KID Project:an internet-based digital video atlas of capsule endoscopy for research purposes

BACKGROUND AND AIMS: Capsule endoscopy (CE) has revolutionized small-bowel (SB) investigation. Computational methods can enhance diagnostic yield (DY); however, incorporating machine learning algorithms (MLAs) into CE reading is difficult as large amounts of image annotations are required for training. Current databases lack graphic annotations of pathologies and cannot be used. A novel database, KID, aims to provide a reference for research and development of medical decision support systems (MDSS) for CE. METHODS: Open-source software was used for the KID database. Clinicians contribute anonymized, annotated CE images and videos. Graphic annotations are supported by an open-access annotation tool (Ratsnake). We detail an experiment based on the KID database, examining differences in SB lesion measurement between human readers and a MLA. The Jaccard Index (JI) was used to evaluate similarity between annotations by the MLA and human readers. RESULTS: The MLA performed best in measuring lymphangiectasias with a JI of 81\u200a\ub1\u200a6\u200a%. The other lesion types were: angioectasias (JI 64\u200a\ub1\u200a11\u200a%), aphthae (JI 64\u200a\ub1\u200a8\u200a%), chylous cysts (JI 70\u200a\ub1\u200a14\u200a%), polypoid lesions (JI 75\u200a\ub1\u200a21\u200a%), and ulcers (JI 56\u200a\ub1\u200a9\u200a%). CONCLUSION: MLA can perform as well as human readers in the measurement of SB angioectasias in white light (WL). Automated lesion measurement is therefore feasible. KID is currently the only open-source CE database developed specifically to aid development of MDSS. Our experiment demonstrates this potential

A semi-virtual two dimensional gel electrophoresis: IF–ESI LC-MS/MS

A method for increasing the productivity of ESI LC-MS/MS (electrospray ionization-liquid chromatography-tandem mass spectrometry) was proposed and applied. After IF (isoelectric focusing) of the sample using IPG (immobilized pH gradient) strip, the strip was cut to sections, and every section was treated according to trypsinolysis protocol for MS/MS analysis. The peptides produced were further analyzed by ESI LC-MS/MS. The procedure allows to: • identify many more proteins and proteoforms compared to shotgun analysis of extracts. • build a semi-virtual 2DE map of identified proteins

Dried Blood Spot in Laboratory: Directions and Prospects

Over the past few years, dried blood spot (DBS) technology has become a convenient tool in both qualitative and quantitative biological analysis. DBS technology consists of a membrane carrier (MC) on the surface of which a biomaterial sample becomes absorbed. Modern analytical, immunological or genomic methods can be employed for analysis after drying the sample. DBS has been described as the most appropriate method for biomaterial sampling due to specific associated inherent advantages, including the small volumes of biomaterials required, the absence of a need for special conditions for samples’ storage and transportation, improved stability of analytes and reduced risk of infection resulting from contaminated samples. This review illustrates information on the current state of DBS technology, which can be useful and helpful for biomedical researchers. The prospects of using this technology to assess the metabolomic profile, assessment, diagnosis of communicable diseases are demonstrated

Variety and Dynamics of Proteoforms in the Human Proteome: Aspects of Markers for Hepatocellular Carcinoma

We have previously developed an approach, where two-dimensional gel electrophoresis (2DE) was used, followed by sectional analysis of the whole gel using high-resolution nano-liquid chromatography-mass spectrometry (ESI LC-MS/MS). In this study, we applied this approach on the panoramic analysis of proteins and their proteoforms from normal (liver) and cancer (HepG2) cells. This allowed us to detect, in a single proteome, about 20,000 proteoforms coded by more than 4000 genes. A set of 3D-graphs showing distribution of these proteoforms in 2DE maps (profiles) was generated. A comparative analysis of these profiles between normal and cancer cells showed high variability and dynamics of many proteins. Among these proteins, there are some well-known features like alpha-fetoprotein (FETA) or glypican-3 (GPC3) and potential hepatocellular carcinoma (HCC) markers. More detailed information about their proteoforms could be used for generation of panels of more specific biomarkers

Association Between Fecal Calprotectin Levels and Small-bowel Inflammation Score in Capsule Endoscopy : A Multicenter Retrospective Study

Accurate inflammation reporting in capsule endoscopy (CE) is important for diagnosis and monitoring of treatment of inflammatory bowel disease (IBD). Fecal calprotectin (FC) is a highly specific biomarker of gut inflammation. Lewis score (LS) was developed to standardize quantification of inflammation in small-bowel (SB) CE images. Multicenter retrospective study aiming to investigate correlation between LS and FC in a large group of patients undergoing CE for suspected or known small-bowel IBD, and to develop a model for prediction of CE results (LS) based on FC levels. Five academic centers and a district general hospital offering CE in UK, Finland, Sweden, Canada, and Israel. In total, 333 patients were recruited. They had small-bowel CE and FC done within 3 months. Overall, correlation between FC and LS was weak (r (s): 0.232, P <0.001). When two clinically significant FC thresholds (100 and 250 mu g/g) were examined, the r (s) between FC and LS was 0.247 (weak) and 0.337 (moderate), respectively (P = 0.307). For clinically significant (LS a parts per thousand yen 135) or negative (LS <135) for SB inflammation, ROC curves gave an optimum cutoff point of FC 76 mu g/g with sensitivity 0.59 and specificity 0.41. Limitations: Retrospective design. LS appears to show low correlation with FC as well as other serology markers of inflammation. FC does not appear to be a reliable biomarker for significant small-bowel inflammation. Nevertheless, FC level a parts per thousand yen 76 mu g/g may be associated with appreciable visual inflammation on small-bowel CE in patients with negative prior diagnostic workup.Peer reviewe

Use of patency capsule in patients with established Crohn's disease.

Background and study aims: Video capsule endoscopy (VCE) is invaluable in the diagnosis of small-bowel pathology. Capsule retention is a major concern in patients with Crohn's disease. The patency capsule was designed to evaluate small-bowel patency before VCE. However, the actual benefit of the patency capsule test in Crohn's disease remains unclear. The aim of this study was to evaluate the clinical impact of patency capsule use on the risk of video capsule retention in patients with established Crohn's disease. Patients and methods: This was a retrospective, multicenter study of patients with established Crohn's disease who underwent VCE for clinical need. The utilization strategy for the patency capsule was classified as selective (only in patients with obstructive symptoms, history of intestinal obstruction or surgery, or per treating physician's request) or nonselective (all patients with Crohn's disease). The main outcome was video capsule retention in the entire cohort and within each utilization strategy. Results: A total of 406 patients who were referred for VCE were included in the study. VCE was performed in 132 /406 patients (32.5 %) without a prior patency capsule test. The patency capsule test was performed in 274 /406 patients (67.5 %) and was negative in 193 patients. Overall, VCE was performed in 343 patients and was retained in the small bowel in 8 (2.3 %). In this cohort, the risk of video capsule retention in the small bowel was 1.5 % without use of a prior patency capsule and 2.1 % after a negative patency test (P = 0.9). A total of 18 patients underwent VCE after a positive patency capsule test, with a retention rate of 11.1 % (P = 0.01). Patency capsule administration strategy (selective vs. nonselective) was not associated with the risk of video capsule retention. Conclusions: Capsule retention is a rare event in patients with established Crohn's disease undergoing VCE. The risk of video capsule retention was not reduced by the nonselective use of the patency capsule. Furthermore, VCE after a positive patency capsule test in patients with Crohn's disease was associated with a high risk of video capsule retention

Small bowel capsule endoscopy in the management of established Crohn's disease: clinical impact, safety, and correlation with inflammatory biomarkers.

Multiple studies have established the superior diagnostic accuracy of video capsule endoscopy (VCE) for the diagnosis of small bowel (SB) Crohn's disease (CD). However, data on the clinical impact of VCE in patients with established CD are scarce. The aim of this study was to examine the impact and safety of VCE on the clinical management of patients with established CD

Targeted Quantitative Screening of Chromosome 18 Encoded Proteome in Plasma Samples of Astronaut Candidates

This work was aimed at estimating the concentrations of proteins encoded by human chromosome 18 (Chr 18) in plasma samples of 54 healthy male volunteers (aged 20–47). These young persons have been certified by the medical evaluation board as healthy subjects ready for space flight training. Over 260 stable isotope-labeled peptide standards (SIS) were synthesized to perform the measurements of proteins encoded by Chr 18. Selected reaction monitoring (SRM) with SIS allowed an estimate of the levels of 84 of 276 proteins encoded by Chr 18. These proteins were quantified in whole and depleted plasma samples. Concentration of the proteins detected varied from 10^–6 M (transthyretin, P02766) to 10^–11 M (P4-ATPase, O43861). A minor part of the proteins (mostly representing intracellular proteins) was characterized by extremely high inter individual variations. The results provide a background for studies of a potential biomarker in plasma among proteins encoded by Chr 18. The SRM raw data are available in ProteomeXchange repository (PXD004374)