Journal: Microbiology Spectrum

Article Title: Performance and practicality of 16S nanopore sequencing for routine bacterial identification in clinical samples

doi: 10.1128/spectrum.00623-26

Figure Lengend Snippet: Overview of the laboratory and bioinformatic workflows. ( A ) Investigated were dilution series of pure liquid cultures of E. coli and S. aureus , as well as over 100 clinical samples from routine diagnostics. The DNA was extracted, and the 16S rRNA was amplified with the Molzym Micro-Dx kit. The resulting amplicons were sequenced with both ONT and Illumina MiSeq. ( B ) All raw sequencing data were quality- and length-filtered. Illumina reads were additionally subsampled to 9,000 reads before further processing. The DADA2 tool was used to generate amplicon sequence variants (ASVs) from the Illumina reads, and the LORCAN pipeline was used for the ONT reads. The taxonomy of the consensus sequences was determined using BLAST. For further analysis, only species associated with more than 100 reads were kept. The figure was created with BioRender ( https://BioRender.com) .

Article Snippet: The commercial Micro-Dx kit (Molzym, Bremen, Germany) was used for automated microbial DNA enrichment, host depletion, microbial DNA extraction, and real-time 16S PCR ( ).

Techniques: Amplification, Sequencing

Journal: International Journal of Neuropsychopharmacology

Article Title: Activation of Extracellular Signal-Regulated Kinases (ERK 1/2) in the Locus Coeruleus Contributes to Pain-Related Anxiety in Arthritic Male Rats

doi: 10.1093/ijnp/pyx005

Figure Lengend Snippet: Phosphorylated extracellular signal-regulated kinase 1/2 (pERK1/2) and tyrosine hydroxylase (TH) levels in the Locus Coeruleus (LC) of control and 1- and 4 -week MA rats (MA1W and MA4W). (A) There were significantly more TH immunoreactive ( IR ) cells in the caudal and total LC of MA4W rats: 2-way ANOVA and Bonferroni posthoc, control vs MA4W for each side (n=5 – 7). (B) The pERK1/2 mean gray values were significant ly higher in the entire rostro-caudal extension of the LC: 2-way ANOVA and Bonferroni posthoc control vs MA1W/MA4W for each side (n=5 – 7). (C) Representative photomicrographs showing TH and detailing the immunolabeling in the amplified inset . Scale bar =100 µm. (D) The increase in TH expression in MA4W rats was also observed in western blots. (Da) Representative regio ns of the immunoblots showing the bands for TH and Tubulin proteins. (E) Representative photomicrographs showing pERK1/2 in the cau dal and rostral dom a ins. Scale bar =100 µm. (F) Photomicrographs showing the pERK1/2 immunolabeling i n TH positive neurons in the LC. Scale bar = 50 µ m. AU, ar bitrary units; C, contralateral; I, ipsilateral. * P <.05, ** P <.01, and *** P <.001.

Article Snippet: Transverse sections of the LC region were washed, blocked , and then incubated with antibodies against tyrosine hydroxylase (TH, raised in sheep, 1:2000; 48 hours, Abcam), the phosphorylated ERK1/2 isoforms (raised in rabbit, pERK1/2, 1:500, 48 hours; Acris Antibodies, Herford, Germany), or both to confirm the nature and localization of pERK1/2 positive cells in the LC, as described elsewhere ( ).

Techniques: Control, Immunolabeling, Amplification, Expressing, Western Blot

Journal: Medicine

Article Title: Prognostic significance of tumor-associated macrophages in patients with nasopharyngeal carcinoma

doi: 10.1097/md.0000000000021999

Figure Lengend Snippet: Figure 2. Forest plots showing hazard ratios (HRs) and 95% CIs for (A) density of CD68+ TAMs in IT and OS; (B) density of CD68+ TAMs in IT and DFS; (C) density of CD163+ M2-like TAMs in IT and OS; and (D) density of CD163+ M2-like TAMs in IT and DFS. CI=confidence interval; DFS=disease-free survival; IT=intratumor; OS=overall survival; TAMs=tumor-associated macrophages.

Article Snippet: Author Year Country Sample size Sex (M/F) Study duration Age mean (range) Detection method Marker Antibody He 1999 China 43 33/10 1985–1990 46.8 (22–71) IHC CD68 (+) Zhongshan Bio-tech Co Ltd, China Cai 2016 China 557 418/139 2001–2003 46 (19–78) IHC CD68 (+) NR Huang (a) 2017 China 580 446/134 2009–2011 45 (24–77) IHC CD68 (+) CD68 (+)CCL18 (+) CD68: Cat No. sc7083 Santa Cruz, USA CCL18: Cat No. MAB394 R&D Systems, USA Huang (b) 2017 China 110 87/23 2008–2012 NR IHC CD163 (+) CD163: Mouse, Abcam, USA Xia 2017 China 107 NR 2009–2010 24–77 IHC CD163 (+) CD206 (+) CD163: Mouse, Zhongshan Golden Bridge, Beijing, China CD206: Mouse, Abcam, USA Yu 2018 China 152 121/31 1999–2000 48 (18–71) IHC CD68 (+) CD163 (+) CD68: Boster, Wuhan, China CD163: Zhongshan Golden Bridge, China Stage Treatment Tissue detection Cut-off value Follow-up (month) Study design Survival analysis NOS score III CCRT IT >10 cells/field (200X) 60–120 Retrospective OS 6 I–IV Mixed IT, TS ROC curve 2–114 Retrospective OS, DFS 7 I–IV Mixed IT >22 cells/field (400 ) 43 (8–58) Retrospective OS, DFS 7 I–IV Mixed IT, TS Median value 53 (10–86) Retrospective OS, DFS 8 I–II Surgery IT >20 cells/field (400 ) To Dec 2015 Retrospective OS, DFS 7 I–IV RT IT >Score 2 130 (5–144) Retrospective OS, DFS 7 CCRT= concurrent chemoradiothrapy; DFS=disease-free survival; F= female; IHC= immunohistochemistry; IT= intratumor; M=male; NOS=Newcastle-Ottawa Scale; NR=not reported; OS= overall survival; RT= radiotherapy; TS= tumor stroma.

Techniques:

Journal: Medicine

Article Title: Prognostic significance of tumor-associated macrophages in patients with nasopharyngeal carcinoma

doi: 10.1097/md.0000000000021999

Figure Lengend Snippet: Figure 3. Sensitivity analysis for the (A) density of CD68+ TAMs in IT and OS; (B) density of CD68+ TAMs in IT and DFS; (C) density of CD163+ M2-like TAMs in IT and OS; and (D) density of CD163+ M2-like TAMs in IT and DFS. CI=confidence interval; DFS=disease-free survival; IT=intratumor; OS=overall survival; TAMs= tumor-associated macrophages.

Article Snippet: Author Year Country Sample size Sex (M/F) Study duration Age mean (range) Detection method Marker Antibody He 1999 China 43 33/10 1985–1990 46.8 (22–71) IHC CD68 (+) Zhongshan Bio-tech Co Ltd, China Cai 2016 China 557 418/139 2001–2003 46 (19–78) IHC CD68 (+) NR Huang (a) 2017 China 580 446/134 2009–2011 45 (24–77) IHC CD68 (+) CD68 (+)CCL18 (+) CD68: Cat No. sc7083 Santa Cruz, USA CCL18: Cat No. MAB394 R&D Systems, USA Huang (b) 2017 China 110 87/23 2008–2012 NR IHC CD163 (+) CD163: Mouse, Abcam, USA Xia 2017 China 107 NR 2009–2010 24–77 IHC CD163 (+) CD206 (+) CD163: Mouse, Zhongshan Golden Bridge, Beijing, China CD206: Mouse, Abcam, USA Yu 2018 China 152 121/31 1999–2000 48 (18–71) IHC CD68 (+) CD163 (+) CD68: Boster, Wuhan, China CD163: Zhongshan Golden Bridge, China Stage Treatment Tissue detection Cut-off value Follow-up (month) Study design Survival analysis NOS score III CCRT IT >10 cells/field (200X) 60–120 Retrospective OS 6 I–IV Mixed IT, TS ROC curve 2–114 Retrospective OS, DFS 7 I–IV Mixed IT >22 cells/field (400 ) 43 (8–58) Retrospective OS, DFS 7 I–IV Mixed IT, TS Median value 53 (10–86) Retrospective OS, DFS 8 I–II Surgery IT >20 cells/field (400 ) To Dec 2015 Retrospective OS, DFS 7 I–IV RT IT >Score 2 130 (5–144) Retrospective OS, DFS 7 CCRT= concurrent chemoradiothrapy; DFS=disease-free survival; F= female; IHC= immunohistochemistry; IT= intratumor; M=male; NOS=Newcastle-Ottawa Scale; NR=not reported; OS= overall survival; RT= radiotherapy; TS= tumor stroma.

Techniques:

Journal: Medicine

Article Title: Prognostic significance of tumor-associated macrophages in patients with nasopharyngeal carcinoma

doi: 10.1097/md.0000000000021999

Figure Lengend Snippet: Figure 4. Publication bias examined by Begg plot test for (A) density of CD68+ TAMs in IT and OS (P=.734); (B) density of CD68+ TAMs in IT and DFS (P=1); (C) density of CD163+ M2-like TAMs in IT and OS (P=.602); and density of CD163+ M2-like TAMs in IT and DFS (P=1). CI=confidence interval; DFS=disease-free survival; IT=intratumor; OS=overall survival; TAMs=tumor-associated macrophages.

Article Snippet: Author Year Country Sample size Sex (M/F) Study duration Age mean (range) Detection method Marker Antibody He 1999 China 43 33/10 1985–1990 46.8 (22–71) IHC CD68 (+) Zhongshan Bio-tech Co Ltd, China Cai 2016 China 557 418/139 2001–2003 46 (19–78) IHC CD68 (+) NR Huang (a) 2017 China 580 446/134 2009–2011 45 (24–77) IHC CD68 (+) CD68 (+)CCL18 (+) CD68: Cat No. sc7083 Santa Cruz, USA CCL18: Cat No. MAB394 R&D Systems, USA Huang (b) 2017 China 110 87/23 2008–2012 NR IHC CD163 (+) CD163: Mouse, Abcam, USA Xia 2017 China 107 NR 2009–2010 24–77 IHC CD163 (+) CD206 (+) CD163: Mouse, Zhongshan Golden Bridge, Beijing, China CD206: Mouse, Abcam, USA Yu 2018 China 152 121/31 1999–2000 48 (18–71) IHC CD68 (+) CD163 (+) CD68: Boster, Wuhan, China CD163: Zhongshan Golden Bridge, China Stage Treatment Tissue detection Cut-off value Follow-up (month) Study design Survival analysis NOS score III CCRT IT >10 cells/field (200X) 60–120 Retrospective OS 6 I–IV Mixed IT, TS ROC curve 2–114 Retrospective OS, DFS 7 I–IV Mixed IT >22 cells/field (400 ) 43 (8–58) Retrospective OS, DFS 7 I–IV Mixed IT, TS Median value 53 (10–86) Retrospective OS, DFS 8 I–II Surgery IT >20 cells/field (400 ) To Dec 2015 Retrospective OS, DFS 7 I–IV RT IT >Score 2 130 (5–144) Retrospective OS, DFS 7 CCRT= concurrent chemoradiothrapy; DFS=disease-free survival; F= female; IHC= immunohistochemistry; IT= intratumor; M=male; NOS=Newcastle-Ottawa Scale; NR=not reported; OS= overall survival; RT= radiotherapy; TS= tumor stroma.

Techniques: