

The case report of an intra-articular calcaneal fracture is presented. The case is noteworthy because the entire anterior process was fractured and dislocated into the subtalar joint. Treatment consisted of open reduction and internal fixation with good results. The literature was reviewed and an aggressive treatment posture adopted in order to prevent the long-term disability often associated with this type of injury.

Use of the Shaw scalpel in podiatric surgery

The Shaw scalpel is an electric device that produces instantaneous hemostasis through the direct transfer of heat in order to seal severed blood vessels. It offers an improved method of surgical hemostasis without the muscle stimulation and tissue damage of conventional electrosurgical units. In this presentation, the authors introduce this new hemostatic scalpel, illustrate its use in podiatric surgery, and review results of investigational trial efficacy.

On-Line Diagnostics of Rear Axle Transmission Errors

This paper describes a methodology suitable for implementation on the production floor, to perform measurement of gear-induced vibrations in assembled axle carriers outside of a vehicle. A dynamic approach to computerized axle testing is described which has resulted in a machine capable of testing more than 100 axle carriers per hour, while exhibiting 95–98 percent correlation with laboratory measurements. The high resolution of measured conjugate gear error of 1 part in 10,000 in terms of angular velocity variations is achieved. The following three major tasks are addressed in the course of the paper: development of an angular sensor; synthesis of a dynamic drive train; configuration of a data processing system. The dynamic concept of the drive train is chosen to measure the conjugate gear error in the most direct possible manner, as torsional oscillations; to ensure adequate transmissibility for both frequency ranges of interest, mesh and boom; and to provide immunity from extraneous inputs. A real-time signal processing technique is developed, employing a peripheral array processor. Along with a decision of acceptability the machine furnishes, whenever needed, a set of supporting indicators to provide for diagnosis of the faults. An efficient method of modeling a drive train for torsional oscillations, and a computer algorithm for rapid and noise-free conjugate gear order analysis, both of general nature, are also described.

Why occupancy isn't the best measure of hospital performance

Occupancy is a time-honored measure of hospital efficiency and bed need, but it is a measure whose chief virtue is its ease of calculation. Specific indicators of cost, quality, and access are more difficult to develop and interpret, but they are far more accurate and important measures of the appropriateness of a hospital's capacity and use.