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Abstract Conventional dendritic cells (cDC) play key roles in immune induction, but what drives their heterogeneity and functional specialization is still ill-defined. Here we show that cDC-specific deletion of the transcriptional repressor Bcl6 in mice alters the phenotype and transcriptome of cDC1 and cDC2, while their lineage identity is preserved. Bcl6-deficient cDC1 are diminished in the periphery but maintain their ability to cross-present antigen to CD8+ T cells, confirming general maintenance of this subset. Surprisingly, the absence of Bcl6 in cDC causes a complete loss of Notch2-dependent cDC2 in the spleen and intestinal lamina propria. DC-targeted Bcl6-deficient mice induced fewer T follicular helper cells despite a profound impact on T follicular regulatory cells in response to immunization and mounted diminished Th17 immunity to Citrobacter rodentium in the colon. Our findings establish Bcl6 as an essential transcription factor for subsets of cDC and add to our understanding of the transcriptional landscape underlying cDC heterogeneity.

Abstract Urinary tract obstruction during renal development leads to inflammation, leukocyte infiltration, tubular cell death, and interstitial fibrosis. Interleukin-10 (IL-10) is an anti-inflammatory cytokine, produced mainly by monocytes/macrophages and regulatory T-cells. IL-10 inhibits innate and adaptive immune responses. IL-10 has a protective role in the adult model of obstructive uropathy. However, its role in neonatal obstructive uropathy is still unclear which led us to study the role of IL-10 in neonatal mice with unilateral ureteral obstruction (UUO). UUO serves as a model for congenital obstructive nephropathies, a leading cause of kidney failure in children. Newborn Il-10 −/− and C57BL/6 wildtype-mice (WT) were subjected to complete UUO or sham-operation on the 2nd day of life. Neonatal kidneys were harvested at day 3, 7, and 14 of life and analyzed for different leukocyte subpopulations by FACS, for cytokines and chemokines by Luminex assay and ELISA, and for inflammation, programmed cell death, and fibrosis by immunohistochemistry and western blot. Compared to WT mice, Il-10 −/− mice showed reduced infiltration of neutrophils, CD11bhi cells, conventional type 1 dendritic cells, and T-cells following UUO. Il-10 −/− mice with UUO also showed a reduction in pro-inflammatory cytokine and chemokine release compared to WT with UUO, mainly of IP-10, IL-1α, MIP-2α and IL-17A. In addition, Il-10 −/− mice showed less necroptosis after UUO while the rate of apoptosis was not different. Finally, α-SMA and collagen abundance as readout for fibrosis were similar in Il-10 −/− and WT with UUO. Surprisingly and in contrast to adult Il-10 −/− mice undergoing UUO, neonatal Il-10 −/− mice with UUO showed a reduced inflammatory response compared to respective WT control mice with UUO. Notably, long term changes such as renal fibrosis were not different between neonatal Il-10 −/− and neonatal WT mice with UUO suggesting that IL-10 signaling is different in neonates and adults with UUO.

Abstract Background Tertiary lymphoid structures (TLSs) are dense accumulations of lymphocytes in inflamed peripheral tissues, including cancer, and are associated with improved survival and response to immunotherapy in various solid tumors. Histological TLS quantification has been proposed as a novel predictive and prognostic biomarker, but lack of standardized methods of TLS characterization hampers assessment of TLS densities across different patients, diseases, and clinical centers. Methods We introduce an approach based on HookNet-TLS, a multi-resolution deep learning model, for automated and unbiased TLS quantification and identification of germinal centers in routine hematoxylin and eosin stained digital pathology slides. We developed HookNet-TLS using n = 1019 manually annotated TCGA slides from clear cell renal cell carcinoma, muscle-invasive bladder cancer, and lung squamous cell carcinoma. Results Here we show that HookNet-TLS automates TLS quantification across multiple cancer types achieving human-level performance and demonstrates prognostic associations similar to visual assessment. Conclusions HookNet-TLS has the potential to be used as a tool for objective quantification of TLS in routine H&E digital pathology slides. We make HookNet-TLS publicly available to promote its use in research.

In this study, we present the design, simulation, and implementation of a DC-DC synchronous buck converter utilizing IISB’s 2 μm 4H-silicon carbide (SiC) complementary metal–oxide–semiconductor (CMOS) technology. The converter is designed to meet the demands of modern integrated circuits, particularly in the field of integrated power management. The SiC technology offers enhanced performance and reliability at high temperatures, making it especially suitable for applications that operate in these conditions, including automotive systems, and aerospace, among others. The power transistors and gate drivers are fully integrated on-chip, optimizing efficiency and minimizing footprint. Additionally, the study contributes to the understanding of SiC technology and its application in integrated circuit design. Simulation results demonstrate a peak efficiency of 86.6% at 120 mA load current and 84.8% at 300 mA load current, showing the converter performance under different operating conditions. Furthermore, at high temperatures (295 °C), the converter achieves an efficiency of 89.6%, demonstrating its robustness and versatility in extreme environments. These findings contribute to the advancement of integrated circuit design and facilitate advancements in more efficient and robust power management solutions.

Introduction: Short educational programs prior to metabolic and bariatric surgery (MBS) provide information to prepare patients adequately for surgery and subsequent changes. Our knowledge of the beneficial effects of these programs on stabilizing and improving mental health of patients with obesity awaiting surgery is incomplete. The objective of this study was to assess the effects of a group-based educational program before MBS on three key factors: i) patients' mental health, ii) the program's perceived helpfulness from the patients' perspective, and iii) the effectiveness of delivering the program online via videoconferencing. Methods: Validated questionnaires for anxiety, depression, stress, and quality of life before and after the program were assessed. Additionally, participants’ perspectives of benefits were assessed. Two subgroups, one participating in face-to-face classes, the other participating online via videoconferencing, were compared. Results: Three hundred five patients with obesity waiting for MBS participated in the program. The dropout rate was 3%. On mean average, symptoms of anxiety (-1.1 units (SD 4.6), p < 0.001), depression (-0.9 units (SD 4.6), p < 0.001), and stress (-4.6 units (SD 15.6), p < 0.001) improved, while physical quality of life (+1.7 (SD 9.7), p = 0.016) and body weight (-0.3 kg (SD 8.7), p = 0.57) remained stable. Patients perceived the program as very beneficial. The results were similar between delivery methods (face-to-face versus videoconferencing). Conclusion: The educational program proved to be effective in bridging the gap in preoperative preparation while also stabilizing participants' mental health. In addition, participants perceived the program as supportive. Online participation via video conferencing can be offered as an equivalent option to face-to-face classes.

Abstract ADP‐ribosylation (ADPR) of proteins is catalyzed by ADP‐ribosyltransferases, which are targeted by inhibitors (i.e. poly(ADP‐ribose) polymerase inhibitors [PARPi]). Although renal cell carcinoma (RCC) cells are sensitive in vitro to PARPi, studies on the association between ADPR levels and somatic loss of function mutations in DNA damage repair genes are currently missing. Here we observed, in two clear cell RCC (ccRCC) patient cohorts (n = 257 and n = 241) stained with an engineered ADP‐ribose binding macrodomain (eAf1521), that decreased cytoplasmic ADPR (cyADPR) levels significantly correlated with late tumor stage, high‐ISUP (the International Society of Urological Pathology) grade, presence of necrosis, dense lymphocyte infiltration, and worse patient survival (p

IntroductionCOVID-19 affected global physical and psychological health. The purpose of this study was to explore the pandemics impact on health-related quality of life (HRQoL), mental health (anxiety, depression, and perceived stress) and eating behavior in people with severe obesity participating in a multimodal conservative behavioral weight loss (BWL) program conducted via videoconferencing. Additionally, the efficacy of the six-month BWL program in a virtual video-based setting during the pandemic was examined.Methods297 participants of a face-to-face multimodal behavioral weight loss program prior to the pandemic (PrePAN, May 2014–September 2019) and 146 participants of the in terms of content same intervention in a videoconference-based setting during the pandemic (PAN, July 2020–April 2022) were questioned and compared using standardized questionnaires for HRQoL, symptoms of depressive and anxiety disorders, perceived stress, and eating behavior at baseline and at the end of treatment.ResultsSymptoms for anxiety, depression and perceived stress were similar between PrePAN and PAN at baseline. In addition, PAN tended to show lower disinhibition of eating behavior and feelings of hunger than PrePAN. During the pandemic, the BWL intervention resulted in body weight loss (67%) or stabilization (16%) in most of the participants. It also contributed by improving physical HRQoL, lower worries, and improved eating behaviors compared to baseline.ConclusionDuring the COVID-19 pandemic, baseline mental health of people with morbid obesity was not worse than before the pandemic. Additionally, the BWL intervention in the virtual video-based setting stabilized and improved physical and mental health during the COVID-19 pandemic.

Families who have children with delays or disabilities are often expected to become advocates for their children. Despite this inherent expectation, there is limited research available focused on advocacy during the early years (birth to three). The purpose of this study was to use qualitative inquiry, specifically semi-structured interviews, to explore 15 parents' meanings of and experiences with advocacy in the early years. Thematic and constant comparative analyses were used and subsequently 22 codes within six major categories were identified. Three major findings related to the meaning and nature of advocacy in the early years involved: (a) education and being a voice for children are critical components of parents' constructed definitions of advocacy; (b) parents engage in a variety of advocacy interactions, across formal and informal settings, prior to and during Early Intervention; and (c) and parental advocacy requires capital resources. Implications for practice and future research are discussed.

Mononuclear phagocytes (MP), i.e., monocytes, macrophages, and dendritic cells (DCs), are essential for immune homeostasis via their capacities to clear pathogens, pathogen components, and non-infectious particles. However, tissue injury-related changes in local microenvironments activate resident and infiltrating MP towards pro-inflammatory phenotypes that contribute to inflammation by secreting additional inflammatory mediators. Efficient control of injurious factors leads to a switch of MP phenotype, which changes the microenvironment towards the resolution of inflammation. In the same way, MP endorses adaptive structural responses leading to either compensatory hypertrophy of surviving cells, tissue regeneration from local tissue progenitor cells, or tissue fibrosis and atrophy. Under certain circumstances, MP contribute to the reversal of tissue fibrosis by clearance of the extracellular matrix. Here we give an update on the tissue microenvironment-related factors that, upon tissue injury, instruct resident and infiltrating MP how to support host defense and recover tissue function and integrity. We propose that MP are not intrinsically active drivers of organ injury and dysfunction but dynamic amplifiers (and biomarkers) of specific tissue microenvironments that vary across spatial and temporal contexts. Therefore, MP receptors are frequently redundant and suboptimal targets for specific therapeutic interventions compared to molecular targets upstream in adaptive humoral or cellular stress response pathways that influence tissue milieus at a contextual level.

Abstract Key message The TreeTrace_spruce database contains images and measurements of 100 Norway spruce (Picea abies (L.) H.Karst.) logs from Northeastern France, each about 4.5 m long. The image database includes RGB images of large and small ends of the logs and hyperspectral and computed tomography (CT) images of wood discs sampled at both log ends. The 100 logs were also fully X-ray scanned with a CT device for roundwoods and their top surface was scanned with a terrestrial LiDAR device. The measurements performed on discs include wood local density, growth ring widths and pith location. This database is complementary to another one (TreeTrace_Douglas) resulting from the same ANR project TreeTrace, but if the objectives are similar, the protocols and conditions of acquisition are not the same for these two databases. TreeTrace_spruce dataset is available at https://doi.org/10.57745/WKLTJI and associated metadata are available at https://metadata-afs.nancy.inra.fr/geonetwork/srv/fre/catalog.search#/metadata/cffee2f1-18e1-4b53-9f5b-6cc4c66f1cb8 .

Studies on cultural ecosystem services (CES) in urban forests using Public Participation GIS mapping are a well-established field of research. However, far fewer studies do exist that also illuminate perceived disservices, thus omitting an important part of human-forest relationships. Advancing knowledge on unpleasant places can promote outdoor recreation and help forest managers focus on disservices that matter. This study aims at spatially identifying people’s perceptions in urban forests with focus on unpleasant experiences. We elicited perceived disservices and CES spatially by collecting Public Participation GIS data (PPGIS) from city dwellers in three urban forests in Germany’s Southwest (755 respondents mapped 1552 places of disservices). We investigated relationships between sociodemographic characteristics and the number of mapped places using Spearman’s rank. We also explored the spatial concurrence between disservices and CES using Spearman’s rank. We identified a hierarchy of importance of forest visitors’ perceived dislikes. We revealed that negative perceptions of urban forest visitors originated broadly from people and their traces and rarely from the ecosystem according to existing ecosystem disservices typologies (EDS). We found a significant relationship between age and the number of mapped services. We found clusters of disliked places and correlations between disservices and CES, indicating that hotspots of CES in turn are also hotspots of disservices. We conclude that city foresters may best address disservices by advancing guidance-concepts for spatial movements of urban forest visitors within the forest to avoid conflicting clusters of various stakeholders. Our results may help city foresters to better manage both the forest and visitors’ various interests.

Although the Individuals With Disabilities Education Improvement Act (IDEA) mandates parent participation in their children's education programs, the implementation of IDEA results in parent effort beyond participation, specifically, an expectation of advocacy. To date, research on the advocacy expectation is mixed, with some parents perceiving advocacy as an obligation to ensure appropriate services for their children, whereas others argue it is unreasonable and has cultural dissonance, disadvantaging some parents. We examined parent perspectives of the advocacy expectation in special education through 19 focus groups with 127 parents of children with disabilities across four states. Findings included a nuanced understanding of the advocacy expectation, with participants reporting the importance of advocacy and some describing that advocacy was part of their social role. However, under adversarial circumstances with school personnel, participants described feeling overwhelmed because the advocacy expectation felt more difficult than it needed to be. We discuss implications for policy and practice.

Industrial-quality inspections, particularly those leveraging AI, require significant amounts of training data. In fields like injection molding, producing a multitude of defective parts for such data poses environmental and financial challenges. Synthetic training data emerge as a potential solution to address these concerns. Although the creation of realistic synthetic 2D images from 3D models of injection-molded parts involves numerous rendering parameters, the current literature on the generation and application of synthetic data in industrial-quality inspection scarcely addresses the impact of these parameters on AI efficacy. In this study, we delve into some of these key parameters, such as camera position, lighting, and computational noise, to gauge their effect on AI performance. By utilizing Blender software, we procedurally introduced the “flash” defect on a 3D model sourced from a CAD file of an injection-molded part. Subsequently, with Blender’s Cycles rendering engine, we produced datasets for each parameter variation. These datasets were then used to train a pre-trained EfficientNet-V2 for the binary classification of the “flash” defect. Our results indicate that while noise is less critical, using a range of noise levels in training can benefit model adaptability and efficiency. Variability in camera positioning and lighting conditions was found to be more significant, enhancing model performance even when real-world conditions mirror the controlled synthetic environment. These findings suggest that incorporating diverse lighting and camera dynamics is beneficial for AI applications, regardless of the consistency in real-world operational settings.

The aim of this first randomized clinical trial (RCT) was to determine whether intraoral scans (IOS) can be used as a visual aid to improve the communication of dental findings in pediatric dentistry. Therefore, 60 children (mean age 10.1 ± 3.3 years) and their accompanying parents/primary caregivers (PGs) were examined between July 2022 and February 2023. Patients were randomly allocated to two groups: half of the participants were informed of the children’s dental findings including treatment plans by verbal explanation alone (control group, n = 30), while the other half were informed using IOS (Trios 4, 3Shape) as a visual aid to support the verbal explanation (study group, n = 30). Both groups then completed a questionnaire regarding their children’s diagnosis, treatment needs, planned therapy, and oral hygiene. Statistical analysis was performed using a t-test (p < 0.05). Overall, there was a significant difference between the two groups (p < 0.001) in terms of understanding the current oral situation of their children. While 85.5 ± 17.3% (mean ± standard deviation) of the answers were correct in the study group, only 57.2 ± 17.8% of the participants in the control group were capable of answering the questions correctly. In particular, the control group had difficulties answering the questions about treatment needs and therapy correctly. Within the limitations of this first pilot study, IOS can be clearly recommended as a visual aid to improve the communication of dental findings with PGs in pediatric dentistry.

Using telehealth in early intervention has the potential to increase family and child outcomes as well as to increase access to family-centered services. Yet, little is known about families' perspectives, including concerns, prior to using telehealth in early intervention. The purpose of this study was to explore families' perceptions and attitudes toward using telehealth in early intervention. Nine focus groups were conducted with 37 families of children with disabilities. Overall, participants preferred in-person visits (versus telehealth) for early intervention services. However, participants recognized some benefits of telehealth in facilitating communication with early intervention professionals and reaching underserved families. In addition to benefits, participants identified barriers to telehealth including limited access to: technology, the internet and materials. Policymakers and professionals should consider the perspectives, priorities and concerns of families before implementing telehealth in early intervention.

The ontogeny of conventional and plasmacytoid dendritic cells (DC) and how these two cell types are related is not fully known. Here the authors identify a pool of bone marrow precursor cells expressing Ly6D Siglec-H and Zbtb46 that can differentiate into either cDC or pDC and show that type I IFN can limit cDC and favor pDC output from these precursors.

Due to systemic barriers, Spanish-speaking (versus English-speaking) parents of children with disabilities are less likely to participate in educational decision-making. However, little research has directly compared special education experiences between both populations. The purpose of this study was to explore the differences and similarities between Spanish-speaking (n = 12) and English-speaking (n = 44) parents of children with disabilities. Specifically, six focus groups were conducted in either English or Spanish in two states. There were three main findings: exacerbated negative experiences (e.g., disempowerment and lack of teacher knowledge) for Spanish-speaking (versus English-speaking) parents, unique communication barriers among Spanish-speaking families and shared barriers among English- and Spanish-speaking parents. Implications for research and practice are discussed.

Parent advocacy has led to improved educational access and outcomes for students with disabilities. Extant research indicates that parents are more likely to participate in individual advocacy than systemic advocacy. Due to the preponderance of individual advocacy, limited research has focused on systemic advocacy. Thus, the purpose of this study was to explore individual and systemic advocacy among parents of children with disabilities. Prior to attending a training on civic engagement, 127 parents from four states participated in English- or Spanish-speaking focus groups. Results indicated participants more frequently engaged in individual advocacy than systemic advocacy and utilized a greater variety of individual advocacy strategies. Additionally, parent advocacy can be developmental, moving from individual to systemic efforts. Participants also identified barriers and facilitators impacting their systemic and individual advocacy. Implications for future research and practice are discussed.

In the past, parents of children with disabilities have spearheaded several policies for individuals with disabilities. However, little is known about their experiences with legislators. To address this gap, focus groups and surveys about legislative advocacy were conducted with 127 parents of individuals with disabilities across four states. The purpose of the study was to explore parent perceptions about experiences with legislative advocacy including the frequency of, strategies for, and barriers to legislative advocacy. Descriptive statistics were conducted to analyze the survey data; constant comparative analysis was used to analyze the focus group data. Participants reported engaging in various forms of legislative advocacy. Participants shared positive and negative experiences interacting with legislators, including individual and collective advocacy efforts. Some participants did not engage in legislative advocacy due to intimidation. Relationships facilitated legislative advocacy for participants. Implications for future research about legislative advocacy and practices to facilitate legislative advocacy are discussed.

Transcriptional changes during prostate cancer progression are not yet fully understood. Here, the authors integrate a transcriptomics atlas of prostate cancer and validate it with preclinical models and single-cell RNA-seq, revealing the role of EZH2 and macrophage polarisation in tumour progression.

BackgroundIn contrast to infection or mechanical issues joint replacement failure following inflammatory adverse reactions is poorly understood.ObjectiveTo assess the association of IL-1β polymorphisms and history of allergy with aseptic non-mechanical complications following arthroplasty.MethodsIn 102 patients with aseptic non-mechanically caused symptomatic knee or hip arthroplasty (SA) and 93 patients with asymptomatic arthroplasty (AA) questionnaire-based history, patch test with at least standard series, lymphocyte transformation test (LTT) with nickel, cobalt and chromium and interleukin-1 polymorphism analysis were done. Three polymorphisms of the IL1B gene [IL-1b -3954 (rs1143634), IL-1b -511 (rs16944) and IL-1b -31 (rs1143627)] and one polymorphism of the IL1RN gene [IL1RN intron 2, variable number of tandem repeats, VNTR (rs2234663)] were assessed by PCR and gel electrophoresis.ResultsWe found no significant difference in smoking history and atopy but 25% versus 10% of self-reported metal allergy in SA versus AA; the patch test (respective, LTT) for metal sensitivity was more often positive in SA patients. The allele 498 bp of the IL1RN polymorphism occurred significantly more often in the SA group (37% versus 11%; p < 0.0001). Upon additional presence of atopy, the difference was even greater (60% vs 10%) (p < 0.000001). There was no association of IL-1 polymorphisms with metal allergy.ConclusionThe IL1RN VNTR allele 498 bp was strongly associated with SA. In patients with a history of atopy, presence of the IL1RN VNTR allele 498 bp led to a four-fold higher SA prevalence compared to patients without this allele.

Abstract Precision fish farming is an emerging concept in aquaculture research and industry, which combines new technologies and data processing methods to enable data-based decision making in fish farming. The concept is based on the automated monitoring of fish, infrastructure, and the environment ideally by contactless methods. The identification of individual fish of the same species within the cultivated group is critical for individualized treatment, biomass estimation and fish state determination. A few studies have shown that fish body patterns can be used for individual identification, but no system for the automation of this exists. We introduced a methodology for fully automatic Atlantic salmon (Salmo salar) individual identification according to the dot patterns on the skin. The method was tested for 328 individuals, with identification accuracy of 100%. We also studied the long-term stability of the patterns (aging) for individual identification over a period of 6 months. The identification accuracy was 100% for 30 fish (out of water images). The methodology can be adapted to any fish species with dot skin patterns. We proved that the methodology can be used as a non-invasive substitute for invasive fish tagging. The non-invasive fish identification opens new posiblities to maintain the fish individually and not as a fish school which is impossible with current invasive fish tagging.

Gene fusions involving the ERG transcription factor and point mutations in the ubiquitin ligase adaptor SPOP are two truncal mutations that are mutually exclusively present in prostate cancer. Here, the authors show that mutations in SPOP render prostate tumor cells sensitive to antiandrogen therapy and that the presence of ERG promotes sensitivity to high dose of androgen and SPOP inhibition.

Type 2 conventional dendritic cells (cDC2) are important immune activators in adults, but their development and functions at the neonatal stage remain unclear. Here the authors show, using fate-mapping and single-cell RNA sequencing, that neonatal cDC2 come from multiple origins, but converge functionally as potent immune activators upon proper stimuli.

Introduction The human microbiota, the community of micro-organisms in different cavities, has been increasingly linked with inflammatory and neoplastic diseases. While investigation into the gut microbiome has been robust, the urinary microbiome has only recently been described. Investigation into the relationship between bladder cancer (BC) and the bladder and the intestinal microbiome may elucidate a pathophysiological relationship between the two. The bladder or the intestinal microbiome or the interplay between both may also act as a non-invasive biomarker for tumour behaviour. While these associations have not yet been fully investigated, urologists have been manipulating the bladder microbiome for treatment of BC for more than 40 years, treating high grade non-muscle invasive BC (NMIBC) with intravesical BCG immunotherapy. Neither the association between the microbiome sampled directly from bladder tissue and the response to BCG-therapy nor the association between response to BCG-therapy with the faecal microbiome has been studied until now. A prognostic tool prior to initiation of BCG-therapy is still needed.Methods and analysis In patients with NMIBC bladder samples will be collected during surgery (bladder microbiome assessment), faecal samples (microbiome assessment), instrumented urine and blood samples (biobank) will also be taken. We will analyse the microbial community by 16S rDNA gene amplicon sequencing. The difference in alpha diversity (diversity of species within each sample) and beta diversity (change in species diversity) between BCG-candidates will be assessed. Subgroup analysis will be performed which will lead to the development of a clinical prediction model estimating risk of BCG-response.Ethics and dissemination The study has been approved by the Cantonal Ethics Committee Zurich (2021-01783) and it is being conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Study results will be disseminated through peer-reviewed journals and national and international scientific conferences.Trial registration number NCT05204199.

Introduction Despite continued efforts, long-term outcomes of kidney transplantation remain unsatisfactory. Kidney graft rejections are independent risk factors for graft failure. At the participating centres of the TRAnsplant BIOpsies study group, a common therapeutic standard has previously been defined for the treatment of graft rejections. The outcomes of this strategy will be assessed in a prospective, observational cohort study.Methods and analysis A total of 800 kidney transplantation patients will be enrolled who undergo a graft biopsy because of deteriorating kidney function. Patients will be stratified according to the Banff classification, and the influence of the treatment strategy on end points will be assessed using regression analysis. Primary end points will be all-cause mortality and graft survival. Secondary end points will be worsening of kidney function (≥30% decline of estimated Glomerular Filtration Rate [eGFR] or new-onset large proteinuria), recurrence of graft rejection and treatment response. Baseline data and detailed histopathology data will be entered into an electronic database on enrolment. During a first follow-up period (within 14 days) and subsequent yearly follow-ups (for 5 years), treatment strategies and clinical course will be recorded. Recruitment at the four participating centres started in September 2016. As of August 2020, 495 patients have been included.Ethics and dissemination Ethical approval for the study has been obtained from the ethics committee of Kiel (AZ B 278/16) and was confirmed by the committees of Munich, Mainz and Stuttgart. The results will be reported in a peer-reviewed journal, according to the Strengthening the Reporting of Observational Studies in Epidemiology criteria.Trial registration number ISRCTN78772632; Pre-results.

Abstract Background Identifying molecular differences between primary and metastatic colorectal cancers—now possible with the aid of omics technologies—can improve our understanding of the biological mechanisms of cancer progression and facilitate the discovery of novel treatments for late-stage cancer. We compared the DNA methylomes of primary colorectal cancers (CRCs) and CRC metastases to the liver. Laser microdissection was used to obtain epithelial tissue (10 to 25 × 106 μm2) from sections of fresh-frozen samples of primary CRCs (n = 6), CRC liver metastases (n = 12), and normal colon mucosa (n = 3). DNA extracted from tissues was enriched for methylated sequences with a methylCpG binding domain (MBD) polypeptide-based protocol and subjected to deep sequencing. The performance of this protocol was compared with that of targeted enrichment for bisulfite sequencing used in a previous study of ours. Results MBD enrichment captured a total of 322,551 genomic regions (249.5 Mb or ~ 7.8% of the human genome), which included over seven million CpG sites. A few of these regions were differentially methylated at an expected false discovery rate (FDR) of 5% in neoplastic tissues (primaries: 0.67%, i.e., 2155 regions containing 279,441 CpG sites; liver metastases: 1%, i.e., 3223 regions containing 312,723 CpG sites) as compared with normal mucosa samples. Most of the differentially methylated regions (DMRs; 94% in primaries; 70% in metastases) were hypermethylated, and almost 80% of these (1882 of 2396) were present in both lesion types. At 5% FDR, no DMRs were detected in liver metastases vs. primary CRC. However, short regions of low-magnitude hypomethylation were frequent in metastases but rare in primaries. Hypermethylated DMRs were far more abundant in sequences classified as intragenic, gene-regulatory, or CpG shelves-shores-island segments, whereas hypomethylated DMRs were equally represented in extragenic (mainly, open-sea) and intragenic (mainly, gene bodies) sequences of the genome. Compared with targeted enrichment, MBD capture provided a better picture of the extension of CRC-associated DNA hypermethylation but was less powerful for identifying hypomethylation. Conclusions Our findings demonstrate that the hypermethylation phenotype in CRC liver metastases remains similar to that of the primary tumor, whereas CRC-associated DNA hypomethylation probably undergoes further progression after the cancer cells have migrated to the liver.

Abstract Retention forestry, which retains a portion of the original stand at the time of harvesting to maintain continuity of structural and compositional diversity, has been originally developed to mitigate the impacts of clear‐cutting. Retention of habitat trees and deadwood has since become common practice also in continuous‐cover forests of Central Europe. While the use of retention in these forests is plausible, the evidence base for its application is lacking, trade‐offs have not been quantified, it is not clear what support it receives from forest owners and other stakeholders and how it is best integrated into forest management practices. The Research Training Group ConFoBi (Conservation of Forest Biodiversity in Multiple‐use Landscapes of Central Europe) focusses on the effectiveness of retention forestry, combining ecological studies on forest biodiversity with social and economic studies of biodiversity conservation across multiple spatial scales. The aim of ConFoBi is to assess whether and how structural retention measures are appropriate for the conservation of forest biodiversity in uneven‐aged and selectively harvested continuous‐cover forests of temperate Europe. The study design is based on a pool of 135 plots (1 ha) distributed along gradients of forest connectivity and structure. The main objectives are (a) to investigate the effects of structural elements and landscape context on multiple taxa, including different trophic and functional groups, to evaluate the effectiveness of retention practices for biodiversity conservation; (b) to analyze how forest biodiversity conservation is perceived and practiced, and what costs and benefits it creates; and (c) to identify how biodiversity conservation can be effectively integrated in multi‐functional forest management. ConFoBi will quantify retention levels required across the landscape, as well as the socio‐economic prerequisites for their implementation by forest owners and managers. ConFoBi's research results will provide an evidence base for integrating biodiversity conservation into forest management in temperate forests.

Neglecting tissue heterogeneity during the analysis of microRNA (miRNA) levels results in average signals from an unknown mixture of different cell types that are difficult to interpret. Here we demonstrate the technical requirements needed to obtain high-quality, quantitative miRNA expression information from tumor tissue compartments obtained by laser microdissection (LMD). Furthermore, we show the significance of disentangling tumor tissue heterogeneity by applying the newly developed protocols for combining LMD of tumor tissue compartments with RT-qPCR analysis to reveal compartment-specific miRNA expression signatures. An important advantage of this strategy is that the miRNA signature can be directly linked to histopathology. In summary, combining LMD and RT-qPCR is a powerful approach for spatial miRNA expression analysis in complex tissues, enabling discovery of disease mechanisms, biomarkers and drug candidates.

Tumour progression is an evolutionary process in which different clones evolve over time, leading to intra-tumour heterogeneity. Interactions between clones can affect tumour evolution and hence disease progression and treatment outcome. Intra-tumoural pairs of mutations that are overrepresented in a co-occurring or clonally exclusive fashion over a cohort of patient samples may be suggestive of a synergistic effect between the different clones carrying these mutations. We therefore developed a novel statistical testing framework, called GeneAccord, to identify such gene pairs that are altered in distinct subclones of the same tumour. We analysed our framework for calibration and power. By comparing its performance to baseline methods, we demonstrate that to control type I errors, it is essential to account for the evolutionary dependencies among clones. In applying GeneAccord to the single-cell sequencing of a cohort of 123 acute myeloid leukaemia patients, we find 1 clonally co-occurring and 8 clonally exclusive gene pairs. The clonally exclusive pairs mostly involve genes of the key signalling pathways.

Early intervention (EI) service providers working with young children with developmental disabilities and delays and their families often utilize coaching practices to engage caregivers in the EI process. Within the literature, the usefulness of coaching has been identified. However, little is known about how coaching practices look in naturalistic settings and service providers' perceptions of these practices. Through the use of an online survey, this study examined beliefs and reported practices of EI service providers. The findings indicated that EI providers considered coaching to be meaningful and offered several benefits to both caregivers and children. Some of the perceived advantages included engaging and empowering caregivers and increased opportunities for children to practice and master skills. Most coaching practices were ranked as highly important and were reportedly utilized frequently by service providers in the sample. However, some coaching practices, such as reflection and feedback, were not implemented as often as joint planning, observation, and action. In addition, the participants identified challenges and facilitators for using coaching as a style of interacting with caregivers. Discussion of EI provider perceptions, limitations, recommendations, implications, and future research directions are presented.