Pancreas Transplantation Outcome Predictions-PTOP: A Risk Prediction Tool for Pancreas and Pancreas-Kidney Transplants Based on a European Cohort.

Background: For patients with complicated type 1 diabetes having, for example, hypoglycemia unawareness and end-stage renal disease because of diabetic nephropathy, combined pancreas and kidney transplantation (PKT) is the therapy of choice. However, the shortage of available grafts and complex impact of risk factors call for individualized, impartial predictions of PKT and pancreas transplantation (PT) outcomes to support physicians in graft acceptance decisions. Methods: Based on a large European cohort with 3060 PKT and PT performed between 2006 and 2021, the 3 primary patient outcomes time to patient mortality, pancreas graft loss, and kidney graft loss were visualized using Kaplan-Meier survival curves. Multivariable Cox proportional hazards models were developed for 5- and 10-y prediction of outcomes based on 26 risk factors. Results: Risk factors associated with increased mortality included previous kidney transplants, rescue allocations, longer waiting times, and simultaneous transplants of other organs. Increased pancreas graft loss was positively associated with higher recipient body mass index and donor age and negatively associated with simultaneous transplants of kidneys and other organs. Donor age was also associated with increased kidney graft losses. The multivariable Cox models reported median C-index values were 63% for patient mortality, 62% for pancreas loss, and 55% for kidney loss. Conclusions: This study provides an online risk tool at https://riskcalc.org/ptop for individual 5- and 10-y post-PKT and PT patient outcomes based on parameters available at the time of graft offer to support critical organ acceptance decisions and encourage external validation in independent populations.

Rescue Allocation Modes in Eurotransplant Kidney Transplantation: Recipient Oriented Extended Allocation Versus Competitive Rescue Allocation-A Retrospective Multicenter Outcome Analysis.

BACKGROUND: Whenever the kidney standard allocation (SA) algorithms according to the Eurotransplant (ET) Kidney Allocation System or the Eurotransplant Senior Program fail, rescue allocation (RA) is initiated. There are 2 procedurally different modes of RA: recipient oriented extended allocation (REAL) and competitive rescue allocation (CRA). The objective of this study was to evaluate the association of patient survival and graft failure with RA mode and whether or not it varied across the different ET countries. METHODS: The ET database was retrospectively analyzed for donor and recipient clinical and demographic characteristics in association with graft outcomes of deceased donor renal transplantation (DDRT) across all ET countries and centers from 2014 to 2021 using Cox proportional hazards methods. RESULTS: Seventeen thousand six hundred seventy-nine renal transplantations were included (SA 15 658 [89%], REAL 860 [4.9%], and CRA 1161 [6.6%]). In CRA, donors were older, cold ischemia times were longer, and HLA matches were worse in comparison with REAL and especially SA. Multivariable analyses showed comparable graft and recipient survival between SA and REAL; however, CRA was associated with shorter graft survival. Germany performed 76% of all DDRTs after REAL and CRA and the latter mode reduced waiting times by up to 2.9 y. CONCLUSIONS: REAL and CRA are used differently in the ET countries according to national donor rates. Both RA schemes optimize graft utilization, lead to acceptable outcomes, and help to stabilize national DDRT programs, especially in Germany.

Diabetes, Obesity, and Pathological Upstaging in Renal Cell Carcinoma: Results From a Large Multi-institutional Consortium.

PURPOSE: We sought to determine whether clinical risk factors and morphometric features on preoperative imaging can be utilized to identify those patients with cT1 tumors who are at higher risk of upstaging (pT3a). MATERIALS AND METHODS: We performed a retrospective international case-control study of consecutive patients treated surgically with radical or partial nephrectomy for nonmetastatic renal cell carcinoma (cT1 N0) conducted between January 2010 and December 2018. Multivariable logistic regression models were used to study associations of preoperative risk factors on pT3a pathological upstaging among all patients, as well as subsets with those with preoperative tumors ≤4 cm, renal nephrometry scores, tumors ≤4 cm with nephrometry scores, and clear cell histology. We also examined association with pT3a subsets (renal vein, sinus fat, perinephric fat). RESULTS: Among the 4,092 partial nephrectomy and 2,056 radical nephrectomy patients, pathological upstaging occurred in 4.9% and 23.3%, respectively. Among each group independent factors associated with pT3a upstaging were increasing preoperative tumor size, increasing age, and the presence of diabetes. Specifically, among partial nephrectomy subjects diabetes (OR=1.65; 95% CI 1.17, 2.29), male sex (OR=1.62; 95% CI 1.14, 2.33), and increasing BMI (OR=1.03; 95% CI 1.00, 1.05 per 1 unit BMI) were statistically associated with upstaging. Subset analyses identified hilar tumors as more likely to be upstaged (partial nephrectomy OR=1.91; 95% CI 1.12, 3.16; radical nephrectomy OR=2.16; 95% CI 1.44, 3.25). CONCLUSIONS: Diabetes and higher BMI were associated with pathological upstaging, as were preoperative tumor size, increased age, and male sex. Similarly, hilar tumors were frequently upstaged.

Kidney Transplantation Outcome Predictions (KTOP): A Risk Prediction Tool for Kidney Transplants from Brain-dead Deceased Donors Based on a Large European Cohort.

BACKGROUND: European kidney donation shortages mandate efficient organ allocation by optimizing the prediction of success for individual recipients. OBJECTIVE: To develop the first European online risk tool for kidney transplant outcomes on the basis of recipient-only and recipient plus donor characteristics. DESIGN, SETTING, AND PARTICIPANTS: We used individual recipient and donor risk factors and three outcomes (death, death with functioning graft [DWFG], and graft loss) for 32 958 transplants within the Eurotransplant kidney allocation system and the Eurotransplant senior program between January 2006 and May 2018 in eight European countries to develop and validate a risk tool. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Cox proportional-hazards models were used to analyze the association of risk factors with overall patient mortality, and proportional subdistribution hazard regression models for their association with graft loss and DWFG. Prediction models were developed with recipient-only and recipient-donor risk factors. Sensitivity analyses based on time-specific area under the receiver operating characteristic curve (AUC) with leave-one-country-out validation were performed and calibration plots were generated. RESULTS AND LIMITATIONS: The 10-yr cumulative incidence rate was 37% for mortality, 12% for DWFG, and 41% for graft loss. In recipient-donor models the leading risk factors for mortality were recipient diabetes (hazard ratio [HR] 10.73), retransplantation (HR 3.08 per transplant), and recipient age (HR 1.08). Effects were similar for DWFG. For graft loss, diabetes (subdistributional HR [SHR] 1.32), increased donor age (SHR 1.02), and prolonged cold ischemia time (SHR 1.02) had increased SHRs. All p values were <0.001. CONCLUSIONS: Previously identified risk factors for outcomes following kidney transplants allow for outcome prediction with 10-yr AUC values of up to 0.81. PATIENT SUMMARY: Using European data, we estimated individual risks to predict the success of kidney transplants and support physicians in decision-making. An online tool is now available (https://riskcalc.org/ktop/) for predicting kidney transplant outcomes both before and after a donor has been identified.

Objective hearing threshold identification from auditory brainstem response measurements using supervised and self-supervised approaches.

Hearing loss is a major health problem and psychological burden in humans. Mouse models offer a possibility to elucidate genes involved in the underlying developmental and pathophysiological mechanisms of hearing impairment. To this end, large-scale mouse phenotyping programs include auditory phenotyping of single-gene knockout mouse lines. Using the auditory brainstem response (ABR) procedure, the German Mouse Clinic and similar facilities worldwide have produced large, uniform data sets of averaged ABR raw data of mutant and wildtype mice. In the course of standard ABR analysis, hearing thresholds are assessed visually by trained staff from series of signal curves of increasing sound pressure level. This is time-consuming and prone to be biased by the reader as well as the graphical display quality and scale.In an attempt to reduce workload and improve quality and reproducibility, we developed and compared two methods for automated hearing threshold identification from averaged ABR raw data: a supervised approach involving two combined neural networks trained on human-generated labels and a self-supervised approach, which exploits the signal power spectrum and combines random forest sound level estimation with a piece-wise curve fitting algorithm for threshold finding.We show that both models work well and are suitable for fast, reliable, and unbiased hearing threshold detection and quality control. In a high-throughput mouse phenotyping environment, both methods perform well as part of an automated end-to-end screening pipeline to detect candidate genes for hearing involvement. Code for both models as well as data used for this work are freely available.

Association between short-term exposure to air pollution and COVID-19 mortality in all German districts: the importance of confounders.

Background: The focus of many studies is to estimate the effect of risk factors on outcomes, yet results may be dependent on the choice of other risk factors or potential confounders to include in a statistical model. For complex and unexplored systems, such as the COVID-19 spreading process, where a priori knowledge of potential confounders is lacking, data-driven empirical variable selection methods may be primarily utilized. Published studies often lack a sensitivity analysis as to how results depend on the choice of confounders in the model. This study showed variability in associations of short-term air pollution with COVID-19 mortality in Germany under multiple approaches accounting for confounders in statistical models. Methods: Associations between air pollution variables PM2.5, PM10, CO, NO, NO2, and O3 and cumulative COVID-19 deaths in 400 German districts were assessed via negative binomial models for two time periods, March 2020-February 2021 and March 2021-February 2022. Prevalent methods for adjustment of confounders were identified after a literature search, including change-in-estimate and information criteria approaches. The methods were compared to assess the impact on the association estimates of air pollution and COVID-19 mortality considering 37 potential confounders. Results: Univariate analyses showed significant negative associations with COVID-19 mortality for CO, NO, and NO2, and positive associations, at least for the first time period, for O3 and PM2.5. However, these associations became non-significant when other risk factors were accounted for in the model, in particular after adjustment for mobility, political orientation, and age. Model estimates from most selection methods were similar to models including all risk factors. Conclusion: Results highlight the importance of adequately accounting for high-impact confounders when analyzing associations of air pollution with COVID-19 and show that it can be of help to compare multiple selection approaches. This study showed how model selection processes can be performed using different methods in the context of high-dimensional and correlated covariates, when important confounders are not known a priori. Apparent associations between air pollution and COVID-19 mortality failed to reach significance when leading selection methods were used. Supplementary Information: The online version contains supplementary material available at 10.1186/s12302-022-00657-5.

Kidney Transplantation After Rescue Allocation-the Eurotransplant Experience: A Retrospective Multicenter Outcome Analysis.

BACKGROUND: At Eurotransplant (ET), kidneys are transferred to "rescue allocation" (RA), whenever the standard allocation (SA) algorithms Eurotransplant Kidney Allocation System (ETKAS) and Eurotransplant Senior Program (ESP) fail. We analyzed the outcome of RA. METHODS: Retrospective patient clinical and demographic characteristics association analyses were performed with graft outcomes for 2422 recipients of a deceased donor renal transplantation (DDRT) after RA versus 25 481 after SA from 71 centers across all ET countries from 2006 to 2018. RESULTS: Numbers of DDRTs after RA increased over the time, especially in Germany. RA played a minor role in ESP versus ETKAS (2.7% versus 10.4%). RA recipients and donors were older compared with SA recipients and donors, cold ischemia times were longer, waiting times were shorter, and the incidence of primary nonfunction was comparable. Among ETKAS recipients, HLA matching was more favorable in SA (mean 3.7 versus 2.5). In multivariate modeling, the incidence of graft loss in ETKAS recipients was reduced in RA compared with SA (subdistribution hazard ratio, 0.80; 95% confidence interval [0.70-0.91], P < 0.001), whereas other outcomes (mortality, death with functioning graft (DwFG)) were not significantly different. None of the 3 outcomes were significantly different when comparing RA with SA within the ESP program. CONCLUSIONS: Facing increased waiting times and mortality on dialysis due to donor shortage, this study reveals encouragingly positive DDRT outcomes following RA. This supports the extension of RA to more patients and as an alternative tool to enable transplantation in patients in countries with prohibitively long waiting times or at risk of deterioration.

Radical Prostatectomy Without Prior Biopsy Following Multiparametric Magnetic Resonance Imaging and Prostate-specific Membrane Antigen Positron Emission Tomography.

A biopsy-free diagnostic pathway in prostate cancer (PC) is limited by the diagnostic accuracy of multiparametric magnetic resonance imaging (mpMRI). The improved accuracy of prostate-specific membrane antigen (PSMA) positron emission tomography (PET) raises the question whether this imaging modality can complement mpMRI to safely avoid biopsy prior to radical prostatectomy (RP). In this case series, we report the feasibility of primary RP without prior biopsy based on a high suspicion of significant PC in both mpMRI (Prostate Imaging Reporting and Data System [PI-RADS] score ≥4) and PSMA-PET (PET score ≥4 on a five-point Likert scale and maximum standardized uptake value ≥4.0) in 25 patients. All patients showed International Society of Urological Pathology (ISUP) grade ≥2 PC in postoperative histopathology. We report patient- and lesion-based comparisons with histopathology of the prostate specimen. Results of our case series may trigger the discussion about RP without prior biopsy as a possible option in well-selected patients. Our case series is limited by retrospective design and small sample size. We want to emphasize clearly that this practice should not be regarded as a standard procedure at the moment. Future studies with larger cohorts only inside a prospective, ethically approved study design are necessary to confirm these results.

Characterising a homozygous two-exon deletion in UQCRH: comparing human and mouse phenotypes.

Mitochondrial disorders are clinically and genetically diverse, with isolated complex III (CIII) deficiency being relatively rare. Here, we describe two affected cousins, presenting with recurrent episodes of severe lactic acidosis, hyperammonaemia, hypoglycaemia and encephalopathy. Genetic investigations in both cases identified a homozygous deletion of exons 2 and 3 of UQCRH, which encodes a structural complex III (CIII) subunit. We generated a mouse model with the equivalent homozygous Uqcrh deletion (Uqcrh-/- ), which also presented with lactic acidosis and hyperammonaemia, but had a more severe, non-episodic phenotype, resulting in failure to thrive and early death. The biochemical phenotypes observed in patient and Uqcrh-/- mouse tissues were remarkably similar, displaying impaired CIII activity, decreased molecular weight of fully assembled holoenzyme and an increase of an unexpected large supercomplex (SXL ), comprising mostly of one complex I (CI) dimer and one CIII dimer. This phenotypic similarity along with lentiviral rescue experiments in patient fibroblasts verifies the pathogenicity of the shared genetic defect, demonstrating that the Uqcrh-/- mouse is a valuable model for future studies of human CIII deficiency.

Dose-dependent long-term effects of a single radiation event on behaviour and glial cells.

PURPOSE: The increasing use of low-dose ionizing radiation in medicine requires a systematic study of its long-term effects on the brain, behaviour and its possible association with neurodegenerative disease vulnerability. Therefore, we analysed the long-term effects of a single low-dose irradiation exposure at 10 weeks of age compared to medium and higher doses on locomotor, emotion-related and sensorimotor behaviour in mice as well as on hippocampal glial cell populations. MATERIALS AND METHODS: We determined the influence of radiation dose (0, 0.063, 0.125 or 0.5 Gy), time post-irradiation (4, 12 and 18 months p.i.), sex and genotype (wild type versus mice with Ercc2 DNA repair gene point mutation) on behaviour. RESULTS: The high dose (0.5 Gy) had early-onset adverse effects at 4 months p.i. on sensorimotor recruitment and late-onset negative locomotor effects at 12 and 18 months p.i. Notably, the low dose (0.063 Gy) produced no early effects but subtle late-onset (18 months) protective effects on sensorimotor recruitment and exploratory behaviour. Quantification and morphological characterization of the microglial and the astrocytic cells of the dentate gyrus 24 months p.i. indicated heightened immune activity after high dose irradiation (0.125 and 0.5 Gy) while conversely, low dose (0.063 Gy) induced more neuroprotective features. CONCLUSION: This is one of the first studies demonstrating such long-term and late-onset effects on brain and behaviour after a single radiation event in adulthood.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density.

The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease.

Survival data on timing of resection of liver metastases in colorectal cancer patients.

Between 2007 and 2016, 140 consecutive patients who underwent resection of colorectal cancer with simultaneous liver metastases at a single university hospital were retrospectively analysed. In order to gather information regarding potential survival differences for n = 68 simultaneous versus n = 72 staged resections of the colorectal primary tumor and the liver metastases, Clinical, histopathological, serological, and survival data were compared for those two patient groups. The rate of simultaneous tumor resections increased from approximately 25% in 2007 to >75% in 2016. There was no difference in tumor specific survival for patients with simultaneous vs. staged resection (p = 0.631). This effect continued after excluding patients with extrahepatic metastases (p = 0.440). Further, neoadjuvant treatment did not lead to differences in the tumor-specific survival (p = 0.123). Factors associated with an increased tumor-specific survival were low ASA score (p < 0.001), low number of tumor-affected lymph nodes (p < 0.001), histological grading G1/2 (p = 0.001), and a low number of liver metastases (p = 0.044). There was no significant survival difference for the primary tumor stage (pT), the Clavien-Dindo complication rate, the resection status (R0), and minor versus major hepatectomies.

Simultaneous Versus Staged Resection of Colorectal Cancer Liver Metastasis: A Retrospective Single-Center Study.

BACKGROUND: For patients with colorectal cancer and synchronous liver metastasis, either a simultaneous, or a two-staged resection of the primary tumor and the liver metastases is possible. There are currently no guidelines preferring one approach to the other. MATERIAL AND METHODS: Consecutive patients who underwent hepatic resection at our university hospital from 2007-2016 were included. Clinical, histopathologic, serologic, and survival data were analyzed. The primary end point was tumor-specific survival for patients with simultaneous versus staged resections. RESULTS: Of all 140 patients, 68 underwent simultaneous resection and 72 underwent staged resection. The characteristics of both groups were comparable. Patients with simultaneous resections had a shorter duration of cumulative operation time (299 versus 460 min; P = 0.003) and a shorter cumulative length of hospital stay (23 versus 43 d; P = 0.002). Perioperative mortality (P = 0.257) did not differ significantly; however, patients with simultaneous resections had higher rates of grade 2 complications according to Clavien-Dindo (P < 0.001). Tumor-specific 1-y survival was 85 ± 5% for simultaneous and 83 ± 5% for staged resection (P = 0.631). On multivariable analysis, pT4 (P = 0.038), pN3 (P = 0.003), and G3/4 (P = 0.041) of the primary tumor and postoperative complications (Clavien-Dindo 3/4/5, P = 0.003) were poor prognostic factors regarding tumor-specific survival. CONCLUSIONS: This is one of the largest and most thoroughly documented retrospective single-center studies of consecutive patients with synchronous hepatic metastases. Simultaneous resection of colorectal cancer together with hepatic metastases is a safe procedure in selected patients and does not have a significant influence on long-term survival.

A comprehensive and comparative phenotypic analysis of the collaborative founder strains identifies new and known phenotypes.

The collaborative cross (CC) is a large panel of mouse-inbred lines derived from eight founder strains (NOD/ShiLtJ, NZO/HILtJ, A/J, C57BL/6J, 129S1/SvImJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ). Here, we performed a comprehensive and comparative phenotyping screening to identify phenotypic differences and similarities between the eight founder strains. In total, more than 300 parameters including allergy, behavior, cardiovascular, clinical blood chemistry, dysmorphology, bone and cartilage, energy metabolism, eye and vision, immunology, lung function, neurology, nociception, and pathology were analyzed; in most traits from sixteen females and sixteen males. We identified over 270 parameters that were significantly different between strains. This study highlights the value of the founder and CC strains for phenotype-genotype associations of many genetic traits that are highly relevant to human diseases. All data described here are publicly available from the mouse phenome database for analyses and downloads.

Soft windowing application to improve analysis of high-throughput phenotyping data.

MOTIVATION: High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors. RESULTS: Here we introduce 'soft windowing', a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources. AVAILABILITY AND IMPLEMENTATION: The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.