The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LITS) organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2016 and International Conference On Medical Image Computing Computer Assisted Intervention (MICCAI) 2017. Twenty four valid state-of-the-art liver and liver tumor segmentation algorithms were applied to a set of 131 computed tomography (CT) volumes with different types of tumor contrast levels (hyper-/hypo-intense), abnormalities in tissues (metastasectomie) size and varying amount of lesions. The submitted algorithms have been tested on 70 undisclosed volumes. The dataset is created in collaboration with seven hospitals and research institutions and manually reviewed by independent three radiologists. We found that not a single algorithm performed best for liver and tumors. The best liver segmentation algorithm achieved a Dice score of 0.96(MICCAI) whereas for tumor segmentation the best algorithm evaluated at 0.67(ISBI) and 0.70(MICCAI). The LITS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource.Comment: conferenc

The Study of Cyclosporin A Nanocrystals Uptake and Transport across an Intestinal Epithelial Cell Model

Cyclosporin A nanocrystals (CsA-NCs) interaction with Caco-2 cells were investigated in this study, including cellular uptake and transport across Caco-2 cell monolayers. CsA-NCs of 165 nm, 240 nm and 450 nm were formulated. The dissolution of CsA-NCs was investigated by paddle method. The effect of size, concentration and incubation time on cellular uptake and dissolution kinetics of CsA-NCs in cells were studied. Uptake mechanisms were also evaluated using endocytotic inhibitors and low temperature (4 °C). The cell monolayers were incubated with each diameter CsA-NCs to evaluate the effect of size on the permeation characteristics of CsA across the intestinal mucosa. The results of dissolution study showed that 165 nm CsA-NC had the highest dissolution rate followed by 240 CsA-NC and finally 450 nm CsA-NC. The saturation of cell uptake of CsA-NCs was observed with the increase of incubation concentration and time. 240 nm and 450 nm CsA-NCs had the lowest and highest uptake efficiency at different time and drug concentration, respectively. The uptake of all three-sized CsA-NCs declined significantly in some different degree after the pre-treatment with different endocytosis inhibitors. 165 nm CsA-NC showed a highest transport capacity across monolayers at the same concentration and time. The results suggest that the size of CsA-NCs can not only affect the efficiency of cellular uptake, but also the type of endocytosis. Decreasing particle size of CsA-NCs can improve transport capacity of CsA through cell monolayer

Data from: Association between COL11A1 (rs1337185) and ADAMTS5 (rs162509) gene polymorphisms and lumbar spine pathologies in Chinese Han population: an observational study

Objectives: A previous study identified a significant association between several single nucleotide polymorphisms (SNPs) and lumbar disc degeneration (LDD) in Indians. To validate the association between these SNPs and specific lumbar spine pathologies, we performed a case-control study in Chinese Han population. Design: An observational study. Setting: University Hospital in Nanning, China. Participants: This study included 428 LDD patients and 400 normal controls. Outcome measures: LDD Patients were classified into 4 subgroups, including disc herniation only (Subgroup 1), discopathies or/and osteochondrosis associated with disc herniation (Subgroup 2), spinal stenosis or/and spondylolisthesis (Subgroup 3), and degenerative scoliosis (Subgroup 4). This study was conducted by examining 2 aspects: environmental factors and SNP genotyping. The environmental factors were evaluated with a questionnaire survey including questions about BMI, smoking habits, the physical demands of their job and exposure to vibrations. Rs1337185, rs5275, rs5277, rs7575934, rs3213718 and rs162509 were genotyped using a PCR-based Invader assay. Results: The physical workload was significantly higher in patients with lumbar spine pathologies than in the normal controls (P=0.035). The genotype and allele frequencies of rs1337185 and rs162509 were significantly different between the LDD patients and the normal controls. In rs1337185, a significant association was found between the C allele (risk allele) and the presence of disc herniation (OR=1.80; 95%CI= 1.21-2.68; P=0.003, adjusted P=0.012), and the presence of spinal stenosis and spondylolisthesis (OR=1.92; 95%CI=1.29-2.89; P= 0.001, adjusted P=0.004). In rs162509, the G allele represented 1.58-fold increased risk to suffer from disc herniation (OR=1.58; 95%CI=1.20-2.09; P=0.001, adjusted P=0.004). Conclusions: The SNPs rs1337185 in COL11A1 and rs162509 in ADAMTS5 are associated with susceptibility to LDD. The C allele of rs1337185 is risky for patients who are affected by lumbar pathologies such as disc herniation, stenosis and spondylolisthesis. The G allele of rs16250 represents a risk factor for the development of disc herniation

Polyacrylamide-Based Block Copolymer Bearing Pyridine Groups Shows Unexpected Salt-Induced LCST Behavior

Thermal-responsive block copolymers are a special type of macromolecule that exhibit a wide range of applications in various fields. In this contribution, we report a new type of polyacrylamide-based block copolymer bearing pyridine groups of polyethylene glycol-block-poly(N-(2-methylpyridine)-acrylamide; Px) that display distinct salt-induced lower critical solution temperature (LCST) behavior. Unexpectedly, the phase-transition mechanism of the salt-induced LCST behavior of Px block copolymers is different from that of the reported LCST-featured analogues. Moreover, their thermo-responsive behavior can be significantly regulated by several parameters such as salt species and concentration, urea, polymerization degree, polymer concentration and pH values. This unique thermal behavior of pyridine-containing block copolymers provides a new avenue for the fabrication of smart polymer materials with potential applications in biomedicine

Proteomic profiling of expression of proteasomal subunits from livers of mice treated with diethylnitrosamine

The liver plays a central role in transforming and clearing chemicals and is susceptible to the toxicity from these agents. Diethylnitrosamine is metabolized primarily in the liver by cytochrome P-450 and can cause DNA damage. The 26S proteasome is a large proteolytic complex that degrades ubiquitinated proteins, and regulates many physiological processes. We used proteomics-based approaches to examine expressional differences of liver proteasomal subunits from diethylnitrosamine-treated mice. The expression of most proteasomal subunits was observed to be upregulated in the analysis of 2DE and MALDI-TOF MS/MS. Some of these differentially expressed proteasomal subunits were further confirmed by Western blot, RT-PCR, and immunohistochemistry. Our results provided useful information on the relationship between the proteasomal complex and related diseases

An LED-Driven AuNPs-PDMS Microfluidic Chip and Integrated Device for the Detection of Digital Loop-Mediated Isothermal DNA Amplification

The sensitive quantification of low-abundance nucleic acids holds importance for a range of clinical applications and biological studies. In this study, we describe a facile microfluidic chip for absolute DNA quantifications based on the digital loop-mediated isothermal amplification (digital LAMP) method. This microfluidic chip integrates a cross-flow channel for droplet generation with a micro-cavity for droplet tiling. DNA templates in the LAMP reagent were divided into ~20,000 water-in-oil droplets at the cross-flow channel. The droplets were then tiled in the micro-cavity for isothermal amplification and fluorescent detection. Different from the existing polydimethylsiloxane (PDMS) microfluidic chips, this study incorporates gold nanoparticles (AuNPs) into PDMS substrate through silica coating and dodecanol modification. The digital LAMP chip prepared by AuNPs-PDMS combines the benefits of the microstructure manufacturing performance of PDMS with the light-to-heat conversion advantages of AuNPs. Upon illumination with a near infrared (NIR) LED, the droplets were stably and efficiently heated by the AuNPs in PDMS. We further introduce an integrated device with a NIR heating unit and a fluorescent detection unit. The system could detect HBV (hepatitis B virus)-DNA at a concentration of 1 × 101 to 1 × 104 copies/μL. The LED-driven digital LAMP chip and the integrated device; therefore, demonstrate high accuracy and excellent performance for the absolute quantification of low-abundance nucleic acids, showing the advantages of integration, miniaturization, cost, and power consumption

Cu-Catalyzed Direct Amidation of Aromatic C–H Bonds: An Access to Arylamines

A Cu-catalyzed aromatic C–H amidation with phthalimide under oxygen as a terminal oxidant without using additional additives has been achieved. This reaction has the broad substrate scope and shows moderate to good yields in most cases. This method is complementary to the previously reported metal-catalyzed C–H amination systems