Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain-wide structural and functional disruption in mice with oligodendrocyte specific Nf1 deletion is rescued by inhibition of NOS

Neurofibromin gene (NF1) mutation causes Neurofibromatosis type 1 (NF1), a disorder in which brain white matter deficits identified by neuroimaging are common, yet of unknown cellular etiology. In mice, Nf1 loss in adult oligodendrocyte causes myelin decompaction, and increases oligodendrocyte nitric oxide (NO) levels. Nitric oxide synthase (NOS) inhibitors rescue this pathology. Whether oligodendrocyte pathology is sufficient to affect brainwide structure and account for NF1 imaging findings is unknown. Here, we show that Nf1 gene inactivation in adult oligodendrocytes (Plp-Nf1fl/+ mice) results in a motor coordination deficit. Magnetic resonance imaging in awake mice shows that fractional anisotropy is reduced in Plp-Nf1fl/+ corpus callosum and that interhemispheric functional connectivity in motor cortex is also reduced, consistent with disrupted myelin integrity. Further, NOS-specific inhibition rescued both measures. These results demonstrate that oligodendrocyte defects account for aspects of brain dysfunction in NF1, which can be identified by neuroimaging and ameliorated by NOS inhibition. Significance statement This study assesses the effects of myelin decompaction on motor behavior and brain-wide structural and functional connectivity, and the effect of nitric oxide synthase (NOS) inhibition by N-nitro-L-arginine methyl ester (L-NAME) on these imaging measures. We report that inducible oligodendrocyte-specific inactivation of the Nf1 gene, which causes myelin decompaction, results in reduced motor coordination. Using diffusion-based MRI we show reduced myelin integrity and using functional MRI we show reduced functional connectivity in awake passive mice. L-NAME administration results in rescue of the pathology at the mesoscopic level using imaging procedures that can be directly applied to humans to study treatment efficacy in clinical trials.
The Na+/K+ ATPase Regulates Glycolysis and Modifies Immune Metabolism in Tumors

Cancer therapies targeting metabolism have been limited due to a lack of understanding of the controlling properties of vulnerable pathways. The Na+/K+ ATPase is responsible for a large portion of cellular energy demands but how these demands influence metabolism and create metabolic liabilities are not known. Using metabolomic approaches, we first show that digoxin, a cardiac glycoside widely used in humans, acts through disruption to central carbon metabolism via on target inhibition of the Na+/K+ ATPase that was fully recovered by expression of an allele resistant to digoxin. We further show in vivo that administration of digoxin inhibits glycolysis in both malignant and healthy cells, particularly within clinically relevant cardiac tissue, while exhibiting tumor-specific cytotoxic activity in an allografted soft tissue sarcoma. Single-cell expression analysis of over 31,000 cells within the sarcoma shows that acute Na+/K+ ATPase inhibition shifts the immune composition of the tumor microenvironment, leading to selective alterations to metabolic programs in specific immune cells thus acting both through tumor cell and microenvironmental (e.g. macrophage) cells. These results provide evidence that altering energy demands can be used to regulate glycolysis with cell-type specific consequences in a multicellular environment of biomedical interest.
Differential effect of value and salience on saccadic reaction times

Express saccades, a mode of visually guided saccades, distinguished from regular saccades by extremely short reaction times, are triggered by inserting a temporal gap between the fixation dot and the saccade target. It is usually assumed that they are produced by a specific pathway in which the superior colliculus plays a key role. Whether and how this pathway deals with information on the subjective value of a saccade target is unknown. We, therefore, studied the influence of varying reward expectancies and compared it with the impact of the presence and absence of a temporal gap between the disappearance of the fixation dot and the appearance of the target on the visually guided saccades of two rhesus macaques (Macaca mulatta). We observed that the introduction of a gap shifted the entire saccadic reaction time distribution to shorter latencies while increasing the probability of express saccades. On the other hand, promoting the monkey’s reward expectancy shortened reaction times and increased peak velocities of regular saccades, and increased the probability of express saccades. Importantly, we observed that the reaction time and peak velocity of express saccades were not sensitive to the value of the saccade target, suggesting that the express pathway does not have access to information on value. We propose a new model on express saccades that treats the salience of visual objects in the scene differently from the subjective value assigned to them.
A two-stage ECG signal denoising method based on deep convolutional network

Electrocardiogram (ECG) is an effective and non-invasive indicator for the detection and prevention of arrhythmia. ECG signals are susceptible to noise contamination, which can lead to errors in ECG interpretation. Therefore, ECG pretreatment is important for accurate analysis. In this paper, a method of noise reduction based on deep learning is proposed. The method is divided into two stages, and two corresponding models are formed. In the first stage, a one-dimensional U-net model is designed for ECG signal denoising to eliminate noise as much as possible. The one-dimensional DR-net model in the second stage is used to reconstruct the ECG signal and to correct the waveform distortion caused by noise removal in the first stage. In this paper, the U-net and the DR-net are constructed by the convolution method to achieve end-to-end mapping from noisy ECG signals to clean ECG signals. The ECG data used in this paper are from CPSC2018, and the noise signal is from MIT-BIH Noise Stress Test Database (NSTDB). In the experiment, the improvement in the signal-to-noise ratio SNRimp, the root mean square error decrease RMSEde, and the correlation coefficient P, are used to evaluate the performance of the network. This two-stage method is compared with FCN and U-net alone. The experimental results show that the two-stage noise reduction method can eliminate complex noise in the ECG signal while retaining the characteristic shape of the ECG signal. According to the results, we believe that the proposed method has a good application prospect in clinical practice.
Resolvin E1 derived from eicosapentaenoic acid prevents hyperinsulinemia and hyperglycemia in a host genetic manner

Eicosapentaenoic acid (EPA) has garnered attention after the success of the REDUCE‐IT trial, which contradicted previous conclusions on EPA for cardiovascular disease risk. Here we first investigated EPA's preventative role on hyperglycemia and hyperinsulinemia. EPA ethyl esters prevented obesity‐induced glucose intolerance, hyperinsulinemia, and hyperglycemia in C57BL/6J mice. Supporting NHANES analyses showed that fasting glucose levels of obese adults were inversely related to EPA intake. We next investigated how EPA improved murine hyperinsulinemia and hyperglycemia. EPA overturned the obesity‐driven decrement in the concentration of 18‐hydroxyeicosapentaenoic acid (18‐HEPE) in white adipose tissue and liver. Treatment of obese inbred mice with RvE1, the downstream immunoresolvant metabolite of 18‐HEPE, but not 18‐HEPE itself, reversed hyperinsulinemia and hyperglycemia through the G‐protein coupled receptor ERV1/ChemR23. To translate the findings, we determined if the effects of RvE1 were dependent on host genetics. RvE1's effects on hyperinsulinemia and hyperglycemia were divergent in diversity outbred mice that model human genetic variation. Secondary SNP analyses further confirmed extensive genetic variation in human RvE1/EPA‐metabolizing genes. Collectively, the data suggest EPA prevents hyperinsulinemia and hyperglycemia, in part, through RvE1's activation of ERV1/ChemR23 in a host genetic manner. The studies underscore the need for personalized administration of RvE1 based on genetic/metabolic enzyme profiles.
Large domains of heterochromatin direct the formation of short mitotic chromosome loops

During mitosis chromosomes reorganise into highly compact, rod-shaped forms, thought to consist of consecutive chromatin loops around a central protein scaffold. Condensin complexes are involved in chromatin compaction, but the contribution of other chromatin proteins, DNA sequence and histone modifications is less understood. A large region of fission yeast DNA inserted into a mouse chromosome was previously observed to adopt a mitotic organisation distinct from that of surrounding mouse DNA. Here we show that a similar distinct structure is common to a large subset of insertion events in both mouse and human cells and is coincident with the presence of high levels of heterochromatic H3 lysine 9 trimethylation (H3K9me3). Hi-C and microscopy indicate that the heterochromatinised fission yeast DNA is organised into smaller chromatin loops than flanking euchromatic mouse chromatin. We conclude that heterochromatin alters chromatin loop size, thus contributing to the distinct appearance of heterochromatin on mitotic chromosomes, such as at centromeres.
Long-term performance of Utah slanted electrode arrays and intramuscular electromyographic leads implanted chronically in human arm nerves and muscles

Objective. We explore the long-term performance and stability of seven percutaneous Utah Slanted Electrode Arrays (USEAs) and intramuscular recording leads (iEMGs) implanted chronically in the residual arm nerves and muscles of three human participants as a means to permanently restore sensorimotor function after transradial amputations. Approach. We quantify the number of functional recording and functional stimulating electrodes over time. We also calculate the signal-to-noise ratio (SNR) of USEA and iEMG recordings and quantify the stimulation current necessary to evoke detectable sensory percepts. Furthermore, we quantify the consistency of the sensory modality, receptive field location, and receptive field size of USEA-evoked percepts. Main results. In the most recent subject, involving USEAs with technical improvements, neural recordings persisted for 502 d (entire implant duration) and the number of functional recording electrodes for one USEA increased over time. However, for six out of seven USEAs across the three participants, the number of functional recording electrodes decreased within the first 2 months after implantation. The SNR of neural recordings and electromyographic recordings stayed relatively consistent over time. Sensory percepts were consistently evoked over the span of 14 months, were not significantly different in size, and highlighted the nerves’ fascicular organization. The percentage of percepts with consistent modality or consistent receptive field location between sessions (∼1 month apart) varied between 0%–86.2% and 9.1%–100%, respectively. Stimulation thresholds and electrode impedances increased initially but then remained relatively stable over time. Significance. This work demonstrates improved performance of USEAs, and provides a basis for comparing the longevity and stability of USEAs to that of other neural interfaces. USEAs provide a rich repertoire of neural recordings and sensory percepts. Although their performance still generally declines over time, functionality can persist long-term. Future work should leverage the results presented here to further improve USEA design or to develop adaptive algorithms that can maintain a high level of performance.
Sex-segregated range use by black-and-white ruffed lemurs (Varecia variegata) in Ranomafana National Park, Madagascar

Ranging behavior is one important strategy by which nonhuman primates obtain access to resources critical to their biological maintenance and reproductive success. As most primates live in permanent social groups, their members must balance the benefits of group living with the costs of intragroup competition for resources. However, some taxa live in more spatiotemporally flexible social groups, whose members modify patterns of association and range use as a method to mitigate these costs. Here, we describe the range use of black-and-white ruffed lemurs (Varecia variegata) at Mangevo, an undisturbed primary rainforest site in Ranomafana National Park, Madagascar and characterize sex-differences in annual home range area, overlap, and daily distances traveled. Moreover, we characterized seasonal variability in range use and ask whether ranging behaviors can be explained by either climatic or reproductive seasonality. We found that females used significantly larger home ranges than males, though sexes shared equal and moderate levels of home range overlap. Overall, range use did not vary across seasons; though within sexes, male range use varied significantly with climatic variation. Moreover, daily path length was best predicted by day length, female reproductive state, and sex. While the patterns of range use and spatial association presented here share some similarities with ‘bisexually bonded’ community models described for chimpanzees, we argue that ruffed lemurs represent yet another community model wherein ‘neighborhoods’ of overlapping males and females affiliate with each other moreso than with other, more distantly located community members, and to the exclusion of members from adjacent communities.
In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity

DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication, closely connected to genomic instability and oncogenesis. We present a stochastic hybrid model of DNA re-replication that accurately portrays the interplay between discrete dynamics, continuous dynamics, and uncertainty. Using experimental data on the fission yeast genome, model simulations show how different regions respond to re-replication, and permit insight into the key mechanisms affecting re-replication dynamics. Simulated and experimental population-level profiles exhibit good correlation along the genome, which is robust to model parameters, validating our approach. At a single-cell level, copy numbers of individual loci are affected by intrinsic properties of each locus, in cis effects from adjoining loci and in trans effects from distant loci. In silico analysis and single-cell imaging reveal that cell-to-cell heterogeneity is inherent in re-replication and can lead to a plethora of genotypic variations. Our thorough in silico analysis of DNA re-replication across a complete genome reveals that heterogeneity at the single cell level and robustness at the population level are emerging and co-existing principles of DNA re-replication. Our results indicate that re-replication can promote genome plasticity by generating many diverse genotypes within a population, potentially offering an evolutionary advantage in cells with aberrations in replication control mechanisms.
Eco-evo-devo implications and archaeobiological perspectives of wild and domesticated grapevines fruits covariating traits

The phenotypic changes that occurred during the domestication and diversification of grapevine are well known, particularly changes in seed morphology, but the functional causes and consequences behind these variations are poorly understood. Wild and domesticate grapes differ, among others, in the form of their pips: wild grapes produce roundish pips with short stalks and cultivated varieties have more elongated pips with longer stalks. Such variations of form are of first importance for archaeobotany since the pip form is, most often, the only remaining information in archaeological settings. This study aims to enlight archaeobotanical record and grapevine pip development by better understanding how size and shape (co)variates between pip and berry in both wild and domesticated Vitis vinifera. The covariation of berry size, number of seeds per berry (“piposity”), pip size and pip shape were explored on 49 grapevine accessions sampled among Euro-Mediterranean traditional cultivars and wild grapevines. We show that for wild grapevine, the higher the piposity, the bigger the berry and the more elongated the pip. For both wild and domesticated grapevine, the longer is the pip, the more it has a “domesticated” shape. Consequences for archaeobotanical studies are tested and discussed, and these covariations allowed the inference of berry dimensions from archaeological pips from a Southern France Roman site. This systematic exploration sheds light on new aspects of pip-berry relationship, in both size and shape, on grapevine eco-evo-devo changes during domestication, and invites to explore further the functional ecology of grapevine pip and berry and notably the impact of cultivation practices and human selection on grapevine morphology.
SCHNEL: Scalable clustering of high dimensional single-cell data

Motivation Single cell data measures multiple cellular markers at the single-cell level for thousands to millions of cells. Identification of distinct cell populations is a key step for further biological understanding, usually performed by clustering this data. Dimensionality reduction based clustering tools are either not scalable to large datasets containing millions of cells, or not fully automated requiring an initial manual estimation of the number of clusters. Graph clustering tools provide automated and reliable clustering for single cell data, but suffer heavily from scalability to large datasets. Results We developed SCHNEL, a scalable, reliable and automated clustering tool for high-dimensional single-cell data. SCHNEL transforms large high-dimensional data to a hierarchy of datasets containing subsets of data points following the original data manifold. The novel approach of SCHNEL combines this hierarchical representation of the data with graph clustering, making graph clustering scalable to millions of cells. Using seven different cytometry datasets, SCHNEL outperformed three popular clustering tools for cytometry data, and was able to produce meaningful clustering results for datasets of 3.5 and 17.2 million cells within workable timeframes. In addition, we show that SCHNEL is a general clustering tool by applying it to single-cell RNA sequencing data, as well as a popular machine learning benchmark dataset MNIST. Availability and Implementation Implementation is available on GitHub (https://github.com/paulderaadt/HSNE-clustering) Contact a.mahfouz@lumc.nl Supplementary information Supplementary data are available at Bioinformatics online.
Recombination and sterility in inversion homo- and heterokaryotypes under a general counting model of chiasma interference

It has long been known that chiasmata are not independently generated along the chromosome, a phenomenon known as chiasma interference. In this paper, I suggest a model of chiasma interference that generalizes the Poisson model, the counting model, the Poisson-skip model and the two-pathway counting model into a single framework, and use it to derive infinite series expressions for the sterility and recombination pattern probabilities in inversion homo- and heterokaryotypes, and a closed-form expression for the special case of the two-pathway counting model in homokaryotypes.
Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis

The human PUF-family proteins, PUM1 and PUM2, post-transcriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3’ UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a ‘rulebook’ of key contextual features that differentiate functional vs. non-functional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.
Comparison of cardiac and lung doses for breast cancer patients with free breathing and deep inspiration breath hold technique in 3 dimensional conformal radiotherapy - a dosimetric study

Abstract Purpose: To investigate the cardio-pulmonary doses between Deep Inspiration Breath Hold (DIBH) and Free Breathing (FB) technique in left sided breast irradiation. Materials & Methods: DIBH CT and FB CT were acquired for 10 left sided breast patients who underwent whole breast irradiation with or without nodal irradiation. Three fields single isocenter technique were used for patients with node positive patients along with two tangential conformal fields whereas only two tangential fields were used in node negative patients. All the critical structures like lungs, heart, esophagus, thyroid, etc., were delineated in both DIBH and FB scan. Both DIBH and FB scans were fused with the Dicom origin as they were acquired with the same Dicom coordinates. Plans were created in the DIBH scan for a dose range between 50 Gy in 25 fractions. Critical structures doses were recorded from the Dose Volume Histogram for both the DIBH and FB data set for evaluation. Results: The average mean heart dose in DIBH vs FB was 13.18 Gy vs 6.97 Gy, (p = 0.0063) significantly with DIBH as compared to FB technique. The relative reduction in average mean heart dose was 47.12%. The relative V5 reduced by 14.70% (i.e. 34.42% vs 19.72%, p = 0.0080), V10 reduced by 13.83% (i.e. 27.79 % vs 13.96%, p = 0.0073). V20 reduced by 13.19% (i.e. 24.54 % vs 11.35%, p = 0.0069), V30 reduced by 12.38% (i.e. 22.27 % vs 9.89 %, p = 0.0073) significantly with DIBH as compared to FB. The average mean left lung dose reduced marginally by 1.43 Gy (13.73 Gy vs 12.30 Gy, p = 0.4599) but insignificantly with DIBH as compared to FB. Other left lung parameters (V5, V10, V20 and V30) shows marginal decreases in DIBH plans compare to FB plans. Conclusion: DIBH shows a substantial reduction of cardiac doses but slight and insignificant reduction of pulmonary doses as compared with FB technique. Using the simple DIBH technique, we can effectively reduce the cardiac morbidity and at the same time radiation induced lung pneumonitis is unlikely to increase.
Electrophysiological signatures of memory reactivation in humans

The reactivation of neural activity that was present during the encoding of an event is assumed to be essential for human episodic memory retrieval and the consolidation of memories during sleep. Pioneering animal work has already established a crucial role of memory reactivation to prepare and guide behaviour. Research in humans is now delineating the neural processes involved in memory reactivation during both wakefulness and sleep as well as their functional significance. Focusing on the electrophysiological signatures of memory reactivation in humans during both memory retrieval and sleep-related consolidation, this review provides an overview of the state of the art in the field. We outline recent advances, methodological developments and open questions and specifically highlight commonalities and differences in the neuronal signatures of memory reactivation during the states of wakefulness and sleep. This article is part of the Theo Murphy meeting issue ‘Memory reactivation: replaying events past, present and future’.