Gland Instance Segmentation by Deep Multichannel Side Supervision

In this paper, we propose a new image instance segmentation method that segments individual glands (instances) in colon histology images. This is a task called instance segmentation that has recently become increasingly important. The problem is challenging since not only do the glands need to be segmented from the complex background, they are also required to be individually identified. Here we leverage the idea of image-to-image prediction in recent deep learning by building a framework that automatically exploits and fuses complex multichannel information, regional and boundary patterns, with side supervision (deep supervision on side responses) in gland histology images. Our proposed system, deep multichannel side supervision (DMCS), alleviates heavy feature design due to the use of convolutional neural networks guided by side supervision. Compared to methods reported in the 2015 MICCAI Gland Segmentation Challenge, we observe state-of-the-art results based on a number of evaluation metrics.Comment: conditionally accepted at MICCAI 201

Apolipoprotein E polymorphism and the risk of intracranial aneurysms in a Chinese population

BACKGROUND: The relationship between the apolipoprotein E (APOE) polymorphism and intracranial aneurysms has previously only been studied in Russia and Japan but not in Chinese populations. The purpose of this study was to investigate the association between APOE polymorphism and the risk of intracranial aneurysms in a Chinese population. METHODS: The study population consisted of 150 intracranial aneurysms patients and 150 matched control subjects. The APOE gene polymorphism was analyzed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). RESULTS: Patients with intracranial aneurysms had a significantly higher frequency of APOE E2/E2 genotype [odds ratio (OR) =9.51, 95 % confidence interval (CI) = 1.19, 76.04; P = 0.03] and APOE E2/E3 genotype (OR = 1.87, 95 % CI = 1.03, 3.40; P = 0.04) than healthy controls. The APOE E4/E4 genotype frequencies (OR = 0.09, 95 % CI = 0.01, 0.74; P = 0.03) in the intracranial aneurysms group were significantly lower than those in the controls group. When stratified by the site, shape, size and the Fisher Grade of intracranial aneurysms, no statistically significant result was observed. CONCLUSION: Our study suggested that APOE polymorphism might be associated with intracranial aneurysms in Chinese population. Additional studies are needed to confirm this finding

Integrated saccade latency as a measure of fatigue

INTRODUCTION: High workload, long working hours and inadequate sleep patterns can have deleterious effects on an individual’s performance. Fatigue is often linked with compromised cognitive and motor function. Our information processing system becomes overloaded and unable to monitor and suppress irrelevant information. Subsequent changes in oculomotor parameters and cortical processing times may therefore provide useful biomarkers to assess one’s state of fatigue. We propose a new non-invasive method to quantify fatigue by measuring Eye Movement And Intrinsic Latencies (EMAIL) without the use of any eye-tracking equipment. METHODS: The test is easy to perform and employs a Landolt C flanked by ring distractors. The test is presented at an eccentricity of 8°, randomly on either side of fixation point within ±5° elevation. The measurement variable is the time of presentation, δT. The subject’s task is to saccade to the peripheral target, register the orientation of the gap and respond by pressing one of four buttons. The EMAIL test measures the presentation time, δT, the subject needs to detect the peripheral target, generate an appropriate eye-movement and register the orientation of the gap. RESULTS: The EMAIL test was used to measure the stimulus presentation times needed to achieve 73% correct responses (using a one up, two down staircase). These times were subject specific and ranged from 165 to 200ms in the absence of fatigue. We investigated how, δT, is affected by exposure to other visually demanding tasks and levels of controlled fatigue. Measured integrated oculomotor responses such as latencies and visual processing times were found to increase significantly following demanding visual tasks by as much as 20ms, but only when fatigued. Preliminary findings using the EMAIL test also show that this technique can be used to investigate the effect of stimulants such as caffeine and depressants, such as alcohol. CONCLUSIONS: The EMAIL test provides a simple method to measure oculomotor parameters and to investigate how these are affected by fatigue. This method can be incorporated in the overall safety management system that is often needed in a number of work areas that involve visually-demanding and safety-critical tasks. The measured parameters provide information about an individual’s level of alertness and may also be of relevance in other industries in order to evaluate drugs developed to control fatigue

The Role of Long Noncoding RNAs in Gene Expression Regulation

Accumulating evidence highlights that noncoding RNAs, especially the long noncoding RNAs (lncRNAs), are critical regulators of gene expression in development, differentiation, and human diseases, such as cancers and heart diseases. The regulatory mechanisms of lncRNAs have been categorized into four major archetypes: signals, decoys, scaffolds, and guides. Increasing evidence points that lncRNAs are able to regulate almost every cellular process by their binding to proteins, mRNAs, miRNA, and/or DNAs. In this review, we present the recent research advances about the regulatory mechanisms of lncRNA in gene expression at various levels, including pretranscription, transcription regulation, and posttranscription regulation. We also introduce the interaction between lncRNA and DNA, RNA and protein, and the bioinformatics applications on lncRNA research

HSP60, a protein downregulated by IGFBP7 in colorectal carcinoma

<p>Abstract</p> <p>Background</p> <p>In our previous study, it was well defined that <it>IGFBP7 </it>was an important tumor suppressor gene in colorectal cancer (CRC). We aimed to uncover the downstream molecules responsible for <it>IGFBP7</it>'s behaviour in this study.</p> <p>Methods</p> <p>Differentially expressed protein profiles between PcDNA3.1(<it>IGFBP7</it>)-transfected RKO cells and the empty vector transfected controls were generated by two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) identification. The selected differentially expressed protein induced by IGFBP7 was confirmed by western blot and ELISA. The biological behaviour of the protein was explored by cell growth assay and colony formation assay.</p> <p>Results</p> <p>Six unique proteins were found differentially expressed in PcDNA3.1(<it>IGFBP7</it>)-transfected RKO cells, including albumin (ALB), 60 kDa heat shock protein(HSP60), Actin cytoplasmic 1 or 2, pyruvate kinase muscle 2(PKM2), beta subunit of phenylalanyl-tRNA synthetase(FARSB) and hypothetical protein. The downregulation of HSP60 by IGFBP7 was confirmed by western blot and ELISA. Recombinant human HSP60 protein could increase the proliferation rate and the colony formation ability of PcDNA3.1(<it>IGFBP7</it>)-RKO cells.</p> <p>Conclusion</p> <p>HSP60 was an important downstream molecule of IGFBP7. The downregulation of HSP60 induced by IGFBP7 may be, at least in part, responsible for IGFBP7's tumor suppressive biological behaviour in CRC.</p

Huperzine A Alleviates Mechanical Allodynia but Not Spontaneous Pain via Muscarinic Acetylcholine Receptors in Mice

Chronic pain is a major health issue and most patients suffer from spontaneous pain. Previous studies suggest that Huperzine A (Hup A), an alkaloid isolated from the Chinese herb Huperzia serrata, is a potent analgesic with few side effects. However, whether it alleviates spontaneous pain is unclear. We evaluated the effects of Hup A on spontaneous pain in mice using the conditioned place preference (CPP) behavioral assay and found that application of Hup A attenuated the mechanical allodynia induced by peripheral nerve injury or inflammation. This effect was blocked by atropine. However, clonidine but not Hup A induced preference for the drug-paired chamber in CPP. The same effects occurred when Hup A was infused into the anterior cingulate cortex. Furthermore, ambenonium chloride, a competitive inhibitor of acetylcholinesterase, also increased the paw-withdrawal threshold but failed to induce place preference in CPP. Therefore, our data suggest that acetylcholinesterase in both the peripheral and central nervous systems is involved in the regulation of mechanical allodynia but not the spontaneous pain

Gland Instance Segmentation by Deep Multichannel Side Supervision

Abstract. In this paper, we propose a new image instance segmentation method that segments individual glands (instances) in colon histology images. This is a task called instance segmentation that has recently become increasingly important. The problem is challenging since not only do the glands need to be segmented from the complex background, they are also required to be individually identified. Here we leverage the idea of image-to-image prediction in recent deep learning by building a framework that automatically exploits and fuses complex multichannel information, regional and boundary patterns, with side supervision (deep supervision on side responses) in gland histology images. Our proposed system, deep multichannel side supervision (DMCS), alleviates heavy feature design due to the use of convolutional neural networks guided by side supervision. Compared to methods reported in the 2015 MICCAI Gland Segmentation Challenge, we observe state-of-the-art results based on a number of evaluation metrics

National Brain Tumour Registry of China (NBTRC) statistical report of primary brain tumours diagnosed in China in years 2019-2020

BACKGROUND: The lack of a well-designed brain tumour registry with standardized pathological diagnoses in underdeveloped countries hinders the ability to compare epidemiologic data across the globe. The National Brain Tumour Registry of China (NBTRC), created in January 2018, is the first multi-hospital-based brain tumour registry in China. Patient data reported to the NBTRC in years 2019-2020 were assessed. METHODS: Tumour pathology was based on the 2016 World Health Organization (WHO) classification of tumours of the central nervous system and ICD-O-3. The anatomical site was coded per the Surveillance, Epidemiology, and End Results (SEER) solid tumour module (version of July 2019). The cases were tabulated by histology and anatomical site. Categorical variables were reported as numbers (percentages). The distribution of tumours by age (0-14, 15-19, 20-39, 40-64, and 65+ years) was analysed. FINDINGS: There were a total of 25,537 brain tumours, foremost among them meningioma (23.63%), followed by tumours of the pituitary (23.42%), and nerve sheath tumours (9.09%). Glioblastoma, the most common and lethal form of primary brain cancer in adults, represented 8.56% of all cases. Of note, 6.48% of the malignant tumours were located in the brain stem. The percentage of malignant brain tumours decreased with increasing age, 24.08% in adults (40+ years), 30.25% in young adults (20-39 years), 35.27% in adolescents (15-19 years), and 49.83% in children (0-14 years). Among the 2107 paediatric patients, the most common sites were ventricle (17.19%), brainstem (14.03%), pituitary and craniopharyngeal duct (13.4%), and cerebellum (12.3%), a distribution that differed from that of the entire cohort. The histology distribution was also unique in children, with glioblastoma much less incident compared to the whole cohort (3% vs. 8.47%, INTERPRETATION: The histological and anatomical site distribution of brain tumours in the NBTRC was statistically different in the subgroup of children (0-14 years). Patient choice of pursuing trans-provincial treatment was common and the in-hospital LOS was longer compared to that reported in similar European and American patient populations, which merits further attention. FUNDING: The National Key Research and Development Program of China (2015BAI12B04, 2013BAI09B03, 2014BAI04B01, and 2021YFF1201104) and Chinese National Natural Science Foundation of China (81971668)