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0.434897
84d60c1ce1e34210b97f318236b222fd
Visualization of posterior distributions of the models.Note: Asian = 1, Black or African American = 2, Hispanic or Latino = 3, Caucasian = 4, Native American or American Indian = 5, Pacific Islander = 6, Other = 7.
PMC9244435
41599_2022_1225_Fig4_HTML.jpg
0.443394
1c74fe551bca44c08a01d6dcf09fcc2b
A diagnostic flowchart for reference. AST aspartate transaminase, ALT alanine transaminase, PT prothrombin time, APTT activated partial thrombin time, INR international standardized ratio, CBC complete blood count, CRP, c-reactive protein, PCT procalcitonin, CK creatine kinase, CT computer tomography, MRI magnetic resonance imaging, EBV Epstein–Barr virus, CMV cytomegalovirus, HHV-6 human herpesvirus-6, HHV-7 human herpesvirus-7, HSV-1 herpes simplex virus type 1, HSV-2 herpes simplex virus type 2, ANA anti-nuclear antibody
PMC9244883
12519_2022_581_Fig1_HTML.jpg
0.404785
75581fa506fb4a30bb72ebacb92b8e1e
AKH inhibits the proliferation of various cancer cells, as demonstrated using CCK-8 assay. (A) Viability of Panc-28, A549, MDA-MB-468, Hela, A875, U87, HCT-116 and LX-2 cells following treatment with the vehicle control or various concentrations of AKH (50, 100, 150, 200, 300 and 400 µg/ml) for 48 h. (B) Time-effects of AKH on (a) Panc-28 and (b) A549 cells. The cells were treated with the vehicle control or AKH at 100, 150, 200, 250, 300 and 400 µg/ml for 24, 48, or 72 h, respectively. The data are representative of three independent experiments (n=3) run in triplicate and are expressed as the mean ± SD. ***P<0.001 vs. LX-2 cells in A and vs. 24 h in B (determined using one-way ANOVA). AKH, Alpinia katsumadai Hayata.
PMC9245070
or-48-02-08353-g00.jpg
0.442757
6e6a5ff51d5f4bf6b7b18592b32ec0a7
Effects of AKH on apoptosis and the expression of apoptosis-related proteins in Panc-28 and A549 cells. (A) The morphological features of apoptosis induced by AKH in Panc-28 by Hoechst 33342/PI staining assay. (B) The morphological features of apoptosis induced by AKH in A549 cells by Hoechst 33342/PI staining assay. (C) Analysis of apoptosis of Panc-28 cells examined by flow cytometry with Annexin-V-FITC/PI double staining assay. (D) Analysis of apoptosis of A549 cells by flow cytometry with Annexin-V-FITC/PI double staining assay. (E) Percentage of apoptotic Panc-28 cells. (F) Percentage of apoptotic A549 cells. (G) The expression of apoptosis-related proteins PARP, cleaved-PARP, caspase-8, pro-caspase-3, cleaved-caspase-3 and caspase-9 in Panc-28 cells by western blot analysis. (H) The expression of apoptosis-related proteins PARP, cleaved-PARP, caspase-8, pro-caspase-3, cleaved-caspase-3 and caspase-9 in A549 cells by western blot analysis. (I) The protein expression of cleaved-PARP/PARP, caspase-8, cleaved-caspase-3/pro-caspase 3 and caspase-9 in Panc-28 cells. (J) The protein expression of cleaved-PARP/PARP, caspase-8, cleaved-caspase-3/pro-caspase-3 and caspase-9 in A549 cells. Actin was used as a loading control. The cells were treated with the vehicle control or AKH at 150, 200 and 250 µg/ml for 48 h. The data are representative of three independent experiments (n=3) run in triplicate and are expressed as the mean ± SD. *P<0.05, **P<0.01 and ***P<0.001 vs. vehicle control (determined using one-way ANOVA). AKH, Alpinia katsumadai Hayata; PARP, poly(ADP-ribose)polymerase.
PMC9245070
or-48-02-08353-g01.jpg
0.469309
675de1c1fade494ba11cd6e83d081542
Alpinia katsumadai Hayata (AKH) induces autophagy in Panc-28 and A549 cells. (A) The formation of GFP-LC3 puncta in Panc-28 and A549 was examined under a fluorescence microscope (magnification, ×200; white arrows indicate autophagic cells). The cells were treated with the vehicle control or AKH (250 µg/ml) for 48 h. (B) The bands of LC3, Beclin-1 and actin in Panc-28 cells were examined using western blot analysis. (C) The bands of LC3, Beclin-1 and actin in A549 cells by western blot analysis. Actin was used as a loading control. (D) Relative protein expression of LC-3 and Beclin-1 in Panc-28 cells. (E) Relative protein expression of LC-3 and Beclin-1 in A549 cells. (B-E) The cells were treated with the vehicle control or AKH at 150, 200 and 250 µg/ml for 48 h. Results are representative of three independent experiments (n=3) run in triplicate and are expressed as the mean ± SD. *P<0.05, **P<0.01 and ***P<0.001 vs. vehicle control (determined using one-way ANOVA).
PMC9245070
or-48-02-08353-g02.jpg
0.41129
3c32e9d00ce947929c254ea3e186916f
Effects of the autophagy inhibitors, 3MA and Baf-A1, on AKH-induced cell growth inhibition, apoptosis, and the expression of apoptosis- and autophagy-related proteins in Panc-28 and A549 cells. (A) The viability of the Panc-28 cells by CCK-8 assay. (B) The viability of the A549 cells by CCK-8 assay. (C) Flow cytometric analysis of Panc-28 cells. (D) Flow cytometric analysis of A549 cells. (E) The bands of apoptosis-related proteins PARP, cleaved-PARP, pro-caspase-3 and cleaved-caspase-3; autophagy-related proteins LC3, Beclin-1 and actin following treatment of 3MA and AKH alone or in combination in Panc-28 and A549 cells by western blot analysis. (F) The bands of apoptosis-related proteins PARP, cleaved-PARP, pro-caspase-3 and cleaved-caspase-3, autophagy-related proteins LC3, Beclin-1 and actin following treatment of Baf-A1 and AKH alone or in combination in Panc-28 and A549 cells by western blot analysis. Actin was used as a loading control. The cells were pre-treated with the vehicle control, 3MA (5 mM) or Baf-A1 (10 nM) for 24 h followed by the vehicle control or AKH (250 µg/ml) for 48 h. The data are representative of three independent experiments (n=3) run in triplicate and are expressed as the mean ± SD. *P<0.05, **P<0.01 and ***P<0.001 vs. vehicle control (determined using one-way ANOVA). AKH, Alpinia katsumadai Hayata; PARP, poly(ADP-ribose)polymerase; 3MA, 3-methyladenine; Baf-A1, baflomycin A1.
PMC9245070
or-48-02-08353-g03.jpg
0.417839
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The effect of AKH on the expression of proteins related to the AMPK and Akt/mTOR/p70S6K singling pathways in Panc-28 and A549 cells by western blot analysis. (A) Bands of Akt, pAkt, AMPK, pAMPK, mTOR, pmTOR, 70S6K p70S6K and Actin in Panc-28 cells. (B) Bands of Akt, pAkt, AMPK, pAMPK, mTOR, pmTOR, 70S6K p70S6K and Actin in A549 cells. Actin was used as a loading control. (C) Relative protein expression of pAkt/Akt, pAMPK/AMPK, pmTOR/mTOR and p70S6K/70S6K in Panc-28 cells. (D) Relative protein expression of pAkt/Akt, pAMPK/AMPK, pmTOR/mTOR and p-p70S6K/p70S6K in A549 cells. The cells were treated with the vehicle control or AKH at 150, 200, and 250 µg/ml for 48 h. The data are representative of three independent experiments (n=3) run in triplicate and are expressed as the mean ± SD. **P<0.01 and ***P<0.001 vs. vehicle control (determined using one-way ANOVA). AKH, Alpinia katsumadai Hayata; AMPK, AMP-activated protein kinase.
PMC9245070
or-48-02-08353-g04.jpg
0.459512
e764f59c742a4ec9bdbb890e367a4eec
AKH inhibits the tumor growth of A549 ×enografts in nude mice in vivo. (A) The kinetics of tumor growth. (B) Images of tumors at the end of experiment. The mice were administered normal saline (vehicle control), cisplatin (5 mg/kg/day, positive control) or AKH (100 and 400 mg/kg/day). AKH and normal saline were orally administered by gavage once a day for 12 days and cisplatin by intraperitoneal injection every 3 days for a total of five times (on days 0, 3, 6, 9 and 12). A total of 5 mice were used in each group. The data are expressed as the mean ± SD. **P<0.01 and ***P<0.001 vs. vehicle control (determined using one-way ANOVA). AKH, Alpinia katsumadai Hayata.
PMC9245070
or-48-02-08353-g05.jpg
0.446802
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Analysis of the composition from AKH by LCMS-IT-TOF. (A) The BPC spectrum of AKH. (B) Chemical structures of AKH compounds detected by LCMS-IT-TOF. The nine compounds (1–9) are indicated in the figure and also listed in Table II. AKH, Alpinia katsumadai Hayata; LCMS-IT-TOF, liquid chromatography mass spectrometry-ion trap-time-of-flight mass spectrometry.
PMC9245070
or-48-02-08353-g06.jpg
0.487151
ffe341e902a14dcd9359cbb5bf028e7d
A proposed schematic model of the underlying molecular mechanism associated with the effects of AKH on apoptosis and autophagy in human cancer cells. The black lines indicate activation and the green lines indicate inhibition. AKH, Alpinia katsumadai Hayata; AMPK, AMP-activated protein kinase; PARP, poly(ADP-ribose)polymerase; 3MA, 3-methyladenine; Baf-A1, baflomycin A1; Casp, caspase.
PMC9245070
or-48-02-08353-g07.jpg
0.465171
e965403af9cb421a9502fbb72359d1bb
A phylogenetic tree of Neomartinella yungshunensis, 25 related species and an outgroup was constructed based on the complete chloroplast genome using the maximum likelihood (ML) method. Numbers in each node indicated the bootstrap support values.
PMC9246043
TMDN_A_2087543_F0001_C.jpg
0.459154
1c26df5f49434fec8758526dec3a8e15
Overview of genetic screens in malaria parasites.(A) Pools of mutants have been generated either through random mutagenesis using N-ethyl-N-nitrosourea (ENU), [23] or the piggyBac transposon system [24], (forward genetics) or with long homology arm gene targeting vectors [25], (reverse genetics). (B) Pools of mutants were selected for and propagated. (C) Mutant phenotypes were analysed through growth assays or other phenotypic assays such as microscopy or fluorescence activated cell sorting (FACS), where next-generation sequencing based methods were used to identify and or quantify the mutants. Quantitative insertion sequencing (QIseq), barcode sequencing (BarSeq). Here forward genetics refers to screens where genetic targets are not predetermined and reverse genetics where genetic targets are predetermined by the use of gene targeting vectors.
PMC9246331
BST-50-1069-g0001.jpg
0.428041
e369b39197bf427cb52b69c968f1b76e
The impact of genetic screens in malaria parasites.Timeline of number of genes with phenotypes reported in (A) P. berghei (Pb) using data from the rodent malaria genetically modified parasite database [RgMDb, release 2022]. The inflection point from the Bushell et al. (2017), [25] genome scale screen is indicated. (B) P. falciparum (Pf) using data from PhenoPlasm [Phenoplasm, release 2022]. The inflection point from the Zhang et al. [24] genome scale forward genetic screen is indicated. (C) P. falciparum split by the genetic approach used, and excluding insertional mutagenesis (i.e. the Zhang et al. screen), showing a recent rise in the use of conditional knockout and knockdown approaches, and with the inflection point from the Maier et al. [6] knockout study indicated. Conditional knockout refers to deleting the gene at a specific time point/stage using dimerisable Cre-recombinase (DiCre). Knockdown here refers to a method where expression is inhibited at either the transcriptional, post-transcriptional, translational level, or the protein is inactivated or mislocalised. Natural deletion refers to spontaneous gene loss in e.g. in vitro culture.
PMC9246331
BST-50-1069-g0002.jpg
0.438627
f579213740624e5188081e1a78d15169
Overview of CRISPR/Cas9 Screens in Toxoplasma gondii.Common to all CRISPR/Cas9 screening strategies is the construction of gene specific gRNA vector libraries. Cas9 can be expressed off the same vector as the gRNA or off a separate, co-transfected vector. Alternatively, the Cas9 enzyme can be integrated into the genome. For systems relying on the repair of Cas9-induced DSBs by homologous recombination the HDR template has to be supplied. Top panel: CRISPR–Cas9 knockout screen in T. gondii where (A) gRNA pools were prepared and (B) transfected into Cas9 expressing parasites that produce a decoy gRNA to minimise Cas9 toxicity. (C) gRNA sequencing was performed to identify genes important for parasite fitness in vitro [49]. Bottom panel: CRISPR/Cas9 knockdown screen in T. gondii where CRISPR/Cas9 was combined with the Auxin inducible degron (AID) system. (A) Pools of vectors carrying the gRNA and a repair template that introduce a mNeongreen (mNG)-AID tag were co-transfected with a Cas9 expressing plasmid. (B) Vector pools were transfected into a TIR1/IMC1 td-tomato line and allowed to propagate before arrayed and (C) pooled phenotypic analysis. The AID-tag targets the tagged protein for degradation by exogenous expression of transport inhibitor response 1 protein (TIR1). Inner membrane complex 1 (imc1) td-tomato expression was used in phenotypic assays [55].
PMC9246331
BST-50-1069-g0003.jpg
0.414266
c64e120d63ac48babab9b2536cfc3613
Overview of the outcomes assessed at the different time points. DBDRS Disruptive Behavior Disorders Rating Scale, IRS Impairment Rating Scale, ODD Oppositional Defiant Disorder, SWAN Strengths and Weaknesses of ADHD and Normal Behavior. aClassroom observations were conducted in a subset of the sample (N = 60). bFor analyses on short term effects, outcomes were averaged over T1 and T2. cLonger term effects were assessed in the intervention conditions only
PMC9246781
10802_2021_892_Fig1_HTML.jpg
0.445183
88afb58ccfa24ec0be410f75b1bdc1eb
Three-dimensional score plot of proteomics profiling in patients with and without late gadolinium enhancement in the hypertrophic cardiomyopathy population. Each green circle represents the proteomic profile of a patient with LGE. Each red circle corresponds to that of a patient without LGE. HCM, hypertrophic cardiomyopathy; LGE, late gadolinium enhancement.
PMC9247183
fcvm-09-839409-g0001.jpg
0.404439
d7d120c602f64bfd96a0d1be092fe121
Receiver-operating-characteristic curves for the 17-protein model to distinguish patients with and without late gadolinium enhancement in the hypertrophic cardiomyopathy population. (A) shows the receiver-operating-characteristic curve in the training set, whereas (B) displays that in the test set. AUC, area under the receiver-operating-characteristic curve; CI, confidence interval.
PMC9247183
fcvm-09-839409-g0002.jpg
0.38757
47c0070446684a1a826c0f95bc8ff9bd
The 17 most discriminant proteins to distinguish patients with and without late gadolinium enhancement in the hypertrophic cardiomyopathy population. A red box indicates that the protein concentration was increased in patients with LGE, while a green box means that the concentration was decreased in patients with LGE. P values were computed using the Mann-Whitney-Wilcoxon test. Fold change was calculated by dividing the median in the cases by the median in the controls. HCM, hypertrophic cardiomyopathy; LGE, late gadolinium enhancement.
PMC9247183
fcvm-09-839409-g0003.jpg
0.409127
aa863078242148c5b5d8325754f9fada
Reported and suspected sites of focal calcium signals during cell division in mammalian cells. A series of cartoons of a stylised mammalian cell as it progresses through mitosis. (A) During prometaphase, the nuclear envelope breaks down in response to a specific calcium signal (pink spheres); (B) During metaphase and into anaphase a focal calcium signal appears at both centrosomes of the dividing cell consistent with the dynamic movement of Annexin 11 from the nucleus to the spindle poles; (C) Based on the localisation of annexin A2 during mitosis, it is speculated that there is localised calcium present at the contractile actin ring (equatorial cortex) of the dividing cell; (D) At telophase, based on the localisation of Annexin 11 and the functional consequences of disrupting CaBP7, Sorcin and S100A6 function, it is speculated that there is a focal calcium signal active at the intercellular bridge/midbody. Green organelles: mitochondria; yellow stacks in A & D: Golgi complex; yellow spheres in B & C: Golgi derived vesicles; Red X’s in B: duplicated chromosomes; Black lines in B, spindle and astral microtubules; Blue spheres: Lysosomes; Red T-shaped organelles: centrosomes; Purple spheres: cell nuclei; Pink spheres and ellipses: localised calcium signals.
PMC9247304
fphys-13-951979-g001.jpg
0.432523
cf75669992a346638a3337f0a8b2c6c4
Study flow diagram. ACE, adverse childhood experiences; fMRI, functional MRI.
PMC9247669
bmjopen-2021-058645f01.jpg
0.421354
af5030bec9fc441181657338d7ded9e2
A-C, Demonstration of expiratory muscle relaxation-induced ventilator triggering (ERIT). Flow, Paw, Pes,total (ie, uncorrected Pes signal), Pes,insp (ie, Pes,total – Pga), Pga, and EAdi waveforms recorded during pressure support ventilation with 6 cm H2O (A), 10 cm H2O (B), and 2 cm H2O (C) of support above a positive end-expiratory pressure of 16 cm H2O. Pao2 to Fio2 ratio was 132 mm Hg, and the patient was receiving continuous sedation (Richmond Agitation Sedation Scale score of –4, with propofol 6.6 mg/kg predicted body weight/h and fentanyl 0.66 μg/kg predicted body weight/h). Before recording, adequate position of the double-balloon catheter and EAdi catheter was confirmed using the Baydur maneuver and esophageal spasms present in the Pes tracing, but not in the Pga tracing, and by using the EAdi positioning tool provided on the Servo-U ventilator (Getinge), respectively. Ventilator flow, Paw, and EAdi waveforms were obtained from the ventilator using Servo-tracker software (release 4.2). Simultaneously, Paw, Pes, and Pga were acquired with a dedicated measurement setup (Biopac MP160; BIOPAC, Inc.). Data were synchronized based on Paw tracings that were acquired simultaneously using both acquisition devices and were processed using a software routine for MATLAB 2020b (Mathworks). The onset for different signals was defined as follows (A, B): (1) onset ventilator triggering (Vent,trigg; black dashed line) was defined as start of inspiratory flow (ie, nadir in Paw); (2) onset expiratory muscle relaxation (orange solid line) was defined as start of continuous decrease in Pga; and (3) onset EAdi (light blue solid line) was defined as start of inspiratory EAdi increase of > 0.5 μV, provided that EAdi peak is > 2 μV (to qualify as a breath). Ttot was defined based on flow zero-crossings (A, blue arrow in flow signal). Total Pes decrease was calculated from the onset in Pga drop (concomitant with start of decrease in Pes,total) to Pes,total nadir. The decrease in Pes,insp (ie, reflecting the patient's true inspiratory effort) was calculated from the onset in Pga drop (concomitant with start of decrease in Pes,insp) to Pes,insp nadir. The Pga drop from expiratory muscle relaxation was calculated from the onset in Pga drop to Pga nadir. A, EAdi onset started after ventilator triggering, whereas the drop in Pga and Pes occurred before ventilator triggering. The start of drop in Pga and Pes was very close to the first time point of the sudden decrease in Paw below set positive end-expiratory pressure (start of triggering phase). B, Example showing that not all ERIT breaths were followed by inspiratory effort (arrow): EAdi < 2 μV and the total Pes decrease was approximately equal to the Pga drop from expiratory muscle relaxation. C, Example of double breaths (gray area) with ERIT in a 2:1 pattern. The first ventilator pressurization was the result of some degree of expiratory muscle relaxation not followed by patient inspiratory effort (absent EAdi indicated by arrow in EAdi signal and the total Pes decrease approximately equal to the Pga drop). Then, complete expiratory muscle relaxation resulted in a ventilator insufflation followed by an inspiratory effort. EAdi = electrical activity of the diaphragm; Paw = airway pressure; Pes = esophageal pressure; Pes,insp = esophageal pressure related to inspiratory effort; Pes,total = total esophageal pressure; Pga = gastric pressure; Ttot = total ventilator cycle duration; Vent,trigg = ventilator triggering.
PMC9248081
gr1.jpg
0.460287
161c5f1b82e844eb89a1f9492ac27f69
Observations obtained 5 days after the recording of Figure 1 (pressure support, 8 cm H2O; positive end-expiratory pressure, 10 cm H2O; respiratory rate, 34 breaths/min; tidal volume, 400-470 mL [5.5-6.3 mL/kg predicted body weight]; and Pao2 to Fio2 ratio, 159 mm Hg under continuous sedation [Richmond Agitation Sedation Scale score, –3; propofol, 2.5 mg/kg predicted body weight/h; fentanyl, 1.33 μg/kg predicted body weight/h]). Patient effort was perfectly synchronous with the ventilator: the onset of Pes decrease and EAdi increase occurred at the same time (orange solid line) and before ventilator triggering (black dashed line) for each breath. No signs of expiratory muscle recruitment (no increase in Pga during expiration) were found. EAdi = electrical activity of the diaphragm; Paw = airway pressure; Pes = esophageal pressure; Pga = gastric pressure.
PMC9248081
gr2.jpg
0.445105
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Study CONSORT diagram. Participants were recruited with screening, consent, and enrollment process. The treatment order was randomized into two groups, one group (red) supplemented with the placebo and the other group (green) supplemented with the prebiotic followed by a washout period and crossover to the other treatment for each group.
PMC9248813
fnut-09-908534-g0001.jpg
0.510629
041eecd1eede4c37b95d77ee2fd70d01
(A) Relative abundance of the gut microbiome at the phylum level and (B) the family level within the phylum Actinobacteria pre- and post-treatment with placebo or prebiotic. (C) Box plots of the genus Bifidobacterium counts pre- and post-treatment with placebo or prebiotic. (D–H) Box plots of Bifidobacterium species counts pre- and post-treatment with placebo or prebiotic (*P <0.05, **P < 0.01).
PMC9248813
fnut-09-908534-g0002.jpg
0.400644
0df47a304b784a6c80047cee0f885419
(A) Volcano plot of all detected genes. Genes with a logFC (post–pre treatment) > 0 and a –log(P-value) > 0.05 are colored blue and genes with a logFC <0 and a –log(P-value) > 0.05 are colored red. All the other genes are colored gray. (B–E) Box plot of gene counts pre- and post-treatment with placebo or prebiotic (P ≤ 0.05, unadjusted). (F–H) Correlation plot of changes (post–pre) in Bifidobacterium abundance against changes (post–pre) in gene counts for both placebo and prebiotic in 20 subjects (prebiotic: P ≤ 0.05, adjusted, Kendall T).
PMC9248813
fnut-09-908534-g0003.jpg
0.531259
202787fb295a435caec02f8c1fb14b66
(A) Volcano plot of all metabolites in human plasma samples. Metabolites with a logFC > 0 and a –log(P-value) > 0.05 are colored blue and metabolites with a logFC <0 and a –log(P-value) > 0.05 are colored red. All the other metabolites are colored gray. (B–J) Box plots of IPA, TMAO, choline, and acylcholines concentrations pre- and post-treatment with placebo or prebiotic (unadjusted P-value).
PMC9248813
fnut-09-908534-g0004.jpg
0.483954
431ded68e71242348b55492f21a200c5
Bioinformatics analysis of 600 genomes of the phylum Bacteroidetes points toward high biosynthetic genetic potential of the Chitinophagia class. (A) Consensus tree based on maximum-likelihood method (RAxML model v8 [108], GTR GAMMA with 1,000 bootstraps) of 600 16S rRNA gene sequences color coded on class level. For each strain the genome size and biosynthetic gene cluster amount and types are depicted. Tree is annotated using iTOL v4 (110). (B) Correlation of the total gene cluster amount with the genome size of each stain. (C) Analysis of the BGC types in the individual classes. BGC types: NRPS, nonribosomal peptide; PKS, polyketide; hybrid, cluster containing more than one BGC type; and other, remaining BGC types not separately listed. (D) Detailed look onto the most essential BGC types responsible for the production of bioactive NPs. Partial BGCs on contigs <10 kb of WGS projects are not included in all graphs.
PMC9248904
spectrum.02479-21-f001.jpg
0.407334
403c08a0d6b24784b7398bfc1b29f7aa
BiG-SCAPE (26) analysis of the phylum Bacteroidetes highlights a giant uncovered genetic potential. (A) A global network of all depicted gene cluster families with a cutoff of 0.6. Known ones are marked, named and are identified by known biosynthetic gene cluster (BGC) deposited at MIBiG (all known and deposited Bacteroidetes BGCs are found). (B) Same BGCs sorted by taxonomy. BiG-SCAPE BGC classes: NRPS, nonribosomal peptide; PKS, polyketide; and RiPPs, ribosomally synthesized and posttranslational modified peptides. Singeltons (unique BGCs without any connection) are not shown. Visualization and manipulation by Cytoscape v3.4.0 (113).
PMC9248904
spectrum.02479-21-f002.jpg
0.404917
827bcc9800b1437f829374a794cc3eb4
Taxonomical arrayed chemotype-barcoding matrix reveals an uncharted chemical space within the genus Chitinophaga. (A) The tree is based on a Clustal W alignment (111) of available 16S rRNA gene sequences of 25 Chitinophaga strains available for cultivation. The tree was calculated using MEGA v7.0.26 with the maximum-likelihood method and GTR-Gamma model (112). Percentage on the tree branches indicate values of 1,000 bootstrap replicates with a bootstrap support of more than 50%. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The bucketing process is depicted as a chemotype-barcode matrix and color coded by the condition each individual bucket was present. (B) Bar blot of the unique “metabolite” buckets of each strain. (C) Bar blot depicting the occurrence of “metabolite” buckets in the data sets.
PMC9248904
spectrum.02479-21-f003.jpg
0.461271
944d400330bc407f904e88b3461b581e
Chemical structures of the chitinopeptins A–D. Compounds 1 and 2 are produced by C. eiseniae DSM 22224, compounds 3 to 6 by C. flava KCTC 62435.
PMC9248904
spectrum.02479-21-f004.jpg
0.417693
fca0912c0a51454ca69fa9325b78f714
Biosynthetic gene clusters responsible for the production of chitinopeptin A to Dand further derivatives. (A) BGCs of strains C. eiseniae, C. flava, C. oryziterrae, and C. niastensis with matching amino acid sequence and additional biosynthetic genes responsible for the hydroxylation of Asp, Phe, and Ile or the in cooperation of 2,3-diaminopropionic acid. Identity was calculated with a standard MAFFT alignment (107). (B) Gene cluster family of this iron chelating cyclic lipodepsipeptides. AA, amino acids; NmVal, N-Me-Val; Hya, β-hydroxyaspartic acid; C, condensation domain; A, adenylation domain; MT, nitrogen methyltransferase; T, peptidyl-carrier protein domain; E, epimerization domain; TE, thioesterase domain; CAL, co-enzyme A ligase domain; ACP, acyl-carrier protein domain; KS, ketosynthase domain; AT, acyltransferase domain.
PMC9248904
spectrum.02479-21-f005.jpg
0.438378
a29ce90996284417b092411e35515dac
Oil Red O staining of aortic root and thoracic aorta. (a) and (b) are representative images (taken at 10x) of aortic root from TIGR4- and PBS- inoculated mice at 28-days post-inoculation (PI). (c) The area of Oil Red O staining was quantified and compared between groups. Significantly more plaques were observed 2 days post TIGR4 inoculation. (d) Quantification of Oil Red O content in thoracic aortas as a percentage of the area of tissue at 2-, 7- and 28- days PI. At 28 days PI, TIGR4 inoculated mice present with significantly more plaque in the thoracic aorta compared to PBS control. (e) and (f) are representative images of thoracic aorta from TIGR4- and PBS-inoculated mice, respectively.
PMC9249762
41598_2022_15507_Fig1_HTML.jpg
0.454016
d9ba06cdaf6a460cb19a717c55495824
Assessment of aortic root remodelling and plaque structure using trichrome staining. (a) Total area of aortic wall was quantified to assess inward and outward remodeling as a result of atherosclerosis. 28 days post-inoculation (PI), TIGR4 inoculated mice present with significantly more aortic wall remodelling. 8 μm tissue sections were stained with modified trichrome stain to identify collagen and smooth muscle cells (SMC). Following colour deconvolution, SMC (b) and collagen (c) intensity per area in aortic root were calculated. Significantly less SMC and collagen were present in the plaques of TIGR4 inoculated mice compared to PBS inoculated mice at 7 days PI. Moreover, aortic remodelling, plaque-SMC and -collagen content in TIGR4-inoculated mice with confirmed pulmonary abnormalities (MRI positive) were compared to PBS-inoculated mice (d), (e) and (f), respectively. Similar significant comparisons were observed. (g) and (h) are representative images of aortic root from TIGR4- and PBS-inoculated mice, respectively (taken at 10x).
PMC9249762
41598_2022_15507_Fig2_HTML.jpg
0.468634
31c53d19d6e04a7f80676030886d5c41
Immunofluorescence staining of aortic root. (a) A representative image (taken at 10x) of aortic root stained for F4/80 (red) and DAPI (blue) from TIGR4- and PBS- inoculated mice at 28-days post-inoculation. (b) Red fluorescence intensity was quantified per area in plaque regions (minus any background fluorescence detected) and compared between groups. (c) Representative image (taken at 10x) of aortic root stained for NLRP3 (green) and DAPI (blue) from TIGR4- and PBS- inoculated mice at 28-days post-inoculation. (d) Green fluorescence intensity was quantified per area in plaque regions (minus any background fluorescence detected) and compared between groups. No significance was observed.
PMC9249762
41598_2022_15507_Fig3_HTML.jpg
0.417098
86b9a9f496244fbd96e8a6dd1e073281
FDG uptake in the aortic arch. TIGR4- and PBS-inoculated mice underwent fluorodeoxyglucose positron emission tomography (FDG-PET) imaging at 2-, 7- or 28-days post-inoculation. The FDG standardised uptake value (SUV)-mean (a) and -max (b) were evaluated for each mouse. No significance was observed. Representative images of TIGR4- (c) and PBS-inoculated mice (d), respectively. Sagittal views with the red and white circles present fluorodeoxyglucose uptake in the ascending aorta.
PMC9249762
41598_2022_15507_Fig4_HTML.jpg
0.524145
19153b9375f649fa992dc7e287757702
Gene expression of inflammatory mediators in the heart apex. Tissues from TIGR4- and PBS-inoculated mice were collected at 2-, 7- or 28-days post-inoculation and mRNA expression levels of (a) tenascin C; at 7 days post-inoculation, there was a trend for increased levels of tenascin C (b) tumor necrosis factor-alpha (TNF-a), (c) chemokine (C-C motif) ligand 3 (CCL3), (d) interleukin-6, (e) NLR family pyrin domain containing 3 (NLRP3) and (f) interleukin-1 were quantified by real-time polymerase chain reaction. Target gene was normalized against the housekeeping gene, HPRT. Solid horizontal line represents the median.
PMC9249762
41598_2022_15507_Fig5_HTML.jpg
0.43104
2d48bf06d60c4c2bbd18d25dbda248ee
(A) Isoacceptor counts of functional cytosolic tRNA genes in Drosophila - pseudogenes and mitochondrial tRNA genes are excluded. Colors distinguish distinct anticodons within each isoacceptor family. Counts for initiator (iMet) and elongator tRNA:Met are shown separately. (B) Summary statistics for all Drosophila tRNA genes. (C) Example of tRNA gene nomenclature syntax. (D) Distribution of tRNA genes across major chromosomal scaffolds; pseudogene numbers are in parentheses. ‘M’ = mitochondrial genome. (E) Example of a tRNA gene cluster from the 2R:6,144,000..6,195,000 genomic region, corresponding to cytological region 42A shown in Figure 3 of Kubli 1982. (Notably, the only significant change to tRNA annotations in this region is the addition of tRNA:Arg-ACG-1-4 in the current version.) Green highlight: tRNA:Arg-ACG-1 isodecoders; orange highlight: tRNA:Lys-CTT-1; yellow highlight: tRNA:Asn-GTT-1; magenta highlight: tRNA:Ile-AAT-1; blue rectangles: protein-coding genes; red rectangle is a lncRNA gene.
PMC9249942
25789430-2022-micropub.biology.000560.jpg
0.443734
f0af1bf99b5840d695b476a00dd70c20
CT with bony reconstruction of the facial skeleton (a–c) Axial, sagittal and coronal planes show complete reorganization of the bone structure with moth-eaten appearance, (c) shows the empty alveolar sockets of the extracted teeth (d, e) Multiplanar 3-D reconstructions showing the complete expansion of the process and the pathological fractures.
PMC9250319
gr1.jpg
0.383981
895099d4c5cc48af9c6c18971235464c
Flow diagram for selection and inclusion criteria.
PMC9251088
BMRI2022-5432743.001.jpg
0.43661
4fed7baaf2a34ce08476128e83802c38
The body posture assessment with classical certified tools in both groups: (a) torso rotation angle (ATR) by pediscoliometer; (b) the depth of thoracic kyphosis and lumbar lordosis angles by a digital Sunders inclinometer TMX–127; (c) the plumb line; (d) position of the scapulas; (e) Mathiass test [30].
PMC9251088
BMRI2022-5432743.002.jpg
0.465718
ddbd4be3c80047fa854d9b3d49491767
Number distribution of hours sitting at school (top) and at home (bottom), in both groups: study (a) and control (b).
PMC9251088
BMRI2022-5432743.003.jpg
0.453738
0527386bcd664d439220bcc84061f9da
Study flow chart
PMC9251918
12958_2022_961_Fig1_HTML.jpg
0.464186
f15d08ccdce8477d850b6b89b16e7fe6
Dynamics in LH (A, B) and FSH (C, D) in FHA women with (B, D) and without (A, C) PCOM
PMC9251918
12958_2022_961_Fig2_HTML.jpg
0.45014
5e24a94d54e3419590c839c4f92c2286
CircASPH expression was identified to be significantly upregulated in HCC tissues and related to patient prognosis. (A, B) Heat maps of differentially expressed circRNAs in HCC tissues and non-tumor tissues obtained from GSE128274 and GSE125469. (C) The numbers of overlapping differentially expressed circRNAs from two GEO databases are shown in the Venn diagram. (D) The level of circASPH expression was evaluated by RT-qPCR in 20 paired HCC tissues and normal tissues. (E) FISH analysis of the expression of circASPH in HCC tissues and normal tissues. (F) CircASPH expression in HCC cell lines compared with THLE-2 cells. (G) Kaplan–Meier analysis showed that the level of circASPH was predictive of overall survival. *p < 0.05, **p < 0.01.
PMC9252593
fonc-12-911715-g001.jpg
0.473128
1a41c94347264840b9847bad7b872d89
CircASPH promoted HCC cell proliferation, migration, and invasion. (A) The expression of the circASPH level was detected by circASPH overexpressed and knocked down in HCC cells. (B, C) Cell Counting Kit-8 (CCK-8) assays and EDU staining assays were used to indicate the function of circASPH in the proliferation of HCC cells. (D) Wound-healing assays showed the role of circASPH in the migration of HCC cells. (E) Transwell assays showed the function of circASPH in the invasion of HCC cells. (F–H) Xenograft tumors composed of shRNA-circASPH-transfected HCC cells were significantly smaller than those composed of shRNA-NC-transfected HCC cells. *p < 0.05, **p < 0.01, ***p < 0.001.
PMC9252593
fonc-12-911715-g002.jpg
0.431589
fb6da6473cc5429d85c9cb8f3c3f5809
CircASPH sponged miR-370-3p. (A) Score list for the circInteractome of predicting miRNAs sponged by circASPH. (B) Predicted binding sites between circASPH and miR-370-3p. (C) Dual-luciferase reporter assay showed that the co-transfection of WT and mimic miR-370-3p markedly decreased the luciferase activity. (D) MiR-370-3p was abundantly pulled down by a circASPH probe. (E, F) Images of circASPH and miR-370-3p co-localized in the cytoplasm; scale bar, 20 μm. *p < 0.05, **p < 0.01, ***p < 0.001.
PMC9252593
fonc-12-911715-g003.jpg
0.408699
6d22dacde9294b2dbdba08fb39b3bd6b
CircASPH regulated the level of the DNMT3b/5mC Axis by sponging miR-370-3p in HCC cells. (A, B) Molecular function and biological process of miR-370-3p target genes in gene ontology analysis. (C) KEGG analysis of miR-370-3p target genes. (D) Heatmap of the expression of the DNMT gene family level in GSE124535. (E) Predicted binding sites between DNMT3b and miR-370-3p. (F) Dual-luciferase reporter assay showed that miR-370-3p could interact with the 3’UTR of DNMT3b mRNA. (G, H) The expression of the DNMT3b level with miR-370-3p overexpression and knockdown was detected by RT-qPCR and Western blot. (I) Images of 5hmC-, 5mC-, and DAPI-stained HCC cells with different levels of miR-370-3p; scale bar = 20 μm. (J, K) The expression of DNMT3b level with circASPH overexpression and knockdown was detected by RT-qPCR and Western blot. (L) Images of 5hmC-, 5mC-, and DAPI-stained HCC cells with different levels of circASPH; scale bar = 20 μm. **p < 0.01, ***p < 0.001.
PMC9252593
fonc-12-911715-g004.jpg
0.422562
fe7ea0b2a3c648ff8d0113b88c2538c5
CircASPH promoted the HCC process via miR-370-3p/DNMT3b/5mC. (A) The level of DNMT3b expression was evaluated by RT-qPCR in 20 paired HCC tumor tissues and normal tissues. (B) Pearson analysis indicated the relationship between circASPH and DNMT3b. (C) Immunohistochemical staining for 5mC in HCC tumor tissues; scale bar = 100 μm. (D, E) Cell Counting Kit-8 (CCK-8) assays and EDU staining assays indicated the proliferation of cells expressing a combination of circASPH, sh-miR-370-3p, and si-DNMT3b. (F, G) Wound-healing assays and Transwell assays indicated the ability of migration and invasion of cells expressing a combination of circASPH, sh-miR-370-3p, and si-DNMT3b. **p < 0.01.
PMC9252593
fonc-12-911715-g005.jpg
0.484711
af360ad2d86e481c932ec639980610f7
CircASPH promoted HCC progression by regulating the DNA methylation and expression of HAO2. (A) Volcano plot of the methylation difference between HCC tumor tissues and normal tissues. (B) CpG island distribution of promoter differential methylated CpG sites. (C, D) Average profiles of 5mC and input DNA coverage across the binding-site motif identified on 5mCþ enhancers. (E) GSEA analysis of the gene enriched in the negative regulation of the growth pathway. (F) IGV profile of 5mC-enriched regions and RNA-seq profiles in HCC tumor tissues. (G, H) The expression of the HAO2 level with miR-370-3p overexpression and knockdown was detected by RT-qPCR and Western blot. (I, J) The expression of the HAO2 level with circASPH overexpression and knockdown was detected by RT-qPCR and Western blot. (K) MeDIP-qPCR assays showed 5mC in HAO2 genes with different circASPH levels. **p < 0.01.
PMC9252593
fonc-12-911715-g006.jpg
0.401537
ba967abbfe52478ca5b2f757785c20b5
CircASPH promoted the HCC process via the miR-370-3p/DNMT3b/5mC/HAO2 axis. (A) The level of HAO2 expression was evaluated by RT-qPCR in 20 paired HCC tumor tissues and normal tissues. (B) Pearson analysis indicated the relationship between circASPH and HAO2. (C) EDU staining assays indicated the proliferation of cells expressing a combination of circASPH, sh-miR-370-3p, and HAO2. (D, E) Wound-healing assays and Transwell assays indicated the ability of migration and invasion of cells by expressing a combination of circASPH, sh-miR-370-3p, and HAO2. **p < 0.01.
PMC9252593
fonc-12-911715-g007.jpg
0.426857
9aa0576b83da43e9b0f4539d9dbbc91b
Browser UI with the multi-panel setting. The browser user interface displays data of different types in each panel, representing different dimensionalities. The panel on the left shows the main, conventional browser window. The panel on the top right is a 3D viewer and shows a 3D genome model. The panel on the bottom right shows an image from a microscopy experiment. (A) The main browser menu, ideogram, and select functions. (B) Ruler, chromHMM, and gene tracks, representing 1D data tracks. (C) Image track in thumbnail mode. (D) Hi-C and wiggle/numerical tracks, representing 2D data tracks. (E) A representative dynamic track, the animation displays the 3 numerical tracks from (D), representing 4D data tracks. (F) 3D viewer, displaying the highlighted gene (HOXA1) as spheres, representing 3D data tracks. (G) One expanded image in its own panel with links to Omero viewer provided by the image source.
PMC9252771
gkac238fig1.jpg
0.445172
34238fe01baa415ba2c1d8612970d0de
Dynamic tracks. Dynamic track displays an animation of data from different time points or samples. One of the newly developed dynamic track type: dBedgraph in text format (A). Browser views show steps to select multiple tracks and combine them into a dynamic track, and the animation displays each track iteratively (B–D). Dynamic track can be configured to adjust the height, speed, y-axis scale, and color via settings (E).
PMC9252771
gkac238fig2.jpg
0.442508
36580d1ac91a4ab2898dee6cf48171a7
3D viewer. An overview of how 3D data is displayed in the Browser. 3D coordinates in text format are converted to the binary g3d data using g3dtools, then the file is submitted to the browser for visualization. The 3D viewer can highlight current browser regions or specific genes. Users can also use numerical and annotation data to decorate the 3D structure.
PMC9252771
gkac238fig3.jpg
0.382792
f3dbb9c38d034678b3bad87736a50b68
Image track. How imaging data is displayed in the browser. Browser view with an image track in thumbnail mode (A). The external image display window by image data source provider (B). The metadata popup menu is associated with one image (C). Configuration menu of the image track in main browser (D). The image track is displayed in density mode (E).
PMC9252771
gkac238fig4.jpg
0.440193
34133b4f96ce48beb76025ed385c6cf4
Browser community engagement. Browser users develop new track types for their own visualization. We provide help and support for users with new function/genome requests, as well as technical support for mirror sites. The Browser provides services for many other genomic tools.
PMC9252771
gkac238fig5.jpg
0.456891
47d484be0c0e42cb96645fb413ac8fe7
New components of WashU Epigenome Browser: 3D chromatin viewer, imaging data viewer and dynamic tracks.
PMC9252771
gkac238figgra1.jpg
0.495382
8ab0ce342c8644e2932b1d8d970bfe05
Joint centers sensed and processed to obtain kinematic, dynamic, and biomechanical metrics
PMC9252943
586_2022_7253_Fig1_HTML.jpg
0.431822
d705194183ec4e54ad492b0340c0bcbd
Box plots for between-group comparison in dSVA, torque, and torso velocities
PMC9252943
586_2022_7253_Fig2_HTML.jpg
0.491318
2f9d4e4df3764b37a19103907f33bd54
Correlations between dSVA and peak spine torque with VAS and ODI
PMC9252943
586_2022_7253_Fig3_HTML.jpg
0.513864
952d8074fb224d3ca2eb093db65cdb3c
Correlations between torso velocity with VAS and ODI
PMC9252943
586_2022_7253_Fig4_HTML.jpg
0.494974
7e8e7a8456814ef9a4e076f5f3a02f3a
Box plots of between-group differences stratified by low and high VAS and ODI for peak spine torque
PMC9252943
586_2022_7253_Fig5_HTML.jpg
0.464981
f1e1183fc05e4140bef8db758fb17aad
Ceramide metabolism in mammals. Schematic representation of the ceramide metabolic pathway highlighting critical enzymes involved in ceramide turnover and their respective inhibitors. Six different ceramide synthases (CerS1-6) produce (dihydro)ceramides of varying acyl chain lengths by catalyzing the N-acylation of sphinganine (derived from the condensation of serine and palmitoyl-CoA; de novo pathway; highlighted in orange) or sphingosine (derived from sphingolipid breakdown; salvage pathway; highlighted in green) with a fatty acyl chain of defined length within the range C14–C26. Ceramides can also be derived from the hydrolysis of sphingomyelin (highlighted in purple). Ceramides serve as substrates for more complex sphingolipid species such as glucosylceramides and galactosylceramides, which can be further modified. Ceramides can also be converted to acylceramide species bearing an additional acyl chain at the 1-hydroxy position. ACSL5 Acyl-CoA synthetase long-chain family member 5, CDase ceramidase, CerS ceramide synthase, CGT ceramide UDP-galactosyltransferase, DEGS dihydroceramide desaturase, DGAT2 diacylglycerol O-acyltransferase 2, GALC galactosylceramidase, GCase glucocerebrosidase, GCS glucosylceramide synthase, KDSR 3-ketodihydrosphingosine reductase, ORMDL orosomucoid-like protein, R Fatty acyl chain moiety, SGPL1 sphingoine-1-phosphate lyase 1, SGPP1 sphingosine-1-phosphate phosphatase 1, SK sphingosine kinase, SMase sphingomyelinase, SMS sphingomyelin synthase, SPT serine palmitoyltransferase, UGCG UDP-glucose ceramide glucosyltransferase, UGT8 UDP glycosyltransferase
PMC9252958
18_2022_4401_Fig1_HTML.jpg
0.49945
338e697ac3d34c319855ddb0dfcbd502
Cellular and molecular mechanisms by which ceramides affect metabolic regulation. Excessive influx of free fatty acid (FFA) mediated by the fatty acid transporter CD36 drives the production of ceramides, which exert multifaceted effects to modulate cellular metabolic homeostasis. Ceramide-dependent effects are shown by black arrows, including regulatory proteins through which they act. The consequences of ceramide accumulation are highlighted in red, and the underlying mechanisms are highlighted in blue. Purple arrows depict conversion of lipids, and dashed lines indicate transport. AKT protein kinase B, BAX Bcl-2-associated X protein, CD1d cluster of differentiation 1d, CD36 cluster of differentiation 36 (fatty acid transporter), CerS ceramide synthase, DES dihydroceramide desaturase, eNOS endothelial NO synthase, ER endoplasmic reticulum, FA-CoA fatty acyl-coenzyme A, FFA free fatty acid, GalCer galactosylceramide, GLUT4 glucose transporter 4, HSL hormone-sensitive lipase, iNKT invariant natural killer T cell, IR insulin receptor, JNK c-Jun-N-terminal kinase, KDSR 3-ketodihydrosphingosine reductase, MFF mitochondrial fission factor, MOMP mitochondrial outer membrane permeabilization, NLRP3 NLR family pyrin domain-containing 3, NO nitric oxide, PC phosphatidylcholine, PERK protein kinase RNA-like ER kinase, PKCζ protein kinase C zeta, PKR protein kinase R, PM plasma membrane, PP2A protein phosphatase 2A, SPT serine palmitoyltransferase, SREBP1 sterol regulatory element-binding protein 1, STARD7 StAR-related lipid transfer protein 7, TAG triacylglycerol, VDAC2 voltage-dependent anion channel 2
PMC9252958
18_2022_4401_Fig2_HTML.jpg
0.441781
d2cf56c30b314210b752f6d59a3b295e
Factors potentially contributing to ceramide accumulation in obesity. In conjunction with the increased availability of precursor fatty acids for ceramide production, several cell-extrinsic and -intrinsic factors have been linked to the control of ceramide turnover rate and may contribute to ceramide accumulation when deregulated in obesity. AMPK AMP-activated protein kinase, Asah N-acylsphingosine aminohydrolase (acid CDase), Acer2 alkaline ceramidase 2, CerS ceramide synthase, FFA free fatty acids, FGF21 fibroblast growth factor 21, FXR farnesoid X receptor, HIF2α hypoxia-induced factor 2α, MYC transcription factor MYC, Neu3 neuraminidase 3, Smpd3 sphingomyelin phosphodiesterase 3 (neutral SMase2), Sptlc serine palmitoyltransferase long-chain base subunit
PMC9252958
18_2022_4401_Fig3_HTML.jpg
0.482777
17626927bced4001b96e6b9dcf99e2c2
Tissue-specific effects of ceramide accumulation and the related health consequences in obesity. Most conclusive observations have been demonstrated in rodent models of obesity or dyslipidemia. Although ceramides have been associated with obesity-related metabolic dysfunction and disease development in all tissues shown, the exact ceramide molecular species involved in these processes often remain undefined. If there is evidence of the ceramide species promoting tissue-specific lipotoxicity, this is indicated accordingly. Red arrows indicate inhibitory effects, and green arrows indicate stimulatory effects. Cer ceramide, CerS ceramide synthase, ER endoplasmic reticulum, FFA free fatty acid, HGP hepatic glucose production, LDL low density lipoprotein, NAFLD non-alcoholic fatty liver disease, NASH non-alcoholic steatohepatitis, NO nitric oxide, PVH paraventricular hypothalamus, VMH ventromedial hypothalamus
PMC9252958
18_2022_4401_Fig4_HTML.jpg
0.49641
c0d134f9603944aaad0a12e6b0cacc24
Miridex putorii gen. nov., sp. nov. A, male, ventral view; B, male, dorsal view, a. aedeagus; C, female, ventral view, b. vulva; D, female, dorsal view; E, gnathosoma, male, dorsal view, c. seta dG, d. seta dF, e. supracoxal spine (seta elc.p), f. genital opening, g. anterior end of aedeagus, h. membrane capitulum; F, gnathosoma, male, dorsal view, i. everted anterior part of aedeagus; G, gnathosoma, male, ventral view, j. spines on palps, k. seta v”F, l. pharyngeal bulb, m. subgnathosomal seta (seta n); H, claw on the leg.
PMC9253041
gr1.jpg
0.463989
423496b71223405094e99f921180d943
Miridex putorii gen. nov., sp. nov., egg and immature stages. A, egg; B, larva, ventral view, a. vimineous seta, b. leg with claws, c. ventral scutum; C, protonymph, ventral view; D, deutonymph, ventral view; E, F, G, claw, various views; H, supracoxal spine of deutonymph, arrow indicate the orientation of left spine as viewed on the gnathosoma.
PMC9253041
gr2.jpg
0.431553
2f4b4b926518410983248bfaf0d11ee6
Miridex putorii gen. nov., sp. nov. A, female, ventral view; B, male, ventral view; C, pharate male, deutonymph with visible male inside, a. anterior end of male gnathosoma, b. posterior end of male opisthosoma; D, pharate female, deutonymph with visible female inside, c. anterior end of female gnathosoma; d. posterior end of female opisthosoma.
PMC9253041
gr3.jpg
0.492151
69e06cb1b17b4d87a11cbb491918d4bc
Study flow chart.
PMC9253399
fpsyt-13-886680-g0001.jpg
0.468109
c98dbaee25684c1a9ba18960d4187cbd
Expression and subcellular distribution of USP7 in neurons(A) Immunostaining of USP7 and GFAP in rat hippocampal cultures at DIV15. Scale bar = 50 μm.(B) Immunostaining of USP7 and GAD67 in rat hippocampal cultures at DIV15.(C) Lysates of cultured neurons were collected on DIV15, and USP7 levels were measured by Westerns. GAPDH was probed as a loading control.(D) Lysates of different brain regions were collected from rats of embryonic day 18. USP7 levels were measured by Western blot.(E) Cultured neurons were treated with USP7 inhibitor HBX41108 (10 μM) for 2 or 4 h at DIV15, and the lysates were probed for ubiquitination.(F) Quantification showed an increase in ubiquitination intensity in the HBX41108 treated group (F(2,9) = 33.13, p < 0.01, One-way ANOVA).(G) Developmental time course of USP7 expression in the brain. Cortical tissues were collected from mice of ages from E10 to P90. Data are represented as mean ± SEM. Error bars represent SEM, ∗∗p < 0.01.
PMC9253496
gr1.jpg
0.389236
8933dd12d5504a65ae0439e6ccc0fcdd
Behavior changes in mice following USP7 overexpression in the brain at P0. Behavioral tests were performed at P30-P55(A and B) Homecage activities including grooming, rearing, digging, climbing, circling, and jumping (Ctrl: n = 9; USP7: n = 13, t-test). Counts of grooming and digging (A), as well as the overall activity events (B), were increased significantly in USP7 infected mice.(C) Track length in the open field test showed no difference between two groups (t-test).(D) A representative example of the test arena at the end of the Marble burying test.(E) USP7 mice buried more marbles during the test (F(1,20) = 13.46, p < 0.01. Ctrl: n = 9; USP7: n = 13, repeated measures ANOVA).(F) Quantification of the number of marbles buried at the end of the test (30 min).(G and J) Paradigm for the social preference test (G) and social novelty test (J), and representative tracing.(H and K) Quantification of time spent in each chamber in the social preference test (H) (Ctrl: n = 8; USP7: n = 12, t-test) and social novelty test (K) (Ctrl: n = 8; USP7: n = 12, t-test).(I and L) Quantification of the preference index in the social preference test (I) and social novelty test (L). The preference for social interaction was increased in USP7 animals compared with the control (t-test) (I).(M and N) The novel object recognition test showed no difference in discrimination index between the two groups (Ctrl: n = 8; USP7: n = 13, t-test).(O and P) Hot plate test. The withdrawal latency was decreased in USP7 mice compared with the control (Ctrl: n = 8; USP7: n = 13, t-test). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr10.jpg
0.387915
c00210ae5b434e0cbceeaf66353acbdf
USP7 regulates dendritic growth and arborization(A–D) Hippocampal neurons were transfected with a control vector or USP7 plasmid at DIV 7, and imaged for morphology at DIV 11 (A). Scale bar = 100 μm. Dendritic arborization was analyzed by Sholl analysis (F(1,56) = 3.865, p = 0.054, Repeated measures ANOVA) (B). The total number of dendritic branches and the sum length of dendrites showed no significant difference between the control (n = 24) and the USP7 group (n = 28) at DIV11 (p > 0.05, t-test) (C and D).(E–H) Neurons were transfected with USP7 or a vector as control at DIV 11, and imaged for morphology at DIV 15 (E). Scale bar = 100 μm. Dendritic arborization was analyzed by sholl analysis (F(1,44) = 13.037, p = 0.001, Repeated measure ANOVA) (F). The total number of dendrites and total length of dendrites were increased in USP7-transfected neurons on DIV15 (Ctrl: n = 18; USP7: n = 22. Number of dendrites, p < 0.01, t-test; sum length of dendrites, p < 0.01, t-test) (G, H). Scale bar = 100 μm.(I–M) Knockdown of USP7 results in a reduction of dendritic arborization.(I) Cortical neurons were transfected with vector (Control, n = 16) or shUSP7 (n = 31) at DIV 11 and imaged for morphology on DIV 15. Scale bar = 100 μm.(J) Sholl analysis of dendritic arborization at DIV 15 (F(1,46) = 7.497, p = 0.009, Repeated measure ANOVA).(K and L) Total number of dendrites and total length of dendrites were decreased in shUSP7 neurons on DIV15 (Number of dendrites, p < 0.05, t-test; sum length of dendrites, p < 0.01, t-test).(M) Mean length of dendrites was decreased in shUSP7 neurons on DIV15 (p < 0.05, t-test). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr2.jpg
0.464852
b8acb2e5627d46029a57539b9d2b9584
USP7 regulates XIAP protein accumulation in neurons(A) Lysates were collected from primary cortical neurons of DIV 0 to DIV 20. Expression levels of USP7 and XIAP were measured by Western blot. GAPDH was probed as a loading control.(B) Quantification of USP7 and XIAP intensity (n = 3).(C–E) Cortical neurons were infected with AAV-GFP or AAV-USP7 on DIV 0 for 15 days, and USP7 and XIAP levels were measured by Western blot. An increased level for both USP7 and XIAP was detected in neurons infected with USP7 virus (GFP-AAV: n = 4; USP7-AAV: n = 4. p< 0.05, t-test).(F and G) Cortical neurons were treated with HBX41108 (USP7 inhibitor) for 2 and 4 h and the lysates were collected to probe for XIAP. Inhibition of USP7 led to a decrease in XIAP amount. (Ctrl: n = 4; HBX 2 h: n = 4; HBX 4 h: n = 4. F(2,9) = 30.88, p < 0.01, one-way ANOVA, Dunnett).(H) Cortical neurons were transfected with USP7 at DIV 11 and immunostained for XIAP at DIV 15. Scale bar = 50 μm.(I) Quantification showed an increase in endogenous XIAP intensity in neurons transfected with USP7 (Ctrl: n = 13; USP7: n = 13. p< 0.01, t-test).(J) Hippocampal neurons were transfected with shUSP7 at DIV 8 and immunostained for XIAP at DIV 15. Scale bar = 50 μm.(K) Quantification showed a decrease in endogenous XIAP in neurons with USP7 knockdown (Ctrl: n = 14; USP7: n = 14. p< 0.01, t-test). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr3.jpg
0.387405
267b1828de0a4c378bcb0981b10674fa
USP7 causes XIAP deubiquitination and stabilization(A) XIAP ubiquitination assay. HEK293 cells were transfected with FLAG-XIAP, HA-ubiquitin, and USP7 for 2 days. XIAP was immunoprecipitated and probed for ubiquitin (ubi). Cell lysates (input) were used to detect protein levels.(B and C) Quantification of Western blot intensities. USP7 caused a decrease in XIAP ubiquitination and a decrease in XIAP protein levels (Ubiquitination Signal: F(2,9) = 20.95, p < 0.01, one-way ANOVA, Tukey; XIAP Signal: F(2,9) = 22.20, p < 0.01, one-way ANOVA, Tukey. XIAP: n = 4; XIAP + Ubi: n = 4; XIAP + Ubi + USP7: n = 4).(D) Degradation assay of XIAP with or without USP7. Transfected HEK cells were treated with cycloheximide (CHX) for various time periods and cell lysates were collected to examine XIAP levels by Western blot.(E) Quantification of the degradation rate of XIAP over time (Treatment: F(1,4) = 10.14, p < 0.05, repeated measure ANOVA).(F) Morphology of primary neurons transfected with USP7 or XIAP alone, or both. Scale bar = 100 μm.(G and H) Dendrite branch number and the total length of dendrite were increased in neurons overexpressing USP7 or XIAP. Co-transfection of USP7 and XIAP had no additional effects compared with USP7 alone or XIAP only group (Ctrl: n = 35; USP7: n = 25; XIAP: n = 34; XIAP + USP7: n = 31. Number of dendrites: F(3,121) = 13.83, p < 0.01, one-way ANOVA, Tukey; Sum dendrite length: F(3,121) = 8.82, p < 0.01. one-way ANOVA, Tukey). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr4.jpg
0.427316
acf56231a8a4473a92e2912654d842d8
Knockdown of XIAP blocks the effect of USP7 on dendritic arborization(A) Cultured neurons were transfected with shXIAP at DIV 7 and immunostained for XIAP at DIV 11. Scale bar = 50 μm.(B) Quantification of XIAP expression (Ctrl: n = 36; shXIAP: n = 36. p< 0.01, t-test).(C) Morphology of primary neurons transfected with USP7 or shXIAP alone, or both at DIV11. Scale bar = 100 μm.(D and E) Dendrite branch number and the total length of dendrite were decreased in XIAP knockdown neurons. Co-transfection of USP7 and shXIAP had no additional effects compared with shXIAP alone group, but decreased significantly compared with USP7 only group (Ctrl: n = 35; USP7: n = 46; shXIAP: n = 46; USP7+shXIAP: n = 35. Number of dendrites: F(3,148) = 10.69, p < 0.01, one-way ANOVA, Tukey; Sum dendrite length: F(3,148) = 10.01, p < 0.01. one-way ANOVA, Tukey).(F) Sholl analysis of dendritic arborization at DIV 11 (Group: F (3, 154) = 11.23, p < 0.01. Ctrl vs. shXIAP: p < 0.01; Ctrl vs. USP7: p > 0.05; USP7+shXIAP vs. USP7: p < 0.01; USP7+shXIAP vs. shXIAP: p > 0.05. Repeated measures ANOVA, Tukey). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr5.jpg
0.449227
0849dceeba8d46a18ecd547eb9464458
USP7 antagonizes E6AP effect on dendritic arborization via control of XIAP ubiquitination(A) HEK293 cells were transfected with FLAG-XIAP, HA-ubiquitin, and USP7 with or without E6AP for 2 d. XIAP was immunoprecipitated and probed for HA-ubiquitin (HA-ubi). Cell lysates (input) were also probed to detect the total protein levels.(B and C) Quantification of western blot intensities. E6AP caused an increase in XIAP ubiquitination (F(3,12) = 19.62, p < 0.01, one-way ANOVA, Tukey) and a decrease in XIAP protein levels in the input (F(3,8) = 43.69, p < 0.01, one-way ANOVA, Tukey). USP7 blocked the effect of E6AP on XIAP protein accumulation and XIAP ubiquitination.(D) Morphology of primary neurons transfected with USP7, E6AP, and USP7+E6AP (DIV 11 - DIV 15). Scale bar = 100 μm.(E and F) Dendritic branch number (F(3,81) = 17.28, p < 0.01, one-way ANOVA, Tukey) and the total length of dendrites (F(3,81) = 17.92, p < 0.01, one-way ANOVA, Tukey) were decreased in neurons with E6AP overexpression (E6AP: n = 19; Ctrl: n = 20. one-way ANOVA, Tukey). USP7 abolished the effect caused by E6AP expression (E6AP + USP7: n = 21; E6AP: n = 19. one-way ANOVA, Tukey).(G) Sholl analysis showed a reduction in the complexity of dendritic arborization in E6AP neurons, which was blocked by co-expression with USP7 in neurons (Group: F(3,77) = 16.833, p < 0.01. Repeated measures ANOVA, Tukey). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr6.jpg
0.44352
f38cec0d89a34432b8ec63e92e7d5c7e
Caspase-3 and microtubules are the downstream effectors mediating the USP7 effect on dendritic arborization(A) Primary hippocampal neurons were transfected with USP7 and immunostained for the cleaved caspase 3. Arrows indicate the transfected neurons. Scale bar = 50 μm.(B) Quantification showed a decrease in cleaved caspase-3 intensity in USP7 overexpressing neurons (Ctrl: n = 15; USP7: n = 19, t-test).(C) HEK cells were transfected with USP7 and shUSP7. Cell lysates were collected to determine the cleaved caspase-3 levels by Westerns.(D) Quantification of Western blot intensities of cleaved caspase-3 (F(2,6) = 16.56, p < 0.01, one-way ANOVA, Tukey).(E) Primary neurons were infected with AAV-USP7 at DIV 0, and neuron lysates were collected for western blot to detect changes in microtubule cleavage.(F) Quantification showed a significant decrease in cleaved microtubules in neurons with USP7 virus infection (Ctrl: n = 3; USP7: n = 3, t-test).(G) Primary neurons were infected with AAV-USP7 at DIV 0 and immunostained at DIV 15 with TubΔCasp6 antibodies. Scale bar = 50 μm.(H and I) Quantification showed that USP7-infected neurons had a decrease in microtubule cleavage intensity (Ctrl: n = 15; USP7: n = 18, t-test), but not in the number of cleavage sites along the dendrite (Ctrl: n = 20; USP7: n = 18, t-test). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr7.jpg
0.394564
b4b79430ff904674887151f5866069a9
USP7 overexpression in the brain affects neuron migration and dendritic arborization(A) Schematic illustration of the procedures for in utero electroporation (IUE) performed at E15 and P0, P15.(B) Brain slices taken at P0 following IUE of DsRed control (Ctrl) or GFP-USP7 at E15. Scale bar = 200 μm.(C) Analysis of neuronal migration at P0 showed that less neurons were distributed in the upCP and more in the loCP and VZ regions compared with controls (Ctrl: n = 12; USP7: n = 14. t-test). More than 1200 GFP+ neurons from four brains were analyzed in each group. 15 slices from five brains were analyzed in each group, and more than 3000 GFP+ neurons were analyzed totally.(D) Representative images showing dendritic arborizations of control and USP7 groups. Scale bar = 50 μm.(E) Sholl analysis of dendritic structure at P15 after IUE showed a significant change in branching (Group: F(1, 48) = 17.06, p < 0.01, Repeated measures ANOVA. Ctrl: n = 27; USP7: n = 22).(F and G) Dendrite numbers and the total length of dendrites were increased in the USP7 overexpressing group compared with the control (Ctrl: n = 27; USP7: n = 22. t-test). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr8.jpg
0.460239
31020cb0e449430d99843aff32dcac5e
USP7 overexpression in vivo in mouse brain at P0 leads to dendrite morphological changes(A) Schematic illustration of the procedures for virus injection at P0 and schedule for behavior tests performed at P30-P55. AAV-USP7 and AAV-GFP were injected into the lateral ventricles in mice at P0, and the mice were perfused around P30 to P60 for cryostat to show the validity of the virus. The expression of GFP (B) or GFP-fused USP7 (left: Scale bar = 1000 μm; right: Scale bar = 200 μm) (C) can be detected in the whole brain around P30 to P60 ( left: Scale bar = 500 μm; right: Scale bar = 100 μm).(D) Western blot showed that the expression of USP7 in the cortex of the AAV USP7 group is significantly higher than in the control group, as well as XIAP.(E–I) Sholl analysis shows the morphological changes. Scale bar = 50 μm. 19 cortical neurons from 5 control mice and 27 neurons from 5 AAV USP7 mice were analyzed. The number of dendrites and the mean and total length of dendrites were all increased significantly in the AAV USP7 group (F, Number of dendrites: Ctrl: n = 19, USP7: n = 27, p < 0.01, t-test; G,Sum length: Ctrl: n = 19, USP7: n = 27, p < 0.01, t-test; H, Mean length: Ctrl: n = 19, USP7: n = 27, p < 0.01. t-test). I, The dendritic arborization was more complex in the AAV USP7 group compared with the control group (Group: F(1, 44) = 37.91, p < 0.01, Repeated measures ANOVA). Data are represented as mean ± SEM. Error bars represent SEM, ∗p < 0.05, ∗∗p < 0.01.
PMC9253496
gr9.jpg
0.545477
447b61ccac734204bd02ba4c5edfe5c2
Characteristics of 125 patients with late-onset Blount’s disease by race.
PMC9254026
10.1177_18632521221091501-fig1.jpg
0.439284
574450b066644ee2baaaf20c7f605dc8
Social perception computing framework.
PMC9256363
CIN2022-8700833.001.jpg
0.479851
e05dac2dd9404526b616d0f9f4a4a592
BP neural network model.
PMC9256363
CIN2022-8700833.002.jpg
0.437097
de35ee1b7fe14aeaacbcda0fff1eb002
Neural network signal adjustment flow chart.
PMC9256363
CIN2022-8700833.003.jpg
0.639591
2c571e908c9843eb8eba81ec92306c4a
Three-dimensional model of innovation service platform.
PMC9256363
CIN2022-8700833.004.jpg
0.435807
b8dc88566294405e875bf83e5b0013d8
Content and service capability of innovation service platform for small and medium-sized enterprises.
PMC9256363
CIN2022-8700833.005.jpg
0.517606
958ef2821d9c4b519f1a5559cdfddd21
Comprehensive evaluation results of innovation service platform for small and medium-sized enterprises.
PMC9256363
CIN2022-8700833.006.jpg
0.428956
ed43a43743814933af6d2c1e2b9aa80d
(A) Action mode of caging PROTACs. (B) Uncaging reaction of caging degrader 1. (C) Degradation of BRD4-EGFP fusion protein through 1 without light irradiation in zebrafish embryos (Adapted with permission from (Xue et al., 2019). Copyright (2019) American Chemical Society). (D) Degradation of BRD4-EGFP fusion protein through 1 with light irradiation in zebrafish embryos (Adapted with permission from (Xue et al., 2019). Copyright (2019) American Chemical Society.).
PMC9257139
fcell-10-921958-g001.jpg
0.460804
26cad83f4bbe443f81c11426a4d48b9c
Chemical structure of caging PROTACs.
PMC9257139
fcell-10-921958-g002.jpg
0.428535
bbb1b94b132148a18daff5fc33e66afb
Two action modes of photoswitching PROTAC strategy.
PMC9257139
fcell-10-921958-g003.jpg
0.623666
577a16d042b94b82b9d559a5d3b1dcd6
(A) Reversible reaction of 6 upon visible light or UV irradiation. (B) and (C) The time-course Western blot assays of trans and cis- 6 at 250 nM, respectively (Adapted with permission from (Jin et al., 2020). Copyright (2020) American Chemical Society). (D) Chemical structure of photoswitching PROTACs.
PMC9257139
fcell-10-921958-g004.jpg
0.46245
a6642a429e93406bbe9ae30930d3b6dc
(A) Structure of antibody-PROTAC Conjugates. (B) Structure of aptamer-PROTAC Conjugates. (C) Structure of folate-PROTAC Conjugates.
PMC9257139
fcell-10-921958-g005.jpg
0.407022
b2fbd7e81a0440f1a3c6bbe8890cc5d4
Chemical structures of irreversible covalent, noncovalent, and reversible covalent PROTACs.
PMC9257139
fcell-10-921958-g006.jpg
0.472802
30585aa23b4a47fd8cbdafb24b0539a6
Chemical structure of novel E3 ligase ligand for covalent PROTACs.
PMC9257139
fcell-10-921958-g007.jpg
0.443129
ffd37a7e7ff348a1b5cb7789fb4fd02a
Chemical structure of trivalent PROTACs.
PMC9257139
fcell-10-921958-g008.jpg
0.460669
e3df36facd304933b79f9d59ee7dd8aa
(A) The action mode and structure of RNA-PROTACs. (B) Structure of TF-PROTACs. (C) Structure of oligonucleotide-based PROTACs (O’PROTACs).
PMC9257139
fcell-10-921958-g009.jpg
0.430306
2e4ac9bae49c419f88d595c510cc2f46
(A) Action mode of LYTAC. (B) Action mode of N-acetylgalactosamine (GalNAc)-LYTAC. (C) Chemical structure of molecular degrader of extracellular proteins through the Asialoglycoprotein receptor (MoDE-A). (D) Action mode of antibody-based PROTAC (AbTAC).
PMC9257139
fcell-10-921958-g010.jpg
0.40119
ddee988059ad4b7488eefce156984a5c
(A) Action mode and chemical structure of autophagy-targeting chimeras (AUTACs). (B) Action mode and chemical structure of autophagosome-tethering compound (ATTEC).
PMC9257139
fcell-10-921958-g011.jpg
0.427204
289f7195195c4e8dbfdb2889dcf20233
(A) Chemical structure of RIBOTACs. (B) Action mode of RIBOTACs. (C) Chemical structure of RIBOTACs and NATACs.
PMC9257139
fcell-10-921958-g012.jpg
0.410984
0d9664225ac9429b9803bd93f0615418
Model testing results.
PMC9257178
fpsyg-13-918734-g001.jpg
0.423811
e24c6db338d146cb885b4792da13e3a5
Ultrasound image of the paravertebral block. Tm: Trapezius muscle; Rm: Rhomboideus muscle; ESm: Erector spinal muscle; TP: Transverse process; SCTL: Superior costotransverse ligament; LA: Local anesthesia agency; P: Pleura.
PMC9258351
WJCC-10-5741-g001.jpg