DnaA is a conserved key regulator of replication initiation in bacteria, and is homologous to ORC proteins in archaea and in eukaryotic cells. The ATPase binds to several high affinity binding sites ...at the origin region and upon an unknown molecular trigger, spreads to several adjacent sites, inducing the formation of a helical super structure leading to initiation of replication. Using FRAP analysis of a functional YFP-DnaA allele in Bacillus subtilis, we show that DnaA is bound to oriC with a half-time of 2.5 seconds. DnaA shows similarly high turnover at the replication machinery, where DnaA is bound to DNA polymerase via YabA. The absence of YabA increases the half time binding of DnaA at oriC, showing that YabA plays a dual role in the regulation of DnaA, as a tether at the replication forks, and as a chaser at origin regions. Likewise, a deletion of soj (encoding a ParA protein) leads to an increase in residence time and to overinitiation, while a mutation in DnaA that leads to lowered initiation frequency, due to a reduced ATPase activity, shows a decreased residence time on binding sites. Finally, our single molecule tracking experiments show that DnaA rapidly moves between chromosomal binding sites, and does not arrest for more than few hundreds of milliseconds. In Escherichia coli, DnaA also shows low residence times in the range of 200 ms and oscillates between spatially opposite chromosome regions in a time frame of one to two seconds, independently of ongoing transcription. Thus, DnaA shows extremely rapid binding turnover on the chromosome including oriC regions in two bacterial species, which is influenced by Soj and YabA proteins in B. subtilis, and is crucial for balanced initiation control, likely preventing fatal premature multimerization and strand opening of DnaA at oriC.
•Extensive integration of widely different spatial scales, as a “mimicry” of how humans approach analogous tasks, boosts the performance of a standard fully convolutional neural network in cancer ...segmentation in histopathology images, as shown on three different publicly available datasets.•A family of U-Net-based architectures as human operator-inspired multi-scale multi-encoder networks is proposed. The approach can be easily adopted to any encoder-decoder segmentation architecture and extended to multiple path fusions.•By use of an additional classification loss, additional encoders for largely different spatial scales as the target scale can be trained in a memory-efficient fashion and with moderate additional cost.
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Histopathologic diagnosis relies on simultaneous integration of information from a broad range of scales, ranging from nuclear aberrations (≈O(0.1μm)) through cellular structures (≈O(10μm)) to the global tissue architecture (⪆O(1mm)).
To explicitly mimic how human pathologists combine multi-scale information, we introduce a family of multi-encoder fully-convolutional neural networks with deep fusion. We present a simple block for merging model paths with differing spatial scales in a spatial relationship-preserving fashion, which can readily be included in standard encoder-decoder networks. Additionally, a context classification gate block is proposed as an alternative for the incorporation of global context.
Our experiments were performed on three publicly available whole-slide images of recent challenges (PAIP 2019: hepatocellular carcinoma segmentation; BACH 2020: breast cancer segmentation; CAMELYON 2016: metastasis detection in lymph nodes). The multi-scale architectures consistently outperformed the baseline single-scale U-Nets by a large margin. They benefit from local as well as global context and particularly a combination of both. If feature maps from different scales are fused, doing so in a manner preserving spatial relationships was found to be beneficial. Deep guidance by a context classification loss appeared to improve model training at low computational costs. All multi-scale models had a reduced GPU memory footprint compared to ensembles of individual U-Nets trained on different image scales. Additional path fusions were shown to be possible at low computational cost, opening up possibilities for further, systematic and task-specific architecture optimisation.
The findings demonstrate the potential of the presented family of human-inspired, end-to-end trainable, multi-scale multi-encoder fully-convolutional neural networks to improve deep histopathologic diagnosis by extensive integration of largely different spatial scales.
Biological membranes have been proposed to contain microdomains of a specific lipid composition, in which distinct groups of proteins are clustered. Flotillin-like proteins are conserved between ...pro-and eukaryotes, play an important function in several eukaryotic and bacterial cells, and define in vertebrates a type of so-called detergent-resistant microdomains. Using STED microscopy, we show that two bacterial flotillins, FloA and FloT, form defined assemblies with an average diameter of 85 to 110 nm in the model bacterium Bacillus subtilis. Interestingly, flotillin microdomains are of similar size in eukaryotic cells. The soluble domains of FloA form higher order oligomers of up to several hundred kDa in vitro, showing that like eukaryotic flotillins, bacterial assemblies are based in part on their ability to self-oligomerize. However, B. subtilis paralogs show significantly different diffusion rates, and consequently do not colocalize into a common microdomain. Dual colour time lapse experiments of flotillins together with other detergent-resistant proteins in bacteria show that proteins colocalize for no longer than a few hundred milliseconds, and do not move together. Our data reveal that the bacterial membrane contains defined-sized protein domains rather than functional microdomains dependent on flotillins. Based on their distinct dynamics, FloA and FloT confer spatially distinguishable activities, but do not serve as molecular scaffolds.
BACKGROUND： Peroral cholangioscopy facilitates diagnosis and therapy of biliary disorders. This study prospectively evaluated a new short access cholangioscopy. METHODS： Consecutive patients were ...included as follows： difficult stones （group 1） underwent cholangioscopy with electrohydraulic lithotripsy and indeterminate biliary strictures （group 2） were evaluated with macroscopic assessment and cholangioscopy guided biopsy sampling. We evaluated the complete stone clearance rate （group 1） and diagnostic accu- racy （group 2）. Follow-up was performed over a median of 13 and I6 months, respectively. RESULTS： Group 1 （n=21）： complete stone clearance defined as lack of stones in cholangiography and stone removal dur- ing cholangioscopy was achieved in 15 （71.4%） patients. Clini- cal stone clearance defined as lack of symptoms, laboratory abnormalities and hospital visits during follow-up, irrespec- tive of stone clearance was evident in 17 （81.0%） patients. One serious adverse event occurred （bile duct perforation）. Group 2 （n=28）： malignancy was confirmed in 15 patients. Sensitiv- ity, specificity and diagnostic accuracy of cholangioscopy were 85.7%, 75.0% and 80.7%, respectively. Sensitivity, specificity and diagnostic accuracy of biopsies were 54.5%, 100.0% and 72.2%, respectively. No serious adverse events occurred, and one patient was lost to follow-up.CONCLUSIONS： The novel system enabled complex stone treatment and biliary stricture diagnosis. Cholangioscopy outperformed direct biopsy regarding characterization of in- determinate strictures.
Endoscopic balloon dilatation and laparoscopic myotomy are established treatments for achalasia. Recently, a new endoscopic technique for complete myotomy was described. Herein, we report the results ...of the first prospective trial of peroral endoscopic myotomy (POEM) in Europe.
POEM was performed under general anesthesia in 16 patients (male:female (12:4), mean age 45 years, range 26-76). The primary outcome was symptom relief at 3 months, defined as an Eckhard score ≤3. Secondary outcomes were procedure-related adverse events, lower esophageal sphincter (LES) pressure on manometry, reflux symptoms, and medication use before and after POEM.
A 3-month follow-up was completed for all patients. Treatment success (Eckhard score ≤3) was achieved in 94% of cases (mean score pre- vs. post-treatment (8.8 vs. 1.4); P<0.001). Mean LES pressure was 27.2 mm Hg pre-treatment and 11.8 mm Hg post-treatment (P<0.001). No patient developed symptoms of gastro-esophageal reflux after treatment, but one patient was found to have an erosive lesion (LA grade A) on follow-up esophagogastroduodenoscopy. No patient required medication with proton pump inhibitors or antacids after POEM.
POEM is a promising new treatment for achalasia resulting in short-term symptom relief in >90% of cases. Studies evaluating long-term efficacy and comparing POEM with established treatments have been initiated.
One-fourth of colorectal neoplasia are missed at screening colonoscopy, representing the main cause of interval colorectal cancer. Deep learning systems with real-time computer-aided polyp detection ...(CADe) showed high accuracy in artificial settings, and preliminary randomized controlled trials (RCTs) reported favorable outcomes in the clinical setting. The aim of this meta-analysis was to summarize available RCTs on the performance of CADe systems in colorectal neoplasia detection.
We searched MEDLINE, EMBASE, and Cochrane Central databases until March 2020 for RCTs reporting diagnostic accuracy of CADe systems in the detection of colorectal neoplasia. The primary outcome was pooled adenoma detection rate (ADR), and secondary outcomes were adenoma per colonoscopy (APC) according to size, morphology, and location; advanced APC; polyp detection rate; polyps per colonoscopy; and sessile serrated lesions per colonoscopy. We calculated risk ratios (RRs), performed subgroup and sensitivity analyses, and assessed heterogeneity and publication bias.
Overall, 5 randomized controlled trials (4354 patients) were included in the final analysis. Pooled ADR was significantly higher in the CADe group than in the control group (791/2163 36.6% vs 558/2191 25.2%; RR, 1.44; 95% confidence interval CI, 1.27-1.62; P < .01; I2 = 42%). APC was also higher in the CADe group compared with control (1249/2163 .58 vs 779/2191 .36; RR, 1.70; 95% CI, 1.53-1.89; P < .01; I2 = 33%). APC was higher for ≤5-mm (RR, 1.69; 95% CI, 1.48-1.84), 6- to 9-mm (RR, 1.44; 95% CI, 1.19-1.75), and ≥10-mm adenomas (RR, 1.46; 95% CI, 1.04-2.06) and for proximal (RR, 1.59; 95% CI, 1.34-1.88), distal (RR, 1.68; 95% CI, 1.50-1.88), flat (RR, 1.78; 95% CI, 1.47-2.15), and polypoid morphology (RR, 1.54; 95% CI, 1.40-1.68). Regarding histology, CADe resulted in a higher sessile serrated lesion per colonoscopy (RR, 1.52; 95% CI, 1.14-2.02), whereas a nonsignificant trend for advanced ADR was found (RR, 1.35; 95% CI, .74-2.47; P = .33; I2 = 69%). Level of evidence for RCTs was graded as moderate.
According to available evidence, the incorporation of artificial intelligence as aid for detection of colorectal neoplasia results in a significant increase in the detection of colorectal neoplasia, and such effect is independent from main adenoma characteristics.
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False positive (FP) results by computer-aided detection (CADe) hamper the efficiency of colonoscopy by extending examination time. Our aim was to develop a classification of the causes and clinical ...relevance of CADe FPs, and to assess the relative distribution of FPs in a real-life setting.
In a post-hoc analysis of a randomized trial comparing colonoscopy with and without CADe (NCT: 04079478), we extracted 40 CADe colonoscopy videos. Using a modified Delphi process, 4 expert endoscopists identified the main domains for the reasons and clinical relevance of FPs. Then, 2 expert endoscopists manually examined each FP and classified it according to the proposed domains. The analysis was limited to the withdrawal phase.
The 2 main domains for the causes of CADe FPs were identified as artifacts due to either the mucosal wall or bowel content, and clinical relevance was defined as the time spent on FPs and the FP rate per minute. The mean number of FPs per colonoscopy was 27.3 ± 13.1, of which 24 ± 12 (88%) and 3.2 ± 2.6 (12%) were due to artifacts in the bowel wall and bowel content, respectively. Of the 27.3 FPs per colonoscopy, 1.6 (5.7%) required additional exploration time of 4.8 ± 6.2 seconds per FP (ie, 0.7% of the mean withdrawal time). In detail, 15 (24.2%), 33 (53.2%), and 14 (22.6%) FPs were classified as being of mild, moderate, or severe clinical relevance. The rate of FPs per minute of withdrawal time was 2.4 ± 1.2, and was higher for FPs due to artifacts from the bowel wall than for those from bowel content (2.4 ± 0.6 vs 0.3 ± 0.2, P < .001).
FPs by CADe are primarily due to artifacts from the bowel wall. Despite a high frequency, FPs result in a negligible 1% increase in the total withdrawal time because most of them are immediately discarded by the endoscopist.
The phase behavior of an embedded-charge model for lysozyme developed by Carlsson and co-workers (J. Phys. Chem. B 2001, 105, 9040) is investigated using grand canonical transition matrix Monte Carlo ...simulation. Within this model, protein−protein interactions are approximated through a combination of hard-sphere repulsion, isotropic hydrophobic attraction, and screened electrostatic interactions through a series of embedded point charges located at the positions of charged amino acid groups within lysozyme. Liquid−liquid phase diagrams are constructed for a wide range of solution conditions and compared with experimental data. Our results indicate that the model is generally capable of describing qualitative trends in the evolution of protein phase behavior with variation of pH and ionic strength. From a quantitative perspective, model estimates for both the change in critical temperature with variation of the solution conditions and the critical concentration do not agree with experimental results. We find the width of model coexistence curves to be independent of solution conditions and narrow relative to experimentally obtained phase envelopes. Connections between the value of the second virial coefficient evaluated at the critical temperature and the location of the liquid−liquid phase envelope are also examined.
Colonoscopy is a widely performed procedure with procedural volumes increasing annually throughout the world. Many procedures are now performed as part of colorectal cancer screening programmes. ...Colonoscopy should be of high quality and measures of this quality should be evidence based. New UK key performance indicators and quality assurance standards have been developed by a working group with consensus agreement on each standard reached. This paper reviews the scientific basis for each of the quality measures published in the UK standards.
We examine the relationship between the macroscopic phase behavior of nanoconfined fluids and the nature of microscopic interactions between a confining substrate and fluid. Two model slit-pore ...systems are explored using grand canonical transition-matrix Monte Carlo simulation. One system consists of a square-well fluid interacting with a square-well substrate, and the other contains an embedded point charge model of lysozyme interacting with a mica surface. Fluid phase diagrams are constructed for a broad range of substrate conditions. Our results indicate that one observes a maximum in the critical temperature of the fluid phase envelope upon variation of substrate strength for a given slit width. Both systems studied exhibit such maxima at intermediate wall strength. The physical rationale for this observation suggests that this behavior should be generally expected. We introduce two metrics that enable one to predict conditions that produce maxima in critical temperature. The first is related to the contact angle a fluid develops at a single confining substrate. The second is based upon virial coefficient information and requires knowledge of the substrate−fluid and fluid−fluid interaction potentials only.
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