Molecular Characterization of the 16S rRNA Gene of Helicobacter fennelliae Isolated from Stools and Blood Cultures from Paediatric Patients in South Africa

Forty strains of H. fennelliae collected from paediatric blood and stool samples over an 18 year period at a children's hospital in Cape Town, South Africa, were amplified by PCR of the 16S rRNA. Two distinct genotypes of H. fennelliae were identified based on the phylogenetic analysis. This was confirmed by sequencing a portion of the beta subunit of the RNA polymerase (rpoB) gene. All isolates from South Africa clustered with a proposed novel Helicobacter strain (accession number AF237612) isolated in Australia, while three H. fennelliae type strains from the northern hemisphere, NCTC 11612, LMG 7546 and CCUG 18820, formed a separate branch. A large (355bp) highly conserved intervening sequence (IVS) in the 16S rRNA was found in all isolates. Predicted secondary structures of the IVS from the 16S rRNA and 23S rRNA were characterised by a primary stem structure formed by base pairing of the 3′ and 5′ ends and internal loops and stems. This phylogenetic analysis is the largest undertaken of H. fennelliae. The South African H. fennelliae isolates are closely related to an Australian isolate previously reported to be a possible novel species of Helicobacter. This study suggests that the latter is strain of H. fennelliae

The use of a novel phage-based technology as a practical tool for the diagnosis of tuberculosis in Africa

Sub-Saharan Africa has experienced a significant increase in tuberculosis cases in recent years, fuelled by high rates of TB-HIV co-infection in the region. The diagnosis of tuberculosis is based largely on clinical assessment, sputum smear microscopy and chest radiography. Although smear microscopy is useful for detecting the most infectious cases, a significant portion of cases are negative on sputum smears, making diagnosis more difficult. New tests are urgently needed. The FASTPlaqueTB test, a bacteriophage-based method, has been evaluated in several studies in Africa and elsewhere. Studies in South Africa and Pakistan reported that between half and two-thirds of smear-negative culture-positive TB cases were detected by the FASTPlaqueTB test within 2 days. This suggests a beneficial role for this test in the early diagnosis of clinically suspected smear-negative cases. The same technology has been applied to develop a rapid test to indicate multi-drug resistant TB, FASTPlaqueTB-MDRi. This test gave equivalent results to conventional drug susceptibility methods, but with more rapid results. The tests are simple to perform and require no specialised equipment, making the technology suitable for widespread implementation. (African Journal of Biotechnology: 2003 2(2): 40-46

Enabling qualitative research data sharing using a natural language processing pipeline for deidentification: Moving beyond HIPAA Safe Harbor identifiers

OBJECTIVE: Sharing health research data is essential for accelerating the translation of research into actionable knowledge that can impact health care services and outcomes. Qualitative health research data are rarely shared due to the challenge of deidentifying text and the potential risks of participant reidentification. Here, we establish and evaluate a framework for deidentifying qualitative research data using automated computational techniques including removal of identifiers that are not considered HIPAA Safe Harbor (HSH) identifiers but are likely to be found in unstructured qualitative data. MATERIALS AND METHODS: We developed and validated a pipeline for deidentifying qualitative research data using automated computational techniques. An in-depth analysis and qualitative review of different types of qualitative health research data were conducted to inform and evaluate the development of a natural language processing (NLP) pipeline using named-entity recognition, pattern matching, dictionary, and regular expression methods to deidentify qualitative texts. RESULTS: We collected 2 datasets with 1.2 million words derived from over 400 qualitative research data documents. We created a gold-standard dataset with 280K words (70 files) to evaluate our deidentification pipeline. The majority of identifiers in qualitative data are non-HSH and not captured by existing systems. Our NLP deidentification pipeline had a consistent F1-score of ∼0.90 for both datasets. CONCLUSION: The results of this study demonstrate that NLP methods can be used to identify both HSH identifiers and non-HSH identifiers. Automated tools to assist researchers with the deidentification of qualitative data will be increasingly important given the new National Institutes of Health (NIH) data-sharing mandate

The effect of duration of untreated psychosis and treatment delay on the outcomes of prolonged early intervention in psychotic disorders

Treatment timing: The earlier the better The duration of untreated psychosis influences the long-term outcomes of treatment. Nikolai Albert, at the Copenhagen Mental Health Centre, and a team of Danish researchers have investigated the effects of a specialized early intervention program (OPUS) in 400 patients diagnosed with schizophrenia spectrum disorders and compared the effects of OPUS after two and five years. Their findings suggest that five years of specialized early intervention was most beneficial when the total duration from symptom start to treatment was shorter than 6 months. The treatment was particularly effective at improving patients’ disorganized behavior and negative symptoms such as blunted emotions and lack of motivation. These findings support previous studies suggesting that patients are more responsive to treatment in the early years of illness and highlight the importance of avoiding delays within the mental health service provision

Vascular responses to radiotherapy and androgen-deprivation therapy in experimental prostate cancer

Background: Radiotherapy (RT) and androgen-deprivation therapy (ADT) are standard treatments for advanced prostate cancer (PC). Tumor vascularization is recognized as an important physiological feature likely to impact on both RT and ADT response, and this study therefore aimed to characterize the vascular responses to RT and ADT in experimental PC. Methods: Using mice implanted with CWR22 PC xenografts, vascular responses to RT and ADT by castration were visualized in vivo by DCE MRI, before contrast-enhancement curves were analyzed both semi-quantitatively and by pharmacokinetic modeling. Extracted image parameters were correlated to the results from ex vivo quantitative fluorescent immunohistochemical analysis (qIHC) of tumor vascularization (9 F1), perfusion (Hoechst 33342), and hypoxia (pimonidazole), performed on tissue sections made from tumors excised directly after DCE MRI. Results: Compared to untreated (Ctrl) tumors, an improved and highly functional vascularization was detected in androgen-deprived (AD) tumors, reflected by increases in DCE MRI parameters and by increased number of vessels (VN), vessel density ( VD), and vessel area fraction ( VF) from qIHC. Although total hypoxic fractions ( HF) did not change, estimated acute hypoxia scores ( AHS) – the proportion of hypoxia staining within 50 μm from perfusion staining – were increased in AD tumors compared to in Ctrl tumors. Five to six months after ADT renewed castration-resistant (CR) tumor growth appeared with an even further enhanced tumor vascularization. Compared to the large vascular changes induced by ADT, RT induced minor vascular changes. Correlating DCE MRI and qIHC parameters unveiled the semi-quantitative parameters area under curve ( AUC) from initial time-points to strongly correlate with VD and VF, whereas estimation of vessel size ( VS) by DCE MRI required pharmacokinetic modeling. HF was not correlated to any DCE MRI parameter, however, AHS may be estimated after pharmacokinetic modeling. Interestingly, such modeling also detected tumor necrosis very strongly. Conclusions: DCE MRI reliably allows non-invasive assessment of tumors’ vascular function. The findings of increased tumor vascularization after ADT encourage further studies into whether these changes are beneficial for combined RT, or if treatment with anti-angiogenic therapy may be a strategy to improve the therapeutic efficacy of ADT in advanced PC.publishedVersio

Five years of specialised early intervention versus two years of specialised early intervention followed by three years of standard treatment for patients with a first episode psychosis:randomised, superiority, parallel group trial in Denmark (OPUS II)

Objective To compare the effects of five years of specialised early intervention (SEI) treatment for first episode schizophrenia spectrum disorder with the standard two years of SEI plus three years of treatment as usual. Design Randomised, superiority, parallel group trial with blinded outcome assessment. Randomisation was centralised and computerised with concealed randomisation sequence carried out at an external site. Setting Participants were recruited from six OPUS teams in Denmark between 2009 and 2012. OPUS teams provide SEI treatment to all patients diagnosed with a schizophrenia spectrum disorder in Denmark. Participants 400 participants (51% women) with a mean age of 25.6 (standard deviation 4.3) were randomised to five years of SEI (experimental intervention; n=197) or to two years of SEI plus three years of treatment as usual (control; n=203). Interventions OPUS treatment consists of three core elements—modified assertive community treatment, family involvement, and social skill training—with a patient-case manager ratio of no more than 12:1. For participants randomised to five years of OPUS treatment, the treatment was largely unchanged. Participants randomised to the control group were mostly referred to community health centres after two years of SEI treatment. Main outcomes Follow-up assessments were conducted five years after start of OPUS treatment. Primary outcome was negative symptoms measured on the scale for assessment of negative symptoms (avolition-apathy, anhedonia, alogia, and affective blunting). Secondary outcomes were remission of both negative and psychotic symptoms, psychotic symptoms, suicidal ideation, substance abuse, compliance with medical treatment, adherence with treatment, client satisfaction, days in hospital care, and labour market affiliation. Results Levels of negative symptoms did not differ between the intervention group and control group (1.72 v 1.81 points; estimated mean difference −0.10 (95% confidence interval 0.33 to 0.13), P=0.39). Participants receiving five years of OPUS treatment were more likely to remain in contact with specialised mental health services (90.4% v 55.6%, P<0.001), had higher client satisfaction (estimated mean difference 2.57 points (95% confidence interval 1.36 to 3.79), P<0.001), and had a stronger working alliance (estimated mean difference 5.56 points (95% confidence interval 2.30 to 8.82), P=0.001) than the control group. Conclusions This trial tests SEI treatment for up to five years for patients with first episode schizophrenia spectrum disorder; previous trials have found treatment effects for programmes lasting from one to three years. The prolonged SEI treatment had few effects, which could be due to the high level of treatment provided to control participants and the late start of specialised treatment. Trial registration Clinicaltrial.gov NCT00914238

Introduction of quality management in a National Reference Laboratory in Germany.

BACKGROUND: High quality diagnostic services are crucial for tuberculosis (TB) diagnosis, treatment and control. A strong laboratory quality management system (QMS) is critical to ensuring the quality of testing and results. Recent initiatives to improve TB laboratory quality have focused on low and middle-income countries, but similar issues also apply to high-income countries. METHODS AND FINDINGS: Using a multipronged approach reviews of facilities, equipment, processes (purchasing, pre-analytic, analytic and post-analytic), staff, health and safety, documentation, information management and organization based on the ISO 15189 and the twelve quality system essentials were conducted between October 2015 and January 2016 at the National TB Reference Laboratory in Germany. Outcome assessment included proportion of smear positive slides, proportion of contaminated liquid cultures and DNA contamination rates before and after implementation of QMS. The odds ratio for these outcomes was calculated using a before/after comparison. Reviews highlighted deficiencies across all twelve quality system essentials and were addressed in order of priority and urgency. Actions aimed at improving analytical quality, health and safety and information management were prioritised for initial implementation in parallel with each other. The odds ratio for a sample to be tested as microscopically positive increased by 2.08 (95%CI 1.41-3.06) comparing the time before with the time after implementation of quality managed fluorescence microscopy. Liquid culture contamination rates decreased from 23.6- 7.6% in April-July 2016 to <10% in November 2017-March 2018. The proportion of negative controls showing evidence of DNA contamination decreased from 38.2% in 2013 to 8.1% in 2017, the corresponding odds ratio was 0.14 (95%CI 0.07-0.29). CONCLUSION: This study showed marked improvement on quality indicators after implementation of a QMS in a National TB Reference Laboratory. The challenges and lessons learned in this study are valuable not just for high-income settings, but are equally generalizable to other laboratories

Doing Identity Work with Transgendered Women

Gender, sexuality and identity in relation to individual freedom and equality go to the core of who we are, as well as shape our actions. By offering a glimpse into the identity work processes of two transgendered women, I hope to make visible some of the forces and mechanisms that influence all of us, regardless of our gender or status. The transgendered are a group of people who have long been excluded, diagnosed, defined and oppressed by our current gender system. By making my interviewees’ stories heard, I hope to contribute to change in the prevailing hetero normative and dichotomic gender system. This thesis is a narrative analysis on identity work and gender. In this thesis I aim at answering how the two transgendered women engage in identity work during our consecutive discussions. I also try to identify what the role of gender is during these discussions and in identity work. I have conducted this thesis by interviewing both women in two consecutive in-depth interviews that took place a little over a year apart. After each interview I constructed a narrative that focused on the interviewee’s working life experiences regarding her gender reassignment process and career. Later on, these narratives have worked as background against which I have reflected the identity work and the practice of narrating identity that took place during our meetings. The concept of identity is based on multiple, always changing and socially constructed identities brought forward in popular queer theory literature. I have also used queer theory as a guide in identifying gender related identity work regarding my interviewees. I use the popular identity work literature and my data to name the dominant elements that are present during identity work. I also present a framework for identity work that shows how the previous identity work episode and the micro-level context have an effect on both: narrative identity practice and identity work. In addition I show how gender was present as a subject that was referred to and discussed about and a force that was always looming in the background when we were having our identity discussions. This thesis adds to current identity work literature and queer theory. By making the gender related identity work visible, it helps us to grasp on and change current gendered practices and to undo gender. It also helps us to see and identify some of the forces that contribute to shaping our identities and action