Diffusion-based generation of Histopathological Whole Slide Images at a Gigapixel scale

We present a novel diffusion-based approach to generate synthetic histopathological Whole Slide Images (WSIs) at an unprecedented gigapixel scale. Synthetic WSIs have many potential applications: They can augment training datasets to enhance the performance of many computational pathology applications. They allow the creation of synthesized copies of datasets that can be shared without violating privacy regulations. Or they can facilitate learning representations of WSIs without requiring data annotations. Despite this variety of applications, no existing deep-learning-based method generates WSIs at their typically high resolutions. Mainly due to the high computational complexity. Therefore, we propose a novel coarse-to-fine sampling scheme to tackle image generation of high-resolution WSIs. In this scheme, we increase the resolution of an initial low-resolution image to a high-resolution WSI. Particularly, a diffusion model sequentially adds fine details to images and increases their resolution. In our experiments, we train our method with WSIs from the TCGA-BRCA dataset. Additionally to quantitative evaluations, we also performed a user study with pathologists. The study results suggest that our generated WSIs resemble the structure of real WSIs

Microwave conductivity in polycrystalline (BEDT-TTF)2I3 material

Polycrystalline material of the &#945;-phase of (BEDT-TTF)2I3 was compressed to small samples (4-mm x 1mm, thickness 0.3 mm typically) at a pressure of 10 kbar. Annealing at 70°C yields the superconducting &#945;t-phase. Microwaves (10,2 GHz) enable the measurements of the conductivity for stepwise annealing after every annealing step in always the same sample. For annealing times 10 min all conductivity versus temperature curves are intersecting in an isosbestlc point at 190 K. This behaviour can be described by a conductivity relation for a two component system, from which was determined the volume fraction of the new grown &#945;t-phase in dependence of the annealing time. Starting annealing (annealing times < 10 min) shows another unexpected phase transformation. After 2 min annealing the conductivity at 200 K increases by more than one order of magnitude, but then decreases of further annealing (5-10 min) down to the value for the unannealed sample

Overexpression of eIF3a in Squamous Cell Carcinoma of the Oral Cavity and Its Putative Relation to Chemotherapy Response

The eukaryotic translation initiation factor eIF3a is one of the core subunits of the translation initiation complex eIF3, responsible for ribosomal subunit joining and mRNA recruitment to the ribosome. It is known to play an important role in general translation initiation as well as in the specific translational regulation of various gene products, among which many influence tumour development, progression, and the therapeutically important pathways of DNA damage repair. Therefore, beyond its role in protein synthesis, eIF3a is emerging as regulator in tumour pathogenesis and therapy response and, therefore, a potential tumor marker. By means of a tissue microarray (TMA) for histopathological and statistical assessment, we here show eIF3a expression in 103 cases of squamous cell carcinoma of the oral cavity (OSCC), representing tissues from 103 independent patients. A subset of the study cohort was treated with platinum based therapy. Our results show that the 170 kDa protein is upregulated in OSCC and correlates with good overall survival. Overexpressing tumors respond better to platinum-based chemotherapy, suggesting eIF3a as a putative predictive as well as prognostic tumor marker in OSCC

Linking provenance and its metadata in multi-organizational environments

Reproducibility issues are widely reported in life sciences. As a response, scientific communities have called for enhanced provenance information documenting the complete research life cycle, starting from biological or environmental material acquisition and ending with translating research results into practice. The integrity and trustworthiness of such provenance can be achieved by applying versioning mechanisms and cryptographic techniques, such as hashes or digital signatures, which are provenance metadata. However, the available provenance literature lacks an analysis of mechanisms for the exchange of provenance and its metadata between organizations as well as a grounded proposal of linking provenance and its metadata. In this work, we provide an in-depth analysis of the approaches for coupling provenance information and its metadata with documented research objects in the context of multi-organizational processes, leading to the categorization of possible approaches, description of their key properties, and derivation of requirements for underlying provenance models. We address the requirements by proposing a mechanism for linking provenance and its metadata by extending the Common Provenance Model, the open conceptual foundation for the ISO 23494 provenance standard series, currently under development. The concepts are demonstrated and validated on two complex use cases. This work is intended as a harmonized source of information on provenance coupling in the context of exchange of provenance between organizations, which can be used when designing or choosing a provenance solution. This type of usage is exemplified in the extension of the Common Provenance Model as another step toward a provenance standard for life sciences

ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

Exchange of research data and samples in biomedical research has become a common phenomenon demanding for their effective quality assessment. At the same time, several reports address reproducibility of research, where history of biological samples (acquisition, processing, transportation, storage, and retrieval) and data history (data generation and processing) defines their fitness for purpose, and hence their quality. The project aims at developing a comprehensive W3C PROV based provenance information standard intended for the biomedical research domain. The standard is being developed by the working group 5 ("data processing and integration") of the ISO (International Standardisation Organisation) technical committee 276 "biotechnology". The outcome of the project will be published in parts as international standards or technical specifications. The poster informs about the goals of the standardisation activity, presents the proposed structure of the standards, briefly describes its current state and outlines its future development and open issues