Mean looking times.

<p>An asterisk denotes a statistically significant difference between the test trials. Error bars indicate standard errors; F3 is the last familiarization trial.</p

Supplementary document for Mirrored Transformation Optics - 6810729.pdf

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Additional file 1 of KDELR2-KIF20A axis facilitates bladder cancer growth and metastasis by enhancing Golgi-mediated secretion

Additional file 1: Figure S1. KDELR2 has a prognostic and diagnostic value in BCa. A-B Receiver operating characteristic (ROC) curves of KDELR2 in the GES3167 (normal, n = 19; tumor, n = 41) and TCGA-BLCA datasets (normal, n = 19; tumor, n = 408). (C) Kaplan–Meier curves of KDELR2 expression in patients with BCa in the GSE32894 dataset (high, n = 112; low, n = 112). (D) Multivariate analysis of KDELR2 mRNA level and DFS in patients with BCa. E ROC curves of KDELR2 in clinical samples (normal, n = 24; tumor, n = 24). F Detection of KDELR2 expression by qRT-PCR analysis in cell lines (n = 4). p < 0.001, ***; p <0.0001, ****

Table_1_Uncovering the biogeographic pattern of the widespread nematode-trapping fungi Arthrobotrys oligospora: watershed is the key.XLSX

Studies of biogeographic patterns of fungi have long been behind those of plants and animals. The presence of worldwide species, the lack of systematic sampling design and adequate sampling effort, and the lack of research units are responsible for this status. This study investigates the biogeographical patterns of Arthrobotrys oligospora, the most widespread globally distributed nematode-trapping fungi (NTF), by stratified collecting and analyzing 2,250 samples from 228 sites in Yunnan Province, China. The A. oligospora was isolated, and 149 strains were subjected to ITS, TUB, TEF and RPB2 gene sequencing and multi-gene association phylogeographic analysis. The results show that at population level A. oligospora is randomly distributed throughout Yunnan Province and has no biogeographical distribution pattern. At the genetic level, the phylogenetic tree of A. oligospora diverges into five major evolutionary clades, with a low degree of gene flow between the five clades. However, the correlation between the phylogenetic diversity of A. oligospora and geographical factors was low. There was no clear pattern in the phylogenetic clades distribution of A. oligospora either without dividing the study unit or when the grid was used as the study unit. When watersheds were used as the study unit, 67.4%, 63.3%, 65.9%, 83.3%, and 66.7% of clade 1–5 strains were distributed in the Jinsha river, Red river, Peal river, Lancang river, and Nujiang-Irawaddy river watersheds, respectively. The clades distribution of A. oligospora was highly consistent with the watersheds distribution. Training predictions of the clades distributions using randomly generated polygons were also less accurate than watersheds. These results suggest that watersheds are key to discovering the biogeographic distribution patterns of A. oligospora. The A. oligospora populations are blocked by mountains in the watershed, and gene flow barriers have occurred, which may have resulted in the formation of multiple cryptic species. Watersheds are also ideal for understanding such speciation processes, explaining factors affecting biodiversity distribution and coupling studies of plant and animal and microbial diversity.</p

Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening

Virtual screening (VS) can be accomplished in either ligand- or structure-based methods. In recent times, an increasing number of 2D fingerprint and 3D shape similarity methods have been used in ligand-based VS. To evaluate the performance of these ligand-based methods, retrospective VS was performed on a tailored directory of useful decoys (DUD). The VS performances of 14 2D fingerprints and four 3D shape similarity methods were compared. The results revealed that 2D fingerprints ECFP_2 and FCFP_4 yielded better performance than the 3D Phase Shape methods. These ligand-based methods were also compared with structure-based methods, such as Glide docking and Prime molecular mechanics generalized Born surface area rescoring, which demonstrated that both 2D fingerprint and 3D shape similarity methods could yield higher enrichment during early retrieval of active compounds. The results demonstrated the superiority of ligand-based methods over the docking-based screening in terms of both speed and hit enrichment. Therefore, considering ligand-based methods first in any VS workflow would be a wise option

Table_2_Uncovering the biogeographic pattern of the widespread nematode-trapping fungi Arthrobotrys oligospora: watershed is the key.XLSX

Studies of biogeographic patterns of fungi have long been behind those of plants and animals. The presence of worldwide species, the lack of systematic sampling design and adequate sampling effort, and the lack of research units are responsible for this status. This study investigates the biogeographical patterns of Arthrobotrys oligospora, the most widespread globally distributed nematode-trapping fungi (NTF), by stratified collecting and analyzing 2,250 samples from 228 sites in Yunnan Province, China. The A. oligospora was isolated, and 149 strains were subjected to ITS, TUB, TEF and RPB2 gene sequencing and multi-gene association phylogeographic analysis. The results show that at population level A. oligospora is randomly distributed throughout Yunnan Province and has no biogeographical distribution pattern. At the genetic level, the phylogenetic tree of A. oligospora diverges into five major evolutionary clades, with a low degree of gene flow between the five clades. However, the correlation between the phylogenetic diversity of A. oligospora and geographical factors was low. There was no clear pattern in the phylogenetic clades distribution of A. oligospora either without dividing the study unit or when the grid was used as the study unit. When watersheds were used as the study unit, 67.4%, 63.3%, 65.9%, 83.3%, and 66.7% of clade 1–5 strains were distributed in the Jinsha river, Red river, Peal river, Lancang river, and Nujiang-Irawaddy river watersheds, respectively. The clades distribution of A. oligospora was highly consistent with the watersheds distribution. Training predictions of the clades distributions using randomly generated polygons were also less accurate than watersheds. These results suggest that watersheds are key to discovering the biogeographic distribution patterns of A. oligospora. The A. oligospora populations are blocked by mountains in the watershed, and gene flow barriers have occurred, which may have resulted in the formation of multiple cryptic species. Watersheds are also ideal for understanding such speciation processes, explaining factors affecting biodiversity distribution and coupling studies of plant and animal and microbial diversity.</p

FISH detection of miR-31* expression in OLK and mtOLK.

<p>(<b>A</b>) ∼ (<b>C</b>), no positive signal is detected in OLK. (<b>D</b>) ∼ (<b>L</b>), the representative positive signals are showed in mtOLK. (<b>D</b>) ∼ (<b>F</b>), tumor nest; (<b>G</b>) ∼ (<b>I</b>), vascular area; (<b>J</b>) ∼ (<b>L</b>), inflammation. FISH signals are visualized in green, while blue depicts nuclear DAPI stain. OLK, oral leukoplakia; mtOLK, malignant transformed oral leukoplakia.</p

Representative results of miR-31* effects on biological functions.

<p>(<b>A</b>) the MTT assay in HIOEC; (<b>B</b>) the Annexin V assay in Leuk-1; (<b>C</b>) flow cytometry analysis for cell cycle in Cal-27; (<b>D</b>) representative field of view of HIOEC invasion inserts at a 100× magnification, (Da) miR-31* mimic, (Db) miR-31* inhibitor, (Dc) negative control, (Dd) Quantification of relative numbers of invading cells representing average counts from 6 fields-of-view per insert per sample ±SD, **p<0.05, ***p<0.001; (<b>E</b>) representative field of view of HIOEC migration inserts at a 100× magnification, (Ea) miR-31* mimic, (Eb) miR-31* inhibitor, (Ec) negative control, (Ed) quantification of relative numbers of invading cells representing average counts from 6 fields-of-view per insert per sample ±SD, **p<0.05, ***p<0.001.</p

Clinical outcomes in OLK and mtOLK.

<p>OLK, oral leukoplakia; mtOLK, malignant transformed oral leukoplakia; ND, no dysplasia; MiD, mild dysplasia; MoD, moderate dysplasia; SD, severe dysplasia; SCC, squamous cell carcinoma; NA, not available.</p

miR-31* mimics/inhibitors regulating mRNA and protein expression of FGF3 in oral cells.

<p>(<b>A</b>) QRT-PCR analysis of FGF3 expression in Leuk-1, HIOEC and Cal-27 cell lines, **p<0.05; (<b>B</b>) Western blot analysis of of FGF3 expression in Leuk-1, HIOEC and Cal-27 cell lines transfected with miR-31* mimic, miR-31* inhibitor and negative control. The representative blot is shown (upper for FGF3). The histogram shows the average volume density normalized by the loading control, GAPDH (lower).</p