Summary:

A public repository of data processed for Mallm, Iskar, Ishaque et. al. 2018 Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks

Website: http://www.cancerepisys.org/cancerepisys/index.html

Github: https://github.com/CancerEpiSys/Mallm-et-al-processing-scripts

Research mission

CancerEpiSys is a BMBF funded research project with the CancerSys program that dissects the epigenetic networks associated with chronic lymphocytic leukemia (CLL) to develop novel diagnostic and therapeutic approaches for the disease. It has been initiated based on the emerging view that signals encoded in the DNA sequence, epigenetic modifications (e.g. DNA methylation, post-translational histone modifications), non-coding RNAs and nucleosome positioning are not independently regulated properties. Rather, these chromatin features are governed by an interconnected network of molecular processes that determine the cellular gene expression program. Any errors that occur in the interplay of these factors can lead to aberrant gene regulation associated with cancer. To rationalize the mode of action of novel ‘epigenetic’ drugs in cancer therapy that change properties of this network, we will dissect experimentally and mathematically the interdependence of these processes, focusing on CLL.

The main objectives of CancerEpiSys are: (i) deciphering the relation of DNA sequence, epigenetic modifications, nucleosome positioning and aberrant gene expression in CLL, (ii) the identification of epigenetic network morphologies that describe the response to the epigenetic drugs panobinostat and 3-deazaneplanocin (DZNep) that inhibit histone deacetylases and methyltransferases, (iii) the characterization of epigenetic markers and chromatin features of CLL patient subgroups, and (iv) the integration of results into an analysis scheme for the epigenetic aberrations most relevant for prognostication, prediction of treatment relapse and stratification of patients with respect to therapeutic options. Moreover, our results will inform novel therapeutic approaches that target gene-expression programs at the epigenetic level to sensitize cancer cells towards apoptosis and anti-growth signals.

Summary: Global reconstructions of particle biovolume, size distribution, and carbon export flux from the seasonal euphotic zone and maximum winter time mixed layer.

Summary: Global reconstruction of surface oceanic N2O disequilibrium and its associated flux. The dataset consists of (1) a global compilation of observed nitrous oxide pressure, concentration, mixing ratio measurements and their associated disequilibrium in the surface ocean; (2) the globally mapped N2O disequilibrium predicted by a supervised learning algorithm, and (3) the reconstructed ocean to atmosphere N2O flux. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/810032

Summary: Remotely-generated submesoscale coherent vortices (SCV) within Argo profiles. The data reveal the date, locations, and identification information of Argo profiles that pierced spicy-core (anomalously warm and salty) and minty-core (anomalously cold and fresh) SCVs. We also include statistics gathered for each SCV, such as core water mass characteristics and height/length scales. These data are described in McCoy et al. (2020); doi: 10.1016/j.pocean.2020.102452 For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/836648

Summary:

IMC-Master-Marlin implements the Master code for the Intelligent Motor Control interface, which enables 3D printers to perform motor control tasks requiring additional horsepower. IMC-Marlin-Master is based on the popular Marlin firmware.

Summary:

The Ball-Larus path profiling technique is a powerful methodology for intraprocedural program analysis. Identifying the hottest paths in the control flow graph of a routine, for instance, can direct optimizations to portions of the code where most resources are consumed. However, a shortcoming of this technique was the inability to profile cyclic paths, making it difficult to mine execution patterns that span multiple loop iterations.

In the paper Ball-Larus path profiling across multiple loop iterations appeared at OOPSLA '13 (28th ACM SIGPLAN Conference on Object-Oriented Programming, Systems, Languages, and Applications), we present a new approach to multi-iteration path profiling that allows the profiling of all executed paths obtained as a concatenation of up to k Ball-Larus acyclic paths, where k is a user-defined parameter.

We provide examples showing that this method can reveal optimization opportunities that acyclic-path profiling would miss, and an extensive experimental evaluation on the Jikes RVM shows that our approach can be even faster than Ball-Larus due to fewer operations on smaller hash tables, producing compact representations of cyclic paths even for large values of k.

The present artifact has been endorsed by the OOPSLA Artifact Evaluation Committee. In the archive we provide:

• a VirtualBox disk image containing a lightweight Linux distribution fully configured for using our profiler
• a thorough Getting started guide
• source code and other materials

Summary: iOS/OSX DSP for audio (with Novocaine)