Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications

The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.

The Menstrual Disorder of Teenagers (MDOT) Study No. 2: Period ImPact and Pain Assessment (PIPPA) Tool Validation in a Large Population-Based Cross-Sectional Study of Australian Teenagers

STUDY OBJECTIVE

To validate the Period ImPact and Pain Assessment (PIPPA) self-screening tool for menstrual disturbance in teenagers.

DESIGN

Cross-sectional study.

SETTING

Three senior high schools in the Australian Capital Territory (ACT), Australia.

PARTICIPANTS

A total of 1066 girls between 15 and 19 years of age.

INTERVENTIONS AND MAIN OUTCOME MEASURES

A quantitative paper survey collected self-reports of menstrual bleeding patterns, typical and atypical symptoms, morbidities, and interference with daily activities. Multiple correspondence analysis was used to examine associations between PIPPA questions. Generalized linear models compared total score and subscores by validation criteria: pain, school absence, and body mass index (BMI). Receiver operating characteristic curves were used to evaluate the predictiveness of menstrual disturbance indicators by total PIPPA score.

RESULTS

Reports of pain, interference, and concern within the PIPPA items and between both the MDOT and PIPPA questionnaires were significantly correlated (P < .0001). The indicator "missing school" was highly associated (P < .0001) with pain and interference. Obesity (BMI ≥30) was associated with higher PIPPA scores, as was underweight (BMI≤18.4). Where 0 = no disturbance, 5 = high disturbance, aggregated PIPPA scores found 75% scoring 0-2 (out of 5) and 25% scoring 3-5 (257/1037). High scores of 4 or 5 (out of 5) were 7% (72/1037) and 3.7% (38/1037), respectively.

CONCLUSION

PIPPA is a valid screening tool for pain-related menstrual disturbance that affects functioning in young women. PIPPA subdomains of pain/interference have good validity relative to indicators of pain and interference and are responsive to age, BMI, and school absence differences.

A mixed methods evaluation of Advanced Life Support in Obstetrics (ALSO) and Basic Life Support in Obstetrics (BLSO) in a resource-limited setting on the Thailand-Myanmar border

Background: Short emergency obstetric care (EmOC) courses have demonstrated improved provider confidence, knowledge and skills but impact on indicators such as maternal mortality and stillbirth is less substantial. This manuscript evaluates Advanced Life Support in Obstetrics (ALSO) and Basic Life Support (BLSO) as an adult education tool, in a protracted, post-conflict and resource-limited setting. Methods: A mixed methods evaluation was used. Basic characteristics of ALSO and BLSO participants and their course results were summarized. Kirkpatrick's framework for assessment of education effectiveness included: qualitative data on participants' reactions to training (level 1); and quantitative health indicator data on change in the availability and quality of EmOC and in maternal and/or neonatal health outcomes (level 4), by evaluation of the post-partum haemorrhage (PPH) related maternal mortality ratio (MMR) and stillbirth rate in the eight years prior and following implementation of ALSO and BLSO. Results: 561 Thailand-Myanmar border health workers participated in ALSO (n=355) and BLSO (n=206) courses 2008-2020. Pass rates on skills exceeded 90% for both courses while 50% passed the written ALSO test. Perceived confidence significantly improved for all items assessed. In the eight-year block preceding the implementation of ALSO and BLSO (2000-07) the PPH related MMR per 100,000 live births was 57.0 (95%CI 30.06-108.3)(9/15797) compared to 25.4 (95%CI 11.6-55.4)(6/23620) eight years following (2009-16), p=0.109. After adjustment, PPH related maternal mortality was associated with birth before ALSO/BLSO implementation aOR 3.825 (95%CI 1.1233-11.870), migrant (not refugee) status aOR 3.814 (95%CI 1.241-11.718) and attending ≤four antenatal consultations aOR 3.648 (95%CI 1.189-11.191). Stillbirth rate per 1,000 total births was 18.2 (95%CI 16.2-20.4)(291/16016) before the courses, and 11.1 (95%CI 9.8-12.5)(264/23884) after, p=0.038. Birth before ALSO/ BLSO implementation was associated with stillbirth aoR 1.235 (95%CI 1.018-1.500). Conclusions: This evaluation suggests ALSO and BLSO are sustainable, beneficial, EmOC trainings for adult education in protracted, post-conflict, resource-limited settings.

A mixed methods evaluation of Advanced Life Support in Obstetrics (ALSO) and Basic Life Support in Obstetrics (BLSO) in a resource-limited setting on the Thailand-Myanmar border

Background: Short emergency obstetric care (EmOC) courses have demonstrated improved provider confidence, knowledge and skills but impact on indicators such as maternal mortality and stillbirth is less substantial. This manuscript evaluates Advanced Life Support in Obstetrics (ALSO) and Basic Life Support (BLSO) as an adult education tool, in a protracted, post-conflict and resource-limited setting. Methods: A mixed methods evaluation was used. Basic characteristics of ALSO and BLSO participants and their course results were summarized. Kirkpatrick's framework for assessment of education effectiveness included: qualitative data on participants' reactions to training (level 1); and quantitative health indicator data on change in the availability and quality of EmOC and in maternal and/or neonatal health outcomes (level 4), by evaluation of the post-partum haemorrhage (PPH) related maternal mortality ratio (MMR) and stillbirth rate in the eight years prior and following implementation of ALSO and BLSO. Results: 561 Thailand-Myanmar border health workers participated in ALSO (n=355) and BLSO (n=206) courses 2008-2020. Pass rates on skills exceeded 90% for both courses while 50% passed the written ALSO test. Perceived confidence significantly improved for all items assessed. In the eight-year block preceding the implementation of ALSO and BLSO (2000-07) the PPH related MMR per 100,000 live births was 57.0 (95%CI 30.06-108.3)(9/15797) compared to 25.4 (95%CI 11.6-55.4)(6/23620) eight years following (2009-16), p=0.109. After adjustment, PPH related maternal mortality was associated with birth before ALSO/BLSO implementation aOR 3.825 (95%CI 1.1233-11.870), migrant (not refugee) status aOR 3.814 (95%CI 1.241-11.718) and attending ≤four antenatal consultations aOR 3.648 (95%CI 1.189-11.191). Stillbirth rate per 1,000 total births was 18.2 (95%CI 16.2-20.4)(291/16016) before the courses, and 11.1 (95%CI 9.8-12.5)(264/23884) after, p=0.038. Birth before ALSO/ BLSO implementation was associated with stillbirth aoR 1.235 (95%CI 1.018-1.500). Conclusions: This evaluation suggests ALSO and BLSO are sustainable, beneficial, EmOC trainings for adult education in protracted, post-conflict, resource-limited settings.

Reducing caesarean delivery: An economic evaluation of routine induction of labour at 39 weeks in low-risk nulliparous women

BACKGROUND

Clinical interventions known to reduce the risk of caesarean delivery include routine induction of labour at 39 weeks, caseload midwifery and chart audit, but they have not been compared for cost-effectiveness.

OBJECTIVE

To assesses the cost-effectiveness of three different interventions known to reduce caesarean delivery rates compared to standard care; and conduct a budget impact analysis.

METHODS

A Markov microsimulation model was constructed to compare the costs and outcomes produced by the different interventions. Costs included all costs to the health system, and outcomes were quality-adjusted life years (QALY) gained. A budget impact analysis was undertaken using this model to quantify the costs (in Australian dollars) over three years for government health system funders.

RESULTS

All interventions, plus standard care, produced similar health outcomes (mean of 1.84 QALYs gained over 105 weeks). Caseload midwifery was the lowest cost option at $15 587 (95% confidence interval [CI] 15 269, 15 905), followed by routine induction of labour ($16 257, 95% CI 15 989, 16 536), and chart audit ($16 325, 95% CI 15 979, 16 671). All produced lower costs on average than standard care ($16 905, 95% CI 16 551, 17 259). Caseload midwifery would produce the greatest savings of $172.6 million over three years if implemented for all low-risk nulliparous women in Australia.

CONCLUSIONS

Caseload midwifery presents the best value for reducing caesarean delivery rates of the options considered. Routine induction of labour at 39 weeks and chart audit would also reduce costs compared to standard care.

The Endometriosis Impact Questionnaire (EIQ): a tool to measure the long-term impact of endometriosis on different aspects of women's lives

Background

Endometriosis is a chronic disease impacting on many aspects of a woman’s life. Because of the chronic and recurring nature, many of the impacts of endometriosis could be missed using existing questionnaires which focus on recent events. Therefore, a questionnaire with a long-term perspective is necessary. This study aimed to develop and evaluate a questionnaire to measure the long-term impact of endometriosis on different aspects of women’s lives.

Methods

Through a methodological design, phase 1 was qualitative and phase 2 was a cross-sectional study. The original 100 EIQ items were developed based on results from an earlier qualitative study and literature review. Through a process of assessing face and content validity this was reduced to 66 items. The psychometric properties of the final 63 item EIQ were evaluated through a web-based survey with data from 423 responders with a self-reported surgically-diagnosed endometriosis.

Results

Participants were aged 16-58 years. Exploratory factor analysis of a 66-item EIQ was established with 423 responders. The final 63-item EIQ contained six dimensions including: 33-item physical-psychosocial; 3-item fertility; 7-item sexual; 11-item employment; 6-item educational; and 3-item lifestyle. Cronbach’s alpha of 0.99 for the whole 63-item EIQ, and 0.84 to 0.98 for the dimensions suggests a very good reliability. High positive correlations between the EIQ and the EHP-5 (altered recall period) indicated good evidence of concurrent validity. High intra-class correlations indicated very good test-retest reliability.

Conclusions

The EIQ, as a disease-specific questionnaire, could be used to provide a better understanding of the impact of endometriosis on different aspects of life, to better meet the needs of women. We recommend additional studies to establish validity evidence for the EIQ, including studies in other countries and languages.

Electronic supplementary material

The online version of this article (10.1186/s12905-019-0762-x) contains supplementary material, which is available to authorized users.

Effects of a midwife psycho-education intervention to reduce childbirth fear on women's birth outcomes and postpartum psychological wellbeing

BACKGROUND

High levels of childbirth fear impact birth preparation, obstetric outcomes and emotional wellbeing for around one in five women living in developed countries. Higher rates of obstetric intervention and caesarean section (CS) are experienced in fearful women. The efficacy of interventions to reduce childbirth fear is unclear, with no previous randomised controlled trials reporting birth outcomes or postnatal psychological wellbeing following a midwife led intervention.

METHOD

Between May 2012 and June 2013 women in their second trimester of pregnancy were recruited. Women with a fear score ≥ 66 on the Wijma Delivery Expectancy / Experience Questionnaire (W-DEQ) were randomised to receive telephone psycho-education by a midwife, or usual maternity care. A two armed non-blinded parallel (1:1) multi-site randomised controlled trial with participants allocated in blocks of ten and stratified by hospital site and parity using an electronic centralised computer service. The outcomes of the RCT on obstetric outcomes, maternal psychological well-being, parenting confidence, birth satisfaction, and future birth preference were analysed by intention to treat and reported here.

RESULTS

1410 women were screened for high childbirth fear (W-DEQ ≥66). Three hundred and thirty-nine (n = 339) women were randomised (intervention n = 170; controls n = 169). One hundred and eighty-four women (54 %) returned data for final analysis at 6 weeks postpartum (intervention n = 91; controls n = 93). Compared to controls the intervention group had a clinically meaningful but not statistically significant reduction in overall caesarean section (34 % vs 42 %, p = 0.27) and emergency CS rates (18 % vs 25 %, p = 0.23). Fewer women in the intervention group preferred caesarean section for a future pregnancy (18 % vs 30 %, p = 0.04). All other obstetric variables remained similar. There were no differences in postnatal depression symptoms scores, parenting confidence, or satisfaction with maternity care between groups, but a lower incidence of flashbacks about their birth in the intervention group compared to controls (14 % vs 26 %, p = 0.05). Postnatally women who received psycho-education reported that the 'decision aid' helped reduce their fear (53 % vs 37 %, p = 0.02).

CONCLUSION

Following a brief antenatal midwife-led psycho-education intervention for childbirth fear women were less likely to experience distressing flashbacks of birth and preferred a normal birth in a future pregnancy. A reduction in overall CS rates was also found. Psycho-education for fearful women has clinical benefits for the current birth and expectations of future pregnancies.

TRIAL REGISTRATION

Australian New Zealand Controlled Trials Registry ACTRN12612000526875 , 17th May 2012.

Impact of endometriosis on women's lives: a qualitative study

BACKGROUND

This study aimed to explore women's experiences of the impact of endometriosis and whether there are differences across three age groups.

METHODS

A qualitative descriptive design was conducted using semi-structured focus group discussions with 35 Australian women with endometriosis, in three age groups. All tape-recorded discussions were transcribed verbatim and read line by line to extract meaningful codes and categories using NVivo 9 software through a thematic analysis approach. Categories were then clustered into meaningful themes.

RESULTS

Participants' ages ranged from 17 to 53 years and had a history of 2 to 40 years living with endometriosis, with an average delay time to diagnosis of 8.1 years. Two main themes emerged: (1) experiences of living with endometriosis, and (2) impact of endometriosis on women's lives, with 14 discrete categories. The results showed similarities and differences of the impact between the three age groups. The most highlighted impacts were on marital/sexual relationships, social life, and on physical and psychological aspects in all three age groups, but with different orders of priority. Education was the second most highlighted for the 16-24 years, life opportunities and employment for the 25-34 years; and financial impact for those 35 years and above.

CONCLUSIONS

Our findings show that endometriosis impacts negatively on different aspects of women's lives. A better understanding of these findings could help to decrease the negative impact of endometriosis by guiding service delivery and future research to meet more effectively the needs of women and teenagers with this condition.

Negative Pressure Wound Therapy on Surgical Site Infections in Women Undergoing Elective Caesarean Sections: A Pilot RCT

Obese women undergoing caesarean section (CS) are at increased risk of surgical site infection (SSI). Negative Pressure Wound Therapy (NPWT) is growing in use as a prophylactic approach to prevent wound complications such as SSI, yet there is little evidence of its benefits. This pilot randomized controlled trial (RCT) assessed the effect of NPWT on SSI and other wound complications in obese women undergoing elective caesarean sections (CS) and also the feasibility of conducting a definitive trial. Ninety-two obese women undergoing elective CS were randomized in theatre via a central web based system using a parallel 1:1 process to two groups i.e., 46 women received the intervention (NPWT PICO™ dressing) and 46 women received standard care (Comfeel Plus(®) dressing). All women received the intended dressing following wound closure. The relative risk of SSI in the intervention group was 0.81 (95% CI 0.38-1.68); for the number of complications excluding SSI it was 0.98 (95% CI 0.34-2.79). A sample size of 784 (392 per group) would be required to find a statistically significant difference in SSI between the two groups with 90% power. These results demonstrate that a larger definitive trial is feasible and that careful planning and site selection is critical to the success of the overall study.

"A patchwork of services"--caring for women who sustain severe perineal trauma in New South Wales--from the perspective of women and midwives

BACKGROUND

Current research into severe perineal trauma (3rd and 4th degree) focuses upon identification of risk factors, preventative practices and methods of repair, with little focus on women's experiences of, and interactions with, health professionals following severe perineal trauma (SPT). The aim of this study is to describe current health services provided to women in New South Wales (NSW) who have experienced SPT from the perspective of Clinical Midwifery Consultants (CMC) and women.

METHODS

This study used a descriptive qualitative design and reports on the findings of a component of a larger mixed methods study. Data were collected through a semi-structured discussion group using a variety of non-directive, open-ended questions leading CMCs of NSW. A survey was distributed prior to the discussion group to collect further information and enable a more comprehensive understanding of services provided. Data from individual interviews with twelve women who had experienced SPT during vaginal birth is used to provide greater insight into their interactions with, and ease of access to, health service providers in NSW. An integrative approach was undertaken in reporting the findings which involved comparing and analysing findings from the three sets of data.

RESULTS

One overarching theme was identified: A Patchwork of Policy and Process which identified that current health services operate in a 'patchwork' manner when caring for women who sustain SPT. They are characterised by lack of consistency in practice and standardisation of care. Within the overarching theme, four subthemes were identified: Falling through the gaps; Qualifications, skills and attitudes of health professionals; Caring for women who have sustained SPT; and Gold standard care: how would it look?

CONCLUSION

The findings from this study suggest that current health services in NSW represent a 'patchwork' of service provision for women who have sustained SPT. It appeared that women seek compassionate and supportive care based upon a clear exchange of information, and this should be considered when reflecting upon health service design. This study highlights the benefits of establishing multi-disciplinary collaborative specialist clinics to support women who experience SPT and associated morbidities, with the aim of providing comprehensive physiological and psychological support.

Study protocol for reducing childbirth fear: a midwife-led psycho-education intervention

BACKGROUND

Childbirth fear has received considerable attention in Scandinavian countries, and the United Kingdom, but not in Australia. For first-time mothers, fear is often linked to a perceived lack of control and disbelief in the body's ability to give birth safely, whereas multiparous women may be fearful as a result of previous negative and/or traumatic birth experiences. There have been few well-designed intervention studies that test interventions to address women's childbirth fear, support normal birth, and diminish the possibility of a negative birth experience.

METHODS/DESIGN

Pregnant women in their second trimester of pregnancy will be recruited and screened from antenatal clinics in Queensland, Australia. Women reporting high childbirth fear will be randomly allocated to the intervention or control group. The psycho-educational intervention is offered by midwives over the telephone at 24 and 34 weeks of pregnancy. The intervention aims to review birth expectations, work through distressing elements of childbirth, discuss strategies to develop support networks, affirm that negative childbirth events can be managed and develop a birth plan. Women in the control group will receive standard care offered by the public funded maternity services in Australia. All women will receive an information booklet on childbirth choices. Data will be collected at recruitment during the second trimester, 36 weeks of pregnancy, and 4-6 weeks after birth.

DISCUSSION

This study aims to test the efficacy of a brief, midwife-led psycho-education counselling (known as BELIEF: Birth Emotions - Looking to Improve Expectant Fear) to reduce women's childbirth fear. 1) Relative to controls, women receiving BELIEF will report lower levels of childbirth fear at term; 2) less decisional conflict; 3) less depressive symptoms; 4) better childbirth self-efficacy; and 5) improved health and obstetric outcomes.

TRIAL REGISTRATION

Australian New Zealand Controlled Trials Registry ACTRN12612000526875.

Trends and risk factors for severe perineal trauma during childbirth in New South Wales between 2000 and 2008: a population-based data study

OBJECTIVES

To determine trends and risk factors for severe perineal trauma between 2000 and 2008.

DESIGN

This was a population-based data study.

SETTING

New South Wales, Australia.

PARTICIPANTS

510 006 women giving birth to a singleton baby during the period 2000-2008.

MAIN OUTCOME MEASURES

Rates of severe perineal trauma between 2000 and 2008 and associated demographic, fetal, antenatal, labour and delivery events and factors.

RESULTS

There was an increase in the overall rate of severe perineal trauma from 2000 to 2008 from 1.4% to 1.9% (36% increase). Compared with women who were intact or had minor perineal trauma (first-degree tear, vaginal graze/tear), women who were primiparous (adjusted OR (AOR) 1.8 CI (1.65 to 1.95), were born in China or Vietnam (AOR 1.1 CI (1.09 to 1.23), gave birth in a private hospital (AOR 1.1 CI (1.03 to 1.20), had an instrumental birth (AOR 1.8 CI (1.65 to 1.95) and male baby (AOR 1.3 CI (1.27 to 1.34) all had a significantly higher risk of severe perineal trauma. Only giving birth to a male baby, adjusted for birth weight (AOR 1.5 CI (1.44 to 1.58), remained significant, when women with severe perineal trauma were compared with all other women not experiencing severe perineal trauma. This association increased over the study period.

CONCLUSIONS

To our knowledge, this is the first time that having a male baby has been found to exert such a strong independent risk for severe perineal trauma and the increasing significance of this in recent years needs further exploration.

The transcriptional control regions of the copia retrotransposon

We have analysed the sequence elements that control expression of the copia retrotransposon. Expression of copia fusion constructs containing DNA sequence deletions and rearrangements was assayed by transient expression analysis. Progressive deletion and linker substitution identifies two regions on either side of the major transcriptional start sites in the copia long terminal repeat These regions are both required for high level expression in a cultured Drosophila melanogaster cell line but only the upstream region is required for copia expression in a Drosophila hydei cell line. A third control region lies downstream of the long terminal repeat in a region previously believed to contain no cis-acting regulatory sequences. We show by displacement and inversion of this region that it contains a transcriptional enhancer.

Diagnosis of pregnancy and prediction of fetal age in red deer by real-time ultrasonic scanning

Sixteen pregnant red deer hinds were scanned using real-time ultra sound at regular intervals during the first 150 days of pregnancy. In the early stages of pregnancy, an intra-rectal linear array transducer was used but later in pregnancy the hinds were scanned externally with a sector scanner. Pregnancy was determined from 30 days of gestation by intra-rectal scanning, and from 50 days by external scanning. With advancing age the size of the fetus increased, and linear regressions of size on age gave residual standard deviations of 0.508 days for head diameter and 0.506 days for trunk diameter. It is concluded that this technique can be used to determine pregnancy with a high degree of accuracy from 30 days of gestation and to predict calving date from fetal measurements within the range 1.5 cm to 7 cm for head diameter or 0.5 cm to 8 cm for trunk diameter, corresponding to a fetal age range of 35 to 150 days.

Endocrine differences between rats bearing simple and malignant mammary tumours induced by 9,10-dimethyl-1,2-benzanthracene

Images

The metabolic clearance rates of dehydroepiandrosterone, testosterone and their sulphate esters in man, rat and rabbit

The disappearance of isotopically labelled dehydroepiandrosterone, testosterone and their sulphates from the peripheral circulation of man, rabbit and rat has been investigated.

Metabolic clearance rates, distribution volumes and half-lives have been determined for these compounds in the above species.

In man, the steroid sulphates have a much lower metabolic clearance rate than the corresponding free steroids. This large difference stems from longer half-lives and lower distribution volumes of the former.

In the rabbit or rat the steroid sulphates and the appropriate free steroids do not show such marked differences in their metabolic clearance rates: the half-lives and distribution volumes are comparable.