Multi-site, Multi-domain Airway Tree Modeling (ATM'22): A Public Benchmark for Pulmonary Airway Segmentation

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.Comment: 32 pages, 16 figures. Homepage: https://atm22.grand-challenge.org/. Submitte

Generation of a human iPSC line from a patient with Marfan syndrome caused by mutation in FBN1

Marfan syndrome (MFS) is a heritable connective tissue disease caused by mutations in FBN1, encoding the extracellular matrix protein fibrillin-1. In this study, we generated human induced pluripotent stem cells (iPSCs) from dermal fibroblasts of an MFS patient with the p. E2130K (c. 6388G > A) mutation. The generated hiPSC line had a normal karyotype, showed robust expression of pluripotency markers and was able to differentiate into all three germ layers in vivo. This cell line can provide a platform for understanding the pathogenic mechanisms of MFS related to FBN1 mutations.Resource table.Unlabelled TableUnique stem cell identifierCMUi001-AAlternative name(s) of stem cell lineFBN1-E2130K-iPSCInstitutionAnzhen Hospital, Capital Medical UniversityContact information of [email protected] of cell lineiPSCOriginHumanAdditional origin infoAge: 25Sex: maleEthnicity: Han nationalityCell sourcePatient derived fibroblastsClonalityClonalMethod of reprogrammingSendai virus. Oct4, Sox2, cMyc, Klf4Genetic modificationNOType of modificationN/AAssociated diseaseMarfan syndrome (aortic root aneurysm)Gene/locusGene: FBN1Locus: 15q21.1Mutation: heterozygote c.6388G > A (p.E2130K)Method of modificationN/AName of transgene or resistanceN/AInducible/constitutive systemN/AData archived/stock date02/2018Cell line repository/bankN/AEthical approvalEthics Committee of Anzhen Hospital, Capital Medical University(#134/18

Establishment and application of a rapid visualization method for detecting Vibrio parahaemolyticus nucleic acid

Background: Swift and accurate detection of Vibrio parahaemolyticus, which is a prominent causative pathogen associated with seafood contamination, is required to effectively combat foodborne disease and wound infections. The toxR gene is relatively conserved within V. parahaemolyticus and is primarily involved in the expression and regulation of virulence genes with a notable degree of specificity. The aim of this study was to develop a rapid, simple, and constant temperature detection method for V. parahaemolyticus in clinical and nonspecialized laboratory settings. Methods: In this study, specific primers and CRISPR RNA were used to target the toxR gene to construct a reaction system that combines recombinase polymerase amplification (RPA) with CRISPR‒Cas13a. The whole-genome DNA of the sample was extracted by self-prepared sodium dodecyl sulphate (SDS) nucleic acid rapid extraction reagent, and visual interpretation of the detection results was performed by lateral flow dipsticks (LFDs). Results: The specificity of the RPA-CRISPR/Cas13a-LFD method was validated using V. parahaemolyticus strain ATCC-17802 and six other non-parahaemolytic Vibrio species. The results demonstrated a specificity of 100%. Additionally, the genomic DNA of V. parahaemolyticus was serially diluted and analysed, with a minimum detectable limit of 1 copy/µL for this method, which was greater than that of the TaqMan-qPCR method (102 copies/µL). The established methods were successfully applied to detect wild-type V. parahaemolyticus, yielding results consistent with those of TaqMan-qPCR and MALDI-TOF MS mass spectrometry identification. Finally, the established RPA-CRISPR/Cas13a-LFD method was applied to whole blood specimens from mice infected with V. parahaemolyticus, and the detection rate of V. parahaemolyticus by this method was consistent with that of the conventional PCR method. Conclusions: In this study, we describe an RPA-CRISPR/Cas13a detection method that specifically targets the toxR gene and offers advantages such as simplicity, rapidity, high specificity, and visual interpretation. This method serves as a valuable tool for the prompt detection of V. parahaemolyticus in nonspecialized laboratory settings

Effect of ERCC1 polymorphisms on the response to platinum-based chemotherapy: A systematic review and meta-analysis based on Asian population.

BackgroundPlatinum-based chemotherapy is one of the most common treatments for many cancers; however, the effect of chemotherapy varies from individual to individual. Excision repair cross complementation group 1 (ERCC1) is widely recognized as a key gene regulating nucleotide excision repair (NER) and is closely associated with platinum response. Many studies have yielded conflicting results regarding whether ERCC1 polymorphisms can affect the response to platinum and overall survival (OS). Therefore, it is necessary to perform a meta-analysis of patients with specific races and cancer types.MethodsEight databases (EMBASE, PubMed, Cochrane Library, Chinese National Knowledge Infrastructure, Scopus, VIP, China Biology Medicine disc and Wanfang databases) were searched. Results were expressed in terms of odds ratios (ORs), hazard ratios (HRs) and 95% CIs.ResultsIn this study, rs11615, rs2298881 and rs3212986 SNPs were studied. In the comparison between CT and TT on the response to platinum, esophageal cancer [I2 = 0%, OR = 6.18, 95% CI(1.89,20.23), P = 0.003] and ovarian cancer [I2 = 0%, OR = 4.94, 95% CI(2.21,11.04), PConclusionThe ERCC1 rs11615 polymorphism was related to the response to platinum and OS, but the correlation is based on specific cancer types in the Asian population

Fabrication and characterization of multimaterial chalcogenide glass fiber tapers with high numerical apertures

This paper reports on the fabrication and characterization of multimaterial chalcogenide fiber tapers that have high numerical apertures (NAs). We first fabricated multimaterial As2Se3-As2S3 chalcogenide fiber preforms via a modified one-step coextrusion process. The preforms were drawn into multi- and single-mode fibers with high NAs (≈1.45), whose core/cladding diameters were 103/207 and 11/246 μm, respectively. The outer diameter of the fiber was tapered from a few hundred microns to approximately two microns through a self-developed automatic tapering process. Simulation results showed that the zero-dispersion wavelengths (ZDWs) of the tapers were shorter than 2 μm, indicating that the tapers can be conveniently pumped by commercial short wavelength infrared lasers. We also experimentally demonstrated the supercontinuum generation (SCG) in a 15-cm-long multimaterial As2Se3-As2S3 chalcogenide taper with 1.9 μm core diameter and the ZDW was shifted to 3.3 μm. When pumping the taper with 100 fs short pulses at 3.4 µm, a 20 dB spectral of the generated supercontinuum spans from 1.5 μm to longer than 4.8 μm