tRigon: an R package and Shiny App for integrative (path-)omics data analysis

BACKGROUND

Pathomics facilitates automated, reproducible and precise histopathology analysis and morphological phenotyping. Similar to molecular omics, pathomics datasets are high-dimensional, but also face large outlier variability and inherent data missingness, making quick and comprehensible data analysis challenging. To facilitate pathomics data analysis and interpretation as well as support a broad implementation we developed tRigon (Toolbox foR InteGrative (path-)Omics data aNalysis), a Shiny application for fast, comprehensive and reproducible pathomics analysis.

RESULTS

tRigon is available via the CRAN repository ( https://cran.r-project.org/web/packages/tRigon ) with its source code available on GitLab ( https://git-ce.rwth-aachen.de/labooratory-ai/trigon ). The tRigon package can be installed locally and its application can be executed from the R console via the command 'tRigon::run_tRigon()'. Alternatively, the application is hosted online and can be accessed at https://labooratory.shinyapps.io/tRigon . We show fast computation of small, medium and large datasets in a low- and high-performance hardware setting, indicating broad applicability of tRigon.

CONCLUSIONS

tRigon allows researchers without coding abilities to perform exploratory feature analyses of pathomics and non-pathomics datasets on their own using a variety of hardware.

Early postpartum treatment strategies and early postpartum relapses in women with active multiple sclerosis

BACKGROUND

Relapse risk after delivery is increased in women with active multiple sclerosis (MS), the best strategy to reduce it is unknown. We aimed to assess the association of four different postpartum strategies with relapses during the first 6 months post partum.

METHODS

This cohort study includes data prospectively collected through structured telephone interviews from the German Multiple Sclerosis and Pregnancy Registry. Pregnancies with active MS (fingolimod or natalizumab treatment OR relapse within 1 year before pregnancy) and postpartum follow-up of ≥6 months were included. We compared four strategies: (1) intention to breastfeed exclusively without disease-modifying therapy (DMT) (exclusive breast feeding ≥2 months or switching to non-exclusive/weaning within 2 weeks after a relapse during the first 2 months), (2) early treatment with natalizumab/fingolimod and (3) other DMT initiated within 6 weeks post partum before a relapse. If women did not or only partially breastfed, or started DMT≤6 weeks after delivery after a relapse or later, we assumed (4) no-DMT-no-exclusive- breastfeeding-strategy. Main outcome was time to postpartum MS relapses.

RESULTS

In 867 women with 911 pregnancies, most (n=416) intended to breastfeed exclusively or had no-DMT-no-exclusive-breastfeeding-strategy (n=290); fewer started fingolimod (n=38), natalizumab (n=74) or another DMT (n=93) early. Recurrent time-to-event analysis showed a statistically significant reduction in relapse hazard only with the natalizumab/fingolimod-strategy as of months 3-4 post partum compared with intention-to-breastfeed-exclusively-strategy. The very early relapse risk was highest in no-DMT-no-exclusive-breastfeeding-strategy.

CONCLUSION

In active MS, an early postpartum treatment strategy should be determined well before delivery. Natalizumab/fingolimod-strategy reduced postpartum relapse hazard from month 3, but none diminished the early postpartum relapse hazard.

Effectiveness of a tablet-based intervention for people living with dementia in primary care-A cluster randomized controlled trial

BACKGROUND

Primary care physicians (PCP) play a key role in the care of people living with dementia. However, the implementation and practicability of the German S3 Dementia Guideline in primary care remain unclear. The main objective of the present study was to evaluate an intervention for improving guideline-based dementia care in primary care.

DESIGN

A two-arm, 9-month follow-up cluster-randomized controlled trial with two parallel groups.

SETTING

28 primary care practices in Berlin and the surrounding area in Germany.

PARTICIPANTS

A total of N = 28 PCP, N = 91 people living with dementia, and N = 88 informal caregivers participated in the trial.

INTERVENTION

A tablet-based intervention to improve adherence to the German S3 Dementia Guideline in primary care was compared to a control group (care as usual plus a handbook on dementia). MeasurementsAdherence to dementia guideline (primary outcome) was measured on PCP' (23 items) and informal caregivers' level (19 items) with a self-developed checklist. Secondary outcomes (quality of life, neuropsychiatric symptoms, activities of daily living, general health status, depression, and caregiver burden) were measured with standardized assessments. Also, post-hoc per-protocol analyses were conducted.

RESULTS

No differences in guideline adherence between the intervention and the control group were observed. Further, no significant impact of the intervention on secondary outcomes was detected.

CONCLUSION

The DemTab Study did not improve self-reported guideline adherence in PCP. However, important implementation barriers such as lack of interoperability and low applicability of existing German S3 Dementia Guideline in the primary care setting were identified and are being discussed.

TRIAL REGISTRATION

The DemTab trial was prospectively registered with the ISRCTN registry (Trial registration number: ISRCTN15854413). Registered 01 April 2019, https://doi.org/10.1186/ISRCTN15854413.

Evaluation of skin cancer screening in Germany - Spatiotemporal associations between skin cancer screening and skin cancer mortality based on ambulatory claims data

BACKGROUND

There are regional differences in skin cancer screening uptake in Germany. So far, it is unclear whether a high uptake of screening services leads to a reduction in mortality. This article presents study results on the investigation of spatiotemporal associations between skin cancer screening and mortality. The methods used are discussed regarding their suitability.

MATERIAL AND METHODS

The basis is ambulatory claims data on the utilization of early skin cancer detection as well as data on skin cancer mortality from the cause-of-death statistics of the years 2011-2015 at county level in Germany. In addition to a descriptive evaluation, spatiotemporal cluster analyses and regression models were used to investigate the relationship between the uptake of early detection and mortality. In addition to age, adjustments were also made for other selected socio-economic and socio-graphical variables.

RESULTS

The descriptive results show striking spatial patterns of skin cancer screening and mortality. Cluster analyses identified regions with significantly higher and lower cases of early detection and skin cancer mortality. The spatiotemporal regression analyses show no clear association. Only early detection by a dermatologist, adjusted for age, shows an association with mortality.

CONCLUSIONS

No clear association between early skin cancer detection and mortality can be derived from the results. However, the study design used with a spatiotemporal cluster and regression analysis has shown that these methods allow in-depth statements about the relationship between early skin cancer detection and mortality.

Piloting an ICU follow-up clinic to improve health-related quality of life in ICU survivors after a prolonged intensive care stay (PINA): feasibility of a pragmatic randomised controlled trial

BACKGROUND

ICU survivors often suffer from prolonged physical and mental impairments resulting in the so called "Post-Intensive Care Syndrome" (PICS). The aftercare of former ICU patients affected by PICS in particular has not been addressed sufficiently in Germany so far. The aim of this study was to evaluate the feasibility of a pragmatic randomised trial (RCT) comparing an intensive care unit (ICU) follow-up clinic intervention to usual care.

METHODS

This pilot study in a German university hospital evaluated the feasibility of a pragmatic RCT. Patients were assigned in a 1:1 ratio to an ICU follow-up clinic intervention or to usual care. The concept of this follow-up clinic was previously developed in a participatory process with patients, next of kin, health care professionals and researchers. We performed a process evaluation and determined acceptability, fidelity, completeness of measurement instruments and practicality as feasibility outcomes. The RCT's primary outcome (health-related quality of life) was assessed six months after ICU discharge by means of the physical component scale of the Short-Form-12 self-report questionnaire.

RESULTS

The pilot study was conducted from June 2020 to May 2021 with 21 and 20 participants in the intervention and control group. Principal findings related to feasibility were 85% consent rate (N = 48), 62% fidelity rate, 34% attrition rate (N = 41) and 77% completeness of outcome measurements. The primary effectiveness outcome (health-related quality of life) could be measured in 93% of participants who completed the study (N = 27). The majority of participants (85%) needed assistance with follow-up questionnaires (practicality). Median length of ICU stay was 13 days and 85% (N = 41) received mechanical ventilation, median Sequential Organ Failure Assessment Score was nine. Six-month follow-up assessment was planned for all study participants and performed for 66% (N = 41) of the participants after 197 days (median).

CONCLUSION

The participatory developed intervention of an ICU follow-up clinic and the pragmatic pilot RCT both seem to be feasible. We recommend to start a pragmatic RCT on the effectiveness of the ICU follow-up clinic.

TRIAL REGISTRATION

ClinicalTrials.gov US NLM, NCT04186468, Submission: 02/12/2019, Registration: 04/12/2019, https://clinicaltrials.gov/ct2/show/NCT04186468.

E-mental health in Germany - what is the current use and what are experiences of different types of health care providers for patients with mental illnesses?

BACKGROUND

As a new and effective support option, e-mental health interventions can be useful in complementing treatment in mental health care. To date, little is known about how health care providers use these programs to treat patients with mental illnesses in Germany. The present study aims to examine the use of and experiences with e-mental health interventions from the point of view of different types of health care providers for patients with mental illnesses.

METHODS

Data from a cross-sectional survey of routine care health care providers in Germany in 2021 were analysed. In this survey, data were collected from n = 107 general practitioners (GPs), n = 114 specialist doctors, n = 102 psychotherapists, and n = 102 inpatient clinicians. Assessments included professional use of digital media, as well as knowledge, use and experiences regarding e-mental health interventions in care of people with mental illness.

RESULTS

In the total sample of n = 425, 65.6% (n = 279) were female. The study participants had an average age of 47.7 years (SD = 11.0) and their average work experience was 20.0 years (SD = 11.1). Overall, the majority (83.8%, n = 353) had heard of e-mental health interventions, but few felt well informed. Only 28.5% (n = 121) had already used e-mental health interventions for treatment support. The most commonly recommended e-mental health interventions in the sample were deprexis (39.7%, n = 48), moodgym (24.8%, n = 30), and iFightDepression (22.3%, n = 27). The use was predominantly considered to be helpful and satisfactory. Insufficient knowledge about e-mental health interventions and lack of informational materials for patients were reported as relevant barriers to the use of e-mental health interventions.

CONCLUSIONS

E-mental health interventions can be a useful support option, but they are rarely used in the treatment of patients with mental illnesses. There is a need to disseminate information specific to the various types of health care providers. Tailored implementation strategies need to be developed in order to capitalize on the potential of effective e-mental health interventions and to improve health care for patients with mental illnesses.

Patients' perspectives on the quality of care of a new complex psycho-oncological care programme in Germany - external mixed methods evaluation results

BACKGROUND

Guideline-compliant provision of psycho-oncological (PO) care is still challenging in Germany. Hence, a new care programme, called integrated cross-sectoral psycho-oncology (isPO), was implemented to improve the integration of needs-oriented PO care. Quality of care (QoC) was externally evaluated from the patient's perspective. We aim to gain insight into patients' experiences with isPO and how their assessment affects relevant patient-reported outcomes (anxiety and depression, health status, and work ability).

METHODS

An explanatory, sequential mixed-methods design was applied. Patients were surveyed twice during their 1-year care trajectory: after 3 (T1) and 12 (T2) months. Data sets were matched using pseudonyms. Care documentation data, including sociodemographic characteristics and the primary outcome variable (anxiety and depression), were matched. In the survey, patients rated their satisfaction with respective isPO service providers and the programme in general (QoC). Health status (EORTC-QLQ-C30) and work ability (WAS) were measured. Descriptive analyses and t-tests for dependent samples were conducted to assess changes in outcome variables over time. Linear regression analyses were conducted to assess whether care satisfaction predicted outcome variables. Patients who completed their isPO care trajectory were asked to participate in semi-structured telephone interviews to share their experiences. Purposeful sampling was applied. All 23 interviews were audiotaped, transcribed, and analysed via content-structuring method.

RESULTS

Patients reported medium-to-high satisfaction with their isPO care. All patient-related outcomes significantly improved over time and QoC measures predicted those outcomes. Needs orientation (e.g., care intensity or mode of delivery) was perceived as essential for high QoC, and outpatient care with fixed contact persons as highly important for care continuity. Furthermore, patients identified programme optimisation needs, such as period of care or extension of care to relatives.

CONCLUSIONS

Patients assessed the isPO programme's QoC positively. They identified facilitators for QoC and optimisation needs. Therefore, data on QoC can function as an indicator for a programme's feasibility and maturity within care reality. As patients' care satisfaction positively influences important patient-related outcomes, it may be routinely considered for quality management. Based on patients' perspectives, isPO seems to be recommendable for routine psycho-oncological care in Germany, if ongoing programme optimisation within structured quality management is guaranteed.

TRIAL REGISTRATION

The study was registered in the German Clinical Trials Register (No. DRKS00015326) on 30.10.2018.

The impact of the COVID-19 pandemic restrictions on the health care utilization of cancer patients

BACKGROUND

COVID-19 has impacted both society and medical care. While Germany entered the first lockdown in spring 2020, the PIKKO study (Patient information, communication and competence empowerment in oncology) was still active. The intervention modules, patient navigator (PN), services of the Saarland Cancer Society (SCS), psycho-social counseling and different courses, and online knowledge database (ODB) continued to be offered, but in an adapted form. It was the aim of this supplementary survey to identify the restrictions and burdens of the pandemic containment strategies on the PIKKO patients and thus on the PIKKO study itself. Furthermore, this work shows how the PIKKO modules were used during the lockdown.

METHODS

All patients in the PIKKO intervention group (IG) were invited to complete a questionnaire, n = 503. Furthermore, utilization of the SCS and log files of the ODB were analyzed. For socio-demographic data and contacts with the PN, data from the regular PIKKO surveys were used. In addition to descriptive statistics, chi²-tests, F-tests and linear regression analyses were performed.

RESULTS

356 patients participated in this supplemental survey. 37.6% reported restrictions. "Restrictions on accompanying persons", "ban on visits to the wards" and "protective mouth-nose-mask" were reported as the greatest burdens. 39.0% expressed fears that the restrictions would have an impact on the course of their disease. Linear regression analyses showed differences in feelings of burden among age groups (more among < 60-year-olds), gender (more among women), children in the household (more with children), and preexisting financial stress (more with financial worries). In April 2020, there was more patient contact with PNs by phone, more SCS psycho-social counseling by phone, adapted SCS course offering, but with significantly fewer participants, and high activity on the ODB.

CONCLUSION

Cancer patients in the IG reported restrictions from the pandemic containment strategies and feared an impact on their recovery. However, whether a burden is perceived as heavy depends more on gender, age, or pre-existing burdens than on whether the lockdown affects PIKKO or not. The utilization of counseling, courses or the ODB despite lockdown shows the need for such services, especially in times of crisis.

TRIAL REGISTRATION

This study was retrospectively registered in the German Clinical Trial Register under DRKS00016703 (21 Feb 2019, retrospectively registered). https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00016703 .

Patient information, communication and competence empowerment in oncology: Results and learnings from the PIKKO study

PURPOSE

Many concepts for accompanying and supporting cancer patients exist and have been studied over time. One of them was PIKKO (a German acronym for "Patient information, communication and competence empowerment in oncology"), which combined a patient navigator, socio-legal and psychological counseling (with psychooncologists), courses dealing with various supportive aspects, and a knowledge database with validated and easy-to-understand disease-related information. The aim was to increase the patients' health-related quality of life (HRQoL), self-efficacy as well as health literacy and to reduce psychological complaints such as depression and anxiety.

METHODS

To this purpose, an intervention group was given full access to the modules in addition to treatment as usual, while a control group received only treatment as usual. Over twelve months, each group was surveyed up to five times. Measurements were taken using the SF12, PHQ-9, GAD, GSE, and HLS-EU-Q47.

RESULTS

No significant differences were found in scores on the mentioned metrics. However, each module was used many times and rated positively by the patients. Further analyses showed a tendency higher score in health literacy with higher intensity of use of the database and higher score in mental HRQoL with higher intensity of use of counseling.

CONCLUSION

The study was affected by several limitations. A lack of randomization, difficulties in recruiting the control group, a heterogeneous sample, and the COVID-19 lockdown influenced the results. Nevertheless, the results show that the PIKKO support was appreciated by the patients and the lack of measurable effects was rather due to the mentioned limitations than to the PIKKO intervention.

TRIAL REGISTRATION

This study was retrospectively registered in the German Clinical Trial Register under DRKS00016703 (21.02.2019, retrospectively registered). https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00016703.

Quality of care for people with multimorbidity: a focus group study with patients and their relatives

BACKGROUND

Prevalence of people with multimorbidity rises. Multimorbidity constitutes a challenge to the healthcare system, and treatment of patients with multimorbidity is prone to high-quality variations. Currently, no set of quality indicators (QIs) exists to assess quality of care, let alone incorporating the patient perspective. We therefore aim to identify aspects of quality of care relevant to the patients' perspective and match them to a literature-based set of QIs.

METHODS

We conducted eight focus groups with patients with multimorbidity and three focus groups with patients' relatives using a semistructured guide. Data were analysed using Kuckartz's qualitative content analysis. We derived deductive categories from the literature, added inductive categories (new quality aspects) and translated them into QI.

RESULTS

We created four new QIs based on the quality aspects relevant to patients/relatives. Two QIs (patient education/self-management, regular updates of medication plans) were consented by an expert panel, while two others were not (periodical check-ups, general practitioner-coordinated care). Half of the literature-based QIs, for example, assessment of biopsychosocial support needs, were supported by participants' accounts, while more technical domains regarding assessment and treatment regimens were not addressed in the focus groups.

CONCLUSION

We show that focus groups with patients and relatives adding relevant aspects in QI development should be incorporated by default in QI development processes and constitute a reasonable addition to traditional QI development. Our QI set constitutes a framework for assessing the quality of care in the German healthcare system. It will facilitate implementation of treatment standards and increase the use of existing guidelines, hereby helping to reduce overuse, underuse and misuse of healthcare resources in the treatment of patients with multimorbidity.

TRIAL REGISTRATION NUMBER

German clinical trials registry (DRKS00015718), Pre-Results.

Predicting patient outcomes in psychiatric hospitals with routine data: a machine learning approach

BACKGROUND

A common problem in machine learning applications is availability of data at the point of decision making. The aim of the present study was to use routine data readily available at admission to predict aspects relevant to the organization of psychiatric hospital care. A further aim was to compare the results of a machine learning approach with those obtained through a traditional method and those obtained through a naive baseline classifier.

METHODS

The study included consecutively discharged patients between 1st of January 2017 and 31st of December 2018 from nine psychiatric hospitals in Hesse, Germany. We compared the predictive performance achieved by stochastic gradient boosting (GBM) with multiple logistic regression and a naive baseline classifier. We tested the performance of our final models on unseen patients from another calendar year and from different hospitals.

RESULTS

The study included 45,388 inpatient episodes. The models' performance, as measured by the area under the Receiver Operating Characteristic curve, varied strongly between the predicted outcomes, with relatively high performance in the prediction of coercive treatment (area under the curve: 0.83) and 1:1 observations (0.80) and relatively poor performance in the prediction of short length of stay (0.69) and non-response to treatment (0.65). The GBM performed slightly better than logistic regression. Both approaches were substantially better than a naive prediction based solely on basic diagnostic grouping.

CONCLUSION

The present study has shown that administrative routine data can be used to predict aspects relevant to the organisation of psychiatric hospital care. Future research should investigate the predictive performance that is necessary to provide effective assistance in clinical practice for the benefit of both staff and patients.

Complex intervention in augmentative and alternative communication (AAC) care in Germany: a study protocol of an evaluation study with a controlled mixed-methods design

INTRODUCTION

The current practice of service delivery in Germany for people with complex communication needs (CCN) who are in need of augmentative and alternative communication (AAC) is characterised by diverse problems, including a lack of clarity in the responsibilities of the service providers involved. To address these issues a new service delivery model has been put in place, implemented in three AAC counselling centres for patients with a particular health insurance across Germany. The implementation of a new service delivery model aims to improve individualised service delivery. The model goes beyond standard care by adding case management, counselling, AAC training and, if needed, AAC therapy. This study aims to evaluate the effectiveness of this complex intervention.

METHODS AND ANALYSIS

In consideration of the complexity of the new service delivery model, formative and summative evaluation will be conducted. The formative evaluation will provide data based on qualitative and quantitative assessments of the competences and perspectives of all involved stakeholders, including a proxy measurement of persons with CCN. The summative evaluation will include a controlled study design as the new service delivery model will be compared against the service delivery in an existing contract and against data gathered from caregivers of AAC users provided with standard care. With the exception of the individual interviews the data will be collected from proxies-that is, informal and formal caregivers.

ETHICS AND DISSEMINATION

Data collection, storage and evaluation meet the currently valid data protection regulations. Consultation by the responsible data protection officer of the Oldenburg Medical School and a positive vote from its Ethics Committee were obtained prior to the start of the study. Dissemination strategies include the presentation of the obtained data and results in the form of publications and at conferences.

TRIAL REGISTRATION NUMBER

DRKS00013628.