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    Performance of the local reconstruction algorithms for the CMS hadron calorimeter with Run 2 data

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    A description is presented of the algorithms used to reconstruct energy deposited in the CMS hadron calorimeter during Run 2 (2015–2018) of the LHC. During Run 2, the characteristic bunch-crossing spacing for proton-proton collisions was 25 ns, which resulted in overlapping signals from adjacent crossings. The energy corresponding to a particular bunch crossing of interest is estimated using the known pulse shapes of energy depositions in the calorimeter, which are measured as functions of both energy and time. A variety of algorithms were developed to mitigate the effects of adjacent bunch crossings on local energy reconstruction in the hadron calorimeter in Run 2, and their performance is compared

    <i>foxj1</i> is expressed in ciliated OSNs of zebrafish and mice.

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    (A) Schematic showing the larval zebrafish OE and OB; l: lateral, m: medial, d: dorsal, v: ventral. (B-J) Confocal images of the larval (3–5 dpf) zebrafish nose and OB. (B) foxj1b (Gt(foxj1b:GFP), green) is expressed in neurons labeled by HuC (magenta). Asterisks show foxj1-expressing neurons in 5 dpf larva. (C) Differential expression of foxj1a (Gt(foxj1a:2A-TagRFP), magenta) and foxj1b (Gt(foxj1b:GFP), green) paralogs in 5 dpf larvae. Note that foxj1a is expressed primarily at the outer rim of the OE. (D) foxj1b-positive cells (Gt(foxj1b:GFP), green) bear a brush of motile cilia marked by glutamylated-tubulin (magenta) in 5 dpf larvae. (E) foxj1b-positive OSNs (Gt(foxj1b:GFP), green) in the nasal pit bear cilia, indicated by the marker Gαolf (magenta) in 3 dpf larva. White arrowheads in insets show Gαolf marked cilia arising from foxj1b-positive OSNs. (F) Overlap of foxj1b-expressing cells (Gt(foxj1b:GFP), green) with the ciliated OSN marker OMP (Tg(OMP:gal4); Tg(UAS:NTR-mCherry), magenta) in 4 dpf larva. (G) Mutually exclusive localization of foxj1b-expressing cells (Gt(foxj1b:GFP), green) and microvilli OSNs in 4 dpf larvae, indicated by the marker trpc2 (Tg(trpc2:gal4); Tg(UAS:NTR-mCherry), magenta). (H) foxj1b-expressing OSNs (Gt(foxj1b:GFP), green) project mainly to Gαolf-labeled glomeruli (magenta) in 3 dpf larvae. Note that foxj1b:GFP and Gαolf do not overlap entirely (dotted region). (I, J) foxj1b-positive OSNs, in 4 dpf larvae, (I) project to more glomeruli than OMP-expressing OSNs (J) (Tg(OMP:ChR-YFP)). Glomeruli are shown by staining with the presynaptic vesicle marker SV2 (magenta). (K) Schematic showing mouse RE, OE, and OB; r: rostral, c: caudal, d: dorsal, v: ventral. (L) In the nasal epithelium of the adult mouse (P30), Foxj1 localizes to MCCs (arrowhead) within the RE and the layer of OSNs in the OE. Dashed line demarcates the lamina propria separating OE from the underlying tissue. (M) Foxj1 is absent from the nasal epithelium of the Foxj1 knockout mouse (P21). The residual puncta likely represent nonspecific staining of blood vessels or mesenchymal tissue located in the lamina propria under the basement membrane. (N) Foxj1 (magenta) localizes to the nuclei of mature OSNs immunostained for the OMP (P30). (O) Expression levels of Foxj1 in OSNs at different ages (newborn P0, day 5 P5, and adult P30) calculated by comparing immunofluorescence in OSNs relative to respiratory MCCs. No significant difference was found (MCC/OSN ratio of 10.87 ± 2.61, P0; 8.74 ± 0.53, P5; 6.83 ± 1.56, P30; fluorescence intensity was measured in 20–30 cells of each type per individual field of view and ratio was calculated per animal, 3 mice in each group) by one-way ANOVA with Kruskal–Wallis test. Scale bars = 10 ÎŒm (B-J), 50 ÎŒm (L, M), and 10 ÎŒm (N). Raw data files are available in Mendeley Data (https://data.mendeley.com/datasets/2pn963jn6y). dpf, days post fertilization; MCC, motile multiciliated cell; OB, olfactory bulb; OE, olfactory epithelium; OMP, olfactory marker protein; OSN, olfactory sensory neuron; RE, respiratory epithelium.</p

    Foxj1 controls the expression of OSN-specific genes, but not ciliary motility genes.

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    (A) Single-cell transcriptome analysis of ciliated OSNs from wild-type zebrafish, mouse, and human showing low expression of genes encoding axonemal dynein and motility-associated components in OSNs as compared to MCCs. (B) Whole-mount in situ hybridization of dnah5, dnah8, and dnah9 in foxj1a,b double mutant zebrafish embryos at 3 dpf showing absence of gene expression in the periphery of the nasal placodes (highlighted with white dashed line) that primarily consists of OSNs, whereas expression in MCCs at the rim of the cavity (n = 10 for each gene). MCCs are depleted in foxj1a/b double mutants, and, therefore, expression of these genes were absent in the nasal placodes (bottom panel) (n = 5 for dnah5, n = 6 for dnah8, n = 4 for dnah9). Scale bars = 10 ÎŒm. (C-C”) Double fluorescent labeling of dnah9 (C), ccdc40 (C’), and odad1 (C”) (green) with ciliated-OSN marker ompb (magenta) and MCC marker cimap1b (blue) by HCR in situ hybridization in wild-type embryo at 3 dpf showing coexpression of dnah9, ccdc40, and odad1 with cimap1b (n = 3), but not with ompb (n = 3). (D, D’) RNA sequencing of foxj1a and foxj1b mutant embryos showed a significant decrease in the expression of the ciliated-OSN marker ompb (D) and cnga4 (D’) in foxj1b mutant embryos but not in foxj1a mutants. (E, F) In situ hybridization in 4 dpf larvae showed reduced expression of ompb (E) and cnga4 (F) in nasal placodes of foxj1a/b double mutant embryos (n = 3). Scale Bars = 20 ÎŒm (A-C”), 10 ÎŒm (E, E’). Raw data files are available in Mendeley Data (https://data.mendeley.com/datasets/2pn963jn6y). dpf, days post fertilization; HCR, hybridization chain reaction; MCC, motile multiciliated cell; OSN, olfactory sensory neuron.</p