Properties and Processing of Aviation Exhaust Aerosol at Cruise Altitude Observed from the IAGOS-CARIBIC Flying Laboratory

The characteristics of aviation-induced aerosol, its processing, and effects on cirrus clouds and climate are still associated with large uncertainties. Properties of aviation-induced aerosol, however, are crucially needed for the assessment of aviation's climate impacts today and in the future. We identified more than 1100 aircraft plume encounters during passenger aircraft flights of the IAGOS-CARIBIC Flying Laboratory from July 2018 to March 2020. The aerosol properties inside aircraft plumes were similar, independent of the altitude (i.e., upper troposphere, tropopause region, and lowermost stratosphere). The exhaust aerosol was found to be mostly externally mixed compared to the internally mixed background aerosol, even at a plume age of 1 to 3 h. No enhancement of accumulation mode particles (diameter >250 nm) could be detected inside the aircraft plumes. Particle number emission indices (EIs) deduced from the observations in aged plumes are in the same range as values reported from engine certifications. This finding, together with the observed external mixing state inside the plumes, indicates that the aviation exhaust aerosol almost remains in its emission state during plume expansion. It also reveals that the particle number EIs used in global models are within the range of the EIs measured in aged plumes.

The growth factor EPIREGULIN promotes basal progenitor cell proliferation in the developing neocortex

Neocortex expansion during evolution is linked to higher numbers of neurons, which are thought to result from increased proliferative capacity and neurogenic potential of basal progenitor cells during development. Here, we show that EREG, encoding the growth factor EPIREGULIN, is expressed in the human developing neocortex and in gorilla cerebral organoids, but not in the mouse neocortex. Addition of EPIREGULIN to the mouse neocortex increases proliferation of basal progenitor cells, whereas EREG ablation in human cortical organoids reduces proliferation in the subventricular zone. Treatment of cortical organoids with EPIREGULIN promotes a further increase in proliferation of gorilla but not of human basal progenitor cells. EPIREGULIN competes with the epidermal growth factor (EGF) to promote proliferation, and inhibition of the EGF receptor abrogates the EPIREGULIN-mediated increase in basal progenitor cells. Finally, we identify putative cis-regulatory elements that may contribute to the observed inter-species differences in EREG expression. Our findings suggest that species-specific regulation of EPIREGULIN expression may contribute to the increased neocortex size of primates by providing a tunable pro-proliferative signal to basal progenitor cells in the subventricular zone.

Mutated IKZF1 is an independent marker of adverse risk in acute myeloid leukemia

Genetic lesions of IKZF1 are frequent events and well-established markers of adverse risk in acute lymphoblastic leukemia. However, their function in the pathophysiology and impact on patient outcome in acute myeloid leukemia (AML) remains elusive. In a multicenter cohort of 1606 newly diagnosed and intensively treated adult AML patients, we found IKZF1 alterations in 45 cases with a mutational hotspot at N159S. AML with mutated IKZF1 was associated with alterations in RUNX1, GATA2, KRAS, KIT, SF3B1, and ETV6, while alterations of NPM1, TET2, FLT3-ITD, and normal karyotypes were less frequent. The clinical phenotype of IKZF1-mutated AML was dominated by anemia and thrombocytopenia. In both univariable and multivariable analyses adjusting for age, de novo and secondary AML, and ELN2022 risk categories, we found mutated IKZF1 to be an independent marker of adverse risk regarding complete remission rate, event-free, relapse-free, and overall survival. The deleterious effects of mutated IKZF1 also prevailed in patients who underwent allogeneic hematopoietic stem cell transplantation (n = 519) in both univariable and multivariable models. These dismal outcomes are only partially explained by the hotspot mutation N159S. Our findings suggest a role for IKZF1 mutation status in AML risk modeling.

Cellular senescence promotes progenitor cell expansion during axolotl limb regeneration

Axolotl limb regeneration is accompanied by the transient induction of cellular senescence within the blastema, the structure that nucleates regeneration. The precise role of this blastemal senescent cell (bSC) population, however, remains unknown. Here, through a combination of gain- and loss-of-function assays, we elucidate the functions and molecular features of cellular senescence in vivo. We demonstrate that cellular senescence plays a positive role during axolotl regeneration by creating a pro-proliferative niche that supports progenitor cell expansion and blastema outgrowth. Senescent cells impact their microenvironment via Wnt pathway modulation. Further, we identify a link between Wnt signaling and senescence induction and propose that bSC-derived Wnt signals facilitate the proliferation of neighboring cells in part by preventing their induction into senescence. This work defines the roles of cellular senescence in the regeneration of complex structures.

Knowledge sharing and discovery across heterogeneous research infrastructures

Research infrastructures play an increasingly essential role in scientific research. They provide rich data sources for scientists, such as services and software packages, via catalog and virtual research environments. However, such research infrastructures are typically domain-specific and often not connected. Accordingly, researchers and practitioners face fundamental challenges introduced by fragmented knowledge from heterogeneous, autonomous sources with complicated and uncertain relations in particular research domains. Additionally, the exponential growth rate of knowledge in a specific domain surpasses human experts' ability to formalize and capture tacit and explicit knowledge efficiently. Thus, a knowledge management system is required to discover knowledge effectively, automate the knowledge acquisition based on artificial intelligence approaches, integrate the captured knowledge, and deliver consistent knowledge to agents, research communities, and end-users. In this study, we present the development process of a knowledge management system for ENVironmental Research Infrastructures, which are crucial pillars for environmental scientists in their quest for understanding and interpreting the complex Earth System. Furthermore, we report the challenges we have faced and discuss the lessons learned during the development process.

Knowledge sharing and discovery across heterogeneous research infrastructures

Research infrastructures play an increasingly essential role in scientific research. They provide rich data sources for scientists, such as services and software packages, via catalog and virtual research environments. However, such research infrastructures are typically domain-specific and often not connected. Accordingly, researchers and practitioners face fundamental challenges introduced by fragmented knowledge from heterogeneous, autonomous sources with complicated and uncertain relations in particular research domains. Additionally, the exponential growth rate of knowledge in a specific domain surpasses human experts' ability to formalize and capture tacit and explicit knowledge efficiently. Thus, a knowledge management system is required to discover knowledge effectively, automate the knowledge acquisition based on artificial intelligence approaches, integrate the captured knowledge, and deliver consistent knowledge to agents, research communities, and end-users. In this study, we present the development process of a knowledge management system for ENVironmental Research Infrastructures, which are crucial pillars for environmental scientists in their quest for understanding and interpreting the complex Earth System. Furthermore, we report the challenges we have faced and discuss the lessons learned during the development process.

The RNA binding protein human antigen R is a gatekeeper of liver homeostasis

BACKGROUND AND AIMS

NAFLD is initiated by steatosis and can progress through fibrosis and cirrhosis to HCC. The RNA binding protein human antigen R (HuR) controls RNAs at the posttranscriptional level; hepatocyte HuR has been implicated in the regulation of diet-induced hepatic steatosis. The present study aimed to understand the role of hepatocyte HuR in NAFLD development and progression to fibrosis and HCC.

APPROACH AND RESULTS

Hepatocyte-specific, HuR-deficient mice and control HuR-sufficient mice were fed either a normal diet or an NAFLD-inducing diet. Hepatic lipid accumulation, inflammation, fibrosis, and HCC development were studied by histology, flow cytometry, quantitative PCR, and RNA sequencing. The liver lipidome was characterized by lipidomics analysis, and the HuR-RNA interactions in the liver were mapped by RNA immunoprecipitation sequencing. Hepatocyte-specific, HuR-deficient mice displayed spontaneous hepatic steatosis and fibrosis predisposition compared to control HuR-sufficient mice. On an NAFLD-inducing diet, hepatocyte-specific HuR deficiency resulted in exacerbated inflammation, fibrosis, and HCC-like tumor development. A multi-omic approach, including lipidomics, transcriptomics, and RNA immunoprecipitation sequencing revealed that HuR orchestrates a protective network of hepatic-metabolic and lipid homeostasis-maintaining pathways. Consistently, HuR-deficient livers accumulated, already at steady state, a triglyceride signature resembling that of NAFLD livers. Moreover, up-regulation of secreted phosphoprotein 1 expression mediated, at least partially, fibrosis development in hepatocyte-specific HuR deficiency on an NAFLD-inducing diet, as shown by experiments using antibody blockade of osteopontin.

CONCLUSIONS

HuR is a gatekeeper of liver homeostasis, preventing NAFLD-related fibrosis and HCC, suggesting that the HuR-dependent network could be exploited therapeutically.

Tig1 regulates proximo-distal identity during salamander limb regeneration

Salamander limb regeneration is an accurate process which gives rise exclusively to the missing structures, irrespective of the amputation level. This suggests that cells in the stump have an awareness of their spatial location, a property termed positional identity. Little is known about how positional identity is encoded, in salamanders or other biological systems. Through single-cell RNAseq analysis, we identified Tig1/Rarres1 as a potential determinant of proximal identity. Tig1 encodes a conserved cell surface molecule, is regulated by retinoic acid and exhibits a graded expression along the proximo-distal axis of the limb. Its overexpression leads to regeneration defects in the distal elements and elicits proximal displacement of blastema cells, while its neutralisation blocks proximo-distal cell surface interactions. Critically, Tig1 reprogrammes distal cells to a proximal identity, upregulating Prod1 and inhibiting Hoxa13 and distal transcriptional networks. Thus, Tig1 is a central cell surface determinant of proximal identity in the salamander limb.

The mechanisms by which cells determine their position within the 3D space are poorly understood. Research in salamanders offers fresh insights into this question, uncovering Tig1 as a central determinant of proximo-distal identity in regeneration.

Distinguishing activated T regulatory cell and T conventional cells by single cell technologies

Resting conventional T cells (Tconv) can be distinguished from T regulatory cells (Treg) by the canonical markers FOXP3, CD25 and CD127. However, the expression of these proteins alters after T‐cell activation leading to overlap between Tconv and Treg. The objective of this study was to distinguish resting and antigen‐responsive T effector (Tconv) and Treg using single‐cell technologies. CD4⁺ Treg and Tconv cells were stimulated with antigen and responsive and non‐responsive populations processed for targeted and non‐targeted single‐cell RNAseq. Machine learning was used to generate a limited set of genes that could distinguish responding and non‐responding Treg and Tconv cells and which was used for single‐cell multiplex qPCR and to design a flow cytometry panel. Targeted scRNAseq clearly distinguished the four‐cell populations. A minimal set of 27 genes was identified by machine learning algorithms to provide discrimination of the four populations at >95% accuracy. In all, 15 of the genes were validated to be differentially expressed by single‐cell multiplex qPCR. Discrimination of responding Treg from responding Tconv could be achieved by a flow cytometry strategy that included staining for CD25, CD127, FOXP3, IKZF2, ITGA4, and the novel marker TRIM which was strongly expressed in Tconv and weakly expressed in both responding and non‐responding Treg. A minimal set of genes was identified that discriminates responding and non‐responding CD4⁺ Treg and Tconv cells and, which have identified TRIM as a marker to distinguish Treg by flow cytometry.

Gene-selective transcription promotes the inhibition of tissue reparative macrophages by TNF

Pro-inflammatory TNF is a highly gene-selective inhibitor of the gene expression program of tissue repair and wound healing macrophages.

Anti-TNF therapies are a core anti-inflammatory approach for chronic diseases such as rheumatoid arthritis and Crohn’s Disease. Previously, we and others found that TNF blocks the emergence and function of alternative-activated or M2 macrophages involved in wound healing and tissue-reparative functions. Conceivably, anti-TNF drugs could mediate their protective effects in part by an altered balance of macrophage activity. To understand the mechanistic basis of how TNF regulates tissue-reparative macrophages, we used RNAseq, scRNAseq, ATACseq, time-resolved phospho-proteomics, gene-specific approaches, metabolic analysis, and signaling pathway deconvolution. We found that TNF controls tissue-reparative macrophage gene expression in a highly gene-specific way, dependent on JNK signaling via the type 1 TNF receptor on specific populations of alternative-activated macrophages. We further determined that JNK signaling has a profound and broad effect on activated macrophage gene expression. Our findings suggest that TNF’s anti-M2 effects evolved to specifically modulate components of tissue and reparative M2 macrophages and TNF is therefore a context-specific modulator of M2 macrophages rather than a pan-M2 inhibitor.

A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ-cells to diabetes recovery in zebrafish

Regeneration-competent species possess the ability to reverse the progression of severe diseases by restoring the function of the damaged tissue. However, the cellular dynamics underlying this capability remain unexplored. Here, we have used single-cell transcriptomics to map de novo β-cell regeneration during induction and recovery from diabetes in zebrafish. We show that the zebrafish has evolved two distinct types of somatostatin-producing δ-cells, which we term δ1- and δ2-cells. Moreover, we characterize a small population of glucose-responsive islet cells, which share the hormones and fate-determinants of both β- and δ1-cells. The transcriptomic analysis of β-cell regeneration reveals that β/δ hybrid cells provide a prominent source of insulin expression during diabetes recovery. Using in vivo calcium imaging and cell tracking, we further show that the hybrid cells form de novo and acquire glucose-responsiveness in the course of regeneration. The overexpression of dkk3, a gene enriched in hybrid cells, increases their formation in the absence of β-cell injury. Finally, interspecies comparison shows that plastic δ1-cells are partially related to PP cells in the human pancreas. Our work provides an atlas of β-cell regeneration and indicates that the rapid formation of glucose-responsive hybrid cells contributes to the resolution of diabetes in zebrafish.

Reproducibility of 10x Genomics single cell RNA sequencing method in the immune cell environment

10x Genomics is a highly accessible single cell RNA sequencing platform that allows for simultaneous gene expression analysis and identification of receptor chain combinations in cells of the adaptive immune system. Here, we asked whether the gene and receptor expression measurements in peripheral blood mononuclear cells (PBMC) are influenced by technical, cell freezing, FACS-processing, and day to day biological variation. No differentially expressed gene was observed between 1. triplicates aliquots taken from the same vial of frozen PBMC; 2. triplicate vials of frozen PBMC; and 3. triplicate aliquots taken from the same vial of frozen PBMC and processed separately for FACS staining and sorting of different PBMC populations. A small number of differentially expressed genes were observed between PBMC sampled, isolated and frozen from the same donor on different days, and these differences were more pronounced in the memory B cells than other cell populations. T cell receptors were recovered in all replicates when at least 5 cells per clonotype were identified. These findings show high reproducibility of 10x Genomics single cell RNA sequencing data in the immune cell context.

Impaired saccadic eye movements in multiple sclerosis are related to altered functional connectivity of the oculomotor brain network

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Impaired eye movements in multiple sclerosis (MS) and functional connectivity (FC)

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Eye movements related to altered FC of the oculomotor brain network.

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Lower (beta band) and higher (theta/delta band) FC related to abnormal eye movements.

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Regional changes were more informative than whole-network measures.

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Eye movement parameters also related to disability and cognitive dysfunction.

Background

Impaired eye movements in multiple sclerosis (MS) are common and could represent a non-invasive and accurate measure of (dys)functioning of interconnected areas within the complex brain network. The aim of this study was to test whether altered saccadic eye movements are related to changes in functional connectivity (FC) in patients with MS.

Methods

Cross-sectional eye movement (pro-saccades and anti-saccades) and magnetoencephalography (MEG) data from the Amsterdam MS cohort were included from 176 MS patients and 33 healthy controls. FC was calculated between all regions of the Brainnetome atlas in six conventional frequency bands. Cognitive function and disability were evaluated by previously validated measures. The relationships between saccadic parameters and both FC and clinical scores in MS patients were analysed using multivariate linear regression models.

Results

In MS pro- and anti-saccades were abnormal compared to healthy controls A relationship of saccadic eye movements was found with FC of the oculomotor network, which was stronger for regional than global FC. In general, abnormal eye movements were related to higher delta and theta FC but lower beta FC. Strongest associations were found for pro-saccadic latency and FC of the precuneus (beta band β = -0.23, p = .006), peak velocity and FC of the parietal eye field (theta band β = -0.25, p = .005) and gain and FC of the inferior frontal eye field (theta band β = -0.25, p = .003). Pro-saccadic latency was also strongly associated with disability scores and cognitive dysfunction.

Conclusions

Impaired saccadic eye movements were related to functional connectivity of the oculomotor network and clinical performance in MS. This study also showed that, in addition to global network connectivity, studying regional changes in MEG studies could yield stronger correlations.

Continuous mitotic activity of primitive hematopoietic stem cells in adult mice

The proliferative activity of aging hematopoietic stem cells (HSCs) is controversially discussed. Inducible fluorescent histone 2B fusion protein (H2B-FP) transgenic mice are important tools for tracking the mitotic history of murine HSCs in label dilution experiments. A recent study proposed that primitive HSCs symmetrically divide only four times to then enter permanent quiescence. We observed that background fluorescence due to leaky H2B-FP expression, occurring in all H2B-FP transgenes independent of label induction, accumulated with age in HSCs with high repopulation potential. We argue that this background had been misinterpreted as stable retention of induced label. We found cell division–independent half-lives of H2B-FPs to be short, which had led to overestimation of HSC divisional activity. Our data do not support abrupt entry of HSCs into permanent quiescence or sudden loss of regeneration potential after four divisions, but show that primitive HSCs of adult mice continue to cycle rarely.

The GridKa tape storage: latest improvements and current production setup

Tape storage remains the most cost-effective system for safe long-term storage of petabytes of data and reliably accessing it on demand. It has long been widely used by Tier-1 centers in WLCG. GridKa uses tape storage systems for LHC and non-LHC HEP experiments. The performance requirements on the tape storage systems are increasing every year, creating an increasing number of challenges in providing a scalable and reliable system. Therefore, providing high-performance, scalable and reliable tape storage systems is a top priority for Tier-1 centers in WLCG.

At GridKa, various performance tests were recently done to investigate the existence of bottlenecks in the tape storage setup. As a result, several bottlenecks were identified and resolved, leading to a significant improvement in the overall tape storage performance. These results were achieved in a test environment and introduction of these achievements in to the production environment required a great effort, among many other things, a new software had to be developed to interact with the tape management software.

This contribution provides detailed information on the latest improvements and changes on the GridKa tape storage setup.

Reactive oligodendrocyte progenitor cells (re-)myelinate the regenerating zebrafish spinal cord

Spinal cord injury (SCI) results in loss of neurons, oligodendrocytes and myelin sheaths, all of which are not efficiently restored. The scarcity of oligodendrocytes in the lesion site impairs re-myelination of spared fibres, which leaves axons denuded, impedes signal transduction and contributes to permanent functional deficits. In contrast to mammals, zebrafish can functionally regenerate the spinal cord. Yet, little is known about oligodendroglial lineage biology and re-myelination capacity after SCI in a regeneration-permissive context. Here, we report that, in adult zebrafish, SCI results in axonal, oligodendrocyte and myelin sheath loss. We find that OPCs, the oligodendrocyte progenitor cells, survive the injury, enter a reactive state, proliferate and differentiate into oligodendrocytes. Concomitantly, the oligodendrocyte population is re-established to pre-injury levels within 2 weeks. Transcriptional profiling revealed that reactive OPCs upregulate the expression of several myelination-related genes. Interestingly, global reduction of axonal tracts and partial re-myelination, relative to pre-injury levels, persist at later stages of regeneration, yet are sufficient for functional recovery. Taken together, these findings imply that, in the zebrafish spinal cord, OPCs replace lost oligodendrocytes and, thus, re-establish myelination during regeneration.

Single-cell transcriptome analysis reveals thyrocyte diversity in the zebrafish thyroid gland

The thyroid gland regulates growth and metabolism via production of thyroid hormone in follicles composed of thyrocytes. So far, thyrocytes have been assumed to be a homogenous population. To uncover heterogeneity in the thyrocyte population and molecularly characterize the non-thyrocyte cells surrounding the follicle, we developed a single-cell transcriptome atlas of the region containing the zebrafish thyroid gland. The 6249-cell atlas includes profiles of thyrocytes, blood vessels, lymphatic vessels, immune cells, and fibroblasts. Further, the thyrocytes show expression heterogeneity, including bimodal expression of the transcription factor pax2a. To validate thyrocyte heterogeneity, we generated a CRISPR/Cas9-based pax2a knock-in line that monitors pax2a expression in the thyrocytes. A population of pax2a-low mature thyrocytes interspersed in individual follicles can be distinguished. We corroborate heterogeneity within the thyrocyte population using RNA sequencing of pax2a-high and pax2a-low thyrocytes, which demonstrates 20% differential expression in transcriptome between the two subpopulations. Our results identify and validate transcriptional differences within the presumed homogenous thyrocyte population.

Exome sequencing identifies frequent genomic loss of TET1 in IDH-wild-type glioblastoma

Glioblastoma (GBM) is the most common and malignant brain tumor in adults. Genomic and epigenomic alterations of multiple cancer-driving genes are frequent in GBM. To identify molecular alterations associated with epigenetic aberrations, we performed whole exome sequencing-based analysis of DNA copy number variations in 55 adult patients with IDH-wild-type GBM. Beside mutations in common GBM driver genes such as TERTp (76%), TP53 (22%) and PTEN (20%), 67% of patients were affected by amplifications of genes associated with RTK/Rb/p53 cell signaling, including EGFR (45%), CDK4 (13%), and MDM2/4 (both 7%). The minimal deleted region at chromosome 10 was detected at the DNA demethylase TET1 (93%), mainly due to a loss-of-heterozygosity of complete chromosome 10 (53%) or by a mono-allelic microdeletion at 10q21.3 (7%). In addition, bi-allelic TET1 deletions, detected in 18 patients (33%), frequently co-occurred with EGFR amplification and were associated with low levels of TET1 mRNA expression, pointing at loss of TET1 activity. Bi-allelic TET1 loss was not associated with global concentrations of 5-hydroxymethylcytosine, indicating a site-specific effect of TET1 for DNA (de)methylation. Focal amplification of EGFR positively correlated with overall mutational burden, tumor size, and poor long-term survival. Bi-allelic TET1 loss was not an independent prognostic factor, but significantly associated with poor survival in patients with concomitant EGFR amplification. Rates of genomic TET1 deletion were significantly lower in a cohort of IDH1-mutated patients. Despite the relevance of TET1 for DNA demethylation and as potential therapeutic target, a frequent genomic loss of TET1 has not previously been reported in GBM.

[Clinical aspects of the abnormal pupillary response; shedding light on pupillary response]

Testing the pupillary response is a quick and valuable diagnostic measure for certain neurological and ophthalmological diseases in patients. The pupillary response can aid in localizing abnormalities in important parts of the visual system and brainstem, provided that the tests are executed and interpreted correctly. When an abnormal pupillary response is found, it is important to differentiate between an afferent problem (eyeball, retina, optical nerve), brain stem pathology, or an efferent problem (parasympathetic fibers of the oculomotor nerve, iris sphincter muscle). We describe the technique of the ophthalmological examination, the normal neurophysiology and the possible abnormal pupil responses in patients with intact and decreased consciousness.

Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro

Recent findings suggest that reduced neurogenesis could be one of the underlying reasons for the exacerbated neuropathology in humans, thus restoring the neural stem cell proliferation and neurogenesis could help to circumvent some pathological aspects of Alzheimer’s disease. We recently identified Interleukin-4/STAT6 signaling as a neuron–glia crosstalk mechanism that enables glial proliferation and neurogenesis in adult zebrafish brain and 3D cultures of human astroglia, which manifest neurogenic properties. In this study, by using single cell sequencing in the APP/PS1dE9 mouse model of AD, we found that IL4 receptor (Il4r) is not expressed in mouse astroglia and IL4 signaling is not active in these cells. We tested whether activating IL4/STAT6 signaling would enhance cell proliferation and neurogenesis in healthy and disease conditions. Lentivirus-mediated expression of IL4R or constitutively active STAT6VT impaired the survival capacity of mouse astroglia in vivo but not in vitro. These results suggest that the adult mouse brain generates a non-permissive environment that dictates a negative effect of IL4 signaling on astroglial survival and neurogenic properties in contrast to zebrafish brains and in vitro mammalian cell cultures. Our findings that IL4R signaling in dentate gyrus (DG) of adult mouse brain impinges on the survival of DG cells implicate an evolutionary mechanism that might underlie the loss of neuroregenerative ability of the brain, which might be utilized for basic and clinical aspects for neurodegenerative diseases.

Lightweight dynamic integration of opportunistic resources

To satisfy future computing demands of the Worldwide LHC Computing Grid (WLCG), opportunistic usage of third-party resources is a promising approach. While the means to make such resources compatible with WLCG requirements are largely satisfied by virtual machines and containers technologies, strategies to acquire and disband many resources from many providers are still a focus of current research. Existing meta-schedulers that manage resources in the WLCG are hitting the limits of their design when tasked to manage heterogeneous resources from many diverse resource providers.

To provide opportunistic resources to the WLCG as part of a regular WLCG site, we propose a new meta-scheduling approach suitable for opportunistic, heterogeneous resource provisioning. Instead of anticipating future resource requirements, our approach observes resource usage and promotes well-used resources. Following this approach, we have developed an inherently robust meta-scheduler, COBalD, for managing diverse, heterogeneous resources given unpredictable resource requirements. This paper explains the key concepts of our approach, and discusses the benefits and limitations of our new approach to dynamic resource provisioning compared to previous approaches.

Predicting resource usage for enhanced job scheduling for opportunistic resources in HEP

To overcome the computing challenge in High Energy Physics available resources must be utilized as efficiently as possible. This targets algorithmic challenges in the workflows itself but also the scheduling of jobs to compute resources. To enable the best possible scheduling, job schedulers require accurate information about resource consumption of a job before it is even executed. It is the responsibility of the user to provide an accurate resource estimate required for jobs. However, this is quite a challenge for users as they (i) want to ensure their jobs to run correctly, (ii) must manage to deal with heterogeneous compute resources and (iii) face intransparent library dependencies and frequent updates. Users therefore tend to specify resource requests with an ample buffer. This inaccuracy results in inefficient utilisation by either blocking unused resources or exceeding reserved resources. Especially in the context of opportunistic resource provisioning the inaccuracies have an even broader impact that does not even target utilisation of resources but also composition of the most suitable resources. The contribution of this paper is an analysis of production and end-user workflows in HEP with regards to optimizing the various resources types. We further propose a method to improve user estimates.

Setup and commissioning of a high-throughput analysis cluster

Current and future end-user analyses and workflows in High Energy Physics demand the processing of growing amounts of data. This plays a major role when looking at the demands in the context of the High-Luminosity-LHC. In order to keep the processing time and turn-around cycles as low as possible analysis clusters optimized with respect to these demands can be used. Since hyper converged servers offer a good combination of compute power and local storage, they form the ideal basis for these clusters. In this contribution we report on the setup and commissioning of a dedicated analysis cluster setup at Karlsruhe Institute of Technology. This cluster was designed for use cases demanding high data-throughput. Based on hyper converged servers this cluster offers 500 job slots and 1 PB of local storage. Combined with the 100 Gb network connection between the servers and a 200 Gb uplink to the Tier-1 storage, the cluster can sustain a data-throughput of 1 PB per day. In addition, the local storage provided by the hyper converged worker nodes can be used as cache space. This allows employing of caching approaches on the cluster, thereby enabling a more efficient usage of the disk space. In previous contributions this concept has been shown to lead to an expected speedup of 2 to 4 compared to conventional setups.

Effective Dynamic Integration and Utilization of Heterogenous Compute Resources

Increased operational effectiveness and the dynamic integration of only temporarily available compute resources (opportunistic resources) becomes more and more important in the next decade, due to the scarcity of resources for future high energy physics experiments as well as the desired integration of cloud and high performance computing resources. This results in a more heterogenous compute environment, which gives rise to huge challenges for the computing operation teams of the experiments.

At the Karlsruhe Institute of Technology (KIT) we design solutions to tackle these challenges. In order to ensure an efficient utilization of opportunistic resources and unified access to the entire infrastructure, we developed the Transparent Adaptive Resource Dynamic Integration System (TARDIS). A scalable multi-agent resource manager providing interfaces to provision as well as dynamically and transparently integrate resources of various providers into one common overlay batch system. Operational effectiveness is guaranteed by relying on COBalD – the Opportunistic Balancing Daemon and its simple approach of taking into account the utilization and allocation of the different resource types, in order to run the individual workflows on the best-suited resource respectively.

In this contribution we will present the current status of integrating various HPC centers and cloud providers into the compute infrastructure at the Karlsruhe Institute of Technology as well as our experiences gained in a production environment.

The GridKa Tape Storage: various performance test results and current improvements

Data growth over several years within HEP experiments requires a wider use of storage systems for WLCG Tiered Centers. It also increases the complexity of storage systems, which includes the expansion of hardware components and thereby complicates existing software products more. To cope with such systems is a non-trivial task and requires highly qualified specialists. Storing petabytes of data on tape storage is a still the most cost-effective way. Year after year, the use of a tape storage increases, consequently a detailed study of its optimal use and verification of performance is a key aspect for such a system. It includes several factors, such as performing various performance tests, identifying and eliminating bottlenecks, properly adjusting and improving the current GridKa setup, etc.

At present, GridKa uses dCache as the storage system in frontend and TSM as the tape storage backend. dCache provides a plugin interface for exchanging data between dcache and tape.

TSS is a TSM-based client developed by the GridKa team. TSS has been in production for over 10 years. The interaction between the GridKa dCache instance and TSM is accomplished using additional scripts that can be further optimized to improve the overall performance of the tape storage.

This contribution provides detailed information on the results of various performance tests performed on the GridKa tape and significant improvements of our tape storage performance.

Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level

CD8⁺ T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8⁺ T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labeled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8⁺ T cells under different antigen presentation conditions. Combined expression of TNFRSF9, XCL1, XCL2, and CRTAM was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8⁺ T cells from unselected populations. Gene response profiles of CD8⁺ T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors.

Objective quantification of vitreous haze on optical coherence tomography scans: no evidence for relationship between uveitis and inflammation in multiple sclerosis

BACKGROUND AND PURPOSE

The occurrence of intermediate uveitis, which is characterized by the presence of vitreous haze (VH), in patients with multiple sclerosis (MS) may be a sign of coexistent inflammatory central nervous system (CNS) disease activity. Using an automated algorithm to quantify VH on optical coherence tomography (OCT) scans, the aim was to investigate whether VH in MS patients is associated with signs of inflammatory CNS disease activity.

METHODS

Vitreous haze was quantified on OCT macular volume scans of 290 MS patients and 85 healthy controls (HCs). The relationship between VH and clinical, retinal OCT and magnetic resonance imaging parameters of inflammatory disease activity was investigated using generalized estimating equations.

RESULTS

Mean VH scores did not differ between patients and HCs (P = 0.629). Six patients (2.1%) showed values higher than the highest of the controls by HCs. VH scores did not differ between the different disease types or between eyes with and without a history of optic neuritis (P = 0.132). VH was not associated with inner nuclear layer volume on OCT (P = 0.233), cerebral T2 lesion load on magnetic resonance imaging (P = 0.416) or the development of new relapses (P = 0.205).

CONCLUSION

In this study, OCT-based automated VH estimation did not detect increased vitreous inflammation in MS patients compared to HCs and did not find an association with CNS inflammatory burden.

Progression of Anterograde Trans-Synaptic Degeneration in the Human Retina Is Modulated by Axonal Convergence and Divergence

In the visual pathway of patients with multiple sclerosis (MS), the inner nuclear layer (INL) of the retina is a tight barrier for retrograde trans-synaptic degeneration. In this observational, retrospective cross-sectional study, segmented macular spectral domain optical coherence tomography (OCT) volume scans were reviewed to investigate if this observation also holds true for anterograde trans-synaptic degeneration. Significant thinning was found in all retinal layers in patients with outer retinal diseases compared with the healthy controls, while there was no significant attenuation of the outer retina in patients with MS. In contrast to the tight barrier function observed with retrograde trans-synaptic degeneration, the INL appears to be more permissive for the propagation of anterograde trans-synaptic degeneration. We speculate that this may be due to the size of the area affected and be explained by convergence and divergence of axons within the retinal layers. These findings are likely relevant to future restorative stem cell treatment of the outer retinal layers, as time may matter.

Author Correction: Transferrin receptor 2 controls bone mass and pathological bone formation via BMP and Wnt signaling

In the version of this article initially published, affiliation 14 was incorrect, and Deutsche Forschungsgemeinschaft grants SFB1036 and SFB1118 were missing from the Acknowledgements. The errors have been corrected in the HTML and PDF versions of the article.

Diagnosing and quantifying a common deficit in multiple sclerosis: Internuclear ophthalmoplegia

OBJECTIVE

We present an objective and quantitative approach for diagnosing internuclear ophthalmoplegia (INO) in multiple sclerosis (MS).

METHODS

A validated standardized infrared oculography protocol (DEMoNS [Demonstrate Eye Movement Networks with Saccades]) was used for quantifying prosaccades in patients with MS and healthy controls (HCs). The versional dysconjugacy index (VDI) was calculated, which describes the ratio between the abducting and adducting eye. The VDI was determined for peak velocity, peak acceleration, peak velocity divided by amplitude, and area under the curve (AUC) of the saccadic trajectory. We calculated the diagnostic accuracy for the several VDI parameters by a receiver operating characteristic analysis comparing HCs and patients with MS. The National Eye Institute Visual Function Questionnaire-25 was used to investigate vision-related quality of life of MS patients with INO.

RESULTS

Two hundred ten patients with MS and 58 HCs were included. The highest diagnostic accuracy was achieved by the VDI AUC of 15° horizontal prosaccades. Based on a combined VDI AUC and peak velocity divided by amplitude detection, the prevalence of an INO in MS calculated to 34%. In the INO group, 35.2% of the patients with MS reported any complaints of double vision, compared to 18.4% in the non-INO group (p = 0.010). MS patients with an INO had a lower overall vision-related quality of life (median 89.9, interquartile range 12.8) compared to patients without an INO (median 91.8, interquartile range 9.3, p = 0.011).

CONCLUSIONS

This study provides an accurate quantitative and clinically relevant definition of an INO in MS. This infrared oculography-based INO standard will require prospective validation. The high prevalence of INO in MS provides an anatomically well described and accurately quantifiable model for treatment trials in MS.

Adoption of ARC-CE and HTCondor at GridKa Tier 1

The GridKa Tier 1 data and computing center hosts a significant share of WLCG processing resources. Providing these resources to all major LHC and other VOs requires efficient, scalable and reliable cluster management. To satisfy this, GridKa has recently migrated its batch resources from CREAM-CE and PBS to ARC-CE and HTCondor. This contribution discusses the key highlights of the adoption of this middleware at the scale of a European Tier 1 center: As the largest WLCG Tier 1 using the ARC-CE plus HTCondor stack, GridKa is exemplary for migrating more than 20 000 cores over the time span of only a few weeks. Supporting multiple VOs, we have extensively studied the constraints and possibilities of scheduling jobs of vastly different requirements. We present a robust and maintainable optimization of resource utilization which still respects constraints desired by VOs. Furthermore, we explore the dynamic extension of our batch system, integrating cloud resources with a lightweight configuration mechanism.

Transferrin receptor 2 controls bone mass and pathological bone formation via BMP and Wnt signaling

Transferrin receptor 2 (Tfr2) is mainly expressed in the liver and controls iron homeostasis. Here, we identify Tfr2 as a regulator of bone homeostasis that inhibits bone formation. Mice lacking Tfr2 display increased bone mass and mineralization independent of iron homeostasis and hepatic Tfr2. Bone marrow transplantation experiments and studies of cell-specific Tfr2 knockout mice demonstrate that Tfr2 impairs BMP-p38MAPK signaling and decreases expression of the Wnt inhibitor sclerostin specifically in osteoblasts. Reactivation of MAPK or overexpression of sclerostin rescues skeletal abnormalities in Tfr2 knockout mice. We further show that the extracellular domain of Tfr2 binds BMPs and inhibits BMP-2-induced heterotopic ossification by acting as a decoy receptor. These data indicate that Tfr2 limits bone formation by modulating BMP signaling, possibly through direct interaction with BMP either as a receptor or as a co-receptor in a complex with other BMP receptors. Finally, the Tfr2 extracellular domain may be effective in the treatment of conditions associated with pathological bone formation.

The GridKa Tape System: status and outlook

Tape storage is still a cost effective way to keep large amounts of data over a long period of time and it is expected that this will continue in the future. The GridKa tape environment is a complex system of many hardware components and software layers. Configuring this system for optimal performance for all use cases is a non-trivial task and requires a lot of experience. We present the current status of the GridKa tape environment, report on recent upgrades and improvements and plans to further develop and enhance the system, especially with regard to the future requirements of the HEP experiments and their large data centers. The short-term planning mainly includes the transition from TSM to HPSS as the backend and the effects on the connection of dCache and xrootd. Recent changes of the vendor situation of certain tape technologies require a precise analysis of the impact and eventual adaptation of the mid-term planning, in particular with respect to scalability challenge that comes with HL-LHC on the horizon.

The Software Defined Online Storage System at the GridKa WLCG Tier-1 Center

The computing center GridKa is serving the ALICE, ATLAS, CMS and LHCb experiments as one of the biggest WLCG Tier-1 centers world wide with compute and storage resources. It is operated by the Steinbuch Centre for Computing at Karlsruhe Institute of Technology in Germany. In April 2017 a new online storage system was put into operation. In its current stage of expansion it offers the HEP experiments a capacity of 34 PB of online storage. The whole storage is partitioned into few large file systems, one for each experiment, using IBM Spectrum Scale as software-defined-storage base layer. The system offers a combined read-write performance of 100 GB/s. It can be scaled transparently both in size and performance allowing to fulfill the growing needs especially of the LHC experiments for online storage in the coming years. In this article we discuss the general architecture of the storage system and present first experiences with the performance of the system in production use.

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits.

Cis-regulatory elements are important factors for morphological changes. Here, the authors show widespread divergence of limb and eye regulatory elements in limb loss in snakes and eye degeneration in subterranean mammals respectively.

A standardized protocol for quantification of saccadic eye movements: DEMoNS

OBJECTIVE

Quantitative saccadic testing is a non-invasive method of evaluating the neural networks involved in the control of eye movements. The aim of this study is to provide a standardized and reproducible protocol for infrared oculography measurements of eye movements and analysis, which can be applied for various diseases in a multicenter setting.

METHODS

Development of a protocol to Demonstrate Eye Movement Networks with Saccades (DEMoNS) using infrared oculography. Automated analysis methods were used to calculate parameters describing the characteristics of the saccadic eye movements. The two measurements of the subjects were compared with descriptive and reproducibility statistics.

RESULTS

Infrared oculography measurements of all subjects were performed using the DEMoNS protocol and various saccadic parameters were calculated automatically from 28 subjects. Saccadic parameters such as: peak velocity, latency and saccade pair ratios showed excellent reproducibility (intra-class correlation coefficients > 0.9). Parameters describing performance of more complex tasks showed moderate to good reproducibility (intra-class correlation coefficients 0.63-0.78).

CONCLUSIONS

This study provides a standardized and transparent protocol for measuring and analyzing saccadic eye movements in a multicenter setting. The DEMoNS protocol details outcome measures for treatment trial which are of excellent reproducibility. The DEMoNS protocol can be applied to the study of saccadic eye movements in various neurodegenerative and motor diseases.