Search results for "script"
showing 10 items of 5143 documents
Manipulating mtDNA in vivo reprograms metabolism via novel response mechanisms.
2019
Mitochondria have been increasingly recognized as a central regulatory nexus for multiple metabolic pathways, in addition to ATP production via oxidative phosphorylation (OXPHOS). Here we show that inducing mitochondrial DNA (mtDNA) stress in Drosophila using a mitochondrially-targeted Type I restriction endonuclease (mtEcoBI) results in unexpected metabolic reprogramming in adult flies, distinct from effects on OXPHOS. Carbohydrate utilization was repressed, with catabolism shifted towards lipid oxidation, accompanied by elevated serine synthesis. Cleavage and translocation, the two modes of mtEcoBI action, repressed carbohydrate rmetabolism via two different mechanisms. DNA cleavage activ…
gcType : a high-quality type strain genome database for microbial phylogenetic and functional research
2020
Abstract Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This …
Global data on earthworm abundance, biomass, diversity and corresponding environmental properties
2021
Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ec…
Network reconstruction for trans acting genetic loci using multi-omics data and prior information.
2022
Background: Molecular measurements of the genome, the transcriptome, and the epigenome, often termed multi-omics data, provide an in-depth view on biological systems and their integration is crucial for gaining insights in complex regulatory processes. These data can be used to explain disease related genetic variants by linking them to intermediate molecular traits (quantitative trait loci, QTL). Molecular networks regulating cellular processes leave footprints in QTL results as so-called trans-QTL hotspots. Reconstructing these networks is a complex endeavor and use of biological prior information can improve network inference. However, previous efforts were limited in the types of priors…
Spatio-temporal Schema Integration with Validation: A Practical Approach
2005
We propose to enhance a schema integration process with a validation phase employing logic-based data models. In our methodology, we validate the source schemas against the data model; the inter-schema mappings are validated against the semantics of the data model and the syntax of the correspondence language. In this paper, we focus on how to employ a reasoning engine to validate spatio-temporal schemas and describe where the reasoning engine is plugged into our integration methodology. The validation phase distinguishes our integration methodology from other approaches. We shift the emphasis on automation from the a priori discovery to the a posteriori checking of the inter-schema mapping…
Descriptive Statistics
2009
A set of medical data is based on a collection of the data of individual cases or objects, also called observation units or statistical units. Every case, for example every study participant, patient, every experimental animal, every tooth or every cell shows comparable parameters (such as body weight, gender, erosion, pH). Each of these parameters, also called variables, has a specific parameter value (gender = male, age = 30 years, weight = 70 kg) for each observation unit (for example the patient). The aim of descriptive statistics is to summarize the data, so that they can be clearly illustrated (1–3). The property of a parameter is specified by its so-called scale of measure. Generally…
The HisClima database: historical weather logs for automatic transcription and information extraction
2021
Knowing the weather and atmospheric conditions from the past can help weather researchers to generate models like the ones used to predict how weather conditions are likely to change as global temperatures continue to rise. Many historical weather records are available from the past registered on a systemic basis. Historical weather logs were registered in ships, when they were on the high seas, recording daily weather conditions such as: wind speed, temperature, coordinates, etc. These historical documents represent an important source of knowledge with valuable information to extract climatic information of several centuries ago. This paper presents a database for researching about the ca…
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.
2019
Background Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data. Results In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTfu…
Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors
2009
Inhibiting a protein that regulates multiple signal transduction pathways in cancer cells is an attractive goal for cancer therapy. Heat shock protein 90 (Hsp90) is one of the most promising molecular targets for such an approach. In fact, Hsp90 is a ubiquitous molecular chaperone protein that is involved in folding, activating and assembling of many key mediators of signal transduction, cellular growth, differentiation, stress-response and apoptothic pathways. With the aim to analyze which molecular descriptors have the higher importance in the binding interactions of these classes, we first performed molecular docking experiments on the 187 Hsp90 inhibitors included in the BindingDB, a pu…
Darbinieku rutīnas izsekotājs
2022
Šī kvalifikācijas darba mērķis ir izstrādāt un dokumentēt darbvirsmas lietojumprogrammas specifikāciju, lai nodrošinātu darbinieku ikdienas rutīnas izsekošanu. Prasību specifikācijas un aplikācijas dizaina autors ir Alfrēds Genkins, Latvijas Universitātes students. Specifikācijā jāapraksta funkcionālās un nefunkcionālās prasības, testēšanas gadījumi un lietojumprogrammu projektēšanas lēmumi. Projektēšanas lēmumi ietver detalizētu pārskatu par lietojumprogrammu moduļiem un datu bāzes entītijām, to attiecībām. Lietojumprogrammas galvenais mērķis ir nodrošināt darbību pabeigšanas izsekošanu uzņēmuma mērogā. Tāpat aplikācijas mērķis ir uzlabot darbinieka izziņu: izkraut atmiņas uzdevumus apkārt…