727 research outputs found
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Mittelalterliche Pflanzenreste von der Marktstätte und Brotlaube in Konstanz [Dataset]
No full textDuring excavations in medieval Konstanz very many samples were taken for archaeobotanical analyses. Samples could be dated to different time layers from High to Late Middle Ages. Spelt, millet and oats were probably the most important cereals. But also flax, hemp, figs and spices were recorded
Risk, time pressure, and selection effects [Dataset]
No full textTime pressure is a central aspect of economic decision making nowadays.
It is therefore natural to ask how time pressure affects decisions, and how to detect
individual heterogeneity in the ability to successfully cope with time pressure. In the
context of risky decisions, we ask whether a person’s performance under time
pressure can be predicted by measurable behavior and traits, and whether such
measurement itself may be affected by selection issues. We find that the ability to
cope with time pressure varies significantly across decision makers, leading to
selected subgroups that differ in terms of their observed behaviors and personal
traits. Moreover, measures of cognitive ability and intellectual efficiency jointly
predict individuals’ decision quality and ability to keep their decision strategy under
time pressure
Raw data and analysis scripts for "Design and application of an MR reference phantom for multicentre lung imaging trials"
No full textThis dataset contains all MRI phantom data discussed in the related publication as well as the python scripts used to analyse them. The format is DICOM files, where institution names and adresses have been anonymized.
Abstract
Introduction:
As there is an increasing number of multicentre lung imaging studies with MRI in patients, dedicated reference phantoms are required to allow for the assessment and comparison of image quality in multi-vendor and multi-centre environments. However, appropriate phantoms for this purpose are so far not available commercially. It was therefore the purpose of this project to design and evaluate a cost-effective and simple to use reference phantom which addresses the specific requirements for imaging the lungs with MRI.
Methods:
We designed and employed a cost-effective and simple to use reference phantom specifically for the demands of chest MRI, simulating 4 compartments (lung, blood, muscle and fat) which reflect the specific conditions in proton-MRI of the chest. Multiple phantom instances were produced and measured at 15 sites using a complete proton-MRI protocol designed for an in vivo COPD study at intervals over the course of the study. Measures of signal- and contrast-to-noise ratio, as well as structure and edge depiction were extracted from conventionally acquired images using software written for this purpose.
Results:
For the signal to noise ratio, low (short-term) intra-scanner variability was found with, 4.5% in the lung compartment, 4.0% for blood, 3.3% for muscle and 3.7% for fat. The inter-scanner variability was substantially higher, with 41%, 32% 27% and 32% for the same order of compartments. In addition, measures of structure and edge depiction were found to both vary significantly among several scanner types and among scanners of the same model which were equipped with different gradient systems.
Conclusion:
The described reference phantom detected substantial inter-scanner variability in a current multicentre proton MRI study of the lung. Accordingly, the use of an appropriate reference phantom is advised and the extent of variability in image quality should be considered when interpreting results of such imaging studies
Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile [Dataset]
No full textLatin Americans are highly heterogeneous regarding the type of Native American ancestry. Consideration of specific associations with common diseases may lead to substantial advances in unraveling of disease etiology and disease prevention.
Here we investigate possible associations between the type of Native American ancestry and leading causes of death. After an aggregate-data study based on genome-wide genotype data from 1805 admixed Chileans and 639,789 deaths, we validate an identified association with gallbladder cancer relying on individual data from 64 gallbladder cancer patients, with and without a family history, and 170 healthy controls. Native American proportions were markedly underestimated when the two main types of Native American ancestry in Chile, originated from the Mapuche and Aymara indigenous peoples, were combined together. Consideration of the type of Native American ancestry was crucial to identify disease associations. Native American ancestry showed no association with gallbladder cancer mortality (P = 0.26). By contrast, each 1% increase in the Mapuche proportion represented a 3.7% increased mortality risk by gallbladder cancer (95%CI 3.1–4.3%, P = 6×10−27). Individual-data results and extensive sensitivity analyses confirmed the association between Mapuche ancestry and gallbladder cancer. Increasing Mapuche proportions were also associated with an increased mortality due to asthma and, interestingly, with a decreased mortality by diabetes. The mortality due to skin, bladder, larynx, bronchus and lung cancers increased with increasing Aymara proportions. Described methods should be considered in future studies on human population genetics and human health. Complementary individual-based studies are needed to apportion the genetic and non-genetic components of associations identified relying on aggregate-data
3D Focusing in Simple Microfluidic Devices for Continuous-flow Single-cell Imaging [data set]
No full textAccompanying data for the manuscript "3D Focusing in Simple Microfluidic Devices for Continuous-flow Single-cell Imaging"
Judging the mood of the crowd: Attention is focused on happy faces [Dataset]
No full textPrevious research on valence biases in face perception revealed inconsistent findings either proposing angry or happy faces to be detected more efficiently. We argue that the typical experimental task in this field, the face-in-the-crowd (FiC) paradigm, lacks ecological validity and leads to ambiguous results. In the present paper, we introduce a new task, the mood-of-the-crowd (MoC) paradigm that can complement existing FiC findings. In the new task, participants have to decide which expression is shown by most faces in a crowd. In Experiment 1, photographs were used as stimuli, whereas computer-generated faces were presented in Experiment 2. While in the first experiments either happy and neutral or angry and neutral emotions were shown within one crowd, in Experiment 3, crowds were composed of angry and happy faces. Gaze position was recorded to gain further insights on attentional processes. In the first experiment, happy moods were identified faster and with a higher accuracy. Although we could only find higher accuracy rates for happy moods in experiment 2, happy faces were fixated more frequently indicating faster processing of more information in the same amount of time. A higher proportion of fixations and first fixation on happy faces occurred in experiment 3. Moreover, target gender was found to be an important moderator. In female crowds, emotion was generally assessed more accurately. Additionally, while emotional faces were overall focused more often than neutral faces, this effect was more pronounced in female crowds. The same pattern emerged in the comparison of happy vs. angry faces: Female happy faces had the highest probability to attract attention. The close connection between femininity and emotionality or rather happiness is discussed as a possible reason for these findings
Automatic evaluation of tumour budding in immunohistochemically stained colorectal carcinomas and correlation to clinical outcome [Dataset]
No full text Data used for the implementation of the proposed tumor budding detection
In the publication “Automatic evaluation of tumour budding in immunohistochemically stained colorectal carcinomas and correlation to clinical outcome” we described a multistep approach to detect tumor buds in immunohistochemically stained images: .
Step 1: Color and size based segmentation.
Step 2: Validation of the detected objects (proposals) by a spatial clustering and a convolutional neural network (MatConvNet by A. Vedaldi et al. [1]).
The Matlab-Code for the project is available on GitHub.
The data for the CNN-training and validation are presented as .mat-file. It contains a struct element with the images in a 4D-matrix, the label (“bud” and “no bud”) and a set (“training” and “validation”).
Please refer to the "Terms" tab below for usage and reproduction terms.
References:
1. Vedaldi, A., K. Lenc, and A. Gupta. MatConvNet: CNNs for MATLAB. 2015; Available from: http://www.vlfeat.org/matconvnet/
Robust logistic regression to narrow down the winner's curse for rare and recessive susceptibility variants [Source Code]
No full textLogistic regression is the most common technique used for genetic case-control association studies. A disadvantage of standard maximum likelihood estimators of the genotype relative risk (GRR) is their strong dependence on outlier subjects, for example, patients diagnosed at unusually young age. Robust methods are available to constrain outlier influence, but they are scarcely used in genetic studies. This article provides a non-intimidating introduction to robust logistic regression, and investigates its benefits and limitations in genetic association studies. We applied the bounded Huber and extended the R package ‘robustbase’ with the re-descending Hampel functions to down-weight outlier influence. Computer simulations were carried out to assess the type I error rate, mean squared error (MSE) and statistical power according to major characteristics of the genetic study and investigated markers. Simulations were complemented with the analysis of real data. Both standard and robust estimation controlled type I error rates. Standard logistic regression showed the highest power but standard GRR estimates also showed the largest bias and MSE, in particular for associated rare and recessive variants. For illustration, a recessive variant with a true GRR=6.32 and a minor allele frequency=0.05 investigated in a 1000 case/1000 control study by standard logistic regression resulted in power=0.60 and MSE=16.5. The corresponding figures for Huber-based estimation were power=0.51 and MSE=0.53. Overall, Hampel- and Huber-based GRR estimates did not differ much. Robust logistic regression may represent a valuable alternative to standard maximum likelihood estimation when the focus lies on risk prediction rather than identification of susceptibility variants
Histopathology of thymectomy specimens from the MGTX-trial
No full textBackground:
The thymectomy specimens from the “thymectomy trial in non-thymomatous myasthenia gravis patients receiving prednisone therapy” (MGTX) [1] underwent rigid and comprehensive work-up, which results in a unique, spatially mapped dataset.
Fig. 1 Specimen work-up:
Work-up scheme for the specimens in the MGTX trial [1, 2]. Thymuses were sub-divided into regions that underwent predefined evaluation (e.g. complete work-up of the central A-region, partial work-up of other regions)
Content:
A xlsx-file with one table for patient data (“dataPatients” with age, gender etc.), one table with histomorphological data for the specimen regions (“dataAllRegions” with grading atrophy, grading overall fat etc.) and one table for the follicle morphology in the A region (“dataARegion” with n follicle with germinal centre etc.).
References:
1. Wolfe, G.I., et al., Randomized Trial of Thymectomy in Myasthenia Gravis. N Engl J Med, 2016. 375(6): p. 511-22.
2. Ströbel, P., et al., The ageing and myasthenic thymus: A morphometric study validating a standard procedure in the histological workup of thymic specimens. Journal of Neuroimmunology, 2008. 201–202: p. 64-73
RNA Sequence Data for Hepatobiliary Cancer Cell Lines
No full textRNA Sequence Data for Hepatobiliary Cancer Cell Line