Deep learning-based feature extraction for prediction and interpretation of sharp-wave ripples in the rodent hippocampus

Local field potential (LFP) deflections and oscillations define hippocampal sharp-wave ripples (SWRs), one of the most synchronous events of the brain. SWRs reflect firing and synaptic current sequences emerging from cognitively relevant neuronal ensembles. While spectral analysis have permitted advances, the surge of ultra-dense recordings now call for new automatic detection strategies. Here, we show how one-dimensional convolutional networks operating over highdensity LFP hippocampal recordings allowed for automatic identification of SWR from the rodent hippocampus. When applied without retraining to new datasets and ultra-dense hippocampus-wide recordings, we discovered physiologically relevant processes associated to the emergence of SWR, prompting for novel classification criteria. To gain interpretability, we developed a method to interrogate the operation of the artificial network. We found it relied in feature-based specialization, which permit identification of spatially segregated oscillations and deflections, as well as synchronous population firing typical of replay. Thus, using deep learning-based approaches may change the current heuristic for a better mechanistic interpretation of these relevant neurophysiological events.This work is supported by grants from Fundación La Caixa (LCF/PR/HR21/52410030; DeepCode). Access to the Artemisa high-performance computing infrastructure (NeuroConvo project) is supported by Universidad de Valencia and co-funded by the European Union through the 2014–2020 FEDER Operative Programme (IDIFEDER/2018/048). ANO and RA are supported by PhD fellowships from the Spanish Ministry of Education (FPU17/03268) and Universidad Autónoma de Madrid (FPI-UAM-2017), respectively. We thank Elena Cid for help with histological confirmation of the probe tracks and Pablo Varona for feedback and discussion. We also thank Aarón Cuevas for clarifications and support while developing the Open Ephys Plugin for online detection

Androgen Receptor Functional Analyses by High Throughput Imaging: Determination of Ligand, Cell Cycle, and Mutation-Specific Effects

Understanding how androgen receptor (AR) function is modulated by exposure to steroids, growth factors or small molecules can have important mechanistic implications for AR-related disease therapies (e.g., prostate cancer, androgen insensitivity syndrome, AIS), and in the analysis of environmental endocrine disruptors.We report the development of a high throughput (HT) image-based assay that quantifies AR subcellular and subnuclear distribution, and transcriptional reporter gene activity on a cell-by-cell basis. Furthermore, simultaneous analysis of DNA content allowed determination of cell cycle position and permitted the analysis of cell cycle dependent changes in AR function in unsynchronized cell populations. Assay quality for EC50 coefficients of variation were 5–24%, with Z' values reaching 0.91. This was achieved by the selective analysis of cells expressing physiological levels of AR, important because minor over-expression resulted in elevated nuclear speckling and decreased transcriptional reporter gene activity. A small screen of AR-binding ligands, including known agonists, antagonists, and endocrine disruptors, demonstrated that nuclear translocation and nuclear “speckling” were linked with transcriptional output, and specific ligands were noted to differentially affect measurements for wild type versus mutant AR, suggesting differing mechanisms of action. HT imaging of patient-derived AIS mutations demonstrated a proof-of-principle personalized medicine approach to rapidly identify ligands capable of restoring multiple AR functions.HT imaging-based multiplex screening will provide a rapid, systems-level analysis of compounds/RNAi that may differentially affect wild type AR or clinically relevant AR mutations

Description and performance of track and primary-vertex reconstruction with the CMS tracker

A description is provided of the software algorithms developed for the CMS tracker both for reconstructing charged-particle trajectories in proton-proton interactions and for using the resulting tracks to estimate the positions of the LHC luminous region and individual primary-interaction vertices. Despite the very hostile environment at the LHC, the performance obtained with these algorithms is found to be excellent. For tbar t events under typical 2011 pileup conditions, the average track-reconstruction efficiency for promptly-produced charged particles with transverse momenta of pT > 0.9GeV is 94% for pseudorapidities of |η| < 0.9 and 85% for 0.9 < |η| < 2.5. The inefficiency is caused mainly by hadrons that undergo nuclear interactions in the tracker material. For isolated muons, the corresponding efficiencies are essentially 100%. For isolated muons of pT = 100GeV emitted at |η| < 1.4, the resolutions are approximately 2.8% in pT, and respectively, 10μm and 30μm in the transverse and longitudinal impact parameters. The position resolution achieved for reconstructed primary vertices that correspond to interesting pp collisions is 10–12μm in each of the three spatial dimensions. The tracking and vertexing software is fast and flexible, and easily adaptable to other functions, such as fast tracking for the trigger, or dedicated tracking for electrons that takes into account bremsstrahlung

Data from: Aberrant activation of the RANK signaling receptor induces murine salivary gland tumors

Unlike cancers of related exocrine tissues such as the mammary and prostate gland, diagnosis and treatment of aggressive salivary gland malignancies have not markedly advanced in decades. Effective clinical management of malignant salivary gland cancers is undercut by our limited knowledge concerning the key molecular signals that underpin the etiopathogenesis of this rare and heterogeneous head and neck cancer. Without knowledge of the critical signals that drive salivary gland tumorigenesis, tumor vulnerabilities cannot be exploited that allow for targeted molecular therapies. This knowledge insufficiency is further exacerbated by a paucity of preclinical mouse models (as compared to other cancer fields) with which to both study salivary gland pathobiology and test novel intervention strategies. Using a mouse transgenic approach, we demonstrate that deregulation of the Receptor Activator of NFkB Ligand (RANKL)/RANK signaling axis results in rapid tumor development in all three major salivary glands. In line with its established role in other exocrine gland cancers (i.e., breast cancer), the RANKL/RANK signaling axis elicits an aggressive salivary gland tumor phenotype both at the histologic and molecular level. Despite the ability of this cytokine signaling axis to drive advanced stage disease within a short latency period, early blockade of RANKL/RANK signaling markedly attenuates the development of malignant salivary gland neoplasms. Together, our findings have uncovered a tumorigenic role for RANKL/RANK in the salivary gland and suggest that targeting this pathway may represent a novel therapeutic intervention approach in the prevention and/or treatment of this understudied head and neck cancer

A bioluminescence reporter mouse that monitors expression of constitutively active β-catenin

<div><p>This short technical report describes the generation and characterization of a bioluminescence reporter mouse that is engineered to detect and longitudinally monitor the expression of doxycycline-induced constitutively active β-catenin. The new responder transgenic mouse contains the TetO-ΔN89β-Cat^TMILA transgene, which consists of the tet-operator followed by a bicistronic sequence encoding a stabilized form of active β-catenin (ΔN89β-catenin), an internal ribosome entry site, and the firefly luciferase gene. To confirm that the transgene operates as designed, TetO-ΔN89β-Cat^TMILA transgenic mouse lines were crossed with an effector mouse that harbors the mouse mammary tumor virus-reverse tetracycline transactivator (MMTV-rtTA) transgene (termed MTB hereon), which primarily targets rtTA expression to the mammary epithelium. Following doxycycline administration, the resultant MTB/Cat^TMILA bigenic reporter exhibited precocious lobuloalveologenesis, ductal hyperplasia, and mammary adenocarcinomas, which were visualized and monitored by <i>in vivo</i> bioluminescence detection. Therefore, we predict that the TetO-ΔN89β-Cat^TMILA transgenic responder mouse—when crossed with the appropriate effector transgenic—will have wide-applicability to non-invasively monitor the influence of constitutively active β-catenin expression on cell-fate specification, proliferation, differentiation, and neoplastic transformation in a broad spectrum of target tissues.</p></div

Three-Dimensional High-Frequency Ultrasonography for Early Detection and Characterization of Embryo Implantation Site Development in the Mouse.

Ultrasonography is a powerful tool to non-invasively monitor in real time the development of the human fetus in utero. Although genetically engineered mice have served as valuable in vivo models to study both embryo implantation and pregnancy progression, such studies usually require sacrifice of parous mice for subsequent phenotypic analysis. To address this issue, we used three-dimensional (3-D) reconstruction in silico of high-frequency ultrasound (HFUS) imaging data for early detection and characterization of murine embryo implantation sites and their development in utero. With HFUS imaging followed by 3-D reconstruction, we were able to precisely quantify embryo implantation site number and embryonic developmental progression in pregnant C57BL6J/129S mice from as early as 5.5 days post coitus (d.p.c.) through to 9.5 d.p.c. using a VisualSonics Vevo 2100 (MS550S) transducer. In addition to measurements of implantation site number, location, volume and spacing, embryo viability via cardiac activity monitoring was also achieved. A total of 12 dams were imaged with HFUS with approximately 100 embryos examined per embryonic day. For the post-implantation period (5.5 to 8.5 d.p.c.), 3-D reconstruction of the gravid uterus in mesh or solid overlay format enabled visual representation in silico of implantation site location, number, spacing distances, and site volume within each uterine horn. Therefore, this short technical report describes the feasibility of using 3-D HFUS imaging for early detection and analysis of post-implantation events in the pregnant mouse with the ability to longitudinally monitor the development of these early pregnancy events in a non-invasive manner. As genetically engineered mice continue to be used to characterize female reproductive phenotypes, we believe this reliable and non-invasive method to detect, quantify, and characterize early implantation events will prove to be an invaluable investigative tool for the study of female infertility and subfertility phenotypes based on a defective uterus

10.1371journal.pone.0128467 SUPPORT INFORMATION

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Bioluminescence monitoring of doxycycline-induced ΔN89β-catenin expression in the salivary gland of the MTB/Cat^TMILA bigenic.

<p>(A) Overlay of whole body bioluminescence and X-ray images of MTB/Cat^TMILA bigenic mouse following doxycycline administration for the indicated time periods. Note the localization of the bioluminescence signal to the submandibular salivary gland of the MTB/Cat^TMILA mouse (G8335). (B-D) and (E-G) panels represent salivary gland tissue immunostained for the transgene-derived myc-tagged ΔN89β-catenin protein and BrdU incorporation respectively. (B) Salivary gland tissue from doxycycline-treated monogenic control does not score positive for myc-tagged ΔN89β-catenin expression. (C) Cystic hyperplasia with strong immunostaining for myc-tagged ΔN89β-catenin expression is evident in salivary gland tissue isolated from the MTB/Cat^TMILA bigenic following 336 hours of doxycycline administration (black arrowhead). (D) is a higher magnification image of (C). (E) Salivary gland epithelial cells positive for BrdU are not evident in salivary gland tissue derived from doxycycline-treated monogenic control mice (black arrowhead). (F) Many cells score positive for BrdU incorporation in salivary gland tissue isolated from the similarly treated MTB/Cat^TMILA bigenic (black arrowhead); a higher magnification is shown in (G (black arrowhead)). Note: To date, we have not detected palable salivary tumors in these mice. Scale bar in (B) and (D) apply to (C, E, and F) and (G) respectively.</p

Doxycycline-induced bioluminescence in the mammary gland of the MTB/Cat^TMILA bigenic.

<p>(A) Overlay of full-body bioluminescence and x-ray images of monogenic control (G6719 (ear tag#)) and MTB/Cat^TMILA bigenic (G6718 (ear tag#)) mice following 0, 24, and 48 hours of doxycycline intake. By 24 hours of doxycycline administration, bioluminescence activity is detected in the #2, #3 (thoracic), and #4 (inguinal) mammary glands of the MTB/Cat^TMILA bigenic (G6718) but not in the monogenic control mouse (G6719). (B) Whole mount of mammary gland from monogenic control mouse (G6719) shows normal ductal morphogenesis (black arrowhead) following 1-week of doxycycline administration. (C) Mammary gland whole mount analysis shows precocious lobuloalveologenesis (white arrowhead) in the similarly treated MTB/Cat^TMILA bigenic (G6718). Scale bar in (B) applies to (C); see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0173014#pone.0173014.s001" target="_blank">S1 Fig</a> for corresponding low magnification images. (D) Myc-epitope tag immunohistochemistry does not detect myc-epitope tagged ΔN89β-catenin expression in the mammary epithelium of the doxycycline treated monogenic (G6719) control (black arrowhead). (E) Myc-tagged ΔN89β-catenin expression is clearly detected in the mammary epithelium of the similarly treated MTB/Cat^TMILA bigenic (white arrowhead); (F) is a higher magnification of (E). (G) Image shows a representative transverse section of an epithelial duct in the mammary gland of the doxycycline-treated monogenic (G6719) control mouse, which scores negative for BrdU incorporation following BrdU immunohistochemistry (black arrowhead). (H) Numerous cells scoring positive for BrdU incorporation are detected in the mammary epithelium of the similarly treated MTB/Cat^TMILA bigenic (white arrowhead); (I) is a higher magnification. Scale bar in (D) and (F) apply to (E, G, and H) and (I) respectively. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0173014#pone.0173014.s001" target="_blank">S1 Fig</a> for more details and quantitation of BrdU positive cells in the mammary epithelium of both genotypes following doxycycline administration.</p