A cautionary tale: the non-causal association between type 2 diabetes risk SNP, rs7756992, and levels of non-coding RNA, CDKAL1-v1

Journal ArticleCopyright © The Author(s) 2015. This article is published with open access at Springerlink.com.Aims/hypothesis: Intronic single nucleotide polymorphisms (SNPs) in the CDKAL1 gene are associated with risk of developing type 2 diabetes. A strong correlation between risk alleles and lower levels of the non-coding RNA, CDKAL1-v1, has recently been reported in whole blood extracted from Japanese individuals. We sought to replicate this association in two independent cohorts: one using whole blood from white UK-resident individuals, and one using a collection of human pancreatic islets, a more relevant tissue type to study with respect to the aetiology of diabetes. Methods: Levels of CDKAL1-v1 were measured by real-time PCR using RNA extracted from human whole blood (n = 70) and human pancreatic islets (n = 48). Expression with respect to genotype was then determined. Results: In a simple linear regression model, expression of CDKAL1-v1 was associated with the lead type 2 diabetes-associated SNP, rs7756992, in whole blood and islets. However, these associations were abolished or substantially reduced in multiple regression models taking into account rs9366357 genotype: a moderately linked SNP explaining a much larger amount of the variation in CDKAL1-v1 levels, but not strongly associated with risk of type 2 diabetes. Conclusions/interpretation: Contrary to previous findings, we provide evidence against a role for dysregulated expression of CDKAL1-v1 in mediating the association between intronic SNPs in CDKAL1 and susceptibility to type 2 diabetes. The results of this study illustrate how caution should be exercised when inferring causality from an association between disease-risk genotype and non-coding RNA expression.MRCNIH

A cautionary tale: the non-causal association between type 2 diabetes risk SNP, rs7756992, and levels of non-coding RNA, CDKAL1-v1

This is the final version of the article. Available from Springer Verlag via the DOI in this record.AIMS/HYPOTHESIS: Intronic single nucleotide polymorphisms (SNPs) in the CDKAL1 gene are associated with risk of developing type 2 diabetes. A strong correlation between risk alleles and lower levels of the non-coding RNA, CDKAL1-v1, has recently been reported in whole blood extracted from Japanese individuals. We sought to replicate this association in two independent cohorts: one using whole blood from white UK-resident individuals, and one using a collection of human pancreatic islets, a more relevant tissue type to study with respect to the aetiology of diabetes. METHODS: Levels of CDKAL1-v1 were measured by real-time PCR using RNA extracted from human whole blood (n = 70) and human pancreatic islets (n = 48). Expression with respect to genotype was then determined. RESULTS: In a simple linear regression model, expression of CDKAL1-v1 was associated with the lead type 2 diabetes-associated SNP, rs7756992, in whole blood and islets. However, these associations were abolished or substantially reduced in multiple regression models taking into account rs9366357 genotype: a moderately linked SNP explaining a much larger amount of the variation in CDKAL1-v1 levels, but not strongly associated with risk of type 2 diabetes. CONCLUSIONS/INTERPRETATION: Contrary to previous findings, we provide evidence against a role for dysregulated expression of CDKAL1-v1 in mediating the association between intronic SNPs in CDKAL1 and susceptibility to type 2 diabetes. The results of this study illustrate how caution should be exercised when inferring causality from an association between disease-risk genotype and non-coding RNA expression.This paper presents independent research funded by the Medical Research Council (grant number MR/J006777/1) and supported by the National Institute for Health Research (NIHR) Exeter Clinical Research Facility. The views expressed are those of the authors and not necessarily those of the Medical Research Council, UK National Health Service, NIHR or the UK Department of Health

Developing an EEG-based on-line closed-loop lapse detection and mitigation system

© 2014 Wang, Huang, Wei, Huang, Ko, Lin, Cheng and Jung. In America, 60% of adults reported that they have driven a motor vehicle while feeling drowsy, and at least 15-20% of fatal car accidents are fatigue-related. This study translates previous laboratory-oriented neurophysiological research to design, develop, and test an On-line Closed-loop Lapse Detection and Mitigation (OCLDM) System featuring a mobile wireless dry-sensor EEG headgear and a cell-phone based real-time EEG processing platform. Eleven subjects participated in an event-related lane-keeping task, in which they were instructed to manipulate a randomly deviated, fixed-speed cruising car on a 4-lane highway. This was simulated in a 1st person view with an 8-screen and 8-projector immersive virtual-reality environment. When the subjects experienced lapses or failed to respond to events during the experiment, auditory warning was delivered to rectify the performance decrements. However, the arousing auditory signals were not always effective. The EEG spectra exhibited statistically significant differences between effective and ineffective arousing signals, suggesting that EEG spectra could be used as a countermeasure of the efficacy of arousing signals. In this on-line pilot study, the proposed OCLDM System was able to continuously detect EEG signatures of fatigue, deliver arousing warning to subjects suffering momentary cognitive lapses, and assess the efficacy of the warning in near real-time to rectify cognitive lapses. The on-line testing results of the OCLDM System validated the efficacy of the arousing signals in improving subjects' response times to the subsequent lane-departure events. This study may lead to a practical on-line lapse detection and mitigation system in real-world environments

Generation of tooth profile for roots rotor based on virtual linkage associated with Assur group

This article, for the first time, presents the generation of Roots rotor tooth profiles based on an Assur-group-associated virtual linkage method. Taking the original Roots rotor as an example, structure and geometry of the Roots rotor are introduced, and based on the principle of inversion, an equivalent virtual linkage is identified for generating dedendum tooth profile of the rotor. Using linkage decomposition associated with elemental Assur groups, algorithm for computing the tooth curve is constructed leading to the explicit expression of rotor profile and the corresponding numerical simulation, verifying the validity of the proposed approach. For demonstration purpose, the virtual linkage method is then extended to the generation of tooth profiles for the variants of Roots rotors with arc-cycloidal curves and arc-involute curves. Integrated with computer-aided design, computer-aided engineering and computer-aided manufacturing software platforms, as well as the three-dimensional printing technology, this article provides an efficient and intuitive approach for Roots rotor system design, analysis and development

Geometry and kinematics for a spherical-base integrated parallel mechanism

Parallel mechanisms, in general, have a rigid base and a moving platform connected by several limbs. For achieving higher mobility and dexterity, more degrees of freedom are introduced to the limbs. However, very few researchers focus on changing the design of the rigid base and making it foldable and reconfigurable to improve the performance of the mechanism. Inspired by manipulating an object with a metamorphic robotic hand, this paper presents for the first time a parallel mechanism with a reconfigurable base. This novel spherical-base integrated parallel mechanism has an enlarged workspace compared with traditional parallel manipulators. Evolution and structure of the proposed parallel mechanism is introduced and the geometric constraint of the mechanism is investigated based on mechanism decomposition. Further, kinematics of the proposed mechanism is reduced to the solution of a univariate polynomial of degree 8. Moreover, screw theory based Jacobian is presented followed by the velocity analysis of the mechanism

The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases

BACKGROUND: Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. Published neuroanatomical atlases provide a spatial framework for these studies. We have built an informatics framework based on these atlases for the representation of neuroanatomical knowledge. This framework not only captures current methods of anatomical data acquisition and analysis, it allows these studies to be collated, compared and synthesized within a single system. RESULTS: We have developed an atlas-viewing application ('NeuARt II') in the Java language with unique functional properties. These include the ability to use copyrighted atlases as templates within which users may view, save and retrieve data-maps and annotate them with volumetric delineations. NeuARt II also permits users to view multiple levels on multiple atlases at once. Each data-map in this system is simply a stack of vector images with one image per atlas level, so any set of accurate drawings made onto a supported atlas (in vector graphics format) could be uploaded into NeuARt II. Presently the database is populated with a corpus of high-quality neuroanatomical data from the laboratory of Dr Larry Swanson (consisting 64 highly-detailed maps of PHAL tract-tracing experiments, made up of 1039 separate drawings that were published in 27 primary research publications over 17 years). Herein we take selective examples from these data to demonstrate the features of NeuArt II. Our informatics tool permits users to browse, query and compare these maps. The NeuARt II tool operates within a bioinformatics knowledge management platform (called 'NeuroScholar') either as a standalone or a plug-in application. CONCLUSION: Anatomical localization is fundamental to neuroscientific work and atlases provide an easily-understood framework that is widely used by neuroanatomists and non-neuroanatomists alike. NeuARt II, the neuroinformatics tool presented here, provides an accurate and powerful way of representing neuroanatomical data in the context of commonly-used brain atlases for visualization, comparison and analysis. Furthermore, it provides a framework that supports the delivery and manipulation of mapped data either as a standalone system or as a component in a larger knowledge management system

Inherent Signals in Sequencing-Based Chromatin-ImmunoPrecipitation Control Libraries

The growth of sequencing-based Chromatin Immuno-Precipitation studies call for a more in-depth understanding of the nature of the technology and of the resultant data to reduce false positives and false negatives. Control libraries are typically constructed to complement such studies in order to mitigate the effect of systematic biases that might be present in the data. In this study, we explored multiple control libraries to obtain better understanding of what they truly represent.First, we analyzed the genome-wide profiles of various sequencing-based libraries at a low resolution of 1 Mbp, and compared them with each other as well as against aCGH data. We found that copy number plays a major influence in both ChIP-enriched as well as control libraries. Following that, we inspected the repeat regions to assess the extent of mapping bias. Next, significantly tag-rich 5 kbp regions were identified and they were associated with various genomic landmarks. For instance, we discovered that gene boundaries were surprisingly enriched with sequenced tags. Further, profiles between different cell types were noticeably distinct although the cell types were somewhat related and similar.We found that control libraries bear traces of systematic biases. The biases can be attributed to genomic copy number, inherent sequencing bias, plausible mapping ambiguity, and cell-type specific chromatin structure. Our results suggest careful analysis of control libraries can reveal promising biological insights

Immunoassays Based on Penicillium marneffei Mp1p Derived from Pichia pastoris Expression System for Diagnosis of Penicilliosis

BACKGROUND: Penicillium marneffei is a dimorphic fungus endemic in Southeast Asia. It can cause fatal penicilliosis in humans, particularly in HIV-infected people. Diagnosis of this infection is difficult because its clinical manifestations are not distinctive. Specialized laboratory tests are necessary to establish a definitive diagnosis for successful management. We have demonstrated previously that a cell wall mannoprotein Mp1p, abundant in P. marneffei, is a potential biomarker for diagnosis of P. marneffei infections. In the present study, we describe immunoassays based on Mp1p derived from the yeast Pichia pastoris expression system. METHODOLOGY/PRINCIPAL FINDINGS: We generated monoclonal antibodies (MAbs) and rabbit polyclonal antibodies (PAbs) against Mp1p expressed in P. pastoris. Subsequently, we developed two Mp1p antigen capture ELISAs which employed MAbs for both the capture and detecting antibodies (MAb-MAb pair) or PAbs and MAbs as the capture and detecting antibodies (PAbs-MAb pair) respectively. The two Mp1p antigen ELISAs detected Mp1p specifically in cultures of P. marneffei yeast phase at 37-40 degrees C and had no cross-reaction with other tested pathogenic fungi. The sensitivities and specificities of the two antigen assays were found to be 55% (11/20) and 99.6% (538/540) for MAb-MAb Mp1p ELISA, and 75% (15/20) and 99.4% (537/540) for PAbs-MAb Mp1p ELISA performed using 20 sera with culture-confirmed penicilliosis, and 540 control sera from 15 other mycosis patients and 525 healthy donors. Meanwhile, we also developed an anti-Mp1p IgG antibody ELISA with an evaluated sensitivity of 30% (6/20) and a specificity of 98.5% (532/540) using the same sera. Furthermore, combining the results of Mp1p antigen and antibody detection improved the sensitivity of diagnosis to 100% (20/20). CONCLUSIONS/SIGNIFICANCE: Simultaneous detection of antigen and antibody using the immunoassays based on Mp1p derived from P. pastoris greatly improves detection sensitivity. The procedures should be useful for the routine diagnosis of penicilliosis.published_or_final_versio

The impact of paratracheal lymph node metastasis in squamous cell carcinoma of the hypopharynx

The aim of this study was to analyze the prevalence and prognostic importance of paratracheal lymph nodes in squamous cell carcinoma of the hypopharynx. A retrospective review of 64 previously untreated patients with squamous cell carcinoma (SCC) of the hypopharynx that underwent surgery was performed. Ipsilateral paratracheal lymph node metastases occurred in 22% (14 out of 64) and the mean number of paratracheal lymph nodes dissected per side was 2.3 (range 1–6). Contralateral paratracheal lymph node metastases were present in 2% (1 out of 42). Sixty-seven percent with postcricoid SCC and 22% with pyriform sinus SCC developed clinical node-positive ipsilateral paratracheal lymph node metastases, whereas 11% with posterior pharyngeal wall SCC developed paratracheal metastases. There was a significant correlation between paratracheal lymph node metastasis and cervical metastasis (p = 0.005), and the primary tumor site (postcricoid, 57.1%; pyriform sinus, 20.0%; posterior pharyngeal wall, 8.3%) (p = 0.039). Patients with no evidence of paratracheal lymph node metastasis may have a survival benefit (5-year disease-specific survival rate, 60 vs. 29%). However, this result did not reach statistical significance (p = 0.071). The patients with SCC of the postcricoid and/or pyriform sinus were at risk for ipsilateral paratracheal lymph node metastasis; furthermore, patients with paratracheal node metastasis had a high frequency of cervical metastasis and a poorer prognosis. Therefore, routine ipsilateral paratracheal node dissection is recommended during the surgical treatment of patients with SCC of the postcricoid and/or pyriform sinus with clinical node metastases