Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome

Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio- generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of nextgeneration sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBiogenerated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome sanalyses to facilitate functional studies into an organism’s biology

Perceptions of labour pain management of Dutch primary care midwives : a focus group study

Background: Labour pain is a major concern for women, their partners and maternity health care professionals. However, little is known about Dutch midwives' perceptions of working with women experiencing labour pain. The aim of this study was to explore midwives' perceptions of supporting women in dealing with pain during labour. Methods: We conducted a qualitative focus group study with four focus groups, including a total of 23 midwives from 23 midwifery practices across the country. Purposive sampling was used to select the practices. The constant comparison method of Glaser and Straus (1967, ren. 1995) was used to gain an understanding of midwives' perceptions regarding labour pain management. Results: We found two main themes. The first theme concerned the midwives' experienced professional role conflict, which was reflected in their approach of labour pain management along a spectrum from "working with pain" to a "pain relief" approach. The second theme identified situational factors, including time constraints; discontinuity of care; role of the partner; and various cultural influences, that altered the context in which care was provided and how midwives saw their professional role. Conclusion: Midwives felt challenged by the need to balance their professional attitude towards normal birth and labour pain, which favours working with pain, with the shift in society towards a wider acceptance of pharmacological pain management during labour. This shift compelled them to redefine their professional identity

Transitions in Parkinson's disease in primary care: Protocol of a longitudinal mixed methods study

Introduction: Parkinson's disease affects many aspects of the lives of patients and their relatives. Patients must adapt continuously to disabilities that necessitate changes in (medical) support, such as domestic adjustments, involvement of (non) professional caregivers or admission to hospital. Such changes mark a transition: a transfer of a patient between levels or locations of care. Transitions are likely to be multifold and complex, given that Parkinson's disease care extends across all echelons of healthcare. Patients and relatives are vulnerable during a transition, which imposes risks for their safety and quality of life. Guidance by the general practitioner, who knows the preferences of the patient, can help to overcome challenges associated with a transition. However, patient-centred primary care requires insight into the transitions patients with Parkinson's disease encounter. We aim to examine these transitions and the way patients, relatives and general practitioners experience them and cope with them. Moreover, we will study the patients' expectations of their general practitioner during a transition and the general practitioners' views on their role. Methods and analysis: A longitudinal mixed methods study will be conducted, using qualitative research methods combined with quantitative data as a validated questionnaire on quality of life. Patients will be asked to make a video diary every 2 weeks for a period of 1 year. Once they encounter a transition, patients and their general practitioners will be interviewed to identify causes and consequences of the transition. The verbatim transcripts of the videos and interviews will be analysed according to the principles of constant comparative analysis. Ethics and dissemination: Ethical approval was not needed according to Dutch legislation. Informed consent of patients, relatives and general practitioners will be obtained. We will disseminate the results in peer-reviewed journals, at research conferences and on the website of the Dutch Parkinson's Disease Association

Satisfaction with caregivers during labour among low risk women in the Netherlands : the association with planned place of birth and transfer of care during labour

Background: The caregiver has an important influence on women's birth experiences. When transfer of care during labour is necessary, care is handed over from one caregiver to the other, and this might influence satisfaction with care. It is speculated that satisfaction with care is affected in particular for women who need to be transferred from home to hospital. We examined the level of satisfaction with the caregiver among women with planned home versus planned hospital birth in midwife-led care. Methods: We used data from the prospective multicentre DELIVER (Data EersteLIjns VERloskunde) cohort-study, conducted in 2009 and 2010 in the Netherlands. Women filled in a postpartum questionnaire which contained elements of the Consumer Quality index. This instrument measures 'general rate of satisfaction with the caregiver' (scale from 1 to 10, with cut-off of below 9) and 'quality of treatment by the caregiver' (containing 7 items on a 4 point Likert scale, with cut-off of mean of 4 or lower). Results: Women who planned a home birth (n = 1372) significantly more often rated 'quality of treatment by caregiver' high than women who planned a hospital birth (n = 829). Primiparous women who planned a home birth significantly more often had a high rate (9 or 10) for 'general satisfaction with caregiver' (adj.OR 1.48; 95% CI 1.1, 2.0). Also, primiparous women who planned a home birth and had care transferred during labour (331/553; 60%) significantly more often had a high rate (9 or 10) for 'general satisfaction' compared to those who planned a hospital birth and who had care transferred (1.44; 1.0-2.1). Furthermore, they significantly more often rated 'quality of treatment by caregiver' high, than 276/414 (67%) primiparous women who planned a hospital birth and who had care transferred (1.65; 1.2-2.3). No differences were observed for multiparous women who had planned home or hospital birth and who had care transferred. Conclusions: Planning home birth is associated to a good experience of quality of care by the caregiver. Transferred planned home birth compared to a transferred planned hospital birth does not lead to a more negative experience of care received from the caregiver

How GPs value guidelines applied to patients with multimorbidity: A qualitative study

Objectives: To explore and describe the value general practitioner (GPs) attribute to medical guidelines when they are applied to patients with multimorbidity, and to describe which benefits GPs experience from guideline adherence in these patients. Also, we aimed to identify limitations from guideline adherence in patients with multimorbidity, as perceived by GPs, and to describe their empirical solutions to manage these obstacles. Design: Focus group study with purposive sampling of participants. Focus groups were guided by an experienced moderator who used an interview guide. Interviews were transcribed verbatim. Data analysis was performed by two researchers using the constant comparison analysis technique and field notes were used in the analysis. Data collection proceeded until saturation was reached. Setting: Primary care, eastern part of The Netherlands. Participants: Dutch GPs, heterogeneous in age, sex and academic involvement. Results: 25 GPs participated in five focus groups. GPs valued the guidance that guidelines provide, but experienced shortcomings when they were applied to patients with multimorbidity. Taking these patients’ personal circumstances into account was regarded as important, but it was impeded by a consistent focus on guideline adherence. Preventative measures were considered less appropriate in (elderly) patients with multimorbidity. Moreover, the applicability of guidelines in patients with multimorbidity was questioned. GPs’ extensive practical experience with managing multimorbidity resulted in several empirical solutions, for example, using their ‘common sense’ to respond to the perceived shortcomings. Conclusions: GPs applying guidelines for patients with multimorbidity integrate patient-specific factors in their medical decisions, aiming for patient-centred solutions. Such integration of clinical experience and best evidence is required to practise evidence-based medicine. More flexibility in pay-for-performance systems is needed to facilitate this integration. Several improvements in guideline reporting are necessary to enhance the applicability of guidelines in patients with multimorbidity

High resolution δ18O seasonality record in a French Eemian tufa stromatolite (Caours, Somme Basin)

International audienc

Exploring the impact of chronic obstructive pulmonary disease (COPD) on diabetes control in diabetes patients: a prospective observational study in general practice

Background:Little is known about the association between COPD and diabetes control parameters.Aims:To explore the association between comorbid COPD and longitudinal glycaemic control (HbA 1C) and systolic blood pressure (SBP) in a primary care cohort of diabetes patients.Methods:This is a prospective cohort study of type 2 diabetes patients in the Netherlands. In a mixed model analysis, we tested differences in the 5-year longitudinal development of HbA 1C and SBP according to COPD comorbidity (present/absent). We corrected for relevant covariates. In subgroup effect analyses, we tested whether potential differences between diabetes patients with/without COPD were modified by age, sex, socio-economic status (SES) and body mass index (BMI).Results:We analysed 610 diabetes patients. A total of 63 patients (10.3%) had comorbid COPD. The presence of COPD was not significantly associated with the longitudinal development of HbA 1C (P=0.54) or SBP (P=0.33), but subgroup effect analyses showed significant effect modification by SES (P<0.01) and BMI (P=0.03) on SBP. Diabetes patients without COPD had a flat SBP trend over time, with higher values in patients with a high BMI. For diabetes patients with COPD, SBP gradually increased over time in the middle-And high-SES groups, and it decreased over time in those in the low-SES group.Conclusions:The longitudinal development of HbA 1C was not significantly associated with comorbid COPD in diabetes patients. The course of SBP in diabetes patients with COPD is significantly associated with SES (not BMI) in contrast to those without COPD. Comorbid COPD was associated with longitudinal diabetes control parameters, but it has complex interactions with other patient characteristics. Further research is needed

The effect of comorbidity on glycemic control and systolic blood pressure in type 2 diabetes: A cohort study with 5 year follow-up in primary care

To explore the longitudinal effect of chronic comorbid diseases on glycemic control (HbA1C) and systolic blood pressure (SBP) in type 2 diabetes patients. Methods In a representative primary care cohort of patients with newly diagnosed type 2 diabetes in The Netherlands (n = 610), we tested differences in the five year trend of HbA1C and SBP according to comorbidity profiles. In a mixed model analysis technique we corrected for relevant covariates. Influence of comorbidity (a chronic disease already present when diabetes was diagnosed) was tested as total number of comorbid diseases, and as presence of specific disease groups, i.e. cardiovascular, mental, and musculoskeletal disease, malignancies, and COPD. In subgroup effect analyses we tested if potential differences were modified by age, sex, socioeconomic status, and BMI. Results The number of comorbid diseases significantly influenced the SBP trend, with highest values after five years for diabetes patients without comorbidity (p = 0.005). The number of diseases did not influence the HbA1C trend (p = 0.075). Comorbid musculoskeletal disease resulted in lower HbA1C at the time of diabetes diagnosis, but in higher values after five years (p = 0.044). Patients with cardiovascular diseases had sustained elevated levels of SBP (p = 0.014). Effect modification by socioeconomic status was observed in some comorbidity subgroups. Conclusions Presence of comorbidity in type 2 diabetes patients affected the long-term course of HbA1C and SBP in this primary care cohort. Numbers and types of comorbidity showed differential effects: not the simple sum of diseases, but specific types of comorbid disease had a negative influence on long-term diabetes control parameters. The complex interactions between comorbidity, diabetes control and effect modifiers require further investigation and may help to personalize treatment goals