A comparison of efficient permutation tests for unbalanced ANOVA in two by two designs--and their behavior under heteroscedasticity

We compare different permutation tests and some parametric counterparts that are applicable to unbalanced designs in two by two designs. First the different approaches are shortly summarized. Then we investigate the behavior of the tests in a simulation study. A special focus is on the behavior of the tests under heteroscedastic variances.Comment: 20 pages, 9 figures, Working Paper of the Department of Management And Enigineering of the University of Padov

Estimation and testing of Wilcoxon–Mann–Whitney effects in factorial clustered data designs

Clustered data arise frequently in many practical applications whenever units are repeatedly observed under a certain condition. One typical example for clustered data are animal experiments, where several animals share the same cage and should not be assumed to be completely independent. Standard methods for the analysis of such data are Linear Mixed Models and Generalized Estimating Equations—however, checking their assumptions is not easy, especially in scenarios with small sample sizes, highly skewed, count, and ordinal or binary data. In such situations, Wilcoxon–Mann–Whitney type effects are suitable alternatives to mean-based or other distributional approaches. Hence, no specific data distribution, symmetric or asymmetric, is required. Within this work, we will present different estimation techniques of such effects in clustered factorial designs and discuss quadratic- and multiple contrast type-testing procedures for hypotheses formulated in terms of Wilcoxon–Mann–Whitney effects. Additionally, the framework allows for the occurrence of missing data: estimation and testing hypotheses are based on all-available data instead of complete-cases. An extensive simulation study investigates the precision of the estimators and the behavior of the test procedures in terms of their type-I error control. One real world dataset exemplifies the applicability of the newly proposed procedures

Magnetic resonance imaging analysis of the bioabsorbable Milagro™ interference screw for graft fixation in anterior cruciate ligament reconstruction

Ligament graft fixation with bioabsorbable interference screws is a standard procedure in cruciate ligament replacement. Previous screw designs may resorb incompletely, and can cause osteolysis and sterile cysts despite being implanted for several years. The aim of this study was to examine the in vivo degradation and biocompatibility of the new Milagro™ interference screw (Mitek, Norderstedt, Germany). The Milagro™ interference screw is made of 30% ß-TCP (TriCalcium phosphate) and 70% PLGA (Poly-lactic-co-glycolic acid). In the period between June 2005 and February 2006, 38 patients underwent graft fixation with Milagro™ screws in our hospital. Arthroscopic ACL reconstruction was performed using hamstring tendon grafts in all the patients. MR imaging was performed on 12 randomly selected patients out of the total of 38 at 3, 6 and 12 months after surgery. During the examination, the volume loss of the screw, tunnel enlargement, presence of osteolysis, fluid lines, edema and postoperative screw replacement by bone tissue were evaluated. There was no edema or signs of inflammation around the bone tunnels. At 3, 6 and 12 months, the tibial screws showed an average volume loss of 0, 8.1% (±7.9%) and 82.6% (±17.2%, P < 0.05), respectively. The femoral screws showed volume losses of 2.5% (±2.1%), 31.3% (±21.6%) and 92.02% (±6.3%, P < 0.05), respectively. The femoral tunnel enlargement was 47.4% (±43.8%) of the original bone tunnel volume after 12 months, and the mean tunnel volume of the tibial tunnel was −9.5% (±58.1%) compared to the original tunnel. Bone ingrowth was observed in all the patients. In conclusion, the resorption behaviour of the Milagro™ screw is closely linked to the graft healing process. The screws were rapidly resorbed after 6 months and, at 12 months, only the screw remnants were detectable. Moreover, the Milagro™ screw is biocompatible and osteoconductive, promoting bone ingrowth during resorption. Tunnel enlargement is not prevented in the first months but is reduced by bone ingrowth after 12 months

On negative results when using sentiment analysis tools for software engineering research

Recent years have seen an increasing attention to social aspects of software engineering, including studies of emotions and sentiments experienced and expressed by the software developers. Most of these studies reuse existing sentiment analysis tools such as SentiStrength and NLTK. However, these tools have been trained on product reviews and movie reviews and, therefore, their results might not be applicable in the software engineering domain. In this paper we study whether the sentiment analysis tools agree with the sentiment recognized by human evaluators (as reported in an earlier study) as well as with each other. Furthermore, we evaluate the impact of the choice of a sentiment analysis tool on software engineering studies by conducting a simple study of differences in issue resolution times for positive, negative and neutral texts. We repeat the study for seven datasets (issue trackers and Stack Overflow questions) and different sentiment analysis tools and observe that the disagreement between the tools can lead to diverging conclusions. Finally, we perform two replications of previously published studies and observe that the results of those studies cannot be confirmed when a different sentiment analysis tool is used

Endothelial dysfunction and altered endothelial biomarkers in patients with post-COVID-19 syndrome and chronic fatigue syndrome (ME/CFS)

BACKGROUND: Fatigue, exertion intolerance and post-exertional malaise are among the most frequent symptoms of Post-COVID Syndrome (PCS), with a subset of patients fulfilling criteria for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). As SARS-CoV-2 infects endothelial cells, causing endotheliitis and damaging the endothelium, we investigated endothelial dysfunction (ED) and endothelial biomarkers in patients with PCS. METHODS: We studied the endothelial function in 30 PCS patients with persistent fatigue and exertion intolerance as well as in 15 age- and sex matched seronegative healthy controls (HCs). 14 patients fulfilled the diagnostic criteria for ME/CFS. The other patients were considered to have PCS. Peripheral endothelial function was assessed by the reactive hyperaemia index (RHI) using peripheral arterial tonometry (PAT) in patients and HCs. In a larger cohort of patients and HCs, including post-COVID reconvalescents (PCHCs), Endothelin-1 (ET-1), Angiopoietin-2 (Ang-2), Endocan (ESM-1), IL-8, Angiotensin-Converting Enzyme (ACE) and ACE2 were analysed as endothelial biomarkers. RESULTS: Five of the 14 post-COVID ME/CFS patients and five of the 16 PCS patients showed ED defined by a diminished RHI (< 1.67), but none of HCs exhibited this finding. A paradoxical positive correlation of RHI with age, blood pressure and BMI was found in PCS but not ME/CFS patients. The ET-1 concentration was significantly elevated in both ME/CFS and PCS patients compared to HCs and PCHCs. The serum Ang-2 concentration was lower in both PCS patients and PCHCs compared to HCs. CONCLUSION: A subset of PCS patients display evidence for ED shown by a diminished RHI and altered endothelial biomarkers. Different associations of the RHI with clinical parameters as well as varying biomarker profiles may suggest distinct pathomechanisms among patient subgroups

Therapeutic implications of improved molecular diagnostics for rare CNS-embryonal tumor entities: results of an international, retrospective study

BACKGROUND: Only few data are available on treatment-associated behavior of distinct rare CNS-embryonal tumor entities previously treated as "CNS-primitive neuroectodermal tumors" (CNS-PNET). Respective data on specific entities, including CNS neuroblastoma, FOXR2 activated (CNS NB-FOXR2), and embryonal tumor with multi-layered rosettes (ETMR) are needed for development of differentiated treatment strategies. METHODS: Within this retrospective, international study, tumor samples of clinically well-annotated patients with the original diagnosis of CNS-PNET were analyzed using DNA methylation arrays (n=307). Additional cases (n=66) with DNA methylation pattern of CNS NB-FOXR2 were included irrespective of initial histological diagnosis. Pooled clinical data (n=292) were descriptively analyzed. RESULTS: DNA methylation profiling of "CNS-PNET" classified 58(19%) cases as ETMR, 57(19%) as HGG, 36(12%) as CNS NB-FOXR2, and 89(29%) cases were classified into 18 other entities. Sixty-seven (22%) cases did not show DNA methylation patterns similar to established CNS tumor reference classes. Best treatment results were achieved for CNS NB-FOXR2 patients (5-year PFS: 63%±7%, OS: 85%±5%, n=63), with 35/42 progression-free survivors after upfront craniospinal irradiation (CSI) and chemotherapy. The worst outcome was seen for ETMR and HGG patients with 5-year PFS of 18%±6% and 22%±7%, and 5-year OS of 24%±6% and 25%±7%, respectively. CONCLUSION: The historically reported poor outcome of CNS-PNET patients becomes highly variable when tumors are molecularly classified based on DNA methylation profiling. Patients with CNS NB-FOXR2 responded well to current treatments and a standard-risk-CSI based regimen may be prospectively evaluated. The poor outcome of ETMR across applied treatment strategies substantiates the necessity for evaluation of novel treatments

Fighting post-COVID and ME/CFS - development of curative therapies

The sequela of COVID-19 include a broad spectrum of symptoms that fall under the umbrella term post-COVID-19 condition or syndrome (PCS). Immune dysregulation, autoimmunity, endothelial dysfunction, viral persistence, and viral reactivation have been identified as potential mechanisms. However, there is heterogeneity in expression of biomarkers, and it is unknown yet whether these distinguish different clinical subgroups of PCS. There is an overlap of symptoms and pathomechanisms of PCS with postinfectious myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). No curative therapies are available for ME/CFS or PCS. The mechanisms identified so far provide targets for therapeutic interventions. To accelerate the development of therapies, we propose evaluating drugs targeting different mechanisms in clinical trial networks using harmonized diagnostic and outcome criteria and subgrouping patients based on a thorough clinical profiling including a comprehensive diagnostic and biomarker phenotyping