Modelling of patient journey in chronic spontaneous urticaria: Increasing awareness and education by shorten patients' disease journey in Germany.

Background: Chronic spontaneous urticaria (CSU) is both physically and emotionally stressful, and guideline recommendations are often not optimally implemented in clinical practice. The objective of this study was to provide an overview on the patient journey in CSU and to develop a mathematical model based on solid data.

Methods: The journey of CSU patients in Germany was traced through literature review and expert meetings that included medical experts, pharmacists and representatives of patient organizations.

Synaptic Mechanisms Underlying Temporally Precise Information Processing in the VNLL, an Auditory Brainstem Nucleus.

Large glutamatergic, somatic synapses mediate temporally precise information transfer. In the ventral nucleus of the lateral lemniscus, an auditory brainstem nucleus, the signal of an excitatory large somatic synapse is sign inverted to generate rapid feedforward inhibition with high temporal acuity at sound onsets, a mechanism involved in the suppression of spurious frequency information. The mechanisms of the synaptically driven input-output functions in the ventral nucleus of the lateral lemniscus are not fully resolved.

Analyzing Patient Trajectories With Artificial Intelligence.

In digital medicine, patient data typically record health events over time (eg, through electronic health records, wearables, or other sensing technologies) and thus form unique patient trajectories. Patient trajectories are highly predictive of the future course of diseases and therefore facilitate effective care. However, digital medicine often uses only limited patient data, consisting of health events from only a single or small number of time points while ignoring additional information encoded in patient trajectories.

A phenomenological spiking model for octopus cells in the posterior-ventral cochlear nucleus.

Octopus cells in the posteroventral cochlear nucleus exhibit characteristic onset responses to broad band transients but are little investigated in response to more complex sound stimuli. In this paper, we propose a phenomenological, but biophysically motivated, modeling approach that allows to simulate responses of large populations of octopus cells to arbitrary sound pressure waves. The model depends on only few parameters and reproduces basic physiological characteristics like onset firing and phase locking to amplitude modulations.

Traditional and Digital Biomarkers: Two Worlds Apart?

The identification and application of biomarkers in the clinical and medical fields has an enormous impact on society. The increase of digital devices and the rise in popularity of health-related mobile apps has produced a new trove of biomarkers in large, diverse, and complex data. However, the unclear definition of digital biomarkers, population groups, and their intersection with traditional biomarkers hinders their discovery and validation.

From hype to reality: data science enabling personalized medicine.

Background: Personalized, precision, P4, or stratified medicine is understood as a medical approach in which patients are stratified based on their disease subtype, risk, prognosis, or treatment response using specialized diagnostic tests. The key idea is to base medical decisions on individual patient characteristics, including molecular and behavioral biomarkers, rather than on population averages. Personalized medicine is deeply connected to and dependent on data science, specifically machine learning (often named Artificial Intelligence in the mainstream media).

Towards a systems approach for chronic diseases, based on health state modeling.

Rising pressure from chronic diseases means that we need to learn how to deal with challenges at a different level, including the use of that better connect across fragments, such as disciplines, stakeholders, institutions, and technologies. By learning from progress in leading areas of health innovation (including oncology and AIDS), as well as complementary indications (Alzheimer's disease), I try to extract the most enabling innovation paradigms, and discuss their extension to additional areas of application within a . To facilitate such work, a Precision, P4 or Systems Medicine platform is proposed, which is centered on the representation of that enable the definition of time in the vision to provide Modeling of such should allow iterative optimization, as longitudinal human data accumulate.

Exploring Glucocorticoid Receptor Agonists Mechanism of Action Through Mass Cytometry and Radial Visualizations.

Recent advances in combining flow cytometry and mass spectrometry have led to the development of mass cytometry, allowing for the interrogation of complex cell populations on an unprecedented scale. The volumes and high dimensionality of mass cytometry data pose significant challenges in terms of analysis and visualization. We implement a method called Radviz, where multidimensional single cell data can be visualized as a projection that maintains the original dimensions and data complexity whilst facilitating analysis and visualization.

Short loop-targeting oligoribonucleotides antagonize Lin28 and enable pre-let-7 processing and suppression of cell growth in let-7-deficient cancer cells.

MicroRNAs (miRNAs) originate from stem-loop-containing precursors (pre-miRNAs, pri-miRNAs) and mature by means of the Drosha and Dicer endonucleases and their associated factors. The let-7 miRNAs have prominent roles in developmental differentiation and in regulating cell proliferation. In cancer, the tumor suppressor function of let-7 is abrogated by overexpression of Lin28, one of several RNA-binding proteins that regulate let-7 biogenesis by interacting with conserved motifs in let-7 precursors close to the Dicer cleavage site.

Measurement by SPR of very low dissociation rates: oxidation-mediated loss of biotin-streptavidin affinity.

Long-term relationship: biotin labels on RNAs, and possibly other biomacromolecules, are easily oxidized causing a dramatic loss of affinity for streptavidin and adversely affecting the measurement of high-affinity interactions. A new SPR method has been developed for measuring the very low rate-dissociation constants of biotin- and biotin oxide-conjugated RNAs with streptavidin.

Miravirsen (SPC3649) can inhibit the biogenesis of miR-122.

MicroRNAs (miRNAs) are short noncoding RNAs, which bind to messenger RNAs and regulate protein expression. The biosynthesis of miRNAs includes two precursors, a primary miRNA transcript (pri-miRNA) and a shorter pre-miRNA, both of which carry a common stem-loop bearing the mature miRNA. MiR-122 is a liver-specific miRNA with an important role in the life cycle of hepatitis C virus (HCV).

Calcium-activated chloride channel ANO1 promotes breast cancer progression by activating EGFR and CAMK signaling.

The calcium-activated chloride channel anoctamin 1 (ANO1) is located within the 11q13 amplicon, one of the most frequently amplified chromosomal regions in human cancer, but its functional role in tumorigenesis has remained unclear. The 11q13 region is amplified in ∼15% of breast cancers. Whether ANO1 is amplified in breast tumors, the extent to which gene amplification contributes to ANO1 overexpression, and whether overexpression of ANO1 is important for tumor maintenance have remained unknown.

Protein sequence databases.

Protein sequence databases do not contain just the sequence of the protein itself but also annotation that reflects our knowledge of its function and contributing residues. In this chapter, we will discuss various public protein sequence databases, with a focus on those that are generally applicable. Special attention is paid to issues related to the reliability of both sequence and annotation, as those are fundamental to many questions researchers will ask.

ProteinArchitect: protein evolution above the sequence level.

Background: While many authors have discussed models and tools for studying protein evolution at the sequence level, molecular function is usually mediated by complex, higher order features such as independently folding domains and linear motifs that are based on or embedded in a particular arrangment of features such as secondary structure elements, transmembrane domains and regions with intrinsic disorder. This 'protein architecture' can, in its most simplistic representation, be visualized as domain organization cartoons that can be used to compare proteins in terms of the order of their mostly globular domains.

Methodology: Here, we describe a visual approach and a webserver for protein comparison that extend the domain organization cartoon concept.

Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors.

Cellular differentiation entails loss of pluripotency and gain of lineage- and cell-type-specific characteristics. Using a murine system that progresses from stem cells to lineage-committed progenitors to terminally differentiated neurons, we analyzed DNA methylation and Polycomb-mediated histone H3 methylation (H3K27me3). We show that several hundred promoters, including pluripotency and germline-specific genes, become DNA methylated in lineage-committed progenitor cells, suggesting that DNA methylation may already repress pluripotency in progenitor cells.

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.

To gain insight into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase occupancy and histone modifications at 16,000 promoters in primary human somatic and germline cells. We find CpG-poor promoters hypermethylated in somatic cells, which does not preclude their activity. This methylation is present in male gametes and results in evolutionary loss of CpG dinucleotides, as measured by divergence between humans and primates.

GABAagent: a system for integrating data on GABA receptors.

Motivation: Scientific data pertaining to GABA receptors, which are of medical importance, are widely scattered throughout numerous heterogeneous Internet resources. This situation has made the integrated acquisition of such data difficult and substantially time consuming even for researchers who are Internet aficionados. Thus, there exists a genuine need for the development of Internet applications, such as GABAagent, which provide efficient and timely access to concise and integrated information.

GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

Motivation: Modern biology is shifting from the 'one gene one postdoc' approach to genomic analyses that include the simultaneous monitoring of thousands of genes. The importance of efficient access to concise and integrated biomedical information to support data analysis and decision making is therefore increasing rapidly, in both academic and industrial research. However, knowledge discovery in the widely scattered resources relevant for biomedical research is often a cumbersome and non-trivial task, one that requires a significant amount of training and effort.

Rapid access to biomedical knowledge with GeneCards and HotMolecBase: implications for the electrophoretic analysis of large sets of gene products.

Rapid access to well-organized information about gene products is important for many studies that simultaneously monitor large sets of those factors, for example with electrophoretic methods. HotMolecBase and GeneCards, Internet resources that may be accessed from our Bioinformatics homepage at http://bioinfo.weizmann.

Developmental expression of tau proteins in the chicken and rat brain: rapid down-regulation of a paired helical filament epitope in the rat cerebral cortex coincides with the transition from immature to adult tau isoforms.

The monoclonal antibodies TAU-1 and AT8 are directed at human microtubule-associated protein tau epitopes that contain a dephosphorylated and phosphorylated Ser202, respectively, while AT180 and AT270 are anti-tau monoclonals with epitopes that require phosphorylated Thr181 and Thr231, respectively. We used these antibodies to study the developmental profiles of tau proteins in rat cerebral cortex and chicken optic lobes. In tau extracts from perinatal rat cerebral cortex.

Muscarinic receptor-mediated induction of actin-driven lamellar protrusions in neuroblastoma cell somata and growth cones. Involvement of protein kinase C.

In SH-SY5Y human neuroblastoma cells, addition of acetylcholine or carbachol rapidly induces a transient protrusion of lamellipodia. The protrusions appear after a delay of 30 sec and persist for a period of about 5 min at the margins of cell somata and at the distal parts of cell processes. They are caused by a strikingly increased, cytochalasin B-sensitive assembly of actin at the cell periphery.

Complementary distribution of tau proteins in different phosphorylation states within growing axons.

Microtubule-associated tau proteins are hyperphosphorylated in brains from patients with Alzheimer's disease compared with normal adult human brain. At least some of the phosphorylated residues are also transiently phosphorylated in juvenile brain, but not in more mature stages. Using the monoclonal anti-tau antibodies TAU-1 and AT8, we found in cultured embryonic chicken and rat neurones a clear differential distribution of immunostaining within growing axons.