Reannotation des Maize oligonucleotide arrays

Die Microarray-Technologie hat sich zu einem etablierten Ansatz der Hochdurchsatz-Genexpressionsanalyse entwickelt. Das „maize oligonucleotide array“ (maizearray) ist eine der wenigen Microarray-Plattformen, welche für die genomweite Genexpressionsanalyse von Mais (Zea mays L.) erzeugt wurden. Die Sonden wurden basierend auf ESTs (expressed sequence tags) generiert. Mittlerweile ist die Genomsequenz von Mais verfügbar und ermöglicht eine genauere Annotation dieser Sonden. In dieser Arbeit wurden die Genompositionen aller Sonden und basierend darauf die zugrunde liegenden Gene sowie deren funktionelle Annotation bestimmt. Durch die Analyse konnten Redundanzen und nicht eindeutig bindende Sonden aufgedeckt und gleichzeitig die Zahl der Gene mit funktioneller Annotation verdoppelt werden. Unsere Reannotation wird funktionelle Analysen bereits existierender und zukünftiger Datensätze stark verbessern

Note on intrinsic metrics on graphs

We study the set of intrinsic metrics on a given graph. This is a convex compact set and it carries a natural order. We investigate existence of largest elements with respect to this order. We show that the only locally finite graphs which admit a largest intrinsic metric are certain finite star graphs. In particular all infinite locally finite graphs do not admit a largest intrinsic metric. Moreover, we give a characterization for the existence of intrinsic metrics with finite balls for weakly spherically symmetric graphs

Complex THz and DC inverse spin Hall effect in YIG/Cu1−x_{1-x}Irx_{x} bilayers across a wide concentration range

We measure the inverse spin Hall effect of Cu$_{1-x}$Ir$_{x}$ thin films on yttrium iron garnet over a wide range of Ir concentrations ($0.05 \leqslant x \leqslant 0.7$). Spin currents are triggered through the spin Seebeck effect, either by a DC temperature gradient or by ultrafast optical heating of the metal layer. The spin Hall current is detected by, respectively, electrical contacts or measurement of the emitted THz radiation. With both approaches, we reveal the same Ir concentration dependence that follows a novel complex, non-monotonous behavior as compared to previous studies. For small Ir concentrations a signal minimum is observed, while a pronounced maximum appears near the equiatomic composition. We identify this behavior as originating from the interplay of different spin Hall mechanisms as well as a concentration-dependent variation of the integrated spin current density in Cu$_{1-x}$Ir$_{x}$. The coinciding results obtained for DC and ultrafast stimuli show that the studied material allows for efficient spin-to-charge conversion even on ultrafast timescales, thus enabling a transfer of established spintronic measurement schemes into the terahertz regime.Comment: 12 pages, 4 figure

Explainable AI in medical imaging:An overview for clinical practitioners - Saliency-based XAI approaches

Since recent achievements of Artificial Intelligence (AI) have proven significant success and promising results throughout many fields of application during the last decade, AI has also become an essential part of medical research. The improving data availability, coupled with advances in high-performance computing and innovative algorithms, has increased AI's potential in various aspects. Because AI rapidly reshapes research and promotes the development of personalized clinical care, alongside its implementation arises an urgent need for a deep understanding of its inner workings, especially in high-stake domains. However, such systems can be highly complex and opaque, limiting the possibility of an immediate understanding of the system's decisions. Regarding the medical field, a high impact is attributed to these decisions as physicians and patients can only fully trust AI systems when reasonably communicating the origin of their results, simultaneously enabling the identification of errors and biases. Explainable AI (XAI), becoming an increasingly important field of research in recent years, promotes the formulation of explainability methods and provides a rationale allowing users to comprehend the results generated by AI systems. In this paper, we investigate the application of XAI in medical imaging, addressing a broad audience, especially healthcare professionals. The content focuses on definitions and taxonomies, standard methods and approaches, advantages, limitations, and examples representing the current state of research regarding XAI in medical imaging. This paper focuses on saliency-based XAI methods, where the explanation can be provided directly on the input data (image) and which naturally are of special importance in medical imaging.</p

Re-annotation of the maize oligonucleotide array

The microarray technology has become an established approach for large-scale gene expression analysis with mature protocols for sample, microarray, and data processing. The maize oligonucleotide array (maizearray) is one of the few microarray platforms designed for genome-wide gene expression analysis in Zea mays L. Many datasets addressing various genetic, physiological and developmental topics generated with this platform are available. The original 57,452 microarray probes were compiled based on expressed sequence tags (ESTs). Meanwhile the maize genome sequence became available providing the possibility for an improved annotation of the microarray probe set. In this study we determined the genome positions of all maize array probes to obtain current gene annotations and generated current Gene Ontology (GO) annotations. These new data allow tracing redundancy of the probe set and interfering cross-hybridizations, and doubled the number of genes with functional GO data. Our re-annotation will largely improve the functional analysis of available and future datasets generated on this microarray platform

Fiber-tip spintronic terahertz emitters

Spintronic terahertz emitters promise terahertz sources with an unmatched broad frequency bandwidth that are easy to fabricate and operate, and therefore easy to scale at low cost. However, current experiments and proofs of concept rely on free-space ultrafast pump lasers and rather complex benchtop setups. This contrasts with the requirements of widespread industrial applications, where robust, compact, and safe designs are needed. To meet these requirements, we present a novel fiber-tip spintronic terahertz emitter solution that allows spintronic terahertz systems to be fully fiber-coupled. Using single-mode fiber waveguiding, the newly developed solution naturally leads to a simple and straightforward terahertz near-field imaging system with a 90%-10% knife-edge-response spatial resolution of 30 ${\mu}m$

Advection of Biomass Burning Aerosols towards the Southern Hemispheric Mid-Latitude Station of Punta Arenas as Observed with Multiwavelength Polarization Raman Lidar

In this paper, we present long-term observations of the multiwavelength Raman lidar PollyXT conducted in the framework of the DACAPO-PESO campaign. Regardless of the relatively clean atmosphere in the southern mid-latitude oceans region, we regularly observed events of long-range transported smoke, originating either from regional sources in South America or from Australia. Two case studies will be discussed, both identified as smoke events that occurred on 5 February 2019 and 11 March 2019. For the first case considered, the lofted smoke layer was located at an altitude between 1.0 and 4.2 km, and apart from the predominance of smoke particles, particle linear depolarization values indicated the presence of dust particles. Mean lidar ratio values at 355 and 532 nm were 49 ± 12 and 24 ± 18 sr respectively, while the mean particle linear depolarization was 7.6 ± 3.6% at 532 nm. The advection of smoke and dust particles above Punta Arenas affected significantly the available cloud condensation nuclei (CCN) and ice nucleating particles (INP) in the lower troposphere, and effectively triggered the ice crystal formation processes. Regarding the second case, the thin smoke layers were observed at altitudes 5.5–7.0, 9.0 and 11.0 km. The particle linear depolarization ratio at 532 nm increased rapidly with height, starting from 2% for the lowest two layers and increasing up to 9.5% for the highest layer, indicating the possible presence of non-spherical coated soot aggregates. INP activation was effectively facilitated. The long-term analysis of the one year of observations showed that tropospheric smoke advection over Punta Arenas occurred 16 times (lasting from 1 to 17 h), regularly distributed over the period and with high potential to influence cloud formation in the otherwise pristine environment of the region

External application of liver compresses to reduce fatigue in patients with metastatic cancer undergoing radiation therapy, a randomized clinical trial

Background: Liver compresses are frequently used in integrative medicine as supportive therapy during cancer treatment in order to reduce fatigue. We performed a pilot study to test whether the external application of yarrow liver compresses impacts fatigue in patients with metastatic cancer undergoing radiation therapy. Methods: A randomized prospective pilot trial was performed including patients with brain metastasis or bone metastasis of solid tumors. Patients underwent either palliative radiation therapy (RT) of the metastatic lesions (control group) over two weeks or the same RT with additional external application of yarrow liver compresses once daily during RT. The primary objective was improvement on the general fatigue subscale of the multidimensional fatigue inventory (MFI-20) at the end of treatment, where a mean difference of two points is considered clinically relevant. Secondary objectives included psychological distress, quality of life and qualitative analysis with self-established visual analogue scales (VAS). Mean differences in general fatigue at the end of treatment compared to baseline were analyzed using the ANCOVA test. Results: From 09/2017 to 08/2019 a total of 39 patients were randomized. Due to drop outs 24 patients (12 per group) were available for analysis. Patients in the intervention group received a mean number of 10.5 (range, 7-14) applications of yarrow liver compresses. The mean improvement at the end of therapy on the general fatigue subscale of the MFI-20 was 2 points in favor of the intervention group (p = 0.13), and all other MFI-20 subscales showed at least a trend towards improvement in favor of the intervention group. Likewise, psychological distress and VAS data was improved, the latter reaching statistical significance for the symptoms fatigue, tension and lack of drive. Major toxicities were not observed. Conclusions: External application of liver compresses appears to reduce fatigue within a clinical relevant range in patients with metastatic cancer undergoing radiation therapy. Trial registration: ISRCTN, ICTRP DRKS0001299