The Identification of the Mid Transcription Factor Regulatory Network Specifying Cell Fate and Regulating Survival in the \u3ci\u3eDrosophila\u3c/i\u3e Eye

The Drosophila melanogaster T-box transcription factor Midline (Mid) exhibits a high degree of structural and functional conservation with its vertebrate homolog Tbx-20. Both Mid and Tbx-20 regulate cell-fate specification with in diverse tissues including the central nervous system (CNS) and heart. Although, some important studies reported that Tbx-20 transcripts express in a wide range of developing mammalian eye tissues including those of the human fetus, the function of this transcription factor is unknown in the development of eye tissue. This current study is the first attempt to show that Mid and its para log H15 are expressed within distinct ommatidial cell types including photoreceptor neurons and sensory organ precursor (SOP) cells during early stages of pupal eye imaginal disc morphogensis and also identities a Mid transcription factor network regulating eye development. Reducing the expression of mid transcripts within eye disc tissues using RNA interference (mid-RNAi) results in the loss of interommatidial bristles (JOBs) in the adult eye due to the misspecification of sensory organ precursor (SOP) cells and increased levels of apoptosis induced during earlier stages of pupal development. Since the Notch-Delta signaling pathway specifies the SOP cell fate, we sought to place mid within the Notch-Delta genetic hierarchy specifying SOP cell fates. We determined that Mid functions downstream of the Notch receptor and upstream of the Enhancer of Split gene complex [E(Spl)]. We also discovered mid collaborates with two Notch pathway members also implicated in the regulation of cell survival, extramacrochaetae (emc) and senseless (sens). Moreover, toward identifying the Mid regulatory transcription factor network specifying cell fate, we found that mid collaborates with dFOXO. The dFOXO transcription factor is distinct in that it regulates cell proliferation and homeostasis within Insulin regulated stress induced pathway. The culmination of these studies suggests that Mid regulates cell fate specification in collaboration with Notch-Delta signaling pathway and also play important role in cell survival pathways essential for maintaining homeostasis

Finitely generated saturated multi-Rees algebras

We study the question of finite generation of saturated multi-Rees algebras and investigate the asymptotic behaviour of related length functions. In the setup of excellent local domains, we show that the saturated multi-Rees algebra of a finite collection of ideals is finitely generated when the analytic spread is not maximal and the associated length function eventually agrees with a polynomial. Similar results are obtained when we restrict to two-dimensional local UFDs with no restrictions on the analytic spread. We further prove that the saturated multi-Rees algebra of finitely many monomial ideals in a polynomial ring modulo an irreducible monomial ideal, is always finitely generated. In this case, the corresponding length function is shown to exhibit piecewise quasi-polynomial behaviour. We also produce multi-ideal versions of a theorem of Amao.Comment: Final version (major changes), 18 pages, 1 figur

Growth and physical property study of single nanowire (diameter ~ 45nm) of half doped Manganite

We report here the growth and characterization of functional oxide nanowire of hole doped manganite of La0.5Sr0.5MnO3 (LSMO). We also report four probe electrical resistance measurement of single nanowire of LSMO (diameter ~ 45nm) using FIB fabricated electrodes. The wires were fabricated by hydrothermal method using autoclave at a temperature of 270 oC. The elemental analysis and physical property like electrical resistivity were studied at individual nanowire level. The quantitative determination of Mn valency and elemental mapping of constituent elements was done by using Electron Energy Loss Spectroscopy (EELS) in the Scanning Transmission Electron Microscopy (STEM) mode. We addressed the important issue of whether as a result of size reduction the nanowires can retain the desired composition, structure and physical properties. The nanowires used were found to have a ferromagnetic transition (TC) at around 325 K which is very close to the bulk value of around 330 K found in single crystal of the same composition confirming that the functional behavior is likely to be retained even after size reduction of the nanowires to a diameter of 45 nm. The electrical resistivity shows insulating behavior within the temperature range measured, which is very much similar to the bulk system.Comment: 11 pages, 7 figures, accepted in Journal of Nanomaterial

Mathematical Modelling and Numerical Simulation for Studying the Trajectory of Dust Particle Approaching Solar Photovoltaic Panel

This research aims to investigate the impact of wind velocity on dust particle accumulation on solar panels, a significant factor influencing its efficiency and contribute to increased maintenance costs. The study focuses on analysing the motion of dust particles subjected to various forces, including gravitational force, buoyant force, drag force, wind force, and Van der Waals force. The analytical investigation involves studying particle motion under different wind speeds and directions. The Runge-Kutta method of order four is employed to solve the problem. Interestingly, at low wind speeds (1-2.6 m/s) and wind directions (0°-60°), particles tend to fall to the ground just before reaching the solar panel. However, at higher wind speeds (3.7-5.6 m/s) and similar wind directions, particles exhibit a tendency to fall onto the panel surface. This finding underscores the significance of wind conditions in determining the trajectory of dust particles and their potential impact on solar panel efficiency

Semantic Web repositories for genomics data using the eXframe platform

Background: With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. Methods: To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Conclusions: Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge

An open annotation ontology for science on web 3.0

Background: There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Methods: Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. Results: This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/. Conclusions: The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors

eXframe: reusable framework for storage, analysis and visualization of genomics experiments

<p>Abstract</p> <p>Background</p> <p>Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types.</p> <p>Results</p> <p>We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple data types including microarrays and next generation sequencing 3) query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples) and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients.</p> <p>Conclusion</p> <p>The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications.</p