Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs.

MOTIVATION: Hi-C technology provides insights into the 3D organization of the chromatin, and the single-cell Hi-C method enables researchers to gain knowledge about the chromatin state in individual cell levels. Single-cell Hi-C interaction matrices are high dimensional and very sparse. To cluster thousands of single-cell Hi-C interaction matrices, they are flattened and compiled into one matrix. Depending on the resolution, this matrix can have a few million or even billions of features; therefore, computations can be memory intensive. We present a single-cell Hi-C clustering approach using an approximate nearest neighbors method based on locality-sensitive hashing to reduce the dimensions and the computational resources. RESULTS: The presented method can process a 10 kb single-cell Hi-C dataset with 2600 cells and needs 40 GB of memory, while competitive approaches are not computable even with 1 TB of memory. It can be shown that the differentiation of the cells by their chromatin folding properties and, therefore, the quality of the clustering of single-cell Hi-C data is advantageous compared to competitive algorithms. AVAILABILITY AND IMPLEMENTATION: The presented clustering algorithm is part of the scHiCExplorer, is available on Github https://github.com/joachimwolff/scHiCExplorer, and as a conda package via the bioconda channel. The approximate nearest neighbors implementation is available via https://github.com/joachimwolff/sparse-neighbors-search and as a conda package via the bioconda channel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Scool: a new data storage format for single-cell Hi-C data.

MOTIVATION: Single-cell Hi-C research currently lacks an efficient, easy to use and shareable data storage format. Recent studies have used a variety of sub-optimal solutions: publishing raw data only, text-based interaction matrices, or reusing established Hi-C storage formats for single interaction matrices. These approaches are storage and pre-processing intensive, require long labour time and are often error-prone. RESULTS: The single-cell cooler file format (scool) provides an efficient, user-friendly and storage-saving approach for single-cell Hi-C data. It is a flavour of the established cooler format and guarantees stable API support. AVAILABILITY AND IMPLEMENTATION: The single-cell cooler format is part of the cooler file format as of API version 0.8.9. It is available via pip, conda and github: https://github.com/mirnylab/cooler. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

pyGenomeTracks: reproducible plots for multivariate genomic datasets.

MOTIVATION: Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using a vector graphic software. RESULTS: pyGenomeTracks (PGT) is a modular plotting tool that easily combines multiple tracks. It enables a reproducible and standardized generation of highly customizable and publication ready images. AVAILABILITY AND IMPLEMENTATION: PGT is available through a graphical interface on https://usegalaxy.eu and through the command line. It is provided on conda via the bioconda channel, on pip and it is openly developed on github: https://github.com/deeptools/pyGenomeTracks. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.

The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publication, Galaxy HiCExplorer has been expanded considerably with new tools to facilitate the analysis of cHi-C and to provide an in-depth analysis of Hi-C data. Moreover, it supports the analysis of scHi-C data by offering a broad range of tools. With the help of the standard graphical user interface of Galaxy, presented workflows, extensive documentation and tutorials, novices as well as Hi-C experts are supported in their Hi-C data analysis with Galaxy HiCExplorer.

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments. Users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-seq signals. Galaxy HiCExplorer is freely usable at: https://hicexplorer.usegalaxy.eu and is available as a Docker container: https://github.com/deeptools/docker-galaxy-hicexplorer.

Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.

A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.

Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.

Loop detection using Hi-C data with HiCExplorer.

BACKGROUND: Chromatin loops are an essential factor in the structural organization of the genome; however, their detection in Hi-C interaction matrices is a challenging and compute-intensive task. The approach presented here, integrated into the HiCExplorer software, shows a chromatin loop detection algorithm that applies a strict candidate selection based on continuous negative binomial distributions and performs a Wilcoxon rank-sum test to detect enriched Hi-C interactions. RESULTS: HiCExplorer's loop detection has a high detection rate and accuracy. It is the fastest available CPU implementation and utilizes all threads offered by modern multicore platforms. CONCLUSIONS: HiCExplorer's method to detect loops by using a continuous negative binomial function combined with the donut approach from HiCCUPS leads to reliable and fast computation of loops. All the loop-calling algorithms investigated provide differing results, which intersect by $\sim 50\%$ at most. The tested in situ Hi-C data contain a large amount of noise; achieving better agreement between loop calling algorithms will require cleaner Hi-C data and therefore future improvements to the experimental methods that generate the data.

Creating employment or keeping them busy? An evaluation of training programs for older workers in Germany.

The authors analyze the effect of participation in short-term training measures on older German recipients of means-tested unemployment benefits. Their analysis uses administrative data of the German Federal Employment Agency, and they estimate the effects of participating in two types of short-term training--classroom and in-firm training--on different outcomes of the participants. Results show that classroom training is not effective in making participants independent of benefit receipt. It has a moderately positive effect on employment outcomes, which are highest for West German men. In contrast, in-firm training significantly raises the participants' likelihood of finding regular jobs and of being independent of unemployment benefit receipt.

Of carrots and sticks: the effect of workfare announcements on the job search behaviour and reservation wage of welfare recipients.

The German workfare scheme 'One-Euro-Jobs', which provides additional jobs of public interest for welfare recipients, has a number of different goals. On the one hand, One-Euro-Jobs are intended to increase the participants' employment prospects in the medium term. On the other hand, they can be used to test welfare recipients' willingness to work. We use survey data from the Panel Study 'Labour Market and Social Security' and propensity score matching methods to study the intention-to-treat effect of receiving a One-Euro-Job announcement on job search behaviour, reservation wage and labour market performance of welfare recipients. We find that receiving a One-Euro-Job announcement increases job search activities significantly and decreases the reservation wage for women and individuals who have been employed within the last 4 years, but does not affect the short-term employment probability.

Community-Driven Data Analysis Training for Biology.

The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.

Synaptic pathology in the cerebellar dentate nucleus in chronic multiple sclerosis.

In multiple sclerosis, cerebellar symptoms are associated with clinical impairment and an increased likelihood of progressive course. Cortical atrophy and synaptic dysfunction play a prominent role in cerebellar pathology and although the dentate nucleus is a predilection site for lesion development, structural synaptic changes in this region remain largely unexplored. Moreover, the mechanisms leading to synaptic dysfunction have not yet been investigated at an ultrastructural level in multiple sclerosis. Here, we report on synaptic changes of dentate nuclei in post-mortem cerebella of 16 multiple sclerosis patients and eight controls at the histological level as well as an electron microscopy evaluation of afferent synapses of the cerebellar dentate and pontine nuclei of one multiple sclerosis patient and one control. We found a significant reduction of afferent dentate synapses in multiple sclerosis, irrespective of the presence of demyelination, and a close relationship between glial processes and dentate synapses. Ultrastructurally, we show autophagosomes containing degradation products of synaptic vesicles within dendrites, residual bodies within intact-appearing axons and free postsynaptic densities opposed to astrocytic appendages. Our study demonstrates loss of dentate afferent synapses and provides, for the first time, ultrastructural evidence pointing towards neuron-autonomous and neuroglia-mediated mechanisms of synaptic degradation in chronic multiple sclerosis.

Long-term effects of neonatal MK-801 treatment on spatial learning and cortical plasticity in adult rats.

RATIONALE AND OBJECTIVES: The long-term effects of neonatal treatment with MK-801 on spatial learning and cortical plasticity were investigated in adult rats. METHODS: Rat pups were injected twice daily with MK-801 (0.1 mg/kg) on postnatal days 7-19, participated in water maze testing between postnatal days 90 and 102, and were then studied electrophysiologically. RESULTS: Treatment with MK-801 in such a low dose resulted in a very slight impairment of performance in the water maze task, but not in the visual cue response. Besides the slight learning impairment, the electrophysiological study revealed a reduction in the capacity for plasticity in the primary motor cortex of the treated animals, which was pronounced in the controls. CONCLUSION: The study demonstrates that even a slight impairment in learning and memory function may be accompanied by a cortical plasticity deficiency that is detectable electrophysiologically.

Comparative studies on the effect of ergot contaminated feed on performance and health of piglets and chickens.

Two dose response trials were conducted with piglets and chickens to study the effects of increasing amounts of ergot (Claviceps purpurea) with a defined alkaloid content and pattern on performance, biochemical serum characteristics and organ weights (of chickens). The ergot was mixed into the cereal-soybean meal based diets at levels of 0, 0.5, 1, 2 and 4 g/kg. The total alkaloid content of the ergot was analysed to be 2775 mg/kg and showed the following composition: ergometrine 8.1%, ergotamine 5.4%, ergocomine 3.2%, alpha-ergocryptine 1.9%, ergocristine 14.9% and residue 66.5%. Each treatment was tested with eight castrated male and eight female piglets over a period of 35 days (8 kg initial live weight) and 28 male chickens for 21 days (43 g initial live weight). Cumulative daily dry matter intake and live weight gain [g/d] were 595, 535, 560, 577 and 490 and 413, 399, 420, 443 and 347 for the piglets fed the unsupplemented control diet and the diets containing 0.5, 1, 2 and 4 g ergot per kg, respectively. Feed intake and live weight gain of the piglets fed the highest ergot supplemented diet were significantly decreased. Serum aspartate aminotransferase activity of the 4 g ergot treatment was significantly increased. Also serum albumin concentrations showed significant linear alterations. Serum activities of glutamate dehydrogenase, gamma-glutamyltransferase, total protein and porcine growth hormone were not significantly influenced by dietary treatment. The experiment with chickens demonstrated no significant effects on performance due to dietary ergot exposure. The serum activities of glutamate dehydrogenase and alanine aminotransferase were not significantly influenced by dietary treatment while serum activities of gamma-glutamyltransferase and aspartate aminotransferase and the concentrations of albumin and total bilirubin were significantly affected. Heart weights showed a significant linear decrease due to ergot feeding. According to these results, piglets seemed to react more sensitively on the occurrence of ergot in the diet as compared to chickens. The critical level of total ergot alkaloids for piglets seemed to be in the range from 5.6 mg to 11.1 mg/kg diet for the present study. Ergot effects on signs of inflammation in the proximal duodenum occurred in chickens fed diets containing 2.8 mg and 11.1 mg total ergot alkaloids/kg although live performance remained unaffected. Further studies are necessary to define the critical level of ergot alkaloids in dependence on alkaloid pattern.