gebhart/patrepeval huggingface dataset:
Microfluidic Screening of Electric Fields for Electroporation (2016)

Electroporation is commonly used to deliver molecules such as drugs, proteins, and/or DNA into cells, but the mechanism remains poorly understood. In this work a rapid microfluidic assay was developed to determine the critical electric field threshold required for inducing bacterial electroporation. The microfluidic device was designed to have a bilaterally converging channel to amplify the electric field to magnitudes sufficient to induce electroporation. The bacterial cells are introduced into the channel in the presence of SYTOX(®), which fluorescently labels cells with compromised membranes. Upon delivery of an electric pulse, the cells fluoresce due to transmembrane influx of SYTOX(®) after disruption of the cell membranes. We calculate the critical electric field by capturing the location within the channel of the increase in fluorescence intensity after electroporation. Bacterial strains with industrial and therapeutic relevance such as Escherichia coli BL21 (3.65 ± 0.09 kV/cm), Corynebacterium glutamicum (5.20 ± 0.20 kV/cm), and Mycobacterium smegmatis (5.56 ± 0.08 kV/cm) have been successfully characterized. Determining the critical electric field for electroporation facilitates the development of electroporation protocols that minimize Joule heating and maximize cell viability. This assay will ultimately enable the genetic transformation of bacteria and archaea considered intractable and difficult-to-transfect, while facilitating fundamental genetic studies on numerous diverse microbes.
Spoken Letter Recognition (1990)

Through the use of neural network classifiers and careful feature selection, we have achieved high-accuracy speaker-independent spoken letter recognition. For isolated letters, a broad-category segmentation is performed Location of segment boundaries allows us to measure features at specific locations in the signal such as vowel onset, where important information resides. Letter classification is performed with a feed-forward neural network. Recognition accuracy on a test set of 30 speakers was 96%. Neural network classifiers are also used for pitch tracking and broad-category segmentation of letter strings. Our research has been extended to recognition of names spelled with pauses between the letters. When searching a database of 50,000 names, we achieved 95% first choice name retrieval. Work has begun on a continuous letter classifier which does frame-by-frame phonetic classification of spoken letters.
Shape Optimization of Potentially Slender Structures (2008)

Shape optimization lies at the heart of modern engineering design. Through shape optimization, computers can, in theory, ‘synthesize’ engineering artifacts in a fully automated fashion. However, a serious limitation today is that the evolving geometry (during optimization) may become slender, i.e., beam or plate-like. Under such circumstances, modern 3-D computational methods, such as finite element analysis (FEA), will fail miserably, and so will the shape optimization process. Indeed, the recommended method for analyzing slender artifacts is to replace them with 1-D beams/ 2-D plates, prior to discretization and computational analysis, a process referred to as geometric dimensional reduction. Unfortunately explicit geometric reduction is impractical and hard to automate during optimization since one cannot predict a priori when an artifact will become slender. In this paper, we develop an implicit dimensional reduction method where the reduction is achieved through an algebraic process. The proposed method of reduction is computationally equivalent to explicit geometric reduction for comparable computational cost. However, the proposed method can be easily automated and integrated within a shape optimization process, and standard off-the-shelf 3-D finite element packages can be used to implement the proposed methodology.
Organic Solvent Nanofiltration (2013)

Abstract Organic solvent nanofiltration (OSN) is a pressure‐driven membrane process discriminating molecules in the range of 200‐1000 Da, providing high quality products through gentle operating conditions. OSN has significant potential in chemical‐related industries employing organic solvents including ionic liquids. The main advantages of OSN technologies include low energy consumption, operation time, and process complexity as well as improved production sustainability, quality, and yield. The article seeks to provide insight into the state‐of‐the‐art research in the field, including the development of new polymeric and ceramic OSN membranes, modeling studies of the transport mechanisms through OSN membranes, engineering of membrane modules, development of new membrane characterization techniques, and novel OSN application.
Non-Parametric Super-Resolution Using a Bi-Sensor Camera (2012)

Multiframe super-resolution is the problem of reconstructing a single high-resolution (HR) image from several low-resolution (LR) versions of it. We assume that the original HR image undergoes different linear transforms, where each transform can be approximated as a set of linear shift-invariant transforms over different subregions of the HR image. The linearly transformed versions of the HR image are then downsampled, resulting in different LR images. Under the assumption of linearity, these LR images can form a basis that spans the set of the polyphase components (PPCs) of the HR image. We propose sampling rate diversity, where a secondary LR image, acquired by a secondary sensor of different (lower) sampling rate, is used as a reference to make known portions (subpolyphase components) of the PPCs of the reconstructed HR image. This setup allows for non-parametric reconstruction of the PPCs, where no knowledge of the underlying transforms is required, by solving for the expansion coefficients of the PPCs, in terms of the LR basis.
Key factors behind autofluorescence changes caused by ablation of cardiac tissue (2020)

Radiofrequency ablation is a commonly used clinical procedure that destroys arrhythmogenic sources in patients suffering from atrial fibrillation and other types of cardiac arrhythmias. To improve the success of this procedure, new approaches for real-time visualization of ablation sites are being developed. One of these promising methods is hyperspectral imaging, an approach that detects lesions based on changes in the endogenous tissue autofluorescence profile. To facilitate the clinical implementation of this approach, we examined the key variables that can influence ablation-induced spectral changes, including the drop in myocardial NADH levels, the release of lipofuscin-like pigments, and the increase in diffuse reflectance of the cardiac muscle beneath the endocardial layer. Insights from these experiments suggested simpler algorithms that can be used to acquire and post-process the spectral information required to reveal the lesion sites. Our study is relevant to a growing number of multilayered clinical targets to which spectral approaches are being applied.
The tobacco wounding-activated mitogen-activated protein kinase is encoded by <i>SIPK</i> (1998)

It has been demonstrated that both salicylic acid and fungal elicitors activate a 48-kDa mitogen-activated protein kinase termed salicylic acid-induced protein kinase (SIPK) in tobacco suspension cells. Here, we show that infiltration of these agents into tobacco leaves also activates SIPK. Of particular interest, infiltration of water alone activated a kinase of the same size, possibly because of wounding and/or osmotic stresses. The kinetics of kinase activation, however, differ for these different treatments. Various mechanical stresses, including cutting and wounding by abrasion, also activated a 48-kDa kinase. By using an immune-complex kinase assay with antibodies specific for SIPK or wounding-induced protein kinase, we demonstrate that this wounding-activated 48-kDa kinase is SIPK, rather than wounding-induced protein kinase, as reported [Seo, S., Okamoto, M., Seto, H., Ishizuka, K., Sano, H. & Ohashi, Y. (1995) Science 270, 1988-1992]. Activation of SIPK after wounding was associated with tyrosine phosphorylation but not with increases in SIPK mRNA or protein levels. Thus, the same mitogen-activated protein kinase, SIPK, appears to facilitate signaling for two distinct pathways that lead to disease resistance responses and wounding responses.
Stratification of coronary artery disease patients for revascularization procedure based on estimating adverse effects (2015)

Percutaneous coronary intervention (PCI) is the most commonly performed treatment for coronary atherosclerosis. It is associated with a higher incidence of repeat revascularization procedures compared to coronary artery bypass grafting surgery. Recent results indicate that PCI is only cost-effective for a subset of patients. Estimating risks of treatment options would be an effort toward personalized treatment strategy for coronary atherosclerosis. In this paper, we propose to model clinical knowledge about the treatment of coronary atherosclerosis to identify patient-subgroup-specific classifiers to predict the risk of adverse events of different treatment options. We constructed one model for each patient subgroup to account for subgroup-specific interpretation and availability of features and hierarchically aggregated these models to cover the entire data. In addition, we deviated from the current clinical workflow only for patients with high probability of benefiting from an alternative treatment, as suggested by this model. Consequently, we devised a two-stage test with optimized negative and positive predictive values as the main indicators of performance. Our analysis was based on 2,377 patients that underwent PCI. Performance was compared with a conventional classification model and the existing clinical practice by estimating effectiveness, safety, and costs for different endpoints (6 month angiographic restenosis, 12 and 36 month hazardous events). Compared to the current clinical practice, the proposed method achieved an estimated reduction in adverse effects by 25.0% (95% CI, 17.8 to 30.2) for hazardous events at 36 months and 31.2% (95% CI, 25.4 to 39.0) for hazardous events at 12 months. Estimated total savings per patient amounted to $693 and $794 at 12 and 36 months, respectively. The proposed subgroup-specific method outperformed conventional population wide regression: The median area under the receiver operating characteristic curve increased from 0.57 to 0.61 for prediction of angiographic restenosis and from 0.76 to 0.85 for prediction of hazardous events. The results of this study demonstrated the efficacy of deployment of bare-metal stents and coronary artery bypass grafting surgery for subsets of patients. This is one effort towards development of personalized treatment strategies for patients with coronary atherosclerosis that could significantly impact associated treatment costs.
Specific characteristics of ultrasound contrast agents (1998)

Ultrasound contrast agents possess acoustical characteristics which differ from the surrounding medium. Specific signatures of the agent, consisting of free or encapsulated gas bubbles, will improve the discrimination between the blood containing the agent and the tissue. One of the specific signatures is the initiation of a volume pulsation when the ultrasound wave hits a free or encapsulated gas bubble. Depending on the magnitude of the ultrasound wave the pulsation will be linear to the applied pressure or nonlinear to the applied pressure. Nonlinear vibration can be split into stationary (harmonic) and transient (power) scattering. Besides the nonlinear vibration (harmonics), specific characteristics include enhanced scattering as a function of the acoustic amplitude, transient scattering which is very useful for measuring flow, LOC (loss of correlation) imaging, and the persistence as a function of ambient parameters like pressure and temperature. Recently, a 2-D echomachine has been adapted for imaging of the nonlinear vibration of contrast agents and further developments in both hardware and software will be advantageous for the many specific characteristics of these agents.
An adaptive subband differential microphone (1994)

In a previous talk, ‘‘A new adaptive differential microphone array’’ by Elko and Pong, a differential microphone has been introduced that adapts its directivity pattern to the particular acoustic environment to provide for a good signal-to-noise ratio. There, the selected pattern remains more or less constant with respect to frequency. In this talk an approach is described that contains one more degree of freedom. The spectrum of the signals is partitioned in uniform subbands and different directivity patterns are adaptively chosen in each subband. This allows to cancel multiple noise sources with nonoverlapping spectra. An LMS-based algorithm will be derived with focus on a low computational load and a short delay for the desired signal. Consequences on the speed of adaptation are discussed. Further, experimental results of a first implementation with 33 subbands on a PC-based DSP32C board will be presented. The measurements verify the ability of the algorithm to cancel multiple noise sources with disjoint spectra without distorting the desired signal.
Biomedical diagnostics with elastic light scattering in cell suspensions and tissues (1997)

We review the principles and applications of elastically scattered light for noninvasive diagnostics and study of biological tissues and cells. The use of wavelengths from the ultraviolet to near-infrared as well as scattering effects of polarized light are discussed.
Fast extraction of resonant vibrational response from CARS spectra with arbitrary nonresonant background (2009)

Abstract We describe a new, robust method of numerically extracting equivalent Raman spectra from coherent anti‐Stokes Raman scattering (CARS) spectra. The extraction procedure requires no a priori information regarding the vibrational resonances or the shape of the nonresonant background (NRB). The method we present here is robust to situations where the NRB is not spectrally flat, and is accurate over a wide range of signal‐to‐background ratios. This simple and quick computation method, which relies primarily on a small number of fast Fourier transforms, could reasonably be used in conjunction with spectral imaging, where millions of spectra must be analyzed. Published 2009 by John Wiley & Sons, Ltd.
Implications of microRNAs in Colorectal Cancer Development, Diagnosis, Prognosis, and Therapeutics (2011)

MicroRNAs (miRNAs) are a class of non-coding small RNAs with critical regulatory functions as post-transcriptional regulators. Due to the fundamental importance and broad impact of miRNAs on multiple genes and pathways, dysregulated miRNAs have been associated with human diseases, including cancer. Colorectal cancer (CRC) is among the most deadly diseases, and miRNAs offer a new frontier for target discovery and novel biomarkers for both diagnosis and prognosis. In this review, we summarize the recent advancement of miRNA research in CRC, in particular, the roles of miRNAs in CRC stem cells, epithelial-to-mesenchymal transition, chemoresistance, therapeutics, diagnosis, and prognosis.
Synthesis of neoalkanes. [R/sub 1/R/sub 2/R/sub 3/CCOOH] (1986)

A process is described for the synthesis of an alkyl-substituted 1,1,1-trialkylalkane of the formula R/sub 1/R/sub 2/R/sub 3/CCH/sub 3/ by hydrogenation, wherein R/sub 1/, R/sub 2/ and R/sub 3/ are the same or different alkyl of 1-10 carbon atoms in the presence of a hydrogenation catalyst and hydrogen, the improvement which comprises hydrogenating a feed of a neoacid of the formula R/sub 1/R/sub 2/R/sub 3/CCOOH, at a temperature from about 325/sup 0/C to about 375/sup 0/C; a hydrogen feed rate of 1500 to 8000 m1/g catalyst/h; a neoacid feed rate of 0.2 to 4.9 mM/g catlyst/h and a hydrogen pressure of 35-140 Kg/cm/sup 2/ over a copper oxide/zinc oxide catalyst comprising 80-95% by weight of copper oxide/zinc oxide in an 8:1 to 1:1 weight ratio and 20-5% by weight alumina to obtain substantially complete conversion of the neoacid and recovering a product containing at least about 15 mol % yield of neoalkane based on the neoacid feed.
A review of oxide, silicon nitride, and silicon carbide brazing (1987)

There is growing interest in using ceramics for structural applications, many of which require the fabrication of components with complicated shapes. Normal ceramic processing methods restrict the shapes into which these materials can be produced, but ceramic joining technology can be used to overcome many of these limitations, and also offers the possibility for improving the reliability of ceramic components. One method of joining ceramics is by brazing. The metallic alloys used for bonding must wet and adhere to the ceramic surfaces without excessive reaction. Alumina, partially stabilized zirconia, and silicon nitride have high ionic character to their chemical bonds and are difficult to wet. Alloys for brazing these materials must be formulated to overcome this problem. Silicon carbide, which has some metallic characteristics, reacts excessively with many alloys, and forms joints of low mechanical strength. The brazing characteristics of these three types of ceramics, and residual stresses in ceramic-to-metal joints are briefly discussed.
Fire-Resistant Polyamides Containing Phosphorus (1988)

Flammability and weight loss reduced. Fire-resistant polymers obtained from 1-{(dialkoxyphosphonyl) methyl}-2, 4- and -2, 6-diaminobenzenes by reaction with acyl or diacyl halides of higher functionality. Incorporation of compounds containing phosphorus into certain polymers shown previously to increase fire retardance. Discovery adds new class of polyamides to group of such polymers.
Gold nanostar substrates for SERS-based chemical sensing in the femtomolar regime (2014)

We report a novel approach for fabricating gold nanostar-functionalized substrates for highly sensitive surface enhanced Raman spectroscopy (SERS)-based chemical sensing. Gold nanostars immobilized on a gold substrate via a Raman silent organic tether serve as the SERS substrate, and facilitate the chemical sensing of analytes that can either be chemisorbed or physisorbed on the nanostars. Our SERS substrates are capable of detecting chemisorbed 4-mercaptobenzoic acid at a concentration as low as 10 fM with a reproducible SERS enhancement factor of 10(9), and enable the semi-quantitative multiplexed identification of analytes from mixtures in which they have been dissolved in variable stoichiometry. Most importantly, they afford the detection of physisorbed analytes, such as crystal violet, with an excellent signal-to-noise ratio, hence serving as a versatile platform for the chemical identification of in principle any molecular analyte. These characteristics make a strong case for the use of our nanostar-based SERS substrate in practical chemical sensing applications.
A new colour space for skin tone detection (2009)

The majority of existing methods have one thing in common which is the de-correlation of luminance from the considered colour channels. It is believed that the luminance is underestimated here since it is seen as the least contributing colour component to skin colour detection. This work questions this claim by showing that luminance can be useful in separating skin and non-skin clusters. To this end, this work uses a new colour space which contains error signals derived from differentiating the grayscale map and the non-encoded-red grayscale version. The advantages of this approach are the reduction of space dimensionality from 3D to 1D space and the construction of a rapid classifier necessary for real time applications. This method is meant to assist digital image steganography to orient the embedding process since skin information is deemed to be psycho-visually redundant.
Layered-givens transforms: Tunable complexity, high-performance approximation of optimal non-separable transforms (2017)

We introduce layered-Givens transforms (LGTs) which are arbitrary-dimensional, tunable-complexity, orthonormal transforms of data. LGTs are formed by layers of data permutations and Givens rotations with the number of layers controlling the overall transform's computational complexity. We propose a novel method for the design of layered-Givens transforms that approximate desired complex transforms (such as KLTs, SOTs, etc.) so that most of the performance of the approximated transform is retained at significantly reduced complexity. Key to the LGT performance is the choice of the permutations that arrange the data prior to the Givens rotations. Despite the very highly combinatorial nature of the LGT design problem, we provide an algorithm that finds the optimal parameters (permutation and Givens rotations) for each layer. Our results show that designed LGTs closely approximate desired non-separable transforms at significantly reduced complexity.
Temporal sub-sampling of depth maps in depth image-based rendering of stereoscopic image sequences (2009)

In depth image based rendering, video sequences and their associated depth maps are used to render new camera viewpoints for stereoscopic applications. In this study, we examined the effect of temporal downsampling of the depth maps on stereoscopic depth quality and visual comfort. The depth maps of four eight-second video sequences were temporally downsampled by dropping all frames, except the first, for every 2, 4, or 8 consecutive frames. The dropped frames were then replaced by the retained frame. Test stereoscopic sequences were generated by using the original image sequences for the left-eye view and the rendered image sequences for the right-eye view. The downsampled versions were compared to a reference version with full depth maps that were not downsampled. Based on the data from 21 viewers, ratings of depth quality for the downsampled versions were lower. Importantly, ratings depended on the content characteristics of the stereoscopic video sequences. Results were similar for visual comfort, except that the differences in ratings between sequences were larger. The present results suggest that more processing, such as interpolation of depth maps, might be required to counter the negative effects of temporal downsampling, especially beyond a downsampling of two.
Fast and accurate wire delay estimation for physical synthesis of large ASICs (2002)

Interconnect delays represent an increasingly dominant portion of overall circuit delays. During timing-driven physical synthesis process, timing analysis is repeatedly performed over several hundred thousand components. Thus, fast and accurate estimation of interconnect delays is crucial. Traditionally, lumped and elmore delay models have been widely used for computing interconnect delays in physical synthesis due to their computational efficiency. However, these delay models are known to be inaccurate since they ignore slew and resistive shielding effects. In this paper, we propose a new iterative refinement based delay estimation approach that considers resistive shielding along with driver slew. Experimental results show that the proposed approach gives not only highly accurate results for far end RC-line delays but also compares very favorably to more difficult to match source end delays and source slews. In addition, use of the proposed delay model in physical synthesis yields significant performance improvement on several large industrial ASICs.