Towards reproducible research of event detection techniques for Twitter

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DenseNet and Support Vector Machine classifications of major depressive disorder using vertex-wise cortical features

Major depressive disorder (MDD) is a complex psychiatric disorder that affects the lives of hundreds of millions of individuals around the globe. Even today, researchers debate if morphological alterations in the brain are linked to MDD, likely due to the heterogeneity of this disorder. The application of deep learning tools to neuroimaging data, capable of capturing complex non-linear patterns, has the potential to provide diagnostic and predictive biomarkers for MDD. However, previous attempts to demarcate MDD patients and healthy controls (HC) based on segmented cortical features via linear machine learning approaches have reported low accuracies. In this study, we used globally representative data from the ENIGMA-MDD working group containing an extensive sample of people with MDD (N=2,772) and HC (N=4,240), which allows a comprehensive analysis with generalizable results. Based on the hypothesis that integration of vertex-wise cortical features can improve classification performance, we evaluated the classification of a DenseNet and a Support Vector Machine (SVM), with the expectation that the former would outperform the latter. As we analyzed a multi-site sample, we additionally applied the ComBat harmonization tool to remove potential nuisance effects of site. We found that both classifiers exhibited close to chance performance (balanced accuracy DenseNet: 51%; SVM: 53%), when estimated on unseen sites. Slightly higher classification performance (balanced accuracy DenseNet: 58%; SVM: 55%) was found when the cross-validation folds contained subjects from all sites, indicating site effect. In conclusion, the integration of vertex-wise morphometric features and the use of the non-linear classifier did not lead to the differentiability between MDD and HC. Our results support the notion that MDD classification on this combination of features and classifiers is unfeasible

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Polishing Structural Bulk Updates in a Native XML Database

BaseX is a native XML database on the foundation of a fixed-length, sequential document encoding. Built with a strong focus on reading performance, this thesis shows that the Pre/Dist/Size encoding is yet perfectly capable of handling massive bulk update transactions. Despite its theoretical limitations regarding structural changes of the tree, we show that performance is indeed restricted by the document order and disk access patterns. During tests with the XQuery Update Facility (XQUF), we delete 1.8 million nodes in 22.4 seconds, evenly distributed over a 1.1GB XMark document instance. Compared to the prior approach, this equals a reduction of processing time by 99.99%. To achieve this, we extend the obligatory implementation of the XQUF pending update list with an additional low-level layer, that pre-calculates tree structure adjustments in-memory. This layer adds little overhead and further enables us to merge update operations and curb fragmentation that finds its origin at the user level. To not violate the document order, the XQUF is only arduously brought together with the concept of efficient bulk updates. A method is introduced that imposes an order on update primitives to finally get a ready-to-apply sequence of atomic updates. The reviewed implementation is fully consistent with the XQUF specification and has already proven rock-solid efficiency in production use. A few theoretical paragraphs on alternative approaches, disk access patterns and memory consumption highlight sleeping potential and prepare further progression

BaseX: Erweiterung einer nativen XML Datenbank um XQuery Update

This Bachelor Thesis describes concepts behind the extension of a native XML database with XQuery Update. BaseX is a compact and highly efficient open source XML database and XQuery processor. Based on a relational document encoding, a generic method is presented, that exploits the sequential encoding scheme to its full advantage. The implementation yields excellent test results. Further optimizations are proposed. A method to speed up the execution of critical structural updates and ways to accelerate the overall process. A discussion on ACID conformity in transactional XML database systems finalizes this work

Efficient Structural Bulk Updates on the Pre/Dist/Size XML Encoding

In order to manage XML documents, native XML databases use specific encodings that map the hierarchical structure of a document to a flat representation. Several encodings have been proposed that differ in terms of their support for certain query workloads. While some encodings are optimized for query processing, others focus on data manipulation. For example, the Pre/Dist/Size XML encoding has been designed to support queries over all XPath axes efficiently, but processing atomic updates in XML documents can be costly. In this paper, we present a technique, so-called structural bulk updates, that works in concert with the XQuery Update Facility to support efficient updates on the Pre/Dist/Size encoding. We demonstrate the benefits of our technique in a detailed performance evaluation based on the XMark benchmark

Optical Coherence Tomography and Ultrasonographical Biomarkers in Papilledema - A Retrospective Study on 267 Patients

The differentiation between papilledema and pseudopapilledema is an essential, non-trivial diagnostic task in neuroophthalmological routine. Retrobulbar optic nerve sheath diameter (NSD) measured by standardized A-scan ultrasound and a widened nerve void (WNV) in B-scan ultrasound provide useful information when differentiating the two conditions and proved to yield a high predictive value for intracranial hypertension. Spectral domain optical coherence (SD-OCT) tomography yields objective morphometric data on peripapillary retinal nerve fiber layer (RNFL). The aim of this study was to evaluate the association of peripapillary RNFL thickness and NSD in papilledema

18F-FDG, 11C-methionine, and 68Ga-pentixafor PET/CT in patients with smoldering multiple myeloma: imaging pattern and clinical features

This study aimed to explore the correlation between imaging patterns and clinical features in patients with smoldering multiple myeloma (SMM) who simultaneously underwent 18F-FDG, 11C-Methionine, and 68Ga-Pentixafor positron emission tomography/computed tomography (PET/CT). We retrieved and analyzed clinical characteristics and PET imaging data of 10 patients with SMM. We found a significant correlation between bone marrow (BM) plasma cell (PC) infiltration and mean standardized uptake values (SUV$_{mean}$) of lumbar vertebrae L2-L4 on 11C-Methionine PET/CT scans (r = 0.676, p = 0.031) and 68Ga-Pentixafor PET/CT scans (r = 0.839, p = 0.002). However, there was no significant correlation between BM involvement and SUV$_{mean}$ of lumbar vertebrae L2-L4 on 18F-FDG PET/CT scans (r = 0.558, p = 0.093). Similarly, mean target-to-background ratios (TBR$_{mean}$) of lumbar vertebrae L2-L4 also correlated with bone marrow plasma cell (BMPC) infiltration in 11C-Methionine PET/CT (r = 0.789, p = 0.007) and 68Ga-Pentixafor PET/CT (r = 0.724, p = 0.018) PET/CT. In contrast, we did not observe a significant correlation between BMPC infiltration rate and TBR$_{mean}$ in 18F-FDG PET/CT (r = 0.355, p = 0.313). Additionally, on 11C-Methionine PET/CT scans, we found a significant correlation between BMPC infiltration and TBR$_{max}$ of lumbar vertebrae L2-L4 (r = 0.642, p = 0.045). In conclusion, 11C-Methionine and 68Ga-Pentixafor PET/CT demonstrate higher sensitivity than 18F-FDG PET/CT in detecting BM involvement in SMM

The link between cytogenetics/genomics and imaging patterns of relapse and progression in patients with relapsed/refractory multiple myeloma: a pilot study utilizing 18F-FDG PET/CT

Utilizing 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography (PET)/computed tomography (CT), we performed this pilot study to evaluate the link between cytogenetic/genomic markers and imaging patterns in relapsed/refractory (RR) multiple myeloma (MM). We retrospectively analyzed data of 24 patients with RRMM who were treated at our institution between November 2018 and February 2020. At the last relapse/progression, patients had been treated with a median of three (range 1–10) lines of therapy. Six (25%) patients showed FDG avid extramedullary disease without adjacency to bone. We observed significantly higher maximum standardized uptake values (SUVmax) in patients harboring del(17p) compared with those without del(17p) (p = 0.025). Moreover, a high SUVmax of >15 indicated significantly shortened progression-free survival (PFS) (p = 0.01) and overall survival (OS) (p = 0.0002). One female patient exhibited biallelic TP53 alteration, i.e., deletion and mutation, in whom an extremely high SUVmax of 37.88 was observed. In summary, this pilot study suggested a link between del(17p)/TP53 alteration and high SUVmax on 18F-FDG PET/CT in RRMM patients. Further investigations are highly warranted at this point