bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concordance of MERFISH Spatial Transcriptomics with Bulk and Single-cell RNA Sequencing
Authors: Liu Jonathan , Tran Vanessa , Vemuri Venkata Naga Pranathi , Byrne Ashley , Borja Michael , Kim Yang Joon , Agarwal Snigdha , Wang Ruofan , Awayan Kyle , Murti Abhishek , Taychameekiatchai Aris , Wang Bruce , Emanuel George , He Jiang , Haliburton John , Pisco Angela Oliveira , Neff Norma 
Published: March 2022

AbstractSpatial transcriptomics extends single cell RNA sequencing (scRNA-seq) by providing spatial context for cell type identification and analysis. Imaging-based spatial technologies such as Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) can achieve single-cell resolution, directly mapping single cell identities to spatial positions. MERFISH produces an intrinsically different data type than scRNA-seq and a technical comparison between the two modalities is necessary to ascertain how to best integrate them. We performed MERFISH on mouse liver and kidney and compared the resulting bulk and single-cell RNA statistics with those from the Tabula Muris Senis cell atlas as well as from two Visium datasets. MERFISH quantitatively reproduced the bulk RNA-seq and scRNA-seq results with improvements in overall dropout rates and sensitivity. Finally, we found that MERFISH independently resolved distinct cell types and spatial structure in both liver and kidney. Computational integration with the Tabula Muris Senis atlas did not enhance these results. We conclude that compared to scRNA-seq, MERFISH provides a quantitatively comparable method for measuring single-cell gene expression and can robustly identify cell types without the need for computational integration with scRNA-seq reference atlases.
Impaired peri-olfactory cerebrospinal fluid clearance mediated cognitive decline after dyssomnia
Authors: Zhou Ying , Ran Wang , Luo Zhongyu , Wang Jianan , Fang Mengmeng , Wei Kai , Sun Jianzhong , Lou Min 
Published: March 2022

AbstractAnimal experiments have demonstrated the dependency of CSF clearance function on age and sleep, which partially underlay the cognitive decline in the elderly. However, evidence is lacking in humans mainly due to limited method to assess CSF clearance function. We aimed to image CSF clearance pathways in human brain by dynamic MRI with intrathecal contrast agent as a CSF tracer. We performed T1-weighted and T2-fluid attenuated inversion recovery imaging with equal sequence parameters before and at multiple time points after intrathecal injection of contrast agent to visualize the putative meningeal lymphatic pathway, peri-olfactory nerve pathway and peri-optic nerve pathway. We defined the CSF clearance function as the percentage change in signal unit ratio of critical locations in these pathways from baseline to 39 hours after intrathecal injection. CSF clearance through the putative meningeal lymphatic and peri-neural pathways were clearly visualized in all 85 patients. The CSF clearance function of meningeal lymphatic and peri-neural pathways were reduced with aging (all P < 0.05). The CSF clearance function through peri-olfactory nerve pathway was positive correlated with sleep quality and cognitive function (both P < 0.05). Moreover, the CSF clearance function through peri-olfactory nerve pathway mediated the association of sleep quality with cognitive function (percent change in β [bootstrap 95% confidence interval]: 35% [−0.220, −0.003]). The study shows promise for dynamic MRI with intrathecal injection of contrast agent as a method to assess CSF clearance function through putative peri-neural pathways, and interprets the impaired clearance through putative peri-olfactory nerve pathway may explain the cognitive decline in patients with dyssomnia.
Cell type-specific prediction of 3D chromatin organization enables high-throughputin silicogenetic screening
Authors: Tan Jimin , Shenker-Tauris Nina , Rodriguez-Hernaez Javier , Wang Eric , Sakellaropoulos Theodore , Boccalatte Francesco , Thandapani Palaniraja , Skok Jane , Aifantis Iannis , Fenyö David , Xia Bo , Tsirigos Aristotelis 
Published: March 2022

AbstractThe mammalian genome is spatially organized in the nucleus to enable cell type-specific gene expression. Investigating how chromatin organization determines this specificity remains a challenge. Methods for measuring the 3D chromatin organization, such as Hi-C, are costly and bear strong technical limitations, restricting their broad application particularly in high-throughput genetic perturbations. In this study, we present C.Origami, a deep neural network model that performsde novoprediction of cell type-specific chromatin organization. The C.Origami model enablesin silicoexperiments to examine the impact of genetic perturbations on chromatin interactions in cancer genomes and beyond. In addition, we propose anin silicogenetic screening framework that enables high-throughput identification of impactful genomic regions on 3D chromatin organization. We demonstrate that cell type-specificin silicogenetic perturbation and screening, enabled by C.Origami, can be used to systematically discover novel chromatin regulatory mechanisms in both normal and disease-related biological systems.
Incorporating the image formation process into deep learning improves network performance in deconvolution applications
Authors: Li Yue , Su Yijun , Guo Min , Han Xiaofei , Liu Jiamin , Vishwasrao Harshad D. , Li Xuesong , Christensen Ryan , Sengupta Titas , Moyle Mark W. , Chen Jiji , Usdin Ted B. , Colón-Ramos Daniel , Liu Huafeng , Wu Yicong , Shroff Hari 
Published: March 2022

AbstractWe present ‘Richardson-Lucy Network’ (RLN), a fast and lightweight deep learning method for 3D fluorescence microscopy deconvolution. RLN combines the traditional Richardson-Lucy iteration with a fully convolutional network structure, improving network interpretability and robustness. Containing only ∼16 thousand parameters, RLN enables 4- to 50-fold faster processing than purely data-driven networks with many more parameters. By visual and quantitative analysis, we show that RLN provides better deconvolution, better generalizability, and fewer artifacts than other networks, especially along the axial dimension. RLN outperforms Richardson-Lucy deconvolution on volumes contaminated with severe out of focus fluorescence or noise and provides 4- to 6-fold faster reconstructions of large, cleared tissue datasets than classic multi-view pipelines. We demonstrate RLN’s performance on cells, tissues, and embryos imaged with widefield-, light sheet-, and structured illumination microscopy.
Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation
Authors: Ge Yichen , Chen Xushen , Nan Nan , Bard Jonathan , Wu Fuguo , Yergeau Donald , Liu Tao , Wang Jie , Mu Xiuqian 
Published: March 2022

ABSTRACTHow the diverse neural cell types emerge from multipotent neural progenitor cells during central nervous system development remains poorly understood. Recent scRNA-seq studies have delineated the developmental trajectories of individual neural cell types in many neural systems including the neural retina. Further understanding of the formation of neural cell diversity requires knowledge about how the epigenetic landscape shifts along individual cell lineages and how key transcription factors regulate these changes. In this study, we dissect the changes in the epigenetic landscape during early retinal cell differentiation by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages. Using CUT&Tag, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2, and Isl1, and uncover their roles in shaping the epigenetic landscape and controlling gene expression in a sequential and combinatorial fashion along individual retinal cell lineages such as retinal ganglion cells (RGCs). Our results reveal a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from multipotent retinal progenitor cells (RPCs).
The reliability of two prospective cortical biomarkers for pain: EEG peak alpha frequency and TMS corticomotor excitability
Authors: Chowdhury Nahian S , Skippen Patrick , Si E , Chiang Alan , Millard Samantha K , Furman Andrew J , Chen Shuo , Seminowicz David A , Schabrun Siobhan M 
Published: March 2022

AbstractMany pain biomarkers fail to move from discovery to clinical application, attributed to poor reliability and feasible classifications of at-risk individuals. Preliminary evidence has shown that higher pain sensitivity is associated with slow peak alpha frequency (PAF) and depression of corticomotor excitability (CME). The present study evaluated the reliability of these measures, specifically whether, over several days of pain, a) PAF remains stable and b) individuals show two stable and distinct CME responses: facilitation and depression. Seventy-five healthy participants were given an injection of nerve growth factor (NGF) into the right masseter muscle on Day 0 and Day 2, inducing sustained pain. Electroencephalography (EEG) to assess PAF and transcranial magnetic stimulation (TMS) to assess CME were recorded on Day 0, Day 2 and Day 5. PAF reliability was in the excellent range even without standard pre-processing and ∼2 minutes recording length. Moreover, two distinct and stable CME responses were demonstrated: facilitation and depression. These findings support the notion that PAF is a stable trait characteristic, with reliability unaffected by pain, and excellent reliability achievable with minimal pre-processing and ∼2 minutes recording, making it a readily translatable biomarker. Furthermore, the study showed novel evidence of two stable corticomotor adaptations to sustained pain. Overall, the study provides support for the reliability of PAF and CME as prospective cortical biomarkers.
Increased frequencies of IgH locus suicide recombination points on Chronic Lymphocytic Leukemia with low rate of AID related somatic mutations, cMYC overexpression and short telomeres
Authors: Al Jamal Israa , Parquet Milène , Boutouil Hend , Guiyedi Kenza , Rizzo David , Dupont Marine , Boulin Mélanie , El Hamel Chahrazed , Lerat Justine , Aoufouchi Saïd , al Hamaoui Samar , Makdissy Nehman , Feuillard Jean , Gachard Nathalie , Peron Sophie 
Published: March 2022

AbstractIn normal activated B-cells, Activation Induced-cytidine deaminase (AID) is absolutely required for immunoglobulin (Ig) class switch recombination (CSR) and IGHV somatic hypermutation (SHM). AID is also implicated in the Locus Suicide Recombination (LSR) of the Ig heavy (IgH) locus, resulting in the deletion of the IgH constant part. Chronic lymphocytic leukemia (CLL) is an indolent non-Hodgkin B-cell lymphoma characterized by tumor CLL B-cells that weakly express a B cell receptor (BCR) on their surface. The great majority of CLL tumor B-cells are non class-switched. Searching for abnormalities of IgH locus recombination in CLL, we investigated CSR and LSR in samples from CLL patients (N=47) with high blood tumor cell infiltration (>98%) and in healthy volunteers (HV) as controls (N=9). LSR was detectable at comparable levels in both HV and CLL groups. CSR counts were decreased in CLL samples as expected. As distribution of LSR counts was bimodal, we separated CLL patients in two groups so called LSRHigh and LSRLow. LSRHigh CLLs exhibited very weak AID expression and low mutation rate of IgHV region and of the AID off-target PIM1 gene. LSR junction diversity, evaluated using the Shannon index, was increased in LSRHigh CLLs suggesting that LSR was on-going in these cells. Also, shorter telomeres were observed in LSRHigh CLLs suggesting an increased number of past mitosis. Consistently, increased levels of cMYC expression were detected in LSRHigh CLLs and treatment free survival of these cases was markedly decreased. We hypothesized that LSR in LSRHigh CLLs is AID independent and could be due to DNA lesion and inaccurate DSB repair within the IgH locus, which could be accessible to recombination machinery due to increased IgH locus transcription. Altogether, our results indicate the accessibility of IgH locus and the proliferation increase LSR rate in LSRHigh CLLs could be related to cMYC resulting in shorter treatment free survival of patients and point on an AID independent mechanism of IgH recombination.
Hierarchical organization of spontaneous co-fluctuations in densely-sampled individuals using fMRI
Authors: Betzel Richard F. , Cutts Sarah A. , Tanner Jacob , Greenwell Sarah A. , Varley Thomas , Faskowitz Joshua , Sporns Olaf 
Published: March 2022

ABSTRACTEdge time series decompose FC into its framewise contributions. Previous studies have focused on characterizing the properties of high-amplitude frames, including their cluster structure. Less is known about middle- and low-amplitude co-fluctuations. Here, we address those questions directly, using data from two dense-sampling studies: the MyConnectome project and Midnight Scan Club. We develop a hierarchical clustering algorithm to group peak co-fluctuations of all magnitudes into nested and multi-scale clusters based on their pairwise concordance. At a coarse scale, we find evidence of three large clusters that, collectively, engage virtually all canonical brain systems. At finer scales, however, each cluster is dissolved, giving way to increasingly refined patterns of co-fluctuations involving specific sets of brain systems. We also find an increase in global co-fluctuation magnitude with hierarchical scale. Finally, we comment on the amount of data needed to estimate co-fluctuation pattern clusters and implications for brain-behavior studies. Collectively, the findings reported here fill several gaps in current knowledge concerning the heterogeneity and richness of co-fluctuation patterns as estimated with edge time series while providing some practical guidance for future studies.
Tracing Diurnal Differences in Brain Anatomy with Voxel-Based Morphometry – Associations with Sleep Characteristics
Authors: Zareba Michal Rafal , Fafrowicz Magdalena , Marek Tadeusz , Oginska Halszka , Beldzik Ewa , Domagalik Aleksandra 
Published: March 2022

AbstractMultiple aspects of brain functioning, including arousal, motivation, and cognitive performance, are governed by circadian rhythmicity. Although the recent rise in the use of magnetic resonance imaging (MRI) has enabled investigations into the macroscopic correlates of the diurnal brain processes, neuroanatomical studies are scarce. The current work investigated how time-of-day (TOD) impacts white (WM) and grey matter (GM) volumes using voxel-based morphometry (VBM) in a large dataset (N = 72) divided into two equal, comparable subsamples to assess the replicability of effects. Furthermore, we aimed to assess how the magnitude of these diurnal differences was related to actigraphy-derived indices of sleep health. The results extend the current knowledge by reporting that TOD is predominantly associated with regional WM volume decreases. Additionally, alongside corroborating previously observed volumetric GM decreases, we provide the first evidence for positive TOD effects. Higher replicability was observed for WM, with the only two replicated GM clusters being volumetric increases in the amygdala and hippocampus, and decreases in the retrosplenial cortex, with the latter more pronounced in individuals with shorter sleep times. These findings implicate the existence of region-specific mechanisms behind GM effects, which might be related to cognitive processes taking place during wakefulness and homeostatic sleep pressure.
Possible Mechanism of Porosome-Mediated Exosome Release
Authors: Cho Won Jin , Formosa Brent , Zhvania Mzia G. , Taatjes Douglas J. , Ghiran Ionita , Jena Bhanu P. 
Published: March 2022

ABSTRACTSupramolecular cup-shaped lipoprotein structures called porosomes embedded in the cell plasma membrane mediate fractional release of intra-vesicular contents from cells during secretion. The presence of porosomes, have been documented in many cell types including neurons, acinar cells of the exocrine pancreas, growth hormone secreting cells of the pituitary, and mouse insulin-secreting beta cell insulinomas called Min6. Electron micrographs of the nerve terminal in rat brain and of Min6 cells, suggest that besides the docking, fusion and content release of neurotransmitter containing synaptic vesicles and insulin containing granules, multi-vesicular bodies and exosome-like vesicles are released at the porosome complex. To test this hypothesis, the porosome-associated calcium transporting ATPase 1 [SPCA1] encoded by the ATP2C1 gene, was knocked-out in Min6 cells using CRISPR, to study glucose-stimulated insulin and exosome release. In agreement with electron micrographs, results from the study demonstrate a loss of both glucose-stimulated insulin and exosome release in the ATP2C1 knockout Min6 cells. These results further confirm the role of the porosome complex in insulin secretion and establishes a new paradigm in porosome-mediated exosome release in beta cells of the endocrine pancreas.
Effect of paclitaxel treatment on cellular mechanics and morphology of human oesophageal squamous cell carcinoma in 2D and 3D environments
Authors: Kiwanuka Martin , Higgins Ghodeejah , Ngcobo Silindile , Nagawa Juliet , Lang Dirk M. , Zaman Muhammad H. , Davies Neil H. , Franz Thomas 
Published: March 2022

AbstractDuring chemotherapy, structural and mechanical changes in malignant cells have been observed in several cancers, including leukaemia and pancreatic and prostate cancer. Such cellular changes may act as physical biomarkers for chemoresistance and cancer recurrence. This study aimed to determine how exposure to paclitaxel affects the intracellular stiffness of human oesophageal cancer of South African originin vitro. A human oesophageal squamous cell carcinoma cell line WHCO1 was cultured on glass substrates (2D) and in collagen gels (3D) and exposed to paclitaxel for up to 48 hours. Cellular morphology and stiffness were assessed with confocal microscopy, visually aided morpho-phenotyping image recognition, and mitochondrial particle tracking microrheology at 24 and 48 hours. In the 2D environment, the intracellular stiffness was higher for the paclitaxel-treated than for untreated cells at 24 and 48 hours. In the 3D environment, the paclitaxel-treated cells were stiffer than the untreated cells at 24 hours, but no statistically significant differences in stiffness were observed at 48 hours. In 2D, paclitaxel-treated cells were significantly larger at 24 and 48 hours and more circular at 24 but not at 48 hours than the untreated controls. In 3D, there were no significant morphological differences between treated and untreated cells. The distribution of cell shapes was not statistically significant different across the different treatment conditions in 2D and 3D environments. Future studies with patient-derived primary cancer cells and prolonged drug exposure will help identify physical cellular biomarkers to detect chemoresistance onset and assess therapy effectiveness in oesophageal cancer patients.InsightMechanical changes in cancer cells by chemotherapeutic drugs exposure offer possible physical biomarkers for chemoresistance and cancer recurrence. This study on human oesophageal squamous cell carcinoma indicated thatin vitropaclitaxel treatment induced stiffening and enlarging of malignant cells in two-dimensional environments at 24 and 48 hours. In physiologically more relevant three-dimensional collagen matrices the paclitaxel treatment led to cellular stiffening at 24 hours but softening thereafter, without significant changes in cellular size at any time. The outcomes need to be confirmed in future studies with prolonged drug exposure and patient-derived primary cancer cells.
Systematic analysis uncovers SYK dependency in NF1LoF melanoma cells
Authors: Abecunas Cara , Whitehead Christopher , Ziemke Elizabeth , Baumann Douglas G. , Frankowski-McGregor Christy , Sebolt-Leopold Judith , Fallahi-Sichani Mohammad 
Published: March 2022

AbstractThe loss of function (LoF) of NF1 is the third most frequent mutation that drives hyperactivated RAS and tumor growth in >10% of melanomas. NF1LoF melanoma cells, however, do not show consistent sensitivity to individual MEK, ERK, or PI3K/mTOR inhibitors. Here, we perform a targeted kinase inhibitor screen and identify a tool compound, named MTX-216, to be highly effective in blocking NF1LoF melanoma cells. Single-cell analysis links drug-induced cytotoxicity to effective co-suppression of proliferation marker Ki-67 and the ribosomal S6 phosphorylation, an integrator of multiple RAS-mediated signaling pathways. Using a combination of kinome selectivity assay, transcriptomic analysis, and genetic experiments, we find the anti-tumor efficacy of MTX-216 to be dependent on its ability to inhibit not only PI3K (its nominal target) but also SYK, and suppression of a group of genes that regulate mitochondrial electron transport chain and whose expression is associated with poor survival in NF1LoF melanoma patients. Furthermore, combinations of inhibitors targeting either MEK or PI3K/mTOR with an independent SYK kinase inhibitor or SYK knockdown show favorable effects. These studies provide a path to exploit SYK dependency to selectively block NF1LoF melanoma cells.Statement of significanceNF1LoF melanomas represent a subtype with hyperactivated RAS signaling, for which currently no targeted therapies are clinically available. Our systems pharmacology studies identify SYK as a new vulnerability in NF1LoF melanoma cells.
Molecular mechanism for strengthening E-cadherin adhesion using a monoclonal antibody
Authors: Xie Bin , Maker Allison , Priest Andrew V. , Dranow David M. , Phan Jenny N. , Edwards Thomas E. , Staker Bart , Myler Peter J , Gumbiner Barry M. , Sivasankar Sanjeevi 
Published: March 2022

AbstractE-cadherin (Ecad) is an essential cell-cell adhesion protein with tumor suppression properties. The adhesive state of Ecad can be modified by the monoclonal antibody 19A11, which has potential applications in reducing cancer metastasis. Using x-ray crystallography, we determine the structure of 19A11 Fab bound to Ecad and show that the antibody binds to the first extracellular domain of Ecad near its primary adhesive motif - the strand-swap dimer interface. Molecular dynamics simulations and single molecule atomic force microscopy demonstrate that 19A11 interacts with Ecad in two distinct modes, one that strengthens the strand-swap dimer and one that does not alter adhesion. We show that adhesion is strengthened by the formation of a salt bridge between 19A11 and Ecad, which in turn stabilizes the swapped β-strand and its complimentary binding pocket. Our results identify mechanistic principles for engineering antibodies to enhance Ecad adhesion.