A CAD-oriented modeling approach of frequency-dependent behavior of substrate noise coupling for mixed-signal IC design

A simple, efficient CAD-oriented equivalent circuit modeling approach of frequency-dependent behavior of substrate noise coupling is presented. It is shown that the substrate exhibits significant frequency-dependent characteristics for high frequency applications using epitaxial layers on a highly doped substrate. Using the proposed modeling approach, circuit topographies consisting of only ideal lumped circuit elements can be synthesized to accurately represent the frequency response using y-parameters. The proposed model is well-suited for use in standard circuit simulators. The extracted model is shown to be in good agreement with rigorous 3D device simulation results. 1

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

MOTIVATION: PIWI-interacting RNAs (piRNAs), 23-36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial computational skills. Additionally, researchers may analyze and interpret the same data differently, generating results that are difficult to reconcile. To address these issues, we developed a coordinated set of pipelines, \u27piPipes\u27, to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field. SUPPLEMENTARY INFORMATION: Supplementary information, including flowcharts and example figures for each pipeline, are available at Bioinformatics online. AVAILABILITY AND IMPLEMENTATION: piPipes is implemented in Bash, C++, Python, Perl and R. piPipes is free, open-source software distributed under the GPLv3 license and is available at http://bowhan.github.io/piPipes/. CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Chopper Is Prodeath Regardless of the Effect of p75ICD on Sensitivity to Oxidative Stress

Background. The intracellular domain (ICD) of the neurotrophin receptor, p75NTR, exhibits variably pro- and antiapoptotic activity and has been implicated in neurodegenerative and neurodestructive disease. The molecular determinants of these cellular effects are not completely understood. The “Chopper” domain of p75ICD has been shown to be proapoptotic in in vitro systems in which p75ICD is proapoptotic. The effects of Chopper in systems in which p75ICD is antiapoptotic and, therefore, whether or not Chopper accounts for the variability of the cellular effects of p75ICD are not known. We therefore examined the effects of deletion of Chopper on the effects of p75ICD on in vitro cell culture systems in which p75ICD is pro- or antiapoptotic, respectively. Results. In HN33.11 murine neuroblastoma-hippocampal neuron hybrid cells, p75ICD is antiapoptotic. In NIH 3T3 cells, p75ICD is proapoptotic. In both cell lines deletion of the Chopper domain from p75ICD decreases the incidence of apoptosis resulting from oxidative stress. Thus, irrespective of the nature of the effects of p75ICD on the cell, its Chopper domain is proapoptotic. Conclusions. Expression of p75ICD can enhance or attenuate oxidative induction of apoptosis. Variability of the effects of p75ICD is not related to variability of the effects of its Chopper domain

Identification of functional modules that correlate with phenotypic difference: the influence of network topology

A gene set enrichment analysis method for including network topology in the identification of genes involved in phenotypic alterations is described. Classifications: Genome studies, Method

Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs

Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3\u27 end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor

Viscous damping of nanobeam resonators: humidity, thermal noise and the paddling effect

The nanobeam resonator is the key mechanical component in the nano-electromechanical system. In addition to its high frequency originating from its low dimension, the performance is significantly influenced by the circumstances, especially at nanoscale where a large surface area of the material is exposed. Molecular dynamics simulations and theoretical analysis are used for a quantitative prediction on the damping behavior, such as the critical damping condition and lifetime, of nanobeam resonators that directly maps the fluid-structure properties and interaction information into dynamical behaviors. We show here how the humidity defines the critical damping condition through viscous forces, marking the transition from under-damping to over-damping regime at elevated humidity. Novel phenomena such as the thermal fluctuation and paddling effects are also discussed.Comment: 15 pages, 5 figure

Spin excitations and the Fermi surface of superconducting FeS

High-temperature superconductivity occurs near antiferromagnetic instabilities and nematic state. Debate remains on the origin of nematic order in FeSe and its relation with superconductivity. Here, we use transport, neutron scatter- ing and Fermi surface measurements to demonstrate that hydro-thermo grown superconducting FeS, an isostructure of FeSe, is a tetragonal paramagnet without nematic order and with a quasiparticle mass significantly reduced from that of FeSe. Only stripe-type spin excitation is observed up to 100 meV. No direct coupling between spin excitation and superconductivity in FeS is found, suggesting that FeS is less correlated and the nematic order in FeSe is due to competing checkerboard and stripe spin fluctuations.Comment: 11 pages, 4 page

A User\u27s Guide to the Encyclopedia of DNA Elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

Computational design of the affinity and specificity of a therapeutic T cell receptor

T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities

A Paul Trap Mass Analyzer Consisting of Two Microfabricated Electrode Plates

We report the design and performance of a novel radiofrequency (RF) ion trap mass analyzer, the planar Paul trap, in which a quadrupolar potential distribution is made between two electrode plates. Each plate consists of a series of concentric, lithographically deposited 100-micrometer-wide metal rings, overlaid with a thin resistive layer. To each ring is applied a different RF amplitude, such that the trapping field produced is similar to that of the conventional Paul trap. The accuracy and shape of the electric fields in this trap are not limited by electrode geometry nor machining precision, as is the case in traps made with metal electrodes. The use of two microfabricated plates for ion trap construction presents a lower-cost alternative to conventional ion traps, with additional advantages in electrode alignment, electric field optimization, and ion trap miniaturization. Experiments demonstrate the effects of ion ejection mode and scan rate on mass resolution for several small organic compounds. The current instrument has a mass range up to ~180 Thompsons (Th), with better than unit mass resolution over the whole range