Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric aggregates

The presence of oligomeric aggregates, which is often observed during the process of amyloid formation, has recently attracted much attention since it has been associated with neurodegenerative conditions such as Alzheimer's and Parkinson's diseases. We provide a description of a sequence-indepedent mechanism by which polypeptide chains aggregate by forming metastable oligomeric intermediate states prior to converting into fibrillar structures. Our results illustrate how the formation of ordered arrays of hydrogen bonds drives the formation of beta-sheets within the disordered oligomeric aggregates that form early under the effect of hydrophobic forces. Initially individual beta-sheets form with random orientations, which subsequently tend to align into protofilaments as their lengths increases. Our results suggest that amyloid aggregation represents an example of the Ostwald step rule of first order phase transitions by showing that ordered cross-beta structures emerge preferentially from disordered compact dynamical intermediate assemblies.Comment: 14 pages, 4 figure

Self-reported losses versus actual losses in online gambling: an empirical study

Many research findings in the gambling studies field rely on self-report data. A very small body of empirical research also suggests that when using self-report, players report their gambling losses inaccurately. The aim of the present study was to evaluate the differences between objective and subjective gambling spent data by comparing gambler’s actual behavioral tracking data with their self-report data over a 1-month period. A total of 17,742 Norwegian online gamblers were asked to participate in an online survey. Of those surveyed, 1335 gamblers answered questions relating to gambling expenditure that could be compared with their actual gambling behavior. The study found that the estimated loss self-reported by gamblers was correlated with the actual objective loss and that players with higher losses tended to have more difficulty estimating their gambling expenditure (i.e., players who spent more money gambling also appeared to have more trouble estimating their expenses accurately). Overall, the findings demonstrate that caution is warranted when using self-report data relating to amount of money spent gambling in any studies that are totally reliant on self-report data

An analysis of consumer protection for gamblers across different online gambling operators in Ireland: a descriptive study

The aim of the present study was to evaluate the responsible gambling tools which are available to online gamblers at Irish online gambling websites. The present study used a similar methodology to a recent study carried out on the world’s most popular websites (Bonello and Griffiths Gaming Law Review and Economics, 21, 278–285, 2017), where 50 of the most advertised online gambling websites were evaluated in relation to their responsible gambling (RG) practices. The present study evaluated 39 gambling websites with either a “.ie” or “.com/ie” domain. Each website was evaluated by checking for a number of RG practices, including presence of a dedicated RG page; age verification; access to gambling account history; the availability of RG tools, such as limit setting facilities and exclusion settings; and links to limit-setting options on the deposit page. Descriptive statistics were then performed on the results from each website. Of the 39 online gambling operators identified, 22 redirected gamblers to a “.com” domain, while 17 operators remained as a “.ie” domain. Thirty-five websites (89.7%) visited had a dedicated RG page. Responsible gambling features were evaluated and demonstrated to be available in an inconsistent manner across online gambling websites. Irish websites were shown to perform poorly in comparison with non-Irish counterparts in the provision of RG tools. The researchers of the present study are not aware of any similar studies conducted to date in Ireland

Functionally relevant white matter degradation in multiple sclerosis: a tract-based spatial meta-analysis

Purpose To identify statistical consensus between published studies for distribution and functional relevance of tract white matter (WM) degradation in multiple sclerosis (MS). Materials and Methods By systematically searching online databases, tract-based spatial statistics studies were identified that compared fractional anisotropy (FA; a marker for WM integrity) in MS patients to healthy control subjects, correlated FA in MS patients with physical disability, or correlated FA in MS patients with cognitive performance. Voxelwise meta-analysis was performed by using the Signed Differential Mapping method for each comparison. Moderating effects of mean age, mean physical disability score, imager magnet strength, lesion load, and number of diffusion directions were assessed by means of meta-regression. Results Meta-analysis was performed on data from 495 patients and 253 control subjects across 12 studies. MS diagnosis was significantly associated with widespread lower tract FA (nine studies; largest cluster, 4379 voxels; z = 7.1; P < .001). Greater physical disability was significantly associated with lower FA in the right posterior cingulum, left callosal splenium, right inferior fronto-occipital fasciculus, and left fornix crus (six studies; 323 voxels; z = 1.7; P = .001). Impaired cognition was significantly associated with lower FA in the callosal genu, thalamus, right posterior cingulum, and fornix crus (seven studies; largest cluster, 980 voxels; z = 2.5; P < .001). Conclusion WM damage is widespread in MS with differential and only minimally overlapping distributions of low FA that relates to physical disability and cognitive impairment. The higher number of clusters of lower FA in relation to cognition and their higher z scores suggest that cerebral WM damage may have a greater relevance to cognitive dysfunction than physical disability in MS, and that low anterior callosal and thalamic FA have specific importance to cognitive status

Lesion topography and microscopic white matter tract damage contribute to cognitive impairment in symptomatic carotid artery disease

Purpose: To investigate associations between neuroimaging markers of cerebrovascular disease, including lesion topography and extent and severity of strategic and global cerebral tissue injury, and cognition in carotid artery disease (CAD). Materials and Methods: All participants gave written informed consent to undergo brain magnetic resonance imaging and the Addenbrooke’s Cognitive Examination–Revised. One hundred eight patients with symptomatic CAD but no dementia were included, and a score less than 82 represented cognitive impairment. Group comparison and interrelations between global cognitive and fluency performance, lesion topography, and ultrastructural damage were assessed with voxel-based statistics. Associations between cognition, medial temporal lobe atrophy (MTA), lesion volumes, and global white matter ultrastructural damage indexed as increased mean diffusivity were tested with regression analysis by controlling for age. Diagnostic accuracy of imaging markers selected from a multivariate prediction model was tested with receiver operating characteristic analysis. Results: Cognitively impaired patients (n = 53 [49.1%], classified as having probable vascular cognitive disorder) were older than nonimpaired patients (P = .027) and had more frequent MTA (P<.001), more cortical infarctions (P = .016), and larger volumes of acute (P = .028) and chronic (P = .009) subcortical ischemic lesions. Lesion volumes did not correlate with global cognitive performance (lacunar infarctions, P = .060; acute lesions, P = .088; chronic subcortical ischemic lesions, P = .085). In contrast, cognitive performance correlated with presence of chronic ischemic lesions within the interhemispheric tracts and thalamic radiation (P< .05, false discovery rate corrected). Skeleton mean diffusivity showed the closest correlation with cognition (R2 = 0.311, P< .001) and promising diagnostic accuracy for vascular cognitive disorder (area under the curve, 0.82 [95% confidence interval: 0.75, 0.90]). Findings were confirmed in subjects with a low risk of preclinical Alzheimer disease indexed by the absence of MTA (n = 85). Conclusion: Subcortical white matter ischemic lesion locations and severity of ultrastructural tract damage contribute to cognitive impairment in symptomatic CAD, which suggests that subcortical disconnection within large-scale cognitive neural networks is a key mechanism of vascular cognitive disorder

Rapid flow-sorting to simultaneously resolve multiplex massively parallel sequencing products

Sample preparation for Roche/454, ABI/SOLiD and Life Technologies/Ion Torrent sequencing are based on amplification of library fragments on the surface of beads prior to sequencing. Commonly, libraries are barcoded and pooled, to maximise the sequence output of each sequence run. Here, we describe a novel approach for normalization of multiplex next generation sequencing libraries after emulsion PCR. Briefly, amplified libraries carrying unique barcodes are prepared by fluorescent tagging of complementary sequences and then resolved by high-speed flow cytometric sorting of labeled emulsion PCR beads. The protocol is simple and provides an even sequence distribution of multiplex libraries when sequencing the flow-sorted beads. Moreover, since many empty and mixed emulsion PCR beads are removed, the approach gives rise to a substantial increase in sequence quality and mean read length, as compared to that obtained by standard enrichment protocols

"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures

<p>Abstract</p> <p>Background</p> <p>Microarray experiments rely on several critical steps that may introduce biases and uncertainty in downstream analyses. These steps include mRNA sample extraction, amplification and labelling, hybridization, and scanning causing chip-specific systematic variations on the raw intensity level. Also the chosen array-type and the up-to-dateness of the genomic information probed on the chip affect the quality of the expression measures. In the accompanying publication we presented theory and algorithm of the so-called hook method which aims at correcting expression data for systematic biases using a series of new chip characteristics.</p> <p>Results</p> <p>In this publication we summarize the essential chip characteristics provided by this method, analyze special benchmark experiments to estimate transcript related expression measures and illustrate the potency of the method to detect and to quantify the quality of a particular hybridization. It is shown that our single-chip approach provides expression measures responding linearly on changes of the transcript concentration over three orders of magnitude. In addition, the method calculates a detection call judging the relation between the signal and the detection limit of the particular measurement. The performance of the method in the context of different chip generations and probe set assignments is illustrated. The hook method characterizes the RNA-quality in terms of the 3'/5'-amplification bias and the sample-specific calling rate. We show that the proper judgement of these effects requires the disentanglement of non-specific and specific hybridization which, otherwise, can lead to misinterpretations of expression changes. The consequences of modifying probe/target interactions by either changing the labelling protocol or by substituting RNA by DNA targets are demonstrated.</p> <p>Conclusion</p> <p>The single-chip based hook-method provides accurate expression estimates and chip-summary characteristics using the natural metrics given by the hybridization reaction with the potency to develop new standards for microarray quality control and calibration.</p

The relevance of WHO injury surveillance guidelines for evaluation: learning from the aboriginal community-centered injury surveillance system (ACCISS) and two institution-based systems

<p>Abstract</p> <p>Background</p> <p>Over the past three decades, the capacity to develop and implement injury surveillance systems (ISS) has grown worldwide and is reflected by the diversity of data gathering environments in which ISS operate. The capacity to evaluate ISS, however, is less advanced and existing evaluation guidelines are ambiguous. Furthermore, the applied relevance of these guidelines to evaluate ISS operating in various settings is unclear. The aim of this paper was to examine how the World Health Organization (WHO) injury surveillance guidelines have been applied to evaluate systems operating in three different contexts.</p> <p>Methods</p> <p>The attributes of a good surveillance system as well as instructions for conducting evaluations, outlined in the WHO injury surveillance guidelines, were used to develop an analytical framework. Using this framework, a comparative analysis of the application of the guidelines was conducted using; the Aboriginal Community-Centered Injury Surveillance System (ACCISS) from Canada, the Shantou-Emergency Department Injury Surveillance Project (S-EDISP) from China, and the Yorkhill-Canadian Hospitals Injury Reporting and Prevention Program (Y-CHIRPP) imported from Canada and implemented in Scotland.</p> <p>Results</p> <p>The WHO guidelines provide only a basic platform for evaluation. The guidelines over emphasize epidemiologic attributes and methods and under emphasize public health and injury prevention perspectives requiring adaptation for context-based relevance. Evaluation elements related to the dissemination and use of knowledge, acceptability, and the sustainability of ISS are notably inadequate. From a public health perspective, alternative reference points are required for re-conceptualizing evaluation paradigms. This paper offers an ISS evaluation template that considers how the WHO guidelines could be adapted and applied.</p> <p>Conclusions</p> <p>Findings suggest that attributes of a good surveillance system, when used as evaluation metrics, cannot be weighted equally across ISS. In addition, the attribute of acceptability likely holds more relevance than previously recognized and should be viewed as a critical underpinning attribute of ISS. Context-oriented evaluations sensitive to distinct operational environments are more likely to address knowledge gaps related to; understanding links between the production of injury data and its use, and the effectiveness, impact, and sustainability of ISS. Current frameworks are predisposed to disassociating epidemiologic approaches from subjective factors and social processes.</p

Accurate Expression Profiling of Very Small Cell Populations

BACKGROUND: Expression profiling, the measurement of all transcripts of a cell or tissue type, is currently the most comprehensive method to describe their physiological states. Given that accurate profiling methods currently available require RNA amounts found in thousands to millions of cells, many fields of biology working with specialized cell types cannot use these techniques because available cell numbers are limited. Currently available alternative methods for expression profiling from nanograms of RNA or from very small cell populations lack a broad validation of results to provide accurate information about the measured transcripts. METHODS AND FINDINGS: We provide evidence that currently available methods for expression profiling of very small cell populations are prone to technical noise and therefore cannot be used efficiently as discovery tools. Furthermore, we present Pico Profiling, a new expression profiling method from as few as ten cells, and we show that this approach is as informative as standard techniques from thousands to millions of cells. The central component of Pico Profiling is Whole Transcriptome Amplification (WTA), which generates expression profiles that are highly comparable to those produced by others, at different times, by standard protocols or by Real-time PCR. We provide a complete workflow from RNA isolation to analysis of expression profiles. CONCLUSIONS: Pico Profiling, as presented here, allows generating an accurate expression profile from cell populations as small as ten cells

Testing the role of predicted gene knockouts in human anthropometric trait variation

National Heart, Lung, and Blood Institute (NHLBI) S.L. is funded by a Canadian Institutes of Health Research Banting doctoral scholarship. G.L. is funded by Genome Canada and Génome Québec; the Canada Research Chairs program; and the Montreal Heart Institute Foundation. C.M.L. is supported by Wellcome Trust (grant numbers 086596/Z/08/Z, 086596/Z/08/A); and the Li Ka Shing Foundation. N.S. is funded by National Institutes of Health (grant numbers HL088456, HL111089, HL116747). The Mount Sinai BioMe Biobank Program is supported by the Andrea and Charles Bronfman Philanthropies. GO ESP is supported by NHLBI (RC2 HL-103010 to HeartGO, RC2 HL-102923 to LungGO, RC2 HL-102924 to WHISP). The ESP exome sequencing was performed through NHLBI (RC2 HL-102925 to BroadGO, RC2 HL- 102926 to SeattleGO). EGCUT work was supported through the Estonian Genome Center of University of Tartu by the Targeted Financing from the Estonian Ministry of Science and Education (grant number SF0180142s08); the Development Fund of the University of Tartu (grant number SP1GVARENG); the European Regional Development Fund to the Centre of Excellence in Genomics (EXCEGEN) [grant number 3.2.0304.11-0312]; and through FP7 (grant number 313010). EGCUT were further supported by the US National Institute of Health (grant number R01DK075787). A.K.M. was supported by an American Diabetes Association Mentor-Based Postdoctoral Fellowship (#7-12-MN- 02). The BioVU dataset used in the analyses described were obtained from Vanderbilt University Medical Centers BioVU which is supported by institutional funding and by the Vanderbilt CTSA grant ULTR000445 from NCATS/NIH. Genome-wide genotyping was funded by NIH grants RC2GM092618 from NIGMS/OD and U01HG004603 from NHGRI/NIGMS. Funding to pay the Open Access publication charges for this article was provided by a block grant from Research Councils UK to the University of Cambridge