gebhart/patrepeval huggingface dataset:
Imaging Single-Cell Signaling Dynamics with a Deterministic High-Density Single-Cell Trap Array (2011)

Stochasticity in gene expression, protein or metabolite levels contributes to cell-cell variations, the analysis of which could lead to a better understanding of cellular processes and drug responses. Current technologies are limited in their throughput, resolution (in space, time, and tracking individual cells instead of population average) and the ability to control cellular environment. A few microfluidic tools have been developed to trap and image cells; however, in most designs available to date, there is a compromise among loading efficiency, speed, the ability to trap single cells, and density or number of trapped cells. To meet the needs of single-cell imaging studies, we developed a microfluidic platform for high-throughput capture and imaging of thousands of single cells. The optimized trapping mechanism enables 95% of the traps to be occupied with single cells, with a trap density of 860 traps/mm(2). The dense array allows up to 800 cells to be imaged simultaneously with a 4x objective and a typical camera setup. Capture occurs with low shear and 94% viability after 24 h. This platform is compatible with other upstream microfluidic components for complex cell stimulation patterns, and we show here the ability to measure heterogeneity in calcium oscillatory behavior in genetically identical cells and monitor kinetic cellular response to chemical stimuli.
In vivo cloning by homologous recombination in yeast using a two‐plasmid‐based system (1995)

In order to reduce the number of classical DNA manipulation and ligation steps in the generation of yeast expression plasmids, a series of vectors is described which facilitate the assembly of such plasmids by the more efficient 'recombination in vivo' technique. Two sets of vectors were developed. The first set, called 'expression vectors', contains an expression cassette with a yeast promoter and the PGK terminator separated by a polylinker, and an Escherichia coli replicon. Subcloning in these vectors of a DNA fragment generates a 'transfer vector' which is compatible with the second set of E. coli-yeast shuttle vectors. This set of 'recombination vectors' contains a cassette for a functional copy of a gene complementing a host strain auxotrophy or a bacterial gene conferring an antibiotic resistance to the plasmid-bearing host. Plasmid copy numbers can be modulated through the use of URA3 or URA3-d as the selective marker together with an ARS/CEN and the 2 microns replicon. Integration of the cloned DNAs into the yeast linearized replicative vectors occurs by recombination between homologous flanking sequences during transformation in yeast or E. coli. All the vectors contain the origin of replication of phage f1 and allow the generation of single-stranded DNA in E. coli for sequencing or site-directed mutagenesis.
Automation for Genomics, Part One: Preparation for Sequencing (2000)

In the past four years, automation for genomics has enabled a 43-fold increase in the total finished human genomic sequence in the world. This two-part noncomprehensive review will provide an overview of different types of automation equipment used in genome sequencing. Part One focuses on equipment involved in DNA preparation, DNA sequencing reactions, and other automated procedures for preparing DNA for running on sequencers or subsequent analysis; it also includes information on the development of these machines at various genome centers. Part Two, to be published in the next issue, will cover sequencing machinery and array technology, and conclude with a look at the future technologies that will revolutionize molecular biology. "Alternate" sequencing technologies (including mass spectrometry, biochips, and single-molecule analysis) will also be examined.
A Voiceband Codec with Digital Filtering (1981)

Oversampling and digital filtering have been used to design a per-channel voiceband codec with resolution that exceeds the typical transmission system requirement by more than 15 dB. This extended dynamic range will allow for the use of digital processing in the management of signal levels and system characteristics in many telecommunication applications. Digital filtering contained in the codec provides rejection of out-of-band inputs and smoothing of the analog output that is sufficient to eliminate the need for analog filtering in most telephone applications. Some analog filtering may be required only to maintain the expanded dynamic range in cases where there is a danger of large amounts of out-of-band energy on the analog input impairing the dynamic range of the modulator. The encoder portion of the oversampled codec comprises an interpolating modulator that samples at 256 kHz followed by digital filtering that produces a 16-bit PCM code at a sample rate of 8 kHz. In the decoder, digital processing is used to raise the sampling rate to 1 MHz prior to demodulation in a 17-level interpolating demodulator. The circuits in the codec are designed to be suitable for large-scale integration. Component matching tolerances required in the analog circuits are of the order of only ± 1 percent, While the digital circuits can be implemented with fewer than 5000 gates with delays on the order of 0.1 μs. In this paper the response of the codec is described mathematically and the results are confirmed by measurements of experimental breadboard models.
Managing the software design documents with XML (1998)

It is hard to manage the software design documents within a distributed development team. The issues include the format, distribution and evolution of data. This paper mainly focuses on the issues of the format and distribution, and addresses how we can manage the software design documents for the distributed software development in the standard based way. In the software engineering community, Unified Modeling Language (UML) has been widely accepted as an object-oriented software analysis/design methodology, since it provides most of the concepts and notations that are essential for documenting object oriented models. UML, however, does not have an explicit format for interchanging its models intentionally. This paper addresses this lack and proposes UXF (UML exchange Format), which is an exchange format for UML models, based on XML (Extensible Markup Language). It is a format powerful enough to express, publish, access and exchange UML models and a natural extension from the existing Internet environment. It serves as a communication vehicle for developers, and as a well-structured data format for development tools. We demonstrate some proof-of-concept applications that show the merits of UXF. We are especially interested in a distributed model management system that manages the software design documents over the Internet with UXF. This system leverages the team development, reuse of design documents and tool interoperability by publishing a set of CORBA interfaces. Our work shows an important step in sharing and exchanging software design documents, and indicates the future direction of the interoperable software development tools.
Tafazzin knockdown causes hypertrophy of neonatal ventricular myocytes (2010)

Mutation of the mitochondrial protein tafazzin causes dilated cardiomyopathy in Barth syndrome. We employed an adenovirus as a vector to transfer tafazzin small hairpin RNA (shRNA) into neonatal ventricular myocytes (NVMs) to investigate the effects of tafazzin knockdown. The tafazzin shRNA adenovirus consistently knocked down tafazzin mRNA and lowered cardiolipin while significantly decreasing the production of ATP by the mitochondria. The phosphorylation of AMP-activated protein kinase and mitochondrial density were both increased in tafazzin knockdown NVMs compared with scrambled shRNA controls. When we tested whether tafazzin knockdown causes hypertrophy in vitro, we found that the surface area of NVMs infected with tafazzin shRNA adenovirus was significantly increased, as were the protein synthesis and expression of the hypertrophic marker gene, brain natriuretic peptide. Taken together, our data support the concept that a decreased tafazzin expression causes cardiomyocyte hypertrophy in vitro.
Image-Based Estimation of Ventricular Fiber Orientations for Personalized Modeling of Cardiac Electrophysiology (2012)

Technological limitations pose a major challenge to acquisition of myocardial fiber orientations for patient-specific modeling of cardiac (dys)function and assessment of therapy. The objective of this project was to develop a methodology to estimate cardiac fiber orientations from in vivo images of patient heart geometries. An accurate representation of ventricular geometry and fiber orientations was reconstructed, respectively, from high-resolution ex vivo structural magnetic resonance (MR) and diffusion tensor (DT) MR images of a normal human heart, referred to as the atlas. Ventricular geometry of a patient heart was extracted, via semiautomatic segmentation, from an in vivo computed tomography (CT) image. Using image transformation algorithms, the atlas ventricular geometry was deformed to match that of the patient. Finally, the deformation field was applied to the atlas fiber orientations to obtain an estimate of patient fiber orientations. The accuracy of the fiber estimates was assessed using six normal and three failing canine hearts. The mean absolute difference between inclination angles of acquired and estimated fiber orientations was 15.4°. Computational simulations of ventricular activation maps and pseudo-ECGs in sinus rhythm and ventricular tachycardia indicated that there are no significant differences between estimated and acquired fiber orientations at a clinically observable level.
Methods for measurement of fatty acid and cholesterol metabolism (1995)

The measurement of dynamic fluxes of lipids (biosynthesis, oxidation, and intermediary metabolism) poses difficult challenges. Two fundamental advances have been made recently for measuring the biosynthesis of lipids, namely mass isotopomer distribution analysis and labeled water incorporation. These techniques have resolved the central methodologic problem in biosynthesis by establishing the true precursor isotope enrichment. Mass isotopomer distribution analysis also permits uncontaminated pulse-chase decay curves and intracellular precursor fluxes to be measured. In contrast, the isotopic measurement of lipid oxidation rates remains unreliable because of the wide variability in the recovery of labeled carbon dioxide.
Escher: A CNN Accelerator with Flexible Buffering to Minimize Off-Chip Transfer (2017)

Convolutional neural networks (CNNs) are used to solve many challenging machine learning problems. Interest in CNNs has led to the design of CNN accelerators to improve CNN evaluation throughput and efficiency. Importantly, the bandwidth demand from weight data transfer for modern large CNNs causes CNN accelerators to be severely bandwidth bottlenecked, prompting the need for processing images in batches to increase weight reuse. However, existing CNN accelerator designs limit the choice of batch sizes and lack support for batch processing of convolutional layers. We observe that, for a given storage budget, choosing the best batch size requires balancing the input and weight transfer. We propose Escher, a CNN accelerator with a flexible data buffering scheme that ensures a balance between the input and weight transfer bandwidth, significantly reducing overall bandwidth requirements. For example, compared to the state-of-the-art CNN accelerator designs targeting a Virtex-7 690T FPGA, Escher reduces the accelerator peak bandwidth requirements by 2.4x across both fully-connected and convolutional layers on fixed-point AlexNet, and reduces convolutional layer bandwidth by up to 10.5x on fixed-point GoogleNet.
WiFi-based indoor positioning (2015)

Recently, several indoor localization solutions based on WiFi, Bluetooth, and UWB have been proposed. Due to the limitation and complexity of the indoor environment, the solution to achieve a low-cost and accurate positioning system remains open. This article presents a WiFibased positioning technique that can improve the localization performance from the bottleneck in ToA/AoA. Unlike the traditional approaches, our proposed mechanism relaxes the need for wide signal bandwidth and large numbers of antennas by utilizing the transmission of multiple predefined messages while maintaining high-accuracy performance. The overall system structure is demonstrated by showing localization performance with respect to different numbers of messages used in 20/40 MHz bandwidth WiFi APs. Simulation results show that our WiFi-based positioning approach can achieve 1 m accuracy without any hardware change in commercial WiFi products, which is much better than the conventional solutions from both academia and industry concerning the trade-off of cost and system complexity.
Measurement of pharmacokinetic parameters in histologically graded invasive breast tumours using dynamic contrast-enhanced MRI (2008)

Dynamic contrast-enhanced MRI (DCE-MRI) has demonstrated high sensitivity for detection of breast cancer. Analysis of correlation between quantitative DCE-MRI findings and prognostic factors (such as histological tumour grade) is important for defining the role of this technique in the diagnosis of breast cancer as well as the monitoring of neoadjuvant therapies. This paper presents a practical clinical application of a quantitative pharmacokinetic model to study histologically confirmed and graded invasive human breast tumours. The hypothesis is that, given a documented difference in capillary permeability between benign and malignant breast tumours, a relationship between permeability-related DCE-MRI parameters and tumour aggressiveness persists within invasive breast carcinomas. In addition, it was hypothesized that pharmacokinetic parameters may demonstrate stronger correlation with prognostic factors than the more conventional black-box techniques, so a comparison was undertaken. Significant correlations were found between pharmacokinetic and black-box parameters in 59 invasive breast carcinomas. However, statistically significant variation with tumour grade was demonstrated in only two permeability-related pharmacokinetic parameters: k(ep) (p<0.05) and K(trans) (p<0.05), using one-way analysis of variance. Parameters k(ep) and K(trans) were significantly higher in Grade 3 tumours than in low-grade tumours. None of the measured DCE-MRI parameters varied significantly between Grade 1 and Grade 2 tumours. Measurement of k(ep) and K(trans) might therefore be used to monitor the effectiveness of neoadjuvant treatment of high-grade invasive breast carcinomas, but is unlikely to demonstrate remission in low-grade tumours.
Characterization of a plasma membrane-associated prenylcysteine-directed alpha carboxyl methyltransferase in human neutrophils. (1994)

Signal transduction in human neutrophils requires prenylcysteine-directed carboxyl methylation of ras-related low molecular weight GTP-binding proteins. We now report the subcellular localization and characterization of a neutrophil prenylcysteine alpha carboxyl methyltransferase. The highest carboxyl methyltransferase activity copurified with biotinylated neutrophil surface membranes, supporting a plasma membrane localization of the enzyme. Neutrophil nuclear fractions contained little or no methyltransferase activity. Methyltransferase activity was detergent-sensitive but could be reconstituted by removal of detergent in the presence of phosphatidyl choline and an anionic phospholipid. N-Acetyl-S-trans,trans-farnesyl-L-cysteine (AFC) and N-acetyl-S-all-trans-geranylgeranyl-L-cysteine (AGGC) were effective substrates for neutrophil prenylcysteine-directed methyltransferase; Vmax values for AFC and AGGC (16.4 and 22.1 pmol of methylated/mg protein/min, respectively) are among the highest yet reported. Although both GTP gamma S and the chemoattractant fMet-Leu-Phe stimulated methylation of ras-related proteins, neither affected methylation of AFC. These data suggest that neutrophil plasma membranes contain a phospholipid-dependent, prenylcysteine-directed carboxyl methyltransferase of relatively high specific activity that modifies ras-related protein substrates in the GTP-bound, activated state.
Large Area, Few-Layer Graphene Films on Arbitrary Substrates by Chemical Vapor Deposition (2008)

In this work we present a low cost and scalable technique, via ambient pressure chemical vapor deposition (CVD) on polycrystalline Ni films, to fabricate large area ( approximately cm2) films of single- to few-layer graphene and to transfer the films to nonspecific substrates. These films consist of regions of 1 to approximately 12 graphene layers. Single- or bilayer regions can be up to 20 mum in lateral size. The films are continuous over the entire area and can be patterned lithographically or by prepatterning the underlying Ni film. The transparency, conductivity, and ambipolar transfer characteristics of the films suggest their potential as another materials candidate for electronics and opto-electronic applications.
Large‐scale production, purification and refolding of the full‐length cellular prion protein from Syrian golden hamster in Escherichia coli using the glutathione S‐transferase‐fusion system (1998)

Until quite recently, high-level expression of full-length cellular prion protein (Prp(c)) in bacterial cells was not possible. We describe here the effective purification of mature Syrian golden hamster PrPc (residues 23-231) as a C-terminal fusion to glutathione S-transferase (GST) from inclusion bodies expressed in Escherichia coli. Purification of the denatured fusion protein was simplified greatly by the introduction of a C-terminal histidine anchor, leading to 255 mg pure GST-PrPc-His6/l bacterial broth, which could be refolded easily by dilution in 20 mM Tris, 5 mM dithiothreitol, 1 mM EDTA, pH 9.0. Refolding was monitored by following GST activity. Mature Syrian hamster PrPc (residues 23-231) was released from the refolded fusion protein by thrombin digestion, yielding 73 mg homogeneous protein/l bacterial culture after purification. The recombinant protein was identified by monoclonal antibodies, Edman sequencing and matrix-assisted laser-desorption/ionization MS. Correct folding was confirmed by near-ultraviolet circular dichroism spectroscopy. Samples resulting from different purification steps were sensitive to proteinase K digestion and showed no signs of infectivity in animal experiments, demonstrating that the PrPc produced is identical with the cellular isoform. The presented purification procedure should prove useful for the production of other GST-fusion proteins.
Transplantation of Human Hepatocytes Cultured with Deleted Variant of Hepatocyte Growth Factor Prolongs the Survival of Mice with Acute Liver Failure (2005)

The present work clearly demonstrates the usefulness of dHGF (100 ng/ml) for maintaining the differentiated functions of human hepatocytes in tissue culture.
RNA Interference: Biology, Mechanism, and Applications (2003)

Double-stranded RNA-mediated interference (RNAi) is a simple and rapid method of silencing gene expression in a range of organisms. The silencing of a gene is a consequence of degradation of RNA into short RNAs that activate ribonucleases to target homologous mRNA. The resulting phenotypes either are identical to those of genetic null mutants or resemble an allelic series of mutants. Specific gene silencing has been shown to be related to two ancient processes, cosuppression in plants and quelling in fungi, and has also been associated with regulatory processes such as transposon silencing, antiviral defense mechanisms, gene regulation, and chromosomal modification. Extensive genetic and biochemical analysis revealed a two-step mechanism of RNAi-induced gene silencing. The first step involves degradation of dsRNA into small interfering RNAs (siRNAs), 21 to 25 nucleotides long, by an RNase III-like activity. In the second step, the siRNAs join an RNase complex, RISC (RNA-induced silencing complex), which acts on the cognate mRNA and degrades it. Several key components such as Dicer, RNA-dependent RNA polymerase, helicases, and dsRNA endonucleases have been identified in different organisms for their roles in RNAi. Some of these components also control the development of many organisms by processing many noncoding RNAs, called micro-RNAs. The biogenesis and function of micro-RNAs resemble RNAi activities to a large extent. Recent studies indicate that in the context of RNAi, the genome also undergoes alterations in the form of DNA methylation, heterochromatin formation, and programmed DNA elimination. As a result of these changes, the silencing effect of gene functions is exercised as tightly as possible. Because of its exquisite specificity and efficiency, RNAi is being considered as an important tool not only for functional genomics, but also for gene-specific therapeutic activities that target the mRNAs of disease-related genes.
Design and Evaluation of Binaural Cue Coding Schemes (2002)

LCAV
Catalytic Hydrolysis of Esters of 2-Hydroxypyridine Derivatives for Cu2+ Detection (2008)

Hydrolysis of activated esters, e.g., picolinic acid and alpha-amino acid esters, in the presence of Cu(2+) salts is a stoichiometric process because products of this reaction bind the catalytic metal ion substantially stronger than starting materials do. Herein we report improved ester substrates, which are cleaved in the presence of catalytic amounts of Cu(2+); 55 turnovers of hydrolysis are observed for the best substrate, acetic acid 2-hydroxypyridine ester. We demonstrate that this reaction can be used for sensitive and selective detection of Cu(2+) by using both absorption and fluorescence spectroscopy.
Polarization and angular effects of femtosecond laser-induced nanostructure-covered large scale waves on metals (2011)

In this paper, we find that nanostructure-covered large scale waves (NC-LSWs) can be produced on metals using both s- and p-polarized femtosecond laser pulses. We show that the period of NC-LSWs can be controlled by laser fluence, the number of irradiating pulses, and the incident beam angle. By modeling angular dependence of NC-LSW period induced by s-polarized light, we reveal that inhomogeneous energy deposition plays an important role in the formation of NC-LSWs. This allows us to establish a three-step model for NC-LSW formation, the formation of laser-induced surface unevenness, inhomogeneous energy deposition due to the interference of the incident light with the scattered light, and nonuniform energy deposition due to shielding by LSWs.
A New Servo Method With Eccentricity Correction Circuit (1987)

A new servo method with eccentricity correction circuit for an optical disc equipment is developed. When eccentricity exists, the relative position between tracks and rotation center of a disc varies sinusoid according to the disc rotation. Eccentricity correction is performed by moving actuater according to the synchronized sinusoidal correction signal. Amplitude and phase of the correction signal are equalized to those of track movement by microcomputer. This eccentricity correction can reduce a 200 &mu;m eccentricity down to 10 &mu;m, improve tracking ability, and shorten track access time.