Plasma Damage on Low-k Dielectric Materials

Low dielectric constant (low-k) materials as an interconnecting insulator in integrated circuits are essential for resistance-capacitance (RC) time delay reduction. Plasma technology is widely used for the fabrication of the interconnects, such as dielectric etching, resisting ashing or stripping, barrier metal deposition, and surface treatment. During these processes, low-k dielectric materials may be exposed to the plasma environments. The generated reactive species from the plasma react with the low-k dielectric materials. The reaction involves physical and chemical effects, causing degradations for low-k dielectric materials. This is called “plasma damage” on low-k dielectric materials. Therefore, this chapter is an attempt to provide an overview of plasma damage on the low-k dielectric materials

Preserving User Preferences in Document-Category Management: An Ontology-based Evolution Approach

Preserving the user’s preference in document-category management is essential because it affects his/her search efficiency, cognitive processing load, and satisfaction. Prior research has investigated automated document category evolution by using lexicon-based documentcategory evolution techniques which take into account the document categories previously created by the user. However, comparing documents at the lexical level cannot solve word mismatch or ambiguity problems effectively. To address such problems inherent to the lexicon-based approach, we propose an ONtology-based Category Evolution (ONCE) technique, which uses an appropriate ontology to support document-category evolution at the conceptual level rather than at the lexical level. Specifically, we develop an Ontology Enrichment (OE) technique for automatic leaning of concept descriptors in the adopted ontology. We empirically evaluate the effectiveness of the proposed ONCE technique, using a lexicon-based document-category evolution technique (i.e., CE2) and the hierarchical agglomerative clustering (HAC) technique for benchmark purposes. According to our empirical results, ONCE appears more effective than CE2 and HAC, and achieves higher clustering recall and precision

Using a microfluidic device for 1 μl DNA microarray hybridization in 500 s

This work describes a novel and simple modification of the current microarray format. It reduces the sample/reagent volume to 1 μl and the hybridization time to 500 s. Both 20mer and 80mer oligonucleotide probes and singly labeled 20mer and 80mer targets, representative of the T-cell acute lymphocytic leukemia 1 (TAL1) gene, have been used to elucidate the performance of this hybridization approach. In this format, called shuttle hybridization, a conventional flat glass DNA microarray is integrated with a PMMA microfluidic chip to reduce the sample and reagent consumption to 1/100 of that associated with the conventional format. A serpentine microtrench is designed and fabricated on a PMMA chip using a widely available CO(2) laser scriber. The trench spacing is compatible with the inter-spot distance in standard microarrays. The microtrench chip and microarray chip are easily aligned and assembled manually so that the microarray is integrated with a microfluidic channel. Discrete sample plugs are employed in the microchannel for hybridization. Flowing through the microchannel with alternating depths and widths scrambles continuous sample plug into discrete short plugs. These plugs are shuttled back and forth along the channel, sweeping over microarray probes while re-circulation mixing occurs inside the plugs. Integrating the microarrays into the microfluidic channel reduces the DNA–DNA hybridization time from 18 h to 500 s. Additionally, the enhancement of DNA hybridization reaction by the microfluidic device is investigated by determining the coefficient of variation (CV), the growth rate of the hybridization signal and the ability to discriminate single-base mismatch. Detection limit of 19 amol was obtained for shuttle hybridization. A 1 μl target was used to hybridize with an array that can hold 5000 probes

ATACgraph: Profiling genome-wide chromatin accessibility from ATAC-seq

Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph