Journal: The Journal of the Acoustical Society of America

Article Title: Segmental intelligibility of synthetic speech produced by rule

doi:

Figure Lengend Snippet: Phonemes accounting for the highest percentage of error in initial position.

Article Snippet: Telesensory Systems, TSI Prototype-1 Prose 2000 The TSI system was an early prototype of the current Prose 2000 text-to-speech system developed by Telesensory Systems, Inc. (The Prose 2000 and other Prose products are now produced by Speech Plus, Inc.) The TSI Prototype-1 was based on the MITalk-77 system but used only an 1100-word dictionary for lexical lookup.

Techniques:

Journal: The Journal of the Acoustical Society of America

Article Title: Segmental intelligibility of synthetic speech produced by rule

doi:

Figure Lengend Snippet: Phonemes accounting for the highest percentage of error in final position.

Article Snippet: Telesensory Systems, TSI Prototype-1 Prose 2000 The TSI system was an early prototype of the current Prose 2000 text-to-speech system developed by Telesensory Systems, Inc. (The Prose 2000 and other Prose products are now produced by Speech Plus, Inc.) The TSI Prototype-1 was based on the MITalk-77 system but used only an 1100-word dictionary for lexical lookup.

Techniques:

Journal: The Journal of the Acoustical Society of America

Article Title: Segmental intelligibility of synthetic speech produced by rule

doi:

Figure Lengend Snippet: MRT overall open error rates and error rates for consonants in initial and final position

Article Snippet: Telesensory Systems, TSI Prototype-1 Prose 2000 The TSI system was an early prototype of the current Prose 2000 text-to-speech system developed by Telesensory Systems, Inc. (The Prose 2000 and other Prose products are now produced by Speech Plus, Inc.) The TSI Prototype-1 was based on the MITalk-77 system but used only an 1100-word dictionary for lexical lookup.

Techniques:

Journal: The Journal of the Acoustical Society of America

Article Title: Segmental intelligibility of synthetic speech produced by rule

doi:

Figure Lengend Snippet: MRT open-response phonemes accounting for the highest percentage of error in initial position.

Article Snippet: Telesensory Systems, TSI Prototype-1 Prose 2000 The TSI system was an early prototype of the current Prose 2000 text-to-speech system developed by Telesensory Systems, Inc. (The Prose 2000 and other Prose products are now produced by Speech Plus, Inc.) The TSI Prototype-1 was based on the MITalk-77 system but used only an 1100-word dictionary for lexical lookup.

Techniques:

Journal: The Journal of the Acoustical Society of America

Article Title: Segmental intelligibility of synthetic speech produced by rule

doi:

Figure Lengend Snippet: MRT open-response phonemes accounting for the highest percentage of error in medial position (vowels).

Article Snippet: Telesensory Systems, TSI Prototype-1 Prose 2000 The TSI system was an early prototype of the current Prose 2000 text-to-speech system developed by Telesensory Systems, Inc. (The Prose 2000 and other Prose products are now produced by Speech Plus, Inc.) The TSI Prototype-1 was based on the MITalk-77 system but used only an 1100-word dictionary for lexical lookup.

Techniques:

Journal: The Journal of the Acoustical Society of America

Article Title: Segmental intelligibility of synthetic speech produced by rule

doi:

Figure Lengend Snippet: MRT open-response phonemes accounting for the highest percentage of error in final position.

Article Snippet: Telesensory Systems, TSI Prototype-1 Prose 2000 The TSI system was an early prototype of the current Prose 2000 text-to-speech system developed by Telesensory Systems, Inc. (The Prose 2000 and other Prose products are now produced by Speech Plus, Inc.) The TSI Prototype-1 was based on the MITalk-77 system but used only an 1100-word dictionary for lexical lookup.

Techniques:

Journal: bioRxiv

Article Title: Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development

doi: 10.1101/2025.08.25.672082

Figure Lengend Snippet: (A) The morphology of ESCs, TBLCs and ESCs, TBLCs in TS medium after 3 days of induction. Scale bars, 250 μm. (B) FACS analysis of the percentage of CDX2 + cells from ESCs and TBLCs, as well as ESCs and TBLCs cultured in TS medium, using V6.5 cell line. (C) FACS analysis of the percentage of CD40 + cells from ESCs and TBLCs, as well as ESCs and TBLCs cultured in TS medium, using TC1 cell line. (D) FACS analysis of the percentage of CD40 + TELCs obtained from the TBLCs after induction with different molecules, including FGF4, Activin A, TGFβ1 and BMP4. The corresponding cell morphology is displayed in the lower panel. (E) Scatterplots displaying the transcriptome comparison of TELCs before and after CD40-based FACS using RNA-seq. Upregulated (FC>2) and downregulated (FC<0.5) genes are shown in red and blue, respectively. (F) The morphology of TBLCs of different passages and long-term culture in TX and TS medium, also the morphology of TBLCs after CD40 FACS after induction. Scale bars, 250 μm. (G) Western blotting was used to detect OCT4, CDX2 and EOMES in TELSCs from different passages. β-Tubulin was used as a loading control. (H) The morphology 8C embryos cultured in TX medium. Scale bars, 250 μm. (I) FACS analysis of the percentage of CD40 + cells in TELSC em s at different passages. (J) Immunofluorescence staining of TFAP2C and PEG10 in TBLCs, TELSCs and TELSC em s. Scale bars, 50 μm. (K) Cell cycle analysis of ESCs, TELSCs and TELSC em s. (L) Heatmap indicating the relative expression of TBLCs, TELSCs and TELSC em s. The representative genes and enrichment of GO terms of these genes is shown. (M) Heatmap indicating the relative expression of characteristic genes in TELSCs, TELSC em s and TSCs. Bubble chart showing the relative expression of these genes in mouse embryos. (N) Heatmap indicating the relative expression of characteristic genes in TELSCs, TSCs cultured in TX medium and TSCs cultured in TS medium. Heatmap on the right demonstrating the expression of each cluster in mouse embryos. The representative genes and enrichment of GO terms of these genes is shown. (O) The scatter plot displays differentially expressed genes between TELSCs and TSCs cultured in various media. The bar graph summarizes the number of differentially expressed genes identified under each comparison condition. (P) GSEA analysis of ESCs, TBLCs, TELCs and TELSCs based on “embryonic placenta development” and “placenta development” geneset. (Q) Heatmap indicating the differentially expressed genes in Hippo pathway of TELSCs and TBLCs. (R) Heatmap indicating the relative expression of characteristic genes in TELSCs, TSCs cultured in TX medium and TSCs cultured in TS medium. Bubble chart showing the relative expression of these genes in mouse embryos. (S) Phase contrast images of TBLCs cultured in TS medium for 24h supplemented with Verteporfin at the indicated concentration. Scale bars, 100 µm. (T) Heatmap indicating the differentially expressed genes of TELCs and TBLCs induction in TS medium plus verteporfin. Bubble chart showing the relative expression of these genes in mouse embryos. (U) GSEA analysis of TELCs, TBLCs induction in TS medium and in TS medium plus verteporfin based on TE geneset. (V) The morphology of TELSCs cultured in TS medium, TS medium plus ITS-X and TS medium plus TGFβ1. (W) Heatmap indicating the differentially expressed genes of TELSCs, TBLCs induction in TX medium withdraw ITS-X, in TS medium and in TS medium plus ITS-X. Heatmap on the right demonstrating the expression of each cluster in mouse embryos. The representative genes and enrichment of GO terms of these genes is shown. (X) GSEA analysis of TBLCs induction in TX medium withdraw ITS-X and in TX medium based on “Positive regulation of stem cell proliferation” and “Positive regulation of cell cycle” geneset.

Article Snippet: All TSLs were cultured on Matrigel-coated plates, in 30% TS medium (RPMI 1640 (GIBCO, 11875119), 20% FBS, 1% GlutaMax (GIBCO, 35050061), 1% penicillin-streptomycin (GIBCO, 15140163), 1% sodium pyruvate (GIBCO, 11360070)) and 70% MEF-conditioned TS medium supplemented with 25 ng/ml human recombinant FGF4 (MCE, HY-P7014) and 1 μg/ml heparin (STEMCELL, 7980).

Techniques: Cell Culture, Comparison, RNA Sequencing, Western Blot, Control, Immunofluorescence, Staining, Cell Cycle Assay, Expressing, Concentration Assay

Journal: bioRxiv

Article Title: The histone demethylase KDM5 is essential for larval growth in Drosophila

doi: 10.1101/297804

Figure Lengend Snippet: (A) Lethality of kdm5 K06801 , kdm5 10424 and kdm5 140 homozygous mutant animals generated from a cross between five female and five male heterozygous parents balanced using CyO-GFP. The column labeled total flies indicates the number of progeny (adult) flies scored from at least three independent crosses. Expected number of progeny is based on Mendelian frequencies and taking into account the lethality of CyO homozygotes, i.e 33% of total adult flies. * p <0.01 (chi-squared test). (B) Position of the NP4707 , 10424 and K06801 P element insertions and molecular mapping of the kdm5 140 deletion. Ab indicates the region used to generated the rabbit polyclonal anti-KDM5 antibody ( S ecombe et al . 2007 ). (C) RT-PCR using primers to the 5’ end of the gene using RNA from whole 3 rd instar larvae. Animals homozygous for kdm5 K06801 or kdm5 10424 show low levels of transcript while kdm5 140 shows none. kdm5 mRNA normalized to wildtype ( w 1118 ) using rp49 . **** p <0.0001. (D) RT-PCR using primers to the 3’ end of the gene using RNA from whole 3 rd instar larvae. kdm5 140 has wildtype levels of the 3’ end of the transcript. **** p <0.0001. ns = not significant. (E) Western from wildtype ( w 1118 ) and kdm5 140 homozygous mutant wing imaginal discs showing KDM5 and alpha tubulin. kdm5 140 animals have no detectable full length or truncated KDM5. *ns indicates non-specific band. (F) Schematic of strain genotype for rescue of kdm5 140 with a genomic rescue transgene. Flies are homozygous for the kdm5 140 mutation on the 2 nd chromosome and homozygous for an 11kb genomic rescue transgene on the 3 rd chromosome. (G) Western blot showing KDM5 protein levels from 3 rd instar larval wing imaginal discs from wildtype ( w 1118 ) and kdm5 140 homozygotes that also have two copies of the kdm5:HA genomic rescue transgene. Anti-KDM5 (top), anti-HA (middle) and anti-histone H3 loading control (bottom). (H) kdm5 140 lethality is rescued by a transgene encoding the kdm5 locus. These data were generated by crossing female and male flies heterozygous for kdm5 140 and homozygous the wildtype genomic rescue transgene (intercross of kdm5 140 /CyO-GFP; kdm5:HA / kdm5:HA males and females).

Article Snippet: Antibodies used were anti-pH3 (Cell signaling #9701, 1/1000), anti-histone H3 (Active Motif #39763 or #39163, 1/5000), anti-alpha Tubulin (Developmental Studies Hybridoma Bank, University of Iowa; 1:5000).

Techniques: Mutagenesis, Generated, Labeling, Reverse Transcription Polymerase Chain Reaction, Western Blot, Control

Journal: bioRxiv

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

doi: 10.1101/2024.03.08.583864

Figure Lengend Snippet: (A) Relative contact probability plot (top panel) and its derivative (bottom panel) calculated from the Hi-C matrices of DMSO (blue) and 6 hours dTAG-V1 (orange) treated ZFP143-FKBP cells. (B) Average cohesin (left), enhancer-promoter (E-P, middle) and promoter-promoter (P-P, right) loops in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. Value in the upper-right corner indicates the interaction strength of the loop over the background. (C) Same as in (B) but for the average ZFP143-associated loops (containing ZFP143 peak in at least one loop anchor). (D) High-resolution 4C-seq data generated for the ZFP143-bound genes Rbm41 (left panel) and Prmt6 (middle panel), and non-ZFP143-bound control gene Sik1 (right panel), using gene promoters as viewpoints. The matrix in the top panel represents interaction frequencies in a previously published high-resolution Micro-C dataset . The arrows point to detected Micro-C chromatin loops. The bottom panel shows 4C contact profiles in DMSO (blue) and in 6 hours dTAG-V1 (orange) treated ZFP143-FKBP cells. Genomic tracks show ZFP143-HA ChIP-seq (red), calibrated CTCF ChIP-seq (blue), TT-seq nascent transcription (yellow for sense and purple for antisense transcription) in control and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (E) Tornado plots of ZFP143-HA ChIP-seq signal centred at CTCF peaks in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (F) Same as in (E) but for the calibrated CTCF ChIP-seq signal centred at ZFP143-HA peaks.

Article Snippet: After systematically re-analysing the ZNF143 ChIP-seq data, we posit that the Proteintech anti-ZNF143 polyclonal antibody recognises CTCF in addition to ZNF143.

Techniques: Hi-C, Generated, Control, ChIP-sequencing

Journal: bioRxiv

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

doi: 10.1101/2024.03.08.583864

Figure Lengend Snippet: (A) Average Hi-C loops in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. Value in the upper-right corner indicates the interaction strength of the loop over the background. (B) Same as in (A) but for the average ZFP143-associated Hi-C loops (containing ZFP143 peak in at least one loop anchor). (C) High-resolution 4C-seq data generated for the Cpox and Cldn1 (left panel) and Zfp111 and Zfp108 (right panel) loci using gene promoters as viewpoints. The matrix in the top panel represents interaction frequencies in a previously published high-resolution Micro-C dataset . The arrows point to detected Micro-C chromatin loops. The bottom panel shows 4C contact profiles in DMSO (blue) and in 6 hours dTAG-V1 (orange) treated ZFP143-FKBP cells. Genomic tracks show ZFP143-HA ChIP-seq (red), calibrated CTCF ChIP-seq (blue), TT-seq nascent transcription (yellow for sense and purple for antisense transcription) in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (D) Tornado plots of calibrated CTCF ChIP-seq signal centred at CTCF peaks in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (E) Genomic tracks showing ZFP143-HA ChIP-seq (red) in DMSO and calibrated CTCF ChIP-seq (blue) in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (F) Venn diagram showing the overlap between ZFP143-HA (red) and CTCF (blue) peaks.

Article Snippet: After systematically re-analysing the ZNF143 ChIP-seq data, we posit that the Proteintech anti-ZNF143 polyclonal antibody recognises CTCF in addition to ZNF143.

Techniques: Hi-C, Generated, ChIP-sequencing

Journal: bioRxiv

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

doi: 10.1101/2024.03.08.583864

Figure Lengend Snippet: (A) Overlap between ZNF143/ZFP143 peaks from re-analysed publicly available data and CTCF peaks from CISTROME for human (left panel) and mouse (right panel) datasets. Box plots for each ZNF143/ZFP143 dataset represent the median overlap with CTCF peaks. Each dot represents the overlap between the indicated ZNF143/ZFP143 peak set with an individual CTCF peak set. Colours represent the antibody used for chromatin immunoprecipitation, as indicated below. (B) Venn diagram showing the overlap between ZNF143 peaks detected by Proteintech (light pink) and FLAG (light green) antibodies in K562 cells. (C) Heatmap showing the enrichment of SBS (i.e. ZNF143) and CTCF motifs in common, Proteintech-specific, and FLAG-specific peaks in K562 cells. (D) Tornado plots of ChIP-seq signals detected by Proteintech (light pink), FLAG (light green), and custom (orange) antibodies, and CTCF signal (blue) in K562 cells. The ChIP-seq signals are centred on common (top) and Proteintech-specific (bottom) peaks. (E) Genomic tracks showing ChIP-seq signals for CTCF (blue) and signals detected by Proteintech (pink), FLAG (light green), and custom12 (orange) antibodies in K562 cells. Rectangles indicate common (left) and Proteintech-specific (middle and right) peaks in the region. (F) Scatter plot of the percentage of loop anchors overlapping the peak (x-axis) against the fold enrichment of peaks in loop anchors (y-axis) for a number of DNA binding proteins and for Proteintech-specific, FLAG-specific and common peaks in K562 cells.

Article Snippet: After systematically re-analysing the ZNF143 ChIP-seq data, we posit that the Proteintech anti-ZNF143 polyclonal antibody recognises CTCF in addition to ZNF143.

Techniques: Chromatin Immunoprecipitation, ChIP-sequencing, DNA Binding Assay

Journal: bioRxiv

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

doi: 10.1101/2024.03.08.583864

Figure Lengend Snippet: (A) Tornado plots of CTCF ChIP-seq signal from two biological replicates in wild-type (WT) and ZNF143-knockout (KO) haematopoietic stem and progenitor cells (HSPC) centred at ZNF143-related (top) and ZNF143-unrelated (bottom) CTCF peaks . (B) Same as in (A) but for the CTCF ChIP-seq signal in HSPC from two orthogonal studies , . (C) Rolling mean of the normalised CTCF motifs scores, annotated for the ZNF143-related (top) and ZNF143-unrelated (bottom) CTCF peaks. (D) Violin plots showing the fraction of ZNF143-related (left) and ZNF143-unrelated (right) CTCF peaks overlapping CTCF peaks from the CISTROME database . (E) GC bias scores calculated for CTCF ChIP-seq data generated from WT and ZNF143-KO HSPC samples . Note the divergence of the first WT CTCF replicate from the rest of the samples. (F) Genomic tracks showing CTCF ChIP-seq signal from two biological replicates in WT and ZNF143-KO HSPC , CTCF ChIP-seq signal from two other HSPC samples , , and GC content. Horizontal bars indicate ZNF143-related and ZNF143-unrelated CTCF peaks . Note the overlap of ZNF143-related peaks with GC-rich regions. (G) Tornado plots of ZNF143 ChIP-nexus signal from control and CTCF-depleted HEC1B cells centred at ZNF143-only (top) and shared ZNF143 and CTCF (bottom) peaks . (H) Genomic tracks showing ZNF143 ChIP-nexus signal from control and CTCF-depleted HEC1B cells . Horizontal bars indicate ZNF143-only and shared ZNF143 and CTCF peaks. Note the specific loss of signal at shared peaks upon CTCF depletion. (I) Venn diagram showing the overlap between ZNF143-CTCF motif pairs located 37 bp apart from each other and SINE/B2 repeat elements in the mouse genome from RepeatMasker. (J) Tornado plots of CTCF and ZNF143 ChIP-seq signal centred at ZNF143-CTCF motif pairs located 37 bp apart from each other .

Article Snippet: After systematically re-analysing the ZNF143 ChIP-seq data, we posit that the Proteintech anti-ZNF143 polyclonal antibody recognises CTCF in addition to ZNF143.

Techniques: ChIP-sequencing, Knock-Out, Generated, Control