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This work describes a new method to extract image features using tensor decomposition to model data. Given a set of sample images, we extract patches from images, compute the covariance tensor for all patches, decompose with the Tucker model, and obtain the most critical features from a tensor core. To extract features, we factorize the covariance tensor (CovTen) into its core and propose a new interpretation of the resultant tensor structure, which holds relevant features in a block-wise arrangement (also named filters, weights, or kernels). This tensorial representation allows preserving the spatial structure, learning multichannel filters, and establishing linear dependence between dimensions, reducing the dimensional complexity (the curse of dimensionality). Thus, the proposed method generates filters by a single feed-forward step using a few samples per class as low as 1. Besides, in kernel generation, labels are not needed. The obtained features were extensively tested using a convolutional neural network for classification. All tests were conducted under the VGG architecture conventions. The experiments helped us identify the proposed method’s advantages versus traditional convolutional neural networks in inference capacity and kernels initialization. We also performed experiments to select hyperparameters (nonLinearity, max pooling, samples, filter size) according to their performance. The inference capacity results showed an increased classification accuracy around 67% with CIFAR 10, 64% with CIFAR 100, and 98% with MNIST, using 10,100,1000 samples with a single feed-forward training. On the other hand, the initialization experiments showed the feature extraction capability versus available initializers (He random, He uniform, Glorot, random), confirming linear tensor constraints’ usefulness to generate features. Using the method as kernel initializer returns comparable findings with state of the art around 91% with CIFAR 10, 72% with CIFAR 100, and 99% with MNIST.

Recently, Hyperbolic Spaces in the context of Non-Euclidean Deep Learning have gained popularity because of their ability to represent hierarchical data. We propose that it is possible to take advantage of the hierarchical characteristic present in the images by using hyperbolic neural networks in a GAN architecture. In this study, different configurations using fully connected hyperbolic layers in the GAN, WGAN, CGAN, and the mapping network of the StyleGAN2 are tested in what we call the HGAN, HWGAN, HCGAN, and HStyleGAN, respectively. Furthermore, we test multiple values of curvature and introduce an exponential way to train it. The results are measured using the Inception Score (IS) and the Fréchet Inception Distance (FID) over the MNIST dataset and with FID over CIFAR-10. Depending on the configuration and space curvature, better results are achieved for each proposed hyperbolic version than their euclidean counterpart.

The measurement of partial discharges (PD) in electrical equipment or machines subjected to high voltage can be considered as one of the most important indicators when assessing the state of an insulation system. One of the main challenges in monitoring these degradation phenomena is to adequately measure a statistically significant number of signals from each of the sources acting on the asset under test. However, in industrial environments the presence of large amplitude noise sources or the simultaneous presence of multiple PD sources may limit the acquisition of the signals and therefore the final diagnosis of the equipment status may not be the most accurate. Although different procedures and separation and identification techniques have been implemented with very good results, not having a significant number of PD pulses associated with each source can limit the effectiveness of these procedures. Based on the above, this research proposes a new algorithm of artificial generation of PD based on a Deep Convolutional Generative Adversarial Networks (DCGAN) architecture which allows artificially generating different sources of PD from a small group of real PD, in order to complement those sources that during the measurement were poorly represented in terms of signals. According to the results obtained in different experiments, the temporal and spectral behavior of artificially generated PD sources proved to be similar to that of real experimentally obtained sources.

Background: Endoscopic retrograde cholangiopancreaticography (ERCP) is the standard endoscopic procedure for the diagnosis and treatment of diseases of the pancreas and bile ducts. Cholangioscopy provides direct visualization of the bile ducts. It offers the possibility of more detailed diagnostic and therapeutic indications. Today, cholangioscopy is often performed as a single-operator (SOC) procedure., Objectives: We were interested in the clinical efficacy of our SOC procedure in comparison with published studies, and performed this retrospective data analysis of all our consecutive patients from 2016 to 2022 to analyze the feasibility, safety, and efficacy of SOC., Design and Methods: A retrospective single-center analysis of patients undergoing SOC at a tertiary center from 2016 to 2022 ( N  = 196) was performed. Demographic data, indication for SOC, exam-specific data, efficacy, and complications were included. Sensitivity and specificity for diagnosing indeterminate biliary strictures were calculated., Results: The most common indications for SOC were indeterminate biliary strictures ( n  = 117; 60%), treatment of biliary stones ( n  = 45; 23%), and other indications ( n  = 34; 17%), for example, foreign body removal or intraoperative SOC. In 97% of the SOC ( n  = 191), the procedure was technically successful. The diagnostic or therapeutic goal was achieved in 91% of SOC ( n  = 173). In the subgroup where the SOC result was confirmed by subsequent surgery ( n  = 93), sensitivity was 86%, specificity 99%, and SOC treatment of stones was successful in 89%. Complications occurred in (20%; n  = 37). The majority of these patients ( n  = 18; 10%) had minor bleeding requiring no intervention., Conclusion: SOC is an effective and safe procedure that should be the standard of care when primary diagnostic and/or therapeutic ERCP has failed. The sensitivity and specificity for determining the dignity of biliary strictures and the efficacy for the treatment of difficult-to-treat stones are reproducibly very high., Competing Interests: The authors declare that there is no conflict of interest., (© The Author(s), 2024.)

This paper presents a general framework for simulating plot data in multi-environment field trials with one or more traits. The framework is embedded within the R package FieldSimR, whose core function generates plot errors that capture global field trend, local plot variation, and extraneous variation at a user-defined ratio. FieldSimR's capacity to simulate realistic plot data makes it a flexible and powerful tool for a wide range of improvement processes in plant breeding, such as the optimisation of experimental designs and statistical analyses of multi-environment field trials. FieldSimR provides crucial functionality that is currently missing in other software for simulating plant breeding programmes and is available on CRAN. The paper includes an example simulation of field trials that evaluate 100 maize hybrids for two traits in three environments. To demonstrate FieldSimR's value as an optimisation tool, the simulated data set is then used to compare several popular spatial models for their ability to accurately predict the hybrids' genetic values and reliably estimate the variance parameters of interest. FieldSimR has broader applications to simulating data in other agricultural trials, such as glasshouse experiments., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Werner, Gemenet and Tolhurst.)

Background: SARS-CoV-2 infection and associated COVID-19 disease can lead to critical illness with a risk of developing a multiple organ failure. Subsequently, this may lead to various pathological sequelae, such as secondary sclerosing cholangitis after surviving COVID-19 (SSC-COVID)., Objective: The aim is to retrospectively analyze a cohort of hospitalized patients with first-wave (February 2020-June 2020) SARS-CoV-2 infection and persisting unclear cholangiopathy to determine the incidence of SSC-COVID and its risk factors., Results: A total of 249 patients were hospitalized at the university hospital in Tübingen, Germany, with SARS-CoV-2 infection during the first wave of the pandemic. Of these, 35.3% (88/249) required intensive care treatment; 16.5% (41/249) of them died due to the complications of COVID-19; 30.8% (64/208) of surviving patients could be followed up und were retrospectively analyzed at our center. The incidence of confirmed SSC-COVID was 7.8% (5/64). All SSC-COVID patients had an ICU stay >20 days, for invasive ventilation, positioning treatment, vasopressor treatment, but possible risk factors for SSC were not significant due to the small number of patients., Conclusions: SSC-COVID is an emerging disease in post-COVID patients with a high incidence in our single-center cohort. SSC-COVID should be considered as a differential diagnosis, if unclear cholangiopathy or cholestasis persists after SARS-CoV-2 infection.

Background and Aims: Postpolypectomy syndrome (PPS) is a relevant adverse event that can appear after polypectomy. Several publications mention postpolypectomy syndrome using different criteria to define it. The aim of this study is to detect potential risk factors and predictors for developing PPS and to define the main criteria of PPS., Methods: In this retrospective monocentric study, 475 out of 966 patients who underwent colonoscopy with polypectomy from October 2015 to June 2020 were included. The main criterion of PPS is defined as the development of postinterventional abdominal pain lasting more than six hours., Results: A total of 9.7% of the patients developed PPS, which was defined as local abdominal pain around the polypectomy area after six hours. A total of 8.6% of the study population had abdominal pain within six hours postintervention. A total of 3.7% had an isolated triad of fever, leukocytosis, and increased CRP in the absence of abdominal pain. Increased CRP combined with an elevated temperature over 37.5 °C seems to be a positive predictor for developing PPS. Four independent risk factors could be detected: serrated polyp morphology, polypoid configurated adenomas, polyp localization in the cecum, and the absence of intraepithelial neoplasia., Conclusions: Four independent risk factors for developing PPS were detected. The combination of increased CRP levels with elevated temperature seems to be a predictor for this pathology. As expected, the increasing use of cold snare polypectomies will reduce the incidence of this syndrome. Key summary: Our monocentric study on 966 patients detected four independent risk factors for developing PPS: pedunculated polyp, resected polyps in the cecum, absence of IEN, and serrated polyp morphology. The combination of increased CRP levels with elevated temperature seems to be a predictor for this pathology.

Key Message: Reciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids. Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis., (© 2023. The Author(s).)

Key Message: For genomic selection in clonally propagated crops with diploid (-like) meiotic behavior to be effective, crossing parents should be selected based on genomic predicted cross-performance unless dominance is negligible. For genomic selection (GS) in clonal breeding programs to be effective, parents should be selected based on genomic predicted cross-performance unless dominance is negligible. Genomic prediction of cross-performance enables efficient exploitation of the additive and dominance value simultaneously. Here, we compared different GS strategies for clonally propagated crops with diploid (-like) meiotic behavior, using strawberry as an example. We used stochastic simulation to evaluate six combinations of three breeding programs and two parent selection methods. The three breeding programs included (1) a breeding program that introduced GS in the first clonal stage, and (2) two variations of a two-part breeding program with one and three crossing cycles per year, respectively. The two parent selection methods were (1) parent selection based on genomic estimated breeding values (GEBVs) and (2) parent selection based on genomic predicted cross-performance (GPCP). Selection of parents based on GPCP produced faster genetic gain than selection of parents based on GEBVs because it reduced inbreeding when the dominance degree increased. The two-part breeding programs with one and three crossing cycles per year using GPCP always produced the most genetic gain unless dominance was negligible. We conclude that (1) in clonal breeding programs with GS, parents should be selected based on GPCP, and (2) a two-part breeding program with parent selection based on GPCP to rapidly drive population improvement has great potential to improve breeding clonally propagated crops., (© 2023. The Author(s).)

Endoscopic negative pressure therapy is an effective treatment strategy for various defects of the gastrointestinal tract. The functional principle is based on an open-pore element, which is placed around a perforated drainage tube and connected to a vacuum source. The resulting open-pore suction device can undergo endoluminal or intracavitary placement. Different open-pore suction devices are used for endoscopic negative pressure therapy of upper gastrointestinal tract defects. Comparative analyses for features and properties of these devices are still lacking. Eight different (six hand-made devices and two commercial devices) open-pore suction devices for endoscopic negative pressure therapy of the upper gastrointestinal tract were used, amount fluid removed was evaluated. The evaluation parameters included the time to reach the target pressure, the time required to remove 100 ml of water, and the material resistance of the device. All open-pore suction devices are able to aspirate the target volume of fluids. The time to reach the target volume varied considerably. Target negative pressure was not achieved with all open-pore suction devices during the aspiration of fluids; however, there was no negative effect on suction efficiency. Of the measurement data, material resistance could be calculated for six open-pore elements. We present a simple experimental, nonphysiologically setup for open-pore suction devices used for endoscopic negative pressure therapy. The expected quantity of fluids secreted into the treated organs should affect open-pore suction device for endoscopic negative pressure therapy., (© 2022. The Author(s).)

Introduction: An esophagojejunal anastomotic leak following an oncological gastrectomy is a life-threatening complication, and its management is challenging. A stent application and endoscopic negative pressure therapy are possible therapeutic options. A clinical comparison of these strategies has been missing until now., Methods: A retrospective analysis of 14 consecutive patients endoscopically treated for an anastomotic leak after a gastrectomy between June 2014 and December 2019 was performed., Results: The mean time of the diagnosis of the leakage was 7.14 days after surgery. Five patients were selected for a covered stent, and nine patients received endoscopic negative pressure therapy. In the stent group, the mean number of endoscopies was 2.4, the mean duration of therapy was 26 days, and the mean time of hospitalization was 30 days. In patients treated with endoscopic negative pressure therapy, the mean number of endoscopies was 6.0, the mean days of therapy duration was 14.78, and the mean days of hospitalization was 38.11. Treatment was successful in all patients in the stent-based therapy group and in eight of nine patients in the negative pressure therapy group., Discussion: Good clinical results in preserving the anastomosis and providing sepsis control was achieved in all patients. Stent therapy resulted in anastomosis healing with a lower number of endoscopies, a shorter time of hospitalization, and rapid oral nutrition.

Background: Since December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a pandemic threat to global health. We are now in the fourth wave of this pandemic. As the pandemic developed, the requirements and therapeutic endoscopic procedures for SARS-CoV-2-positive patients underwent changes., Methods: Analysis of implications for an endoscopy unit during the first and second/third waves of the COVID-19 pandemic with a focus on COVID-19-related process changing. Addressed are number of SARS-CoV-2-positive patients and endoscopic examinations performed in patients who tested positive for SARS-CoV-2 during the various waves, adherence to scheduled examinations, rotation of staff to COVID-dedicated structures and, finally, impact of vaccination on infection rate among endoscopic staff., Results: During the first wave, 10 SARS-CoV-2-positive in-house patients underwent a total of 22 gastrointestinal (GI) endoscopic procedures. During the second and third waves, 59 GI endoscopies were performed in 38 patients. While in the first wave, GI bleeding was the main indication for endoscopy (82%), in the second and third waves the main indication for endoscopy was endoscopic insertion of deep feeding tubes (78%; p  < 0.001). During the first wave, 5 (17%) of 29 Interdisciplinary Endoscopy Unit (IEU) staff members were moved to designated COVID wards, which was not necessary during the following waves. Lack of protective clothing was critical during the first wave, but not in the later waves. Screening tests for patients and staff were widely available after the first wave, and IEU staff was vaccinated during the second wave., Conclusion: Strategies to ensure safe endoscopies with respect to preventing transmission of SARS-CoV-2 from patients to staff were effective. Organizational adjustments allowed the routine program to continue unaffected. Indications for GI endoscopies changed over time: during the first wave, GI endoscopies were performed for life-threatening indications, whereas later supportive procedures were the main indication., Competing Interests: Conflict of interest statement: The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s), 2022.)

Background: After intestinal transplantation, close allograft monitoring especially during the early postoperative period is crucial since the intestine is a highly immunogenic organ. Current protocols are based on endoscopic and histologic examination with the latter one being linked to the risk of bleeding and perforation., Aims: Evaluation of the diagnostic value of endoscopy utilizing magnification to predict acute cellular rejection compared to routine allograft biopsies., Methods: Fourteen patients underwent the protocol with longitudinal zoom endoscopic and histological graft monitoring during the first year after transplantation. The intestinal mucosa was analyzed during endoscopy utilizing the SASAKI score while a minimum of two biopsies were taken during each examination. A new graduation of severity for acute cellular rejection based on the findings of the SASAKI score is established., Results: Endoscopic findings of 385 examinations and more than 1000 intestinal allograft biopsies were analyzed. A total of 7 acute cellular rejection episodes in 6/14 patients occurred. Allograft endoscopy was able to diagnose ACR with a sensitivity of 76% and a specificity of 82%., Conclusions: Our results will be critical for refining protocols for allograft monitoring after intestinal transplantation thus paving the way towards less invasive measures., Competing Interests: Conflict of interest We acknowledge support by the Open Access Publishing Fund of the University of Tübingen. The funders were neither involved in study design nor in collection, analysis, interpretation of data or writing the manuscript. The authors have no conflicts of interest or financial ties to disclose in regard to this study., (Copyright © 2022. Published by Elsevier Ltd.)

Background: Esophageal cancer (EC) is the sixth-leading cause of cancer-related deaths in the world. Esophagectomy is the most effective treatment for patients without invasion of adjacent organs or distant metastasis. Complications and relevant problems may occur in the early post-operative course or in a delayed fashion. Here, innovative endoscopic techniques for the treatment of postsurgical problems were developed during the past 20 years., Methods: Endoscopic treatment strategies for the following postoperative complications are presented: anastomotic bleeding, anastomotic insufficiency, delayed gastric passage and anastomotic stenosis. Based on a literature review covering the last two decades, therapeutic procedures are presented and analyzed., Results: Addressing the four complications mentioned, clipping, stenting, injection therapy, dilatation, and negative pressure therapy are successfully utilized as endoscopic treatment techniques today., Conclusion: Endoscopic treatment plays a major role in both early-postoperative and long-term aftercare. During the past 20 years, essential therapeutic measures have been established. A continuous development of these techniques in the field of endoscopy can be expected.

Background: Endoscopic negative pressure therapy is a novel and successful treatment method for a variety of gastrointestinal leaks. This therapy mode has been frequently described for rectal and esophageal leakages. Duodenal diverticular perforations are rare but life-threatening events. The early diagnosis of duodenal diverticular perforation is often complicated by inconclusive symptoms. This is the first report about endoscopic negative pressure therapy in patients with perforated duodenal diverticula., Case Presentation: We present two cases of duodenal diverticula perforations treated with endoscopic negative pressure therapy as stand-alone treatment. Start of symptoms varied from one to three days before hospital admission. Early sectional imaging led to the diagnosis of duodenal diverticular perforation. Both patients were treated with endoluminal endoscopic negative pressure therapy with simultaneous feeding option. Three respective changes of the suction device were performed. Both patients were treated with antibiotics and antimycotics during their hospital stay and be discharged from hospital after 20 days., Conclusions: This is the first description of successful stand-alone treatment by endoscopic negative pressure therapy in two patients with perforated duodenal diverticulum. We thus strongly recommend to attempt interventional therapy with endoluminal endoscopic negative pressure therapy in patients with duodenal diverticular perforations upfront to surgery., (© 2021. The Author(s).)

Background and Study Aims: Since December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of coronavirus disease 2019 (COVID-19), has posed a pandemic threat to global health and has challenged health care system in all affected countries., Patients and Methods: This is a combined study including a descriptive part about the changes in the daily work routine of an Interdisciplinary Endoscopic Unit (IEU) and a prospective analysis of patients tested positive for SARS-CoV-2 who required endoscopic interventions. Conclusively, we present the finding of a point-prevalence analysis in the staff of the IEU., Results: We present effects of the COVID-19-related restructuring of processes in our interdisciplinary endoscopy unit (IEU) with respect to cancelation of examinations, relocation of staff to other departments, impact of SARS-CoV-2 on medical staff of the IEU, and supply of protective clothing. Additionally, we analyzed the cohort of COVID-19 patients: Sixteen endoscopic interventions were done in ten patients. In all patients with confirmed infection with SARS-CoV-2, emergency endoscopies were required for relevant bleeding situations. Re-endoscopies were required only in critically ill COVID-19 patients., Conclusions: The restructuring of processes in the IEU was feasible in short time, effective, and can also be applied broadly at least in developed countries [Garbe et al. in Gastroenterology 159:778-780, 2020; Repici A, Pace F, Gabbiadini R, Colombo M, Hassan C, Dinelli M, Group IG-CW, Maselli R, Spadaccini M, Mutignani M, Gabbrielli A, Signorelli C, Spada C, Leoni P, Fabbri C, Segato S, Gaffuri N, Mangiavillano B, Radaelli F, Salerno R, Bargiggia S, Maroni L, Benedetti A, Occhipinti P, De Grazia F, Ferraris L, Cengia G, Greco S, Alvisi C, Scarcelli A, De Luca L, Cereatti F, Testoni PA, Mingotto R, Aragona G, Manes G, Beretta P, Amvrosiadis G, Cennamo V, Lella F, Missale G, Lagoussis P, Triossi O, Giovanardi M, De Roberto G, Cantu P, Buscarini E, Anderloni A, Carrara S, Fugazza A, Galtieri PA, Pellegatta G, Antonelli G, Rosch T, Sharma P (2020) Endoscopy units and the COVID-19 Outbreak: a Multi-Center Experience from Italy. Gastroenterology;]. The endoscopy-related rate of SARS-CoV-2 infection of staff is low, but supply of protective equipment is crucial for this. Endoscopic procedures in COVID-19 patients were not directly related to SARS-CoV-2 infection, but to other underlying diseases or typical complications of long-term ICU treatment., (© 2020. The Author(s).)

Alcohol abuse after liver transplantation can seriously impact graft and patient survival. However, to date, there is no defined standard procedure to identify patients consuming alcohol after liver transplantation. The aim of this study was to analyze the diagnostic value and clinical impact of routinely measured urinary ethyl glucuronide (uEtG) - a metabolite of ethanol - in patients after liver transplantation. Data of 362 consecutive patients after liver transplantation who visited the University Hospital of Tuebingen for outpatient follow-up were analyzed. Forty-eight patients (13%) displayed positive uEtG results. The uEtG positive group contained significantly more patients with pretransplant alcoholic liver disease. However, two thirds of the uEtG positive patients had no history of pretransplant alcoholic liver disease. Several clinical parameters were significantly associated with positive uEtG. In order to enable a more cost-effective application of uEtG in the future, a clinical risk score was developed (specificity 0.95). In conclusion, routine testing for uEtG reveals a considerable percentage of patients practicing alcohol intake after liver transplantation. Application of our proposed risk score could help focusing uEtG testing on patients at risk., (© 2021 The Authors. Transplant International published by John Wiley & Sons Ltd on behalf of Steunstichting ESOT.)

Healing of gastrointestinal ulcers after Hemospray application was reported in literature. The pathophysiological mechanism of action of hemostatic powders is not elucidated so far. A prospective animal model was performed to evaluate the effect of Hemospray application on the healing process of artificially induced ulcers of the upper and lower gastrointestinal tract. In 10 pigs, 20 ulcers were created in each the upper and the lower gastrointestinal tract by endoscopic mucosal resection. 50% of the pigs were immediately treated with Hemospray application, the others were not treated. Ulcer size was measured endoscopically on day 0, 2, and 7. On day 7 the ulcers were histopathological evaluated for capillary ingrowth and the thickness of the collagen layer. After 7 days the sizes of the ulcers decreased significantly (stomach: - 22.8% with Hemospray application, - 19% without Hemospray application; rectum: - 50.8% with Hemospray application, - 49.5% without Hemospray application; p = 0.005-0.037), but without significant difference between both groups. This study shows no significant effect of the hemostatic powder Hemospray on ulcer healing in the upper and lower gastrointestinal tract compared with untreated controls, neither harmful nor beneficial. However, some trends merit further trials in patients and may indicate a possible mechanism of accelerated mucosal healing., (© 2021. The Author(s).)

Background: Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds., Methods: Data comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White, Landrace, Pietrain, Hampshire, Duroc, and synthetic lines) genotyped and imputed for 71,324 single-nucleotide polymorphisms (SNPs). For each line, we estimated SNP associations using a univariate linear mixed model that accounted for genomic relationships. SNPs with significant associations were identified using a threshold of p < 10 -6 and used to define genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model., Results: We found significant associations with backfat thickness for 264 SNPs across 27 genomic regions. Six genomic regions were detected in three or more lines. The average estimate of the SNP-based heritability was 0.48, with estimates by line ranging from 0.30 to 0.58. The genomic regions jointly explained from 3.2 to 19.5% of the additive genetic variance of backfat thickness within a line. Individual genomic regions explained up to 8.0% of the additive genetic variance of backfat thickness within a line. Some of these 27 genomic regions also explained up to 1.6% of the additive genetic variance in lines for which the genomic region was not statistically significant. We identified 64 candidate genes with annotated functions that can be related to fat metabolism, including well-studied genes such as MC4R, IGF2, and LEPR, and more novel candidate genes such as DHCR7, FGF23, MEDAG, DGKI, and PTN., Conclusions: Our results confirm the polygenic architecture of backfat thickness and the role of genes involved in energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs. The results also suggest that several less well-understood metabolic pathways contribute to backfat development, such as those of phosphate, calcium, and vitamin D homeostasis., (© 2021. The Author(s).)

Key Message: Regional association analysis of 50 re-sequenced Chinese semi-winter rapeseed accessions in combination with co-expression analysis reveal candidate genes affecting oil accumulation in Brassica napus. One of the breeding goals in rapeseed production is to enhance the seed oil content to cater to the increased demand for vegetable oils due to a growing global population. To investigate the genetic basis of variation in seed oil content, we used 60 K Brassica Infinium SNP array along with phenotype data of 203 Chinese semi-winter rapeseed accessions to perform a genome-wide analysis of haplotype blocks associated with the oil content. Nine haplotype regions harbouring lipid synthesis/transport-, carbohydrate metabolism- and photosynthesis-related genes were identified as significantly associated with the oil content and were mapped to chromosomes A02, A04, A05, A07, C03, C04, C05, C08 and C09, respectively. Regional association analysis of 50 re-sequenced Chinese semi-winter rapeseed accessions combined with transcriptome datasets from 13 accessions was further performed on these nine haplotype regions. This revealed natural variation in the BnTGD3-A02 and BnSSE1-A05 gene regions correlated with the phenotypic variation of the oil content within the A02 and A04 chromosome haplotype regions, respectively. Moreover, co-expression network analysis revealed that BnTGD3-A02 and BnSSE1-A05 were directly linked with fatty acid beta-oxidation-related gene BnKAT2-C04, thus forming a molecular network involved in the potential regulation of seed oil accumulation. The results of this study could be used to combine favourable haplotype alleles for further improvement of the seed oil content in rapeseed.

Key Message: Complementing or replacing genetic markers with transcriptomic data and use of reproducing kernel Hilbert space regression based on Gaussian kernels increases hybrid prediction accuracies for complex agronomic traits in canola. In plant breeding, hybrids gained particular importance due to heterosis, the superior performance of offspring compared to their inbred parents. Since the development of new top performing hybrids requires labour-intensive and costly breeding programmes, including testing of large numbers of experimental hybrids, the prediction of hybrid performance is of utmost interest to plant breeders. In this study, we tested the effectiveness of hybrid prediction models in spring-type oilseed rape (Brassica napus L./canola) employing different omics profiles, individually and in combination. To this end, a population of 950 F 1 hybrids was evaluated for seed yield and six other agronomically relevant traits in commercial field trials at several locations throughout Europe. A subset of these hybrids was also evaluated in a climatized glasshouse regarding early biomass production. For each of the 477 parental rapeseed lines, 13,201 single nucleotide polymorphisms (SNPs), 154 primary metabolites, and 19,479 transcripts were determined and used as predictive variables. Both, SNP markers and transcripts, effectively predict hybrid performance using (genomic) best linear unbiased prediction models (gBLUP). Compared to models using pure genetic markers, models incorporating transcriptome data resulted in significantly higher prediction accuracies for five out of seven agronomic traits, indicating that transcripts carry important information beyond genomic data. Notably, reproducing kernel Hilbert space regression based on Gaussian kernels significantly exceeded the predictive abilities of gBLUP models for six of the seven agronomic traits, demonstrating its potential for implementation in future canola breeding programmes.

Intercrop breeding programs using genomic selection can produce faster genetic gain than intercrop breeding programs using phenotypic selection. Intercropping is an agricultural practice in which two or more component crops are grown together. It can lead to enhanced soil structure and fertility, improved weed suppression, and better control of pests and diseases. Especially in subsistence agriculture, intercropping has great potential to optimize farming and increase profitability. However, breeding for intercrop varieties is complex as it requires simultaneous improvement of two or more component crops that combine well in the field. We hypothesize that genomic selection can significantly simplify and accelerate the process of breeding crops for intercropping. Therefore, we used stochastic simulation to compare four different intercrop breeding programs implementing genomic selection and an intercrop breeding program entirely based on phenotypic selection. We assumed three different levels of genetic correlation between monocrop grain yield and intercrop grain yield to investigate how the different breeding strategies are impacted by this factor. We found that all four simulated breeding programs using genomic selection produced significantly more intercrop genetic gain than the phenotypic selection program regardless of the genetic correlation with monocrop yield. We suggest a genomic selection strategy which combines monocrop and intercrop trait information to predict general intercropping ability to increase selection accuracy in the early stages of a breeding program and to minimize the generation interval., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Bančič, Werner, Gaynor, Gorjanc, Odeny, Ojulong, Dawson, Hoad and Hickey.)

Over the last two decades, the application of genomic selection has been extensively studied in various crop species, and it has become a common practice to report prediction accuracies using cross validation. However, genomic prediction accuracies obtained from random cross validation can be strongly inflated due to population or family structure, a characteristic shared by many breeding populations. An understanding of the effect of population and family structure on prediction accuracy is essential for the successful application of genomic selection in plant breeding programs. The objective of this study was to make this effect and its implications for practical breeding programs comprehensible for breeders and scientists with a limited background in quantitative genetics and genomic selection theory. We, therefore, compared genomic prediction accuracies obtained from different random cross validation approaches and within-family prediction in three different prediction scenarios. We used a highly structured population of 940 Brassica napus hybrids coming from 46 testcross families and two subpopulations. Our demonstrations show how genomic prediction accuracies obtained from among-family predictions in random cross validation and within-family predictions capture different measures of prediction accuracy. While among-family prediction accuracy measures prediction accuracy of both the parent average component and the Mendelian sampling term, within-family prediction only measures how accurately the Mendelian sampling term can be predicted. With this paper we aim to foster a critical approach to different measures of genomic prediction accuracy and a careful analysis of values observed in genomic selection experiments and reported in literature., Competing Interests: AA and TK were employed by the company NPZ Innovation GmbH. GL was employed by the company German Seed Alliance GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Werner, Gaynor, Gorjanc, Hickey, Kox, Abbadi, Leckband, Snowdon and Stahl.)

Competing Interests: Disclosure The authors report no conflicts of interest in this work.

Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species., Results: We used the 60 K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation., Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

A major challenge of plant biology is to unravel the genetic basis of complex traits. We took advantage of recent technical advances in high-throughput phenotyping in conjunction with genome-wide association studies to elucidate genotype-phenotype relationships at high temporal resolution. A diverse Brassica napus population from a commercial breeding programme was analysed by automated non-invasive phenotyping. Time-resolved data for early growth-related traits, including estimated biovolume, projected leaf area, early plant height and colour uniformity, were established and complemented by fresh and dry weight biomass. Genome-wide SNP array data provided the framework for genome-wide association analyses. Using time point data and relative growth rates, multiple robust main effect marker-trait associations for biomass and related traits were detected. Candidate genes involved in meristem development, cell wall modification and transcriptional regulation were detected. Our results demonstrate that early plant growth is a highly complex trait governed by several medium and many small effect loci, most of which act only during short phases. These observations highlight the importance of taking the temporal patterns of QTL/allele actions into account and emphasize the need for detailed time-resolved analyses to effectively unravel the complex and stage-specific contributions of genes affecting growth processes that operate at different developmental phases., (© 2019 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

The ongoing global intensification of wheat production will likely be accompanied by a rising pressure of Fusarium diseases. While utmost attention was given to Fusarium head blight (FHB) belowground plant infections of the pathogen have largely been ignored. The current knowledge about the impact of soil borne Fusarium infection on plant performance and the underlying genetic mechanisms for resistance remain very limited. Here, we present the first large-scale investigation of Fusarium root rot (FRR) resistance using a diverse panel of 215 international wheat lines. We obtained data for a total of 21 resistance-related traits, including large-scale Real-time PCR experiments to quantify fungal spread. Association mapping and subsequent haplotype analyses discovered a number of highly conserved genomic regions associated with resistance, and revealed a significant effect of allele stacking on the stembase discoloration. Resistance alleles were accumulated in European winter wheat germplasm, implying indirect prior selection for improved FRR resistance in elite breeding programs. Our results give first insights into the genetic basis of FRR resistance in wheat and demonstrate how molecular parameters can successfully be explored in genomic prediction. Ongoing work will help to further improve our understanding of the complex interactions of genetic factors influencing FRR resistance.

Genomic selection (GS) has revolutionized breeding for quantitative traits in plants, offering potential to optimize resource allocation in breeding programs and increase genetic gain per unit of time. Modern high-density single nucleotide polymorphism (SNP) arrays comprising up to several hundred thousand markers provide a user-friendly technology to characterize the genetic constitution of whole populations and for implementing GS in breeding programs. However, GS does not build upon detailed genotype profiling facilitated by maximum marker density. With extensive genome-wide linkage disequilibrium (LD) being a common characteristic of breeding pools, fewer representative markers from available high-density genotyping platforms could be sufficient to capture the association between a genomic region and a phenotypic trait. To examine the effects of reduced marker density on genomic prediction accuracy, we collected data on three traits across 2 yr in a panel of 203 homozygous Chinese semiwinter rapeseed ( L.) inbred lines, broadly encompassing allelic variability in the Asian genepool. We investigated two approaches to selecting subsets of markers: a trait-dependent strategy based on genome-wide association study (GWAS) significance thresholds and a trait-independent method to detect representative tag SNPs. Prediction accuracies were evaluated using cross-validation with ridge-regression best linear unbiased predictions (rrBLUP). With semiwinter rapeseed as a model species, we demonstrate that low-density marker sets comprising a few hundred to a few thousand markers enable high prediction accuracies in breeding populations with strong LD comparable to those achieved with high-density arrays. Our results are valuable for facilitating routine application of cost-efficient GS in breeding programs., (Copyright © 2018 Crop Science Society of America.)

Objectives: The aim of this multicenter retrospective study was to investigate safety and efficacy of direct acting antiviral (DAA) treatment in the rare subgroup of patients with HCV/HIV-coinfection and advanced liver cirrhosis on the liver transplant waiting list or after liver transplantation, respectively., Methods: When contacting 54 German liver centers (including all 23 German liver transplant centers), 12 HCV/HIV-coinfected patients on antiretroviral combination therapy were reported having received additional DAA therapy while being on the waiting list for liver transplantation (patient characteristics: Child-Pugh A (n = 6), B (n = 5), C (n = 1); MELD range 7-21; HCC (n = 2); HCV genotype 1a (n = 8), 1b (n = 2), 4 (n = 2)). Furthermore, 2 HCV/HIV-coinfected patients were denoted having received DAA therapy after liver transplantation (characteristics: HCV genotype 1a (n = 1), 4 (n = 1))., Results: Applied DAA regimens were SOF/DAC (n = 7), SOF/LDV/RBV (n = 3), SOF/RBV (n = 3), PTV/r/OBV/DSV (n = 1), or PTV/r/OBV/DSV/RBV (n = 1), respectively. All patients achieved SVR 12, in the end. In one patient, HCV relapse occurred after 24 weeks of SOF/DAC therapy; subsequent treatment with 12 weeks PTV/r/OBV/DSV achieved SVR 12. One patient underwent liver transplantation while on DAA treatment. Analysis of liver function revealed either stable parameters or even significant improvement during DAA therapy and in follow-up. MELD scores were found to improve in 9/13 therapies in patients on the waiting list for liver transplantation; in only 2 patients a moderate increase of MELD scores persisted at the end of follow-up., Conclusion: DAA treatment was safe and highly effective in this nation-wide cohort of patients with HCV/HIV-coinfection awaiting liver transplantation or being transplanted., Competing Interests: The authors have declared that no competing interests exist.

Key Message: Genomic prediction using the Brassica 60 k genotyping array is efficient in oilseed rape hybrids. Prediction accuracy is more dependent on trait complexity than on the prediction model. In oilseed rape breeding programs, performance prediction of parental combinations is of fundamental importance. Due to the phenomenon of heterosis, per se performance is not a reliable indicator for F 1 -hybrid performance, and selection of well-paired parents requires the testing of large quantities of hybrid combinations in extensive field trials. However, the number of potential hybrids, in general, dramatically exceeds breeding capacity and budget. Integration of genomic selection (GS) could substantially increase the number of potential combinations that can be evaluated. GS models can be used to predict the performance of untested individuals based only on their genotypic profiles, using marker effects previously predicted in a training population. This allows for a preselection of promising genotypes, enabling a more efficient allocation of resources. In this study, we evaluated the usefulness of the Illumina Brassica 60 k SNP array for genomic prediction and compared three alternative approaches based on a homoscedastic ridge regression BLUP and three Bayesian prediction models that considered general and specific combining ability (GCA and SCA, respectively). A total of 448 hybrids were produced in a commercial breeding program from unbalanced crosses between 220 paternal doubled haploid lines and five male-sterile testers. Predictive ability was evaluated for seven agronomic traits. We demonstrate that the Brassica 60 k genotyping array is an adequate and highly valuable platform to implement genomic prediction of hybrid performance in oilseed rape. Furthermore, we present first insights into the application of established statistical models for prediction of important agronomical traits with contrasting patterns of polygenic control.

In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.

A 35-year-old woman who had previously undergone a lung transplantation presented with severe abdominal pain and vomiting. The gastroscopy showed diffuse ulcerative gastric lesions. Tests for varicella zoster virus and Epstein-Barr virus via polymerase chain reactions (PCR) on endoscopically obtained gastric biopsies were found to be positive and confirmed varicella gastritis. Intravenous antiviral therapy with acyclovir was administered resulting in a normalization of all clinical symptoms, especially of abdominal pain and inflammation parameters.

History and admission findings: We report on a 76-year-old man presenting with painless jaundice who developed dialysis-dependent acute kidney injury. Investigations: Biliary tract was examined with endoscopy, in addition kidney biopsy was performed. Diagnosis, treatment and course: A stenosing process could be seen in the biliary tract, leading to stent implantation. However, jaundice did not resolve. Kidney biopsy revealed bile casts indicating cholemic nephropathy. After switch of concomitant medication, hyperbilirubinemia resolved and kidney function was completely restored. Conclusion: Cholestatic liver disease can cause acute kidney injury by formation of bile casts in the tubuli defining cholemic nephropathy. Resolution of cholestasis can restore kidney function., (© Georg Thieme Verlag KG Stuttgart · New York.)

Aim: To gather data on the antiviral efficacy and safety of second generation direct acting antiviral (DAA) treatment with respect to sustained virological response (SVR) 12 wk after conclusion of treatment, and to determine predictors of SVR12 in this setting., Methods: Two hundred and sixty patients treated with SOF combination partners PR (n = 51), R (n = 10), SMV (n = 30), DCV (n = 81), LDV (n = 73), or 3D (n = 15). 144/260 were pre-treated, 89/260 had liver cirrhosis, 56/260 had portal hypertension with platelets < 100/nL, 25/260 had a MELD score ≥ 10 and 17/260 were post-liver transplantation patients. 194/260 had HCV GT1, 44/260 HCV GT3., Results: Two hundred and forty/256 (93.7%) patients achieved SVR12 (mITT); 4/260 were lost to follow-up. SVR12 rates for subgroups were: 92% for SOF/DCV, 93% for each SOF/SMV, SOF/PR, 94% for SOF/LDV, 100% for 3D, 94% for pretreated, 87% for liver cirrhosis, 82% for patients with platelets < 100/nL, 88% post-liver transplantation, 95% for GT1a, 93% for GT1b, 90% for GT3, 100% for GT2, 4, and 6. 12 patients suffered from relapse, 6 prematurely discontinued treatment, of which 4 died. Negative predictors of SVR12 were a platelet count < 100/nL, MELD score ≥ 10 (P < 0.0001), liver cirrhosis (P = 0.005) at baseline. In Interferon-free treatment GT3 had significantly lower SVR rates than GT1 (P = 0.016). Side effects were mild., Conclusion: Excellent SVR12 rates and the favorable side-effect profile of DAA-combination therapy can be well translated into "real-world". Patients with advanced liver disease, signs of portal hypertension, especially with platelets < 100/nL and patients with GT3 are in special need for further research efforts to overcome comparatively higher rates of virological failure., Competing Interests: Conflict-of-interest statement: Werner CR received travel grants from Gilead, Bristol-Myers-Squibb, Roche, and Janssen-Cilag, and lecture fees from Roche; Schwarz JM and Beck R declare no conflict; Egetemeyr DP received travel grants, and lecture fees from Roche; Malek NP declares no conflict; Lauer UM received travel grants from Roche; Berg CP received travel grants from Gilead, Bristol-Myers-Squibb, Roche, and Janssen-Cilag, and lecture fees from Gilead, Bristol-Myers-Squibb, Roche, and Janssen-Cilag. The authors received no financial support. No funding source exists.