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Abstract Background Infraocclusion of deciduous teeth is a frequent dental anomaly caused by ankylosis accompanied by local growth disturbance. During puberal growth spurt an increasing progression of infraocclusion is detected. The clinical classification of ankylosed deciduous teeth varies considerably among scientific studies. The aim of this paper is to present an up-to-date overview of the variety of methods. Methods The systematic literature search followed the PRISMA guidelines and included the analysis of the following databases and study registries: PubMed (MEDLINE), the Cochrane Library, Web of Science, Embase.com and ClinicalTrials.gov from database inception until September 23, 2024. Studies that investigated at least one ankylosed deciduous tooth per participant in a quantitative or qualitative manner were included. Studies that evaluated only histological data were excluded. Controlled and uncontrolled clinical studies, retrospective studies, observational studies and cross-sectional studies were included. The studies were restricted to English and German languages. Case reports, case series, comments, expert opinions, letters to the editor, literature reviews and studies enrolling less than 10 patients or 10 infraoccluded teeth in total were excluded. Results Of 5645 records, 42 papers qualified for the final analysis. The evaluation of infraoccluded deciduous teeth was mainly (n = 37) performed by quantitative and semiquantitative assessment of the extent of infraposition at the occlusal level. The measurement reference differed considerably. Fewer studies have analyzed ankylosed deciduous teeth at the alveolar level by examining the contour of the alveolar ridge (n = 7) or the height of the alveolar process (n = 5). Even fewer studies (n = 4) have performed qualitative analysis at the skeletal level by evaluating the influence of the vertical skeletal growth pattern on the incidence of ankylosed deciduous teeth. Conclusions To carry out a comprehensive evaluation of infraoccluded deciduous teeth, an assessment of the occlusal, alveolar and potentially skeletal levels is advisable. Radiographic investigations i.e. panoramic radiographs are therefore essential as a supplement to clinical examination. There is a need for standardization and objectification of the methods for the classification of infraoccluded deciduous teeth to give a general recommendation of clinical performance. Registration This systematic review has been registered in the international prospective register of systematic reviews (PROSPERO) under the registration number: CRD42024555842.

Abstract Purpose More accurate prediction of phenotype traits can increase the success of genomic selection in both plant and animal breeding studies and provide more reliable disease risk prediction in humans. Traditional approaches typically use regression models based on linear assumptions between the genetic markers and the traits of interest. Non-linear models have been considered as an alternative tool for modeling genomic interactions (i.e. non-additive effects) and other subtle non-linear patterns between markers and phenotype. Deep learning has become a state-of-the-art non-linear prediction method for sound, image and language data. However, genomic data is better represented in a tabular format. The existing literature on deep learning for tabular data proposes a wide range of novel architectures and reports successful results on various datasets. Tabular deep learning applications in genome-wide prediction (GWP) are still rare. In this work, we perform an overview of the main families of recent deep learning architectures for tabular data and apply them to multi-trait regression and multi-class classification for GWP on real gene datasets. Methods The study involves an extensive overview of recent deep learning architectures for tabular data learning: NODE, TabNet, TabR, TabTransformer, FT-Transformer, AutoInt, GANDALF, SAINT and LassoNet. These architectures are applied to multi-trait GWP. Comprehensive benchmarks of various tabular deep learning methods are conducted to identify best practices and determine their effectiveness compared to traditional methods. Results Extensive experimental results on several genomic datasets (three for multi-trait regression and two for multi-class classification) highlight LassoNet as a standout performer, surpassing both other tabular deep learning models and the highly efficient tree based LightGBM method in terms of both best prediction accuracy and computing efficiency. Conclusion Through series of evaluations on real-world genomic datasets, the study identifies LassoNet as a standout performer, surpassing decision tree methods like LightGBM and other tabular deep learning architectures in terms of both predictive accuracy and computing efficiency. Moreover, the inherent variable selection property of LassoNet provides a systematic way to find important genetic markers that contribute to phenotype expression.

Abstract β-TCP ceramics are versatile bone substitute materials and show many interactions with cells of the monocyte-macrophage-lineage. The possibility of monocytes entering microporous β-TCP ceramics has however not yet been researched. In this study, we used a model approach to investigate whether monocytes might enter β-TCP, providing a possible explanation for the origin of CD68-positive osteoclast-like giant cells found in earlier works. We used flow chambers to unidirectionally load BC, PRP, or PPP into slice models of either 2 mm or 6 mm β-TCP. Immunofluorescence for CD68 and live/dead staining was performed after the loading process. Our results show that monocytes were present in a relevant number of PRP and BC slices representing the inside of our 2 mm slice model and also present on the actual inside of our 6 mm model. For PPP, monocytes were not found beyond the surface in either model. Our results indicate the possibility of a new and so far neglected constituent in β-TCP degradation, perhaps causing the process of ceramic degradation also starting from inside the ceramics as opposed to the current understanding. We also demonstrated flow chambers as a possible new in vitro model for interactions between blood and β-TCP.

Abstract Fluorescence analysis of β-TCP ceramics is often used to describe cells found on said ceramics. However, we found, to our knowledge, so far undescribed artifacts which might sometimes be hard to differentiate from cells due to shape and fluorescence behavior. We tried prolonged ultrasound washing as well as Technovit 9100 fixation to reduce these artifacts. While untreated dowels showed no reduction in artifacts no matter the further treatment, Technovit fixation reduced the artifacts with even further reduction achieved by mechanical cleaning. As a consequence, scientists working with these dowels and likely even other types should try to avoid creating false positive results by considering the existence of these artifacts, checking additional filters for unusual fluorescence and by reducing them by using Technovit fixation when possible.

Abstract Background A national colorectal cancer (CRC) screening programme was launched in 2002 in Germany. A comprehensive evaluation of the programme effectiveness using real-world data is still lacking. In addition, there are regional reports on increasing colorectal cancer incidence in younger populations. Therefore, we aimed to describe and compare the overall, age- and stage-specific incidence trends for colorectal, colon and rectal cancer. Methods We used data from seven population-based cancer registries in Germany. We report absolute and relative changes in incidence rates between the early screening phase (2003–2005) and the most recent time period available (2015–2017), as well as annual percent changes. We analysed incidences according to tumour site (colorectum, colon, and rectum) and to six age groups (young adults: 15–34, 35–39, 40–49, screening-entitled/older adults: 50–54, 55–69 and 70 + years old). Results In our sample of 271,011 colorectal adenocarcinomas, about two-thirds were located in the colon and 95% of them occurred in the age group 50+ (50–54: 5%, 55–69: 32.8%, 70+: 57.2%). For the time period 2003–2005 the age-specific incidence rates of individuals in the age group 55–69 were about 76/100,00 for colon and 54/100,000 for rectal cancer (age group 70 + colon: 179/100,000; rectum: 84/100,000). The incidence rates in young adults were less than 13% of that of individuals in the age group 55–69 (

Abstract Background Children of families with a parent with a mental illness have an increased risk of developing social and mental health problems resulting in decreased quality of life. Therefore, children and adolescents living in families with a parent with mental illness are regarded as a target group for preventive interventions. To date, only a few economic evaluation studies for interventions directed at preventing the intergenerational transmission of mental health problems exist. In this investigation we estimated the cost utility of an intervention for the support of children and adolescents with a parent having a mental illness from the perspective of the German health and social care system. Methods We randomly assigned a total of 214 families with 337 children and adolescents to the intervention (INT) group (108/170) or the control (TAU) group (106/167). Families in the intervention group received on average eight intervention sessions (50–90 min) over 6 months. We estimated total cost of illness by means of the Children and Adolescent Mental Health Service Receipt Inventory (CAMHSRI) over 24 months. For the estimation of Quality-Adjusted Live Years (QALYs) we applied the KIDSCREEN-10. For estimating the incremental cost-utility of the intervention compared to treatment as usual we used the net-benefit approach. Results We estimated the annual cost of illness amounting to € 3784.59 (SD € 8581.11) in the TAU group and € 3264.44 (SD € 9431.89) in the INT group. The annual cost difference between INT and TAU was € − 516.14 (SE 1124.95) which was not significant (p ≤ 0.05). We estimated the average QALY to be 0.759 (SD 0.073) in the TAU group and 0.763 (SD 0.072). The QALY difference between INT and TAU was 0.0037 (SE 0.0092) which was not significant (p ≤ 0.05). The incremental cost utility ratio (ICUR) indicated that the gain of one additional year in full health by means of the intervention was associated with the saving of € 139.49. However, the stochastic insecurity of the ICUR did not allow a unique decision about the cost-utility of the intervention. Conclusions More information on the economic value of the intervention for families with a parent with mental illness in comparison to treatment as usual in Germany is needed. Trial registration: ClinicalTrials.gov, identifier NCT02308462; German Clinical Trials Register: DRKS00006806.

Abstract Background Perioperative hypothermia is a common occurrence, particularly with the elderly and pediatric age groups. Hypothermia is associated with an increased risk of perioperative complications. One method of preventing hypothermia is warming the infused fluids given during surgery. The enFlow™ intravenous fluid warmer has recently been reintroduced with a parylene coating on its heating blocks. In this paper, we evaluated the impact of the parylene coating on the new enFlow’s fluid warming capacity. Methods Six coated and six uncoated enFlow cartridges were used. A solution of 10% propylene glycol and 90% distilled H2O was infused into each heating cartridge at flow rates of 2, 10, 50, 150, and 200 ml/min. The infused fluid temperature was set at 4 °C, 20 °C, and 37 °C. Output temperature was recorded at each level. Data for analysis was derived from 18 runs at each flow rate (six cartridges at three temperatures). Results The parylene coated fluid warming cartridge delivered very stable output of 40 °C temperatures at flow rates of 2, 10, and 50 ml/min regardless of the temperature of the infusate. At higher flow rates, the cartridges were not able to achieve the target temperature with the colder fluid. Both cartridges performed with similar efficacy across all flow rates at all temperatures. Conclusions At low flow rates, the parylene coated enFlow cartridges was comparable to the original uncoated cartridges. At higher flow rates, the coated and uncoated cartridges were not able to achieve the target temperature. The parylene coating on the aluminum heating blocks of the new enFlow intravenous fluid warmer does not negatively affect its performance compared to the uncoated model.

Abstract Background The genetic basis of phenotypic traits is highly variable and usually divided into mono-, oligo- and polygenic inheritance classes. Relatively few traits are known to be monogenic or oligogeneic. The majority of traits are considered to have a polygenic background. To what extent there are mixtures between these classes is unknown. The rapid advancement of genomic techniques makes it possible to directly map large amounts of genomic markers (GWAS) and predict unknown phenotypes (GWP). Most of the multi-marker methods for GWAS and GWP falls into one of two regularization frameworks. The first framework is based on $$\ell _1$$ ℓ 1 -norm regularization (e.g. the LASSO) and is suitable for mono- and oligogenic traits, whereas the second framework regularize with the $$\ell _2$$ ℓ 2 -norm (e.g. ridge regression; RR) and thereby is favourable for polygenic traits. A general framework for mixed inheritance is lacking. Results We have developed a proximal operator algorithm based on the recent LAVA regularization method that jointly performs $$\ell _1$$ ℓ 1 - and $$\ell _2$$ ℓ 2 -norm regularization. The algorithm is built on the alternating direction method of multipliers and proximal translation mapping (LAVA ADMM). When evaluated on the simulated QTLMAS2010 data, it is shown that the LAVA ADMM together with Bayesian optimization of the regularization parameters provides an efficient approach with lower test prediction mean-squared-error (65.89) than the LASSO (66.11), Ridge regression (83.41) and Elastic net (66.11). For the real pig data the test MSE of the LAVA ADMM is 0.850 compared to the LASSO, RR and EN with 0.875, 0.853 and 0.853, respectively. Conclusions This study presents the LAVA ADMM that is capable of joint modelling of monogenic major genetic effects and polygenic minor genetic effects which can be used for both genome-wide assoiciation and prediction purposes. The statistical evaluations based on both simulated and real pig data set shows that the LAVA ADMM has better prediction properies than the LASSO, RR and EN. Julia code for the LAVA ADMM is available at: https://github.com/patwa67/LAVAADMM .

Abstract Background Human T cell Leukemia virus type 1 (HTLV-I) is etiologically linked to adult T cell leukemia/lymphoma (ATL) and an inflammatory neurodegenerative disease called HTLV-I-associated myelopathy or tropical spastic paraparesis (HAM/TSP). The exact genetic or epigenetic events and/or environmental factors that influence the development of ATL, or HAM/TSP diseases are largely unknown. The tumor suppressor gene, Fragile Histidine Triad Diadenosine Triphosphatase (FHIT), is frequently lost in cancer through epigenetic modifications and/or deletion. FHIT is a tumor suppressor acting as genome caretaker by regulating cellular DNA repair. Indeed, FHIT loss leads to replicative stress and accumulation of double DNA strand breaks. Therefore, loss of FHIT expression plays a key role in cellular transformation. Methods Here, we studied over 400 samples from HTLV-I-infected individuals with ATL, TSP/HAM, or asymptomatic carriers (AC) for FHIT loss and expression. We examined the epigenetic status of FHIT through methylation specific PCR and bisulfite sequencing; and correlated these results to FHIT expression in patient samples. Results We found that epigenetic alteration of FHIT is specifically found in chronic and acute ATL but is absent in asymptomatic HTLV-I carriers and TSP/HAM patients’ samples. Furthermore, the extent of FHIT methylation in ATL patients was quantitatively comparable in virus-infected and virus non-infected cells. We also found that longitudinal HTLV-I carriers that progressed to smoldering ATL and descendants of ATL patients harbor FHIT methylation. Conclusions These results suggest that germinal epigenetic mutation of FHIT represents a preexisting mark predisposing to the development of ATL diseases. These findings have important clinical implications as patients with acute ATL are rarely cured. Our study suggests an alternative strategy to the current “wait and see approach” in that early screening of HTLV-I-infected individuals for germinal epimutation of FHIT and early treatment may offer significant clinical benefits.

Abstract Background The Family Reported Outcome Measure (FROM-16) assesses the impact of a patient’s chronic illness on the quality of life (QoL) of the patient’s partner or family members. The aim of the study was to translate, explore the structure of and validate the FROM-16. Methods The questionnaire was translated from English into German (forward, backward, four independent translators). Six interviews with family members were conducted to confirm the questionnaire for linguistic, conceptual, semantic and experiential equivalence and its practicability. The final German translation was tested for internal consistency, reproducibility and test validity. Criterion validity was tested by correlating the scores of the FROM-16 and the Global Health Scale (GHS). Principal component analysis, factor analysis, and confirmatory factor analysis was used to assess the questionnaire’s structure and its domains. Reliability and reproducibility were tested computing the intraclass correlation coefficient (ICC) using one sample t-test for testing the hypothesis that the difference between the scores was not different from zero. Results Overall, 83 family members (61% female, median age: 61 years) completed the questionnaire at two different times (mean interval: 22 days). Internal consistency was good for the FROM-16 scores (Cronbach’s α for total score = 0.86). In those with stable GHS, the ICC for the total score was 0.87 and the difference was not different from zero (p = 0.262) indicating reproducible results. A bi-factor model with a general factor including all items, and two sub-factors comprising the items from the original 2-factor construct had the best fit. Conclusions The German FROM-16 has good reliability, test validity and practicability. It can be considered as an appropriate and generic tool to measure QoL of a patient’s partner or family member. Due to the presence of several cross-loadings we do not recommend the reporting of the scores of the two domains proposed for the original version of FROM-16 when using the German version. Thus, in reporting the results emphasis should be put on the total score. Trial registration: Retrospectively registered: DRKS00021070.

Abstract Background Children of parents with mental illness have a higher risk of developing mental health problems when compared with the general population. Therefore, families with parents with mental illness are a suitable target group for selective prevention. In order to plan and evaluate the health economic consequences of preventive interventions for this target group, data on the societal costs related to parenthood under the condition of mental disorders are needed. To date, within Germany there has been a lack of research evaluating the costs of mental health treatment and use of social services by children and adolescents with parents with mental illness. Methods As part of a multicentre randomised controlled trial, use and costs of health and social services were assessed for a sample of 332 children and adolescents with parents with mental illness in six regions of Germany. Service use at baseline was assessed by the German version of the Children and Adolescent Mental Health Service Receipt Inventory. Costs were calculated for 12 months based on diagnosis and service user status and described separately. Cost drivers were identified by means of a two-part regression model. Results Total mean costs for 12 months for the total sample amount of € 3736.35 (95% CI: € 2816.84–4813.83) per person. Children with a psychiatric diagnosis generated a total of € 5691.93 (95% CI: € 4146.27–7451.38) of costs per person, compared to € 1245.01 (95% CI: € 657.44–1871.49) for children without a psychiatric diagnosis. The logit part indicates significant odds ratios for individual functioning and diagnosis of the child as well as for family functioning. The linear part reveals that increasing individual functioning in the child is related to decreasing costs. Conclusions Children of families with parents with mental illness use a broad spectrum of mental health care, school-based support and youth welfare services even if they are not yet diagnosed as having a mental disorder. Further research should examine whether these institutions are sufficiently qualified and interlinked to meet the support needs of this vulnerable group. Trial registration The study was registered at the 07/10/2014 before the start of data collection (04/11/2014) at the German clinical trials register (Deutsches Register Klinischer Studien, DRKS, nr: DRKS00006806, https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00006806 ).

Abstract Serotyping is the most common method to characterize field isolates of Actinobacillus (A.) pleuropneumoniae, the etiological agent of porcine pleuropneumonia. Based on serology, many farms seem to be infected and antibodies against a wide variety of serovars are detectable, but, so far it is unknown to what degree respective serovars contribute to outbreaks of clinical manifest disease. In this study, 213 German A. pleuropneumoniae field isolates retrieved for diagnostic purposes from outbreaks of porcine pleuropneumonia between 2010 and 2019 were genetically serotyped and analyzed regarding their apx-toxin gene profile using molecular methods. Serotyping revealed a prominent role of serovar 2 in clinical cases (64% of all isolates) and an increase in the detection of this serovar since 2010 in German isolates. Serovar 9/11 followed as the second most frequent serovar with about 15% of the isolates. Furthermore, very recently described serovars 16 (n = 2) and 18 (n = 8) were detected. Most isolates (93.4%) showed apx-profiles typical for the respective serovar. However, this does not hold true for isolates of serovar 18, as 75% (n = 6) of all isolates of this serovar deviated uniformly from the “typical” apx-gene profile of the reference strain 7311555. Notably, isolates from systemic lesions such as joints or meninges did not harbor the complete apxICABD operon which is considered typical for highly virulent strains. Furthermore, the extremely low occurrence (n = 1) of NAD independent (biovar II) isolates in German A. pleuropneumoniae was evident in our collection of clinical isolates.

Abstract Background On farms, the currently approved and most widely practised method of euthanising non-viable piglets is blunt force trauma to the head followed by exsanguination. However, the use of this method is criticised due to public perceptions and aversion to the methodology by caretakers. Therefore, electrocution after electrical stunning was examined as an alternative approach in 80 hybrid piglets. Initially, electrocution was simulated with finite element analysis using a computer piglet-model, where current density in the heart was visualised and size and position of the electrodes were defined. The following step investigated electrical parameters for electrocution in anaesthetised piglets; first, with a constant voltage power source and then with a constant current power source. The electrical stunning was examined using the constant current supply. Finally, the results of electrical stunning and electrocution were verified in 25 healthy piglets with a body weight between 1 and 2 kg. Unconsciousness was proven by testing palpebral, corneal and nociceptive reflexes. Time of death was confirmed by electroencephalography (EEG) and electrocardiography (ECG) records. Results Stunning succeeded with the preset of 1.3 A and 50 Hz, placing the electrodes on both sides of the head between the eyes and ears using different timespans between 8 and 20 s. Prolonged electrical flow resulted in reduced paddling movements after the epileptic seizure, and allowed undisturbed reflex tests and installation of electrodes for EEG and ECG recording during electrocution. Using 0.75 A and 400 Hz, pin-shaped electrodes were first positioned on both sides of the chest for 5 s, followed by a break of 20–30 s and a second current flow, whereby the electrodes were placed above the withers and the sternum for 5 s. Cardiac arrest and an isoelectric EEG were induced within 3 min after the onset of the electrical flow through the chest. The most obvious indicator of effective stunning and electrocution was termination of rhythmic breathing. Piglets with cardiac arrest showed only single gasps lasting up to 3 min after electrocution. Conclusions The evaluated stunning and electrocution protocol might ease concerns about timely piglet euthanasia. However, this should be verified in non-viable piglets to exclude influencing factors like dehydration and diseases.

Abstract Background More than half of the unaccompanied young refugees (UYRs) resettled in Europe report elevated levels of posttraumatic stress symptoms (PTSS) and comorbid symptoms. Earlier studies have highlighted the effectiveness of the trauma-focused preventive group intervention “Mein Weg” (English “My Way”), and the feasibility of trauma-focused cognitive behavioral therapy (TF-CBT) for UYRs. Both interventions are deemed to be empirically supported treatments (ESTs). However, UYRs seldom receive ESTs or, in fact, any treatment at all. In view of the high need and the limited treatment resources available, a stepped-care approach is indicated but has not been evaluated so far. The purpose of this trial is to compare the stepped-care approach BETTER CARE with usual care enhanced with screening and indication (usual care+). Methods In a cluster randomized controlled trial involving N = 540 UYRs living in up to N = 54 child and youth welfare service (CYWS) facilities, BETTER CARE will be compared with usual care+. We will randomize clusters comprising a CYWS facility with at least one eligible psychotherapist. BETTER CARE consists of step (1) screening and indication and either step (2) preventive trauma-focused group intervention “Mein Weg” delivered by trained CYWS staff or step (3) TF-CBT delivered by trained community therapists and supported by trained translators if necessary. Participants will be assessed 6 and 12 months after randomization. The primary outcome is the severity of PTSS after 12 months. Secondary outcomes are depressive and anxiety symptoms, quality of life, and proxy reported PTSS. Furthermore, drug use, health costs, benefits, and long-term effects on integration/acculturation will be assessed. Discussion The trial will directly integrate a stepped-care approach into existing structures of the German child welfare and (mental) health system. It could, therefore, serve as a blueprint for how to implement ESTs for UYRs. If successful, screening, prevention, and intervention will be sustainably implemented in CYWS in southern Germany. Trial registration German Clinical Trials Register DRKS00017453 . Registered on 11 December 2019.

Abstract Glaesserella parasuis is an important pathogen in swine production. It acts as a primary pathogen in systemic Glässer´s disease and as a secondary pathogen in Porcine Respiratory Disease Complex. In this study, a collection of 308 isolates from carrier animals and individuals with respiratory or Glässer´s disease isolated 2012–2019 in Germany was analysed. Isolates were characterized for serovar implementing two different PCR methods. Additionally, two different PCR methods for pathotyping isolates were applied to the collection and results compared. Serovar 6 (p

Abstract Background Oestrous synchronisation of cattle has been widely applied to accomplish simultaneous ovulation in animals and facilitate timed artificial insemination. The main aim of this study was to investigate the ovarian follicular growth and ovulatory response to oestrus and ovulation synchronisation in Norwegian Red heifers and cows. Oestrous cycles in 34 heifers and 10 cows from 4 herds were synchronised with two PGF2α analogue treatments 11 days apart, followed by GnRH analogue treatment for induction of ovulation. Thereafter, the ovaries were examined by ultrasonography at 3 h intervals until ovulation. Results The luteolytic effect of the PGF2α analogue was verified in 9 of 10 cows by progesterone contents in milk. Maximum physical activity of the cows occurred on average 69 h after PGF2α analogue treatment. An ovulatory response was recorded in 95.5% (42/44) of the animals. A significant difference in follicle size at ovulation was found between 2 of the herds. Animals with medium sized and large follicles and heifers aged > 16 months ovulated earlier than other animals. Conclusions The applied sequence of treatments in the study was shown to be effective in synchronizing and inducing ovulation within a relatively narrow time interval in the Norwegian Red heifers and cows, consistent with findings in other cattle breeds.

Abstract Background Genome-wide prediction has become the method of choice in animal and plant breeding. Prediction of breeding values and phenotypes are routinely performed using large genomic data sets with number of markers on the order of several thousands to millions. The number of evaluated individuals is usually smaller which results in problems where model sparsity is of major concern. The LASSO technique has proven to be very well-suited for sparse problems often providing excellent prediction accuracy. Several computationally efficient LASSO algorithms have been developed, but optimization of hyper-parameters can be demanding. Results We have developed a novel automatic adaptive LASSO (AUTALASSO) based on the alternating direction method of multipliers (ADMM) optimization algorithm. The two major hyper-parameters of ADMM are the learning rate and the regularization factor. The learning rate is automatically tuned with line search and the regularization factor optimized using Golden section search. Results show that AUTALASSO provides superior prediction accuracy when evaluated on simulated and real bull data compared to the adaptive LASSO, LASSO and ridge regression implemented in the popular glmnet software. Conclusions The AUTALASSO provides a very flexible and computationally efficient approach to GWP, especially when it is important to obtain high prediction accuracy and genetic gain. The AUTALASSO also has the capability to perform GWAS of both additive and dominance effects with smaller prediction error than the ordinary LASSO.

Abstract Background The pressure-volume (P-V) curve has been suggested as a bedside tool to set mechanical ventilation; however, it reflects a global behavior of the lung without giving information on the regional mechanical properties. Regional P-V (PVr) curves derived from electrical impedance tomography (EIT) could provide valuable clinical information at bedside, being able to explore the regional mechanics of the lung. In the present study, we hypothesized that regional P-V curves would provide different information from those obtained from global P-V curves, both in terms of upper and lower inflection points. Therefore, we constructed pressure-volume curves for each pixel row from non-dependent to dependent lung regions of patients affected by acute hypoxemic respiratory failure (AHRF) and acute respiratory distress syndrome (ARDS). Methods We analyzed slow-inflation P-V maneuvers data from 12 mechanically ventilated patients. During the inflation, the pneumotachograph was used to record flow and airway pressure while the EIT signals were recorded digitally. From each maneuver, global respiratory system P-V curve (PVg) and PVr curves were obtained, each one corresponding to a pixel row within the EIT image. PVg and PVr curves were fitted using a sigmoidal equation, and the upper (UIP) and lower (LIP) inflection points for each curve were mathematically identified; LIP and UIP from PVg were respectively called LIPg and UIPg. From each measurement, the highest regional LIP (LIPrMAX) and the lowest regional UIP (UIPrMIN) were identified and the pressure difference between those two points was defined as linear driving pressure (ΔP LIN). Results A significant difference (p

Abstract Background Genome-wide marker data are used both in phenotypic genome-wide association studies (GWAS) and genome-wide prediction (GWP). Typically, such studies include high-dimensional data with thousands to millions of single nucleotide polymorphisms (SNPs) recorded in hundreds to a few thousands individuals. Different machine-learning approaches have been used in GWAS and GWP effectively, but the use of neural networks (NN) and deep-learning is still scarce. This study presents a NN model for genomic SNP data. Results We show, using both simulated and real pig data, that regularization is obtained using weight decay and dropout, and results in an approximate Bayesian (ABNN) model that can be used to obtain model averaged posterior predictions. The ABNN model is implemented in mxnet and shown to yield better prediction accuracy than genomic best linear unbiased prediction and Bayesian LASSO. The mean squared error was reduced by at least 6.5% in the simulated data and by at least 1% in the real data. Moreover, by comparing NN of different complexities, our results confirm that a shallow model with one layer, one neuron, one-hot encoding and a linear activation function performs better than more complex models. Conclusions The ABNN model provides a computationally efficient approach with good prediction performance and in which the weight components can also provide information on the importance of the SNPs. Hence, ABNN is suitable for both GWP and GWAS.

Abstract Background Electrical impedance tomography (EIT) has been used to guide mechanical ventilation in ICU patients with lung collapse. Its use in patients with obstructive pulmonary diseases has been rare since obstructions could not be monitored on a regional level at the bedside. The current study therefore determines breath-by-breath regional expiratory time constants in intubated patients with chronic obstructive pulmonary disease (COPD) and acute respiratory distress syndrome (ARDS). Methods Expiratory time constants calculated from the global impedance EIT signal were compared to the pneumatic volume signals measured with an electronic pneumotachograph. EIT-derived expiratory time constants were additionally determined on a regional and pixelwise level. However, regional EIT signals on a single pixel level could in principle not be compared with similar pneumatic changes since these measurements cannot be obtained in patients. For this study, EIT measurements were conducted in 14 intubated patients (mean Simplified Acute Physiology Score II (SAPS II) 35 ± 10, mean time on invasive mechanical ventilation 36 ± 26 days) under four different positive end-expiratory pressure (PEEP) levels ranging from 10 to 17 cmH2O. Only patients with moderate-severe ARDS or COPD exacerbation were included into the study, preferentally within the first days following intubation. Results Spearman’s correlation coefficient for comparison between EIT-derived time constants and those from flow/volume curves was between 0.78 for tau (τ) calculated from the global impedance signal up to 0.83 for the mean of all pixelwise calculated regional impedance changes over the entire PEEP range. Furthermore, Bland-Altman analysis revealed a corresponding bias of 0.02 and 0.14 s within the limits of agreement ranging from − 0.50 to 0.65 s for the aforementioned calculation methods. In addition, exemplarily in patients with moderate-severe ARDS or COPD exacerbation, different PEEP levels were shown to have an influence on the distribution pattern of regional time constants. Conclusions EIT-based determination of breath-by-breath regional expiratory time constants is technically feasible, reliable and valid in invasively ventilated patients with severe respiratory failure and provides a promising tool to individually adjust mechanical ventilation in response to the patterns of regional airflow obstruction. Trial registration German Trial Register DRKS 00011650, registered 01/31/17.

Abstract Background Physical exercise and nutritional treatment are promising measures to prevent muscle wasting that is frequently observed in advanced-stage cancer patients. However, conventional exercise is not always suitable for these patients due to physical weakness and therapeutic side effects. In this pilot study, we examined the effect of a combined approach of the novel training method whole-body electromyostimulation (WB-EMS) and individualized nutritional support on body composition with primary focus on skeletal muscle mass in advanced cancer patients under oncological treatment. Methods In a non-randomized controlled trial design patients (56.5% male; 59.9 ± 12.7 years) with advanced solid tumors (UICC III/IV, N = 131) undergoing anti-cancer therapy were allocated to a usual care control group (n = 35) receiving individualized nutritional support or to an intervention group (n = 96) that additionally performed a supervised physical exercise program in form of 20 min WB-EMS sessions (bipolar, 85 Hz) 2×/week for 12 weeks. The primary outcome of skeletal muscle mass and secondary outcomes of body composition, body weight and hand grip strength were measured at baseline, in weeks 4, 8 and 12 by bioelectrical impedance analysis and hand dynamometer. Effects of WB-EMS were estimated by linear mixed models. Secondary outcomes of physical function, hematological and blood chemistry parameters, quality of life and fatigue were assessed at baseline and week 12. Changes were analyzed by t-tests, Wilcoxon signed-rank or Mann-Whitney-U-tests. Results Twenty-four patients of the control and 58 of the WB-EMS group completed the 12-week trial. Patients of the WB-EMS group had a significantly higher skeletal muscle mass (0.53 kg [0.08, 0.98]; p = 0.022) and body weight (1.02 kg [0.05, 1.98]; p = 0.039) compared to controls at the end of intervention. WB-EMS also significantly improved physical function and performance status (p

Abstract Background Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in “SweepFinder”, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F ST , to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. Results Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. Conclusion The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.

Abstract Background We have previously reported an antigen-specific protocol to induce transplant tolerance and linked suppression to human embryonic stem cell (hESC)-derived tissues in immunocompetent mice through coreceptor and costimulation blockade. However, the exact mechanisms of acquired immune tolerance in this model have remained unclear. Methods We utilize the NOD.Foxp3 hCD2 reporter mouse line and an ablative anti-hCD2 antibody to ask if CD4+FOXP3+ regulatory T cells (Treg) are required for coreceptor and costimulation blockade-induced immune tolerance. We also perform genome-wide single-cell RNA-sequencing to interrogate Treg during immune rejection and tolerance and to indicate possible mechanisms involved in sustaining Treg function. Results We show that Treg are indispensable for tolerance induced by coreceptor and costimulation blockade as depletion of which with an anti-hCD2 antibody resulted in rejection of hESC-derived pancreatic islets in NOD.Foxp3 hCD2 mice. Single-cell transcriptomic profiling of 12,964 intragraft CD4+ T cells derived from rejecting and tolerated grafts reveals that Treg are heterogeneous and functionally distinct in the two outcomes of transplant rejection and tolerance. Treg appear to mainly promote chemotactic and ubiquitin-dependent protein catabolism during transplant rejection while seeming to harness proliferative and immunosuppressive function during tolerance. We also demonstrate that this form of acquired transplant tolerance is associated with increased proliferation and PD-1 expression by Treg. Blocking PD-1 signaling with a neutralizing anti-PD-1 antibody leads to reduced Treg proliferation and graft rejection. Conclusions Our results suggest that short-term coreceptor and costimulation blockade mediates immune tolerance to hESC-derived pancreatic islets by promoting Treg proliferation through engagement of PD-1. Our findings could give new insights into clinical development of hESC-derived pancreatic tissues, combined with immunotherapies that expand intragraft Treg, as a potentially sustainable alternative treatment for T1D.

Abstract Actinobacillus (A.) pleuropneumoniae is normally considered strictly adapted to the respiratory tract of swine. Despite this, scattered case reports of arthritis, osteomyelitis, hepatitis, meningitis or nephritis exist, in which A. pleuropneumoniae remained the only detectable pathogen. Therefore, the aim of this study was to investigate whether spreading to other organs than the lungs is incidental or may occur more frequently. For this, organ samples (blood, liver, spleen, kidney, tarsal and carpal joints, meninges, pleural and pericardial fluids) from weaners (n = 47) infected experimentally with A. pleuropneumoniae serovar 7 by aerosol infection (infection dose: 10.9 × 103 cfu/animal) were examined by culture during the first week after infection. In addition, tissue samples of eight weaners were examined by histology and immunohistochemistry (IHC). A. pleuropneumoniae was isolated in all examined sample sites (86.7% pleural fluids, 73.3% pericardial fluids, 50.0% blood, 61.7% liver, 51.1% spleen, 55.3% kidney, 14.9% tarsal joints, 12.8% carpal joints, 27.7% meninges). These results were also obtained from animals with only mild clinical symptoms. IHC detection confirmed these findings in all locations except carpal joints. Histological examination revealed purulent hepatitis (n = 2), nephritis (n = 1) and beginning meningitis (n = 2). Isolation results were significantly correlated (p

Abstract Background Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. Methods ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. Results In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. Conclusions Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps.

Abstract Background Porcine pleuropneumonia, caused by Actinobacillus pleuropneumoniae, is a bacterial respiratory disease of swine. Acute outbreaks of the disease are often accompanied by high mortality and economic losses. As severe cases of the disease frequently require parenteral antibiotic treatment of the animals, the efficacy of a single, high dose of marbofloxacin was compared to a three-time application of a dose of enrofloxacin under experimental conditions. Methods A blinded, controlled, randomized and blocked dose confirmation study was conducted to test the efficacy and safety of a single dose of 8 mg/kg marbofloxacin (160 mg/ml, Forcyl® Swine, Vetoquinol SA, France) to treat acute porcine pleuropneumonia after experimental aerosol inoculation of pigs with A. pleuropneumoniae serotype 2. The results were compared to a three consecutive day treatment of 2.5 mg/kg enrofloxacin and a mock (saline) treatment. Criteria for the assessment of efficacy were severity of lung lesions, bacteriological cure and the course of clinical disease after treatment. Results: Thirty six nursery pigs were divided into three treatment groups: marbofloxacin (T1), enrofloxacin (T2) and mock (T3). Statistically significant superiority (p

Abstract Background Assessing alveolar recruitment at different positive end-expiratory pressure (PEEP) levels is a major clinical and research interest because protective ventilation implies opening the lung without inducing overdistention. The pressure-volume (P-V) curve is a validated method of assessing recruitment but reflects global characteristics, and changes at the regional level may remain undetected. The aim of the present study was to compare, in intubated patients with acute hypoxemic respiratory failure (AHRF) and acute respiratory distress syndrome (ARDS), lung recruitment measured by P-V curve analysis, with dynamic changes in poorly ventilated units of the dorsal lung (dependent silent spaces [DSSs]) assessed by electrical impedance tomography (EIT). We hypothesized that DSSs might represent a dynamic bedside measure of recruitment. Methods We carried out a prospective interventional study of 14 patients with AHRF and ARDS admitted to the intensive care unit undergoing mechanical ventilation. Each patient underwent an incremental/decremental PEEP trial that included five consecutive phases: PEEP 5 and 10 cmH2O, recruitment maneuver + PEEP 15 cmH2O, then PEEP 10 and 5 cmH2O again. We measured, at the end of each phase, recruitment from previous PEEP using the P-V curve method, and changes in DSS were continuously monitored by EIT. Results PEEP changes induced alveolar recruitment as assessed by the P-V curve method and changes in the amount of DSS (p

Abstract Background Postoperative pulmonary complications are a leading cause of morbidity and mortality after cardiac surgery. There are no recommendations on mechanical ventilation associated with cardiopulmonary bypass (CPB) during surgery and anesthesiologists perform either no ventilation (noV) at all during CPB or maintain low tidal volume (LTV) ventilation. Indirect evidence points towards better pulmonary outcomes when LTV is performed but no large-scale prospective trial has yet been published in cardiac surgery. Design The MECANO trial is a single-center, double-blind, randomized, controlled trial comparing two mechanical ventilation strategies, noV and LTV, during cardiac surgery with CPB. In total, 1500 patients are expected to be included, without any restrictions. They will be randomized between noV and LTV on a 1:1 ratio. The noV group will receive no ventilation during CPB. The LTV group will receive 5 breaths/minute with a tidal volume of 3 mL/kg and positive end-expiratory pressure of 5 cmH2O. The primary endpoint will be a composite of all-cause mortality, early respiratory failure defined as a ratio of partial pressure of oxygen/fraction of inspired oxygen

Abstract Background Urological diseases and their treatment may negatively influence continence, potency, and health-related quality of life (HRQOL). Although current guidelines recommend HRQOL assessment in clinical urology, specific guidance on how to assess HRQOL is frequently absent. We evaluated whether and how urologists assess HRQOL and how they determine its practicality. Methods A random sample of 4500 (from 5200 identified German urologists) was drawn and invited to participate in a postal survey (an initial letter followed by one reminder after six weeks). The questionnaire included questions on whether and how HRQOL is assessed, general attitudes towards the concept of HRQOL, and socio-demographics. Due to the exploratory character of the study we produced mainly descriptive statistics. Chi2-tests and logistic regression were used for subgroup-analysis. Results 1557 urologists (85% male, with a mean age of 49 yrs.) participated. Most of them (87%) considered HRQOL assessment as ‘important’ in daily work, while only 7% reported not assessing HRQOL. Patients with prostate carcinoma, incontinence, pain, and benign prostate hyperplasia were the main target groups for HRQOL assessment. The primary aim of HRQOL assessment was to support treatment decisions, monitor patients, and produce a ‘baseline measurement’. Two-thirds of urologists used questionnaires and interviews to evaluate HRQOL and one-quarter assessed HRQOL by asking: ‘How are you?’. The main barriers to HRQOL assessment were anticipated questionnaire costs (77%), extensive questionnaire length (52%), and complex analysis (51%). Conclusions The majority of German urologists assess HRQOL as part of their clinical routine. However, knowledge of HRQOL assessment, analysis, and interpretation seems to be limited in this group. Therefore, urologists may benefit from a targeted education program. Trial registration The clinical trial was registered with the code VfD_13_003629 at the German Healthcare Research Registry ( www.versorgungsforschung-deutschland.de ).

Abstract Background Shiga toxin (Stx) producing Escherichia coli (E. coli) (STEC) is the most frequent cause of diarrhoea-positive haemolytic uraemic syndrome (D + HUS) in humans. In 2011, a huge outbreak with an STEC O104:H4 strain in Germany highlighted the limited possibilities for causative treatment of this syndrome. The responsible STEC strain was found to combine Stx production with adherence mechanisms normally found in enteroaggregative E. coli (EAEC). Pathotypes of E. coli evolve and can exhibit different adhesion mechanisms. It has been shown previously that neonatal gnotobiotic piglets are susceptible for infection with STEC, such as STEC O157:H7 as well as for EAEC, which are considered to be the phylogenetic origin of E. coli O104:H4. This study was designed to characterise the host response to infection with the STEC O104:H4 outbreak strain in comparison to an STEC O157:H7 isolate by evaluating clinical parameters (scoring) and markers of organ dysfunction (biochemistry), as well as immunological (flow cytometry, assessment of cytokines/chemokines and acute phase proteins) and histological alterations (light- and electron microscopy) in a gnotobiotic piglet model of haemolytic uraemic syndrome. Results We observed severe clinical symptoms, such as diarrhoea, dehydration and neurological disorders as well as attaching-and-effacing lesions (A/E) in the colon in STEC O157:H7 infected piglets. In contrast, STEC O104:H4 challenged animals exhibited only mild clinical symptoms including diarrhoea and dehydration and HUS-specific/severe histopathological, haematological and biochemical alterations were only inconsistently presented by individual piglets. A specific adherence phenotype of STEC O104:H4 could not be observed. Flow cytometric analyses of lymphocytes derived from infected animals revealed an increase of natural killer cells (NK cells) during the course of infection revealing a potential role of this subset in the anti-bacterial activity in STEC disease. Conclusions Unexpectedly, E. coli O104:H4 infection caused only mild symptoms and minor changes in histology and blood parameters in piglets. Outcome of the infection trial does not reflect E. coli O104:H4 associated human disease as observed during the outbreak in 2011. The potential role of cells of the innate immune system for STEC related disease pathogenesis should be further elucidated.

Abstract Background Different measures of non-adherence to immunosuppressant (IS) medication have been found to be associated with rejection episodes after successful transplantation. The aim of the current study was to investigate whether graft rejection after renal transplantation is associated with patient-reported IS medication non-adherence and IS trough level variables (IS trough level variability and percentage of sub-therapeutic IS trough levels). Methods Patient-reported non-adherence, IS trough level variability, percentage of sub-therapeutic IS trough levels, and acute biopsy-proven late allograft rejections were assessed in 267 adult renal transplant recipients who were ≥12 months post-transplantation. Results The rate of rejection was 13.5%. IS trough level variability, percentage of sub-therapeutic IS trough levels as well as patient-reported non-adherence were all significantly and positively associated with rejection, but not with each other. Logistic regression analyses revealed that only the percentage of sub-therapeutic IS trough levels and age at transplantation remained significantly associated with rejection. Conclusions Particularly, the percentage of sub-therapeutic IS trough levels is associated with acute rejections after kidney transplantation whereas IS trough level variability and patient-reported non-adherence seem to be of subordinate importance. Patient-reported non-adherence and IS trough level variables were not correlated; thus, non-adherence should always be measured in a multi-methodological approach. Further research concerning the best combination of non-adherence measures is needed.

Abstract Background The aim of the study was to test the effect of two treatments in cases of acute puerperal metritis (APM) and clinical metritis (CM). Methods Cows with APM and CM (n = 40)) were matched according to plasma fibrinogen levels (Fb) into three groups. Two negative control groups D (n = 11) and E (n = 17) were composed of healthy cows. The proportion of animals with APM and CM was similar within the groups. Treatment was started on the 3rd day postpartum (PP). In group A (n = 15), intramuscular (i.m.) administration of ceftiofur was used for five days in combination with flunixin for three days. Group B (n = 15) received i.m. administration of ceftiofur for five days followed by two injections of prostaglandin F2α, with an interval of 8 h, on the 8th day PP. Group C (n = 10) served as a control group with no treatment. The general health status, body temperature (BT) and vaginal discharge were evaluated daily. Endometrial biopsies for bacteriology were taken once a week for seven weeks PP. Blood samples for the analysis of acute phase proteins were collected once a week for six weeks PP. Samples for progesterone analysis were taken twice a week for seven weeks PP. Fertility performance data were recorded. Results The area under the curve of BT was higher in group B than in group D cows (P Conclusions Regardless of more severe uterine inflammation found in animals from group B, these cows showed the same fertility parameters as healthy animals.

Abstract Background In pigs, diseases of the respiratory tract like pleuropneumonia due to Actinobacillus pleuropneumoniae (App) infection have led to high economic losses for decades. Further research on disease pathogenesis, pathogen-host-interactions and new prophylactic and therapeutic approaches are needed. In most studies, a large number of experimental animals are required to assess lung alterations at different stages of the disease. In order to reduce the required number of animals but nevertheless gather information on the nature and extent of lung alterations in living pigs, a computed tomographic scoring system for quantifying gross pathological findings was developed. In this study, five healthy pigs served as control animals while 24 pigs were infected with App, the causative agent of pleuropneumonia in pigs, in an established model for respiratory tract disease. Results Computed tomographic (CT) findings during the course of App challenge were verified by radiological imaging, clinical, serological, gross pathology and histological examinations. Findings from clinical examinations and both CT and radiological imaging, were recorded on day 7 and day 21 after challenge. Clinical signs after experimental App challenge were indicative of acute to chronic disease. Lung CT findings of infected pigs comprised ground-glass opacities and consolidation. On day 7 and 21 the clinical scores significantly correlated with the scores of both imaging techniques. At day 21, significant correlations were found between clinical scores, CT scores and lung lesion scores. In 19 out of 22 challenged pigs the determined disease grades (not affected, slightly affected, moderately affected, severely affected) from CT and gross pathological examination were in accordance. Disease classification by radiography and gross pathology agreed in 11 out of 24 pigs. Conclusions High-resolution, high-contrast CT examination with no overlapping of organs is superior to radiography in the assessment of pneumonic lung lesions after App challenge. The new CT scoring system allows for quantification of gross pathological lung alterations in living pigs. However, computed tomographic findings are not informative of the etiology of respiratory disease.

Abstract Background Missing data on tumour stage information is a common problem in population-based cancer registries. Statistical analyses on the level of tumour stage may be biased, if no adequate method for handling of missing data is applied. In order to determine a useful way to treat missing data on tumour stage, we examined different imputation models for multiple imputation with chained equations for analysing the stage-specific numbers of cases of malignant melanoma and female breast cancer. Methods This analysis was based on the malignant melanoma data set and the female breast cancer data set of the cancer registry Schleswig-Holstein, Germany. The cases with complete tumour stage information were extracted and their stage information partly removed according to a MAR missingness-pattern, resulting in five simulated data sets for each cancer entity. The missing tumour stage values were then treated with multiple imputation with chained equations, using polytomous regression, predictive mean matching, random forests and proportional sampling as imputation models. The estimated tumour stages, stage-specific numbers of cases and survival curves after multiple imputation were compared to the observed ones. Results The amount of missing values for malignant melanoma was too high to estimate a reasonable number of cases for each UICC stage. However, multiple imputation of missing stage values led to stage-specific numbers of cases of T-stage for malignant melanoma as well as T- and UICC-stage for breast cancer close to the observed numbers of cases. The observed tumour stages on the individual level, the stage-specific numbers of cases and the observed survival curves were best met with polytomous regression or predictive mean matching but not with random forest or proportional sampling as imputation models. Conclusions This limited simulation study indicates that multiple imputation with chained equations is an appropriate technique for dealing with missing information on tumour stage in population-based cancer registries, if the amount of unstaged cases is on a reasonable level.

Abstract Background Covalent histone modifications are central to all DNA-dependent processes. Modifications of histones H3 and H4 are becoming well characterised, but knowledge of how H2A modifications regulate chromatin dynamics and gene expression is still very limited. Results To understand the function of H2A modifications, we performed a systematic analysis of the histone H2A methylation status. We identified and functionally characterised two new methylation sites in H2A: R11 (H2AR11) and R29 (H2AR29). Using an unbiased biochemical approach in combination with candidate assays we showed that protein arginine methyltransferase (PRMT) 1 and PRMT6 are unique in their ability to catalyse these modifications. Importantly we found that H2AR29me2 is specifically enriched at genes repressed by PRMT6, implicating H2AR29me2 in transcriptional repression. Conclusions Our data establishes R11 and R29 as new arginine methylation sites in H2A. We identified the specific modifying enzymes involved, and uncovered a novel functional role of H2AR29me2 in gene silencing in vivo. Thus this work reveals novel insights into the function of H2A methylation and in the mechanisms of PRMT6-mediated transcriptional repression.

Abstract Background Reproduction is the single greatest factor limiting beef cattle production. Previous research on beef suckler luteal activity has largely focused on the mechanisms, and duration, of postpartum anoestrus. However, the temporal pattern of luteal activity after resumption of post-partum ovarian activity, and the impact of pattern type on days open (DO) in purebred beef suckler cows, are unknown. Methods Progesterone concentration was measured in milk samples taken thrice weekly from 120 lactations, in 87 animals, on 3 farms, over two years. Onset of luteal activity (OLA) was defined as the first day milk progesterone concentration exceeded 3 ng/ml for two successive measurements, or exceeded 5 ng/ml once. It was defined as delayed if it occurred more than 61 days postpartum. A short initial luteal phase consisted of progesterone concentrations which exceeded 3 ng/ml for fewer than 4 sequential measurements. Temporal progesterone patterns were classified as: 1) Normal cyclicity; 2) Cessation of luteal activity; 3) Prolonged luteal activity; 4) Erratic phase: failure to conform to 1, 2 or 3. Data concerning parity, previous calving interval, breeding values, calf birth and 200-d weight were obtained from the Norwegian Beef Cattle Recording System database. Results The mean (SD) OLA was 41 d (20). Parity and calf birth weight were inversely correlated with OLA. Delayed OLA occurred in 14.4% of lactations. A short first luteal phase occurred in 61.5% of lactations, but this was unrelated to irregular luteal phase occurrence, pregnancy or DO. Irregular luteal phases occurred in 22% of lactations. The irregularities were: prolonged luteal phase (11%); cessation of luteal activity (5%); erratic luteal activity (6%). Early OLA was associated with prolonged luteal phases. DO was positively correlated with irregular luteal phases and negatively correlated with calf 200-d weight. Conclusions This study demonstrates that irregular luteal phases negatively affect reproductive performance in purebred beef suckler cattle. A moderate incidence of irregular luteal phases was seen in the study population. Whilst a positive relationship was seen between OLA and DO, unfavourable associations between early OLA and incidence of irregular luteal phases should be considered when developing breeding programmes.

Abstract Background The combination of optimized contribution dynamic selection and various mating schemes was investigated over seven generations for a typical tree breeding scenario. The allocation of mates was optimized using a simulated annealing algorithm for various object functions including random mating (RM), positive assortative mating (PAM) and minimization of pair-wise coancestry between mates (MCM) all combined with minimization of variance in family size and coancestry. The present study considered two levels of heritability (0.05 and 0.25), two restrictions on relatedness (group coancestry; 1 and 2%) and two maximum permissible numbers of crosses in each generation (100 and 400). The infinitesimal genetic model was used to simulate the genetic architecture of the trait that was the subject of selection. A framework of the long term genetic contribution of ancestors was used to examine the impacts of the mating schemes on population parameters. Results MCM schemes produced on average, an increased rate of genetic gain in the breeding population, although the difference between schemes was small but significant after seven generations (up to 7.1% more than obtained with RM). In addition, MCM reduced the level of inbreeding by as much as 37% compared with RM, although the rate of inbreeding was similar after three generations of selection. PAM schemes yielded levels of genetic gain similar to those produced by RM, but the increase in the level of inbreeding was substantial (up to 43%). Conclusion The main reason why MCM schemes yielded higher genetic gains was the improvement in managing the long term genetic contribution of founders in the population; this was achieved by connecting unrelated families. In addition, the accumulation of inbreeding was reduced by MCM schemes since the variance in long term genetic contributions of founders was smaller than in the other schemes. Consequently, by combining an MCM scheme with an algorithm that optimizes contributions of the selected individuals, a higher long term response is obtained while reducing the risk within the breeding program.

Abstract Background The PORPUS-P is a short questionnaire for measuring prostate-specific quality of life (QoL), which was designed in Canada for use in prostate cancer (PC) patients. We aimed to generate a German version and compare PORPUS-P scores of German reference men from the general population, and German and Canadian patients with newly diagnosed PC who were scheduled to receive radical prostatectomy (RP) or radiotherapy (RT). Methods The study sample consisted of 988 reference men, 121 German and 66 Canadian PC patients scheduled for RT, and 371 German and 68 Canadian PC patients scheduled for RP. All men completed the PORPUS-P (German postal questionnaire, Canada personal interview). Data were gathered from PC patients before the start of therapy. Results Canadian patients were better educated than the German patients, and fewer were retired. Patients scheduled to receive RT were older and more were retired. German RT patients had lower D'Amico risk scores and pre-treatment Gleason scores than RP patients, and Canadian RT patients had higher pre-treatment PSA than RP patients. Urinary and sexual dysfunction were seen in PC patients (especially RT patients), but were also common in the German reference men. Crude mean PORPUS-P scores differed statistically significant between German RT and RP and Canadian RP and RT patients, with RT patients having higher QoL scores. The differences in age-adjusted mean PORPUS-P scores between reference men and RP patients were not clinically significant, while RT patients had (clinically) significantly lower scores than the reference men. Conclusion The German translation of the PORPUS-P appears to be a short and feasible tool for assessing prostate-specific QoL. Although we found a similar response pattern, Canadian and German PC patients scheduled to receive RT or RP rated their pre-treatment quality of life on different levels, which reveals the need for national reference data. Problems in several QoL domains exist before treatment, and differ between PC patients scheduled for RT and RP.

Abstract Background The main objective of this study was to estimate the effect of supplementation with Saccaromyces cerevisiae (SC) (Yea-Sacc® 1026) on milk production, metabolic parameters and the resumption of ovarian activity in early lactation dairy cows. Methods The experiment was conducted during 2005/2006 in a commercial tied-house farm with an average of 200 milking Estonian Holstein Friesian cows. The late pregnant multiparous cows (n = 46) were randomly divided into two groups; one group received 10 g yeast culture from two weeks before to 14 weeks after calving. The groups were fed a total mixed ration with silages and concentrates. Milk recording data and blood samples for plasma metabolites were taken. Resumption of luteal activity was determined using milk progesterone (P4) measurements. Uterine bacteriology and ovarian ultrasonography (US) were performed and body condition scores (BCS) and clinical disease occurrences were recorded. For analysis, the statistical software Stata 9.2 and R were used to compute Cox proportional hazard and linear mixed models. Results The average milk production per cow did not differ between the groups (32.7 ± 6.4 vs 30.7 ± 5.3 kg/day in the SC and control groups respectively), but the production of milk fat (P < 0.001) and milk protein (P < 0.001) were higher in the SC group. There was no effect of treatment on BCS. The analysis of energy-related metabolites in early lactation showed no significant differences between the groups. In both groups higher levels of β-hydroxybutyrate (BHB) appeared from days 14 to 28 after parturition and the concentration of non-esterfied fatty acid (NEFA) was higher from days 1–7 post partum (PP). According to US and P4 results, all cows in both groups ovulated during the experimental period. The resumption of ovarian activity (first ovulations) and time required for elimination of bacteria from the uterus did not differ between the groups. Conclusion Supplementation with SC had an effect on milk protein and fat production, but did not influence the milk yield. No effects on PP metabolic status, bacterial elimination from the uterus nor the resumption of ovarian activity were found.

Abstract Background Bacterial lung infections are a major cause of economic losses in the pig industry; they are responsible for approximately 50% of the antibiotics used in pigs and, therefore, also present an increasing concern to consumer protection agencies. In response to this changing market we investigated the feasibility of an old approach aimed at the breeding selection of more resistant pigs. As a first step in this direction we applied a new respiratory health score system to study the susceptibility of four different pig breeding lines (German Landrace, Piétrain, Hampshire, Large White) towards the respiratory tract pathogen Actinobacillus (A.) pleuropneumoniae. Results A controlled experimental aerosol infection with an A. pleuropneumoniae serotype 7 isolate was performed using 106 weaning pigs of defined breeding lines from the breeds German Landrace, Piétrain, Hamphire, and Large White. Pigs were clinically assessed on days 4 and 20 post infection following a novel scoring system, the Respiratory Health Score (RHS), which combines clinical, sonographic and radiographic examination results. The ranking on day 4 was significantly correlated with the ranking based on the pathomorphological Lung Lesion Score (LLS; Spearman Rank Correlation Coefficient of 0.86 [p < 0.0001]). Based on their RHS pigs were assigned to the different quartiles independent of the breeding line. The RHS-based rankings of pigs on day 4 and on day 20 were highly correlated (Spearman Rank Correlation Coefficient of 0.82 [p < 0.0001]) independent of the breeding line. Pigs of the Hampshire line were predominantly found in the lowest scoring quartile (47.6%) and absent in the highest scoring quartile. In contrast, pigs of the German Landrace and Piétrain breeding lines were predominantly found in the highest scoring quartile (32.3% and 35.7%, respectively). Conclusion These results demonstrate that the RHS obtained from live pigs shows a highly significant correlation to the lung lesion score considered as a "gold standard". The correlation of the ranking at days 4 and 20 post infection implies that the course of disease is highly dependent on the acute lung damage. The different severity of signs among the tested pig breeding lines clearly suggests a genetic difference in the susceptibility of pigs to A. pleuropneumoniae infection.

Abstract Introduction Predictive genetic screening and regular screening programs in patients with multiple endocrine neoplasia type 1 are intended to detect and treat malignant tumors at the earliest stage possible. Malignant neuroendocrine pancreatic tumors are the most frequent cause of death in these patients. However, the extent and intervals of screening in patients with multiple endocrine neoplasia type 1 are controversial as neuroendocrine tumors are usually slow growing. Here we report the case of a patient who developed a fast-growing neuroendocrine carcinoma within 15 months of a laparoscopic distal pancreatic resection. Case presentation We followed a group of 45 patients with multiple endocrine neoplasia type 1 by an annual screening program in the Department of Visceral, Thoracic, and Vascular Surgery at the University Hospital Marburg in cooperation with the Department of Radiology and the Division of Endocrinology. A man with multiple endocrine neoplasia type 1 who was diagnosed with a recurrent primary hyperparathyroidism underwent a distal pancreatic resection for a non-functional neuroendocrine tumor. In the context of our regular screening program, a large non-functional neuroendocrine tumor was diagnosed in the pancreatic head 15 months after the first pancreatic surgery. Therefore, we performed an enucleation and regional lymph node resection. At histology, the diagnosis of a neuroendocrine carcinoma with one lymph node metastasis was established. There was no evidence of recurrence 9 months after re-operation. Conclusion Fast-growing neuroendocrine tumors are rare in patients with multiple endocrine neoplasia type 1. The intervals, both postoperative and in newly diagnosed pancreatic lesions, in patients with multiple endocrine neoplasia type 1 should be reduced to 6 months to establish the early diagnosis of rapidly progressive disease in a small subset of patients.

Abstract Background The ageing of the population is expected to bring an enormous growth in demand for oncological health care. In order to anticipate and respond to future trends, cancer care needs to be critically evaluated. The present study explores the possibility of conducting representative and population-based research on cancer care on the basis of data drawn from the Cancer Registry. Methods A population-based state-wide cohort study (OVIS) has been carried out in Schleswig-Holstein, Germany. All patients with malignant melanoma, breast, or prostate cancer were identified in the Cancer Registry. Epidemiological data were obtained for all the patients and screened for study eligibility. A postal questionnaire requesting information on diagnosis, therapy, QoL and aftercare was sent to eligible patients. Results A total of 11,489 persons diagnosed with the cancer types of interest in the period from January 2002 to July 2004 were registered in the Cancer Registry. Of the 5,354 (47%) patients who gave consent for research, 4,285 (80% of consenters) completed the questionnaire. In terms of relevant epidemiological variables, participants with melanoma were not found to be different from non-participants with the same diagnosis. However, participants with breast or prostate cancer were slightly younger and had smaller tumours than patients who did not participate in our study. Conclusion Population-based cancer registry data proved to be an invaluable resource for both patient recruitment and non-participant analysis. It can help improve our understanding of the strength and nature of differences between participants and non-respondents. Despite minor differences observed in breast and prostate cancer, the OVIS-sample seems to represent the source population adequately.

Abstract Background A major challenge in the application of marrow transplantation as a route to immunological tolerance of a transplanted organ is to achieve hematopoietic stem cell (HSC) engraftment with minimal myelosuppressive treatments. Results We here describe a combined antibody protocol which can achieve long-term engraftment with clinically relevant doses of MHC-mismatched bone marrow, without the need for myelosuppressive drugs. Although not universally applicable in all strains, we achieved reliable engraftment in permissive strains with a two-stage strategy: involving first, treatment with anti-CD8 and anti-CD4 in advance of transplantation; and second, treatment with antibodies targeting CD4, CD8 and CD40L (CD154) at the time of marrow transplantation. Long-term mixed chimerism through co-receptor and co-stimulation blockade facilitated tolerance to donor-type skin grafts, without any evidence of donor-antigen driven regulatory T cells. Conclusion We conclude that antibodies targeting co-receptor and co-stimulatory molecules synergise to enable mixed hematopoietic chimerism and central tolerance, showing that neither cytoreductive conditioning nor 'megadoses' of donor bone marrow are required for donor HSC to engraft in permissive strains.

Abstract Background In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis. Availability: http://www.megx.net/tetra Results TETRA provides a statistical analysis of tetranucleotide usage patterns in genomic fragments, either via a web-service or a stand-alone program. With respect to discriminatory power, such an analysis outperforms the assignment of genomic fragments based on the (G+C)-content, which is a widely-used sequence-based measure for assessing fragment relatedness. While the web-service is restricted to the calculation of correlation coefficients between tetranucleotide usage patterns of submitted DNA sequences, the stand-alone program generates a much more detailed output, comprising all raw data and graphical plots. The stand-alone program is controlled via a graphical user interface and can batch-process a multitude of sequences. Furthermore, it comes with pre-computed tetranucleotide usage patterns for 166 prokaryote chromosomes, providing a useful reference dataset and source for data-mining. Conclusions Up to now, the analysis of skewed oligonucleotide distributions within DNA sequences is not a commonly used tool within metagenomics. With the TETRA web-service and stand-alone program, the method is now accessible in an easy to use manner for a broad audience. This will hopefully facilitate the interrelation of genomic fragments from metagenome libraries, ultimately leading to new insights into the genetic potentials of yet uncultured microorganisms.