gebhart/patrepeval huggingface dataset:
Caffeic acid production enhancement by engineering a phenylalanine over‐producing <i>Escherichia coli</i> strain (2013)

Caffeic acid is a plant-specific phenylpropanoic acid with multiple health-improving effects reported, and its therapeutic derivatives have also been studied throughout the last decade. To meet its market need and achieve high-level production, microbial production of caffeic acid approaches have been developed in metabolically engineered Escherichia coli. In our previous work, we have established the first artificial pathway that realized de novo production of caffeic acid using E. coli endogenous 4-hydroxyphenylacetate 3-hydroxylase (4HP3H). In this work, we exploited the catalytic potential of 4HPA3H in the whole-cell bioconversion study and produced 3.82 g/L (461.12 mg/L/OD) caffeic acid from p-coumaric acid, a direct precursor. We further engineered a phenylalanine over-producer into a tyrosine over-producer and then introduced the artificial pathway. After adjusting the expression strategy and optimizing the inoculants timing, de novo production of caffeic acid reached 766.68 mg/L. Both results from the direct precursor and simple carbon sources represent the highest titers of caffeic acid from microbial production so far.
The mode of substrate entry into the 5‐lipoxygenase active site (769.3) (2014)

Leukotrienes are potent immune‐modulatory compounds involved in the inflammatory response. 5‐Lipoxygenase (5‐LOX) is the enzyme that catalyzes the production of Leukotriene A 4 (LTA 4 ), which is further metabolized to pro and anti‐inflammatory compounds from the substrate Arachidonic Acid (AA), a polyunsaturated fatty acid. The crystal structure of a stabilized form of 5‐LOX has been recently reported (Gilbert et al , 2011). However, the structure does not reveal the mode of substrate recognition. The first step in the enzymatic reaction involves the removal of a hydrogen from the central carbon of a pentadiene present in the substrate. It is not known how 5‐LOX distinguishes among three such chemically equivalent pentadienes in AA to produce only 5‐ S ‐HPETE, which is subsequently transformed to LTA 4 . The crystal structure suggests a somewhat crescent shaped active site lined with invariant Leucines and Isoleucines, with no clear access port visible for substrate entry. A series of site directed mutants were produced and the activities of these mutants evaluated. Product analyses of these mutants with AA and substrate analogs suggest entry of the substrate by the opening of the so‐called Phenylalanine (F)‐Tyrosine(Y) ‘cork’. The data is also consistent with the orientation of AA as carboxyl innermost, as predicted from the stereochemistry of the product and mechanistic models of lipoxygenase function. Grant Funding Source : Supported by NIH Grant # HL107887
Efficient and Bright Colloidal Quantum Dot Light-Emitting Diodes via Controlling the Shell Thickness of Quantum Dots (2013)

In this paper, we use a simple device architecture based on solution-processed ZnO nanoparticles (NPs) as the electron injection/transport layer and bilayer structure of poly(ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS)/poly[9,9-dioctylfluorene-co-N-[4-(3-methylpropyl)]-diphenylamine] (TFB) as the hole injection/transport layer to assess the effect of shell thickness on the properties of quantum-dot-based light emitting diodes (QD-LEDs), comprising CdSe/CdS/ZnS core-shell QDs as the emitting layer. QDs with varying shell thickness were assessed to determine the best option of shell thickness, and the best improvement in device performance was observed when the shell thickness was 2.1 nm. Thereafter, different emissions of QDs, but with optimized same shell thickness (∼2.1 nm), were selected as emitters to be fabricated into same structured QD-LEDs. Highly bright orange-red and green QD-LEDs with peak luminances up to ∼30 000 and ∼52 000 cd m(-2), and power efficiencies of 16 and 19.7 lm W(-1), respectively, were demonstrated successfully. These results may demonstrate a striking basic prototype for the commercialization of QD-based displays and solid-state lightings.
Micromolar affinity CAR T cells to ICAM-1 achieves rapid tumor elimination while avoiding systemic toxicity (2017)

Adoptive transfer of high-affinity chimeric antigen receptor (CAR) T cells targeting hematological cancers has yielded impressive clinical results. However, safety concerns regarding target expression on healthy tissue and poor efficacy have hampered application to solid tumors. Here, a panel of affinity-variant CARs were constructed targeting overexpressed ICAM-1, a broad tumor biomarker, using its physiological ligand, LFA-1. Anti-tumor T cell potency in vitro was directly proportional to CAR affinity and ICAM-1 density. In a solid tumor mouse model allowing simultaneous monitoring of anti-tumor potency and systemic off-tumor toxicity, micromolar affinity CAR T cells demonstrated superior anti-tumor efficacy and safety compared to their nanomolar counterparts. Longitudinal T cell tracking by PET/CT and concurrent cytokine measurement revealed superior expansion and contraction kinetics of micromolar affinity CAR T cells. Therefore, we developed an ICAM-1 specific CAR with broad anti-tumor applicability that utilized a reduced affinity targeting strategy to significantly boost efficacy and safety.
Sounds of Synthesis: Acoustic Real‐Time Analysis of Laser‐Induced Graphene (2022)

Abstract Laser‐induced graphene (LIG) can be patterned on a variety of substrates using a laser scriber/cutter. The quality and morphology of LIG is currently analyzed using Raman spectroscopy and electron microscopy. Here a method is presented to enable analysis of LIG in real‐time during the synthesis using a microphone attached to the laser writing head, followed by a simple acoustic signal processing scheme. It is demonstrated that it is possible to use the same energy input to simultaneously drive the conversion process and probe the formation of LIG in situ by applying Fourier and integral analyses, thus allowing rapid, high‐throughput determination of the local quality and morphology of the produced LIG.
Facile Chemoenzymatic Strategies for the Synthesis and Utilization of<i>S</i>‐Adenosyl‐<scp>L</scp>‐Methionine Analogues (2014)

A chemoenzymatic platform for the synthesis of S-adenosyl-L-methionine (SAM) analogues compatible with downstream SAM-utilizing enzymes is reported. Forty-four non-native S/Se-alkylated Met analogues were synthesized and applied to probing the substrate specificity of five diverse methionine adenosyltransferases (MATs). Human MAT II was among the most permissive of the MATs analyzed and enabled the chemoenzymatic synthesis of 29 non-native SAM analogues. As a proof of concept for the feasibility of natural product "alkylrandomization", a small set of differentially-alkylated indolocarbazole analogues was generated by using a coupled hMAT2-RebM system (RebM is the sugar C4'-O-methyltransferase that is involved in rebeccamycin biosynthesis). The ability to couple SAM synthesis and utilization in a single vessel circumvents issues associated with the rapid decomposition of SAM analogues and thereby opens the door for the further interrogation of a wide range of SAM utilizing enzymes.
Combined Regression and Classification Models for Accurate Estimation of Walking Speed Using a Wrist-worn IMU (2018)

Walking speed is an important quantity not only in fitness applications but also for Iifestyle and health monitoring purposes. With the recent advances in MEMS technology, miniature body-worn sensors have been used for ambulatory walking speed estimation using regression models. However, studies show that these models are more prone to errors in slow walking regime compared to normal and fast walking regimes. To address this issue, our study proposes a combined classification and regression walking speed estimation model. An experimental evaluation was performed on 10 healthy subjects during treadmill walking trials using a smartwatch. The experimental results show that including the classification model can improve the accuracy of walking speed estimation in the slow speed regime by about 22%. The results show that the proposed combined model has error of less than around 13% for various walking speed regimes.
Association of “Greenness” in Corn with Yield and Leaf Nitrogen Concentration (2011)

Efficient use of N fertilizer has become crucial due to fertilizer costs and the impact of excessive N on the environment. Diagnostic tools for estimating plant N status have an important role in reducing N inputs while maintaining yield. The objective of our study was to quantify corn ( Zea mays L.) leaf greenness with a digital camera and image‐analysis software and establish the relationship with yield, leaf N concentration, and chlorophyll meter (or SPAD, soil plant analysis development) values. In 2008 and 2009, field experiments were conducted at five sites with N treatments ranging from 0 to 336 kg N ha −1 At tasseling, the ear leaf was sampled for color analysis and SPAD measurements, and then analyzed for total N. Hue, saturation, and brightness (HSB) values from digital images were processed into a dark green color index (DGCI), which combines HSB values into one composite number. Including calibration disks in images and changing the background color in photographs to pink greatly improved DGCI precision in 2009 over 2008. There was a close relationship (typically r 2 ≥ 0.70) of SPAD and DGCI with leaf N concentration. Within a location, yield increased linearly in most cases with both SPAD (average r 2 = 0.79) and DGCI (average r 2 = 0.78). Digital‐image analysis was a simple method of determining corn N status that has potential as a diagnostic tool for determining crop N needs.
Super-Resolution using a Multi-Mixture Imaging System (2006)

Pixel mixture accelerates a read-out rate of an image, but it lowers the resolution. Although super-resolution is famous technique to improve the resolution, the super-resolution can not improve the resolution from the pixel mixture images because the pixel mixture images are low-passed to reduce aliasing. Therefore, we propose a novel imaging system that we call "multi-mixture". The proposed imaging system can generate two types of image sequences. This paper demonstrates that the super-resolution using the multi-mixture imaging system greatly improves the image resolution.
Challenges in tissue characterization from backscattered intravascular ultrasound signals (2007)

Plaque characterization through backscattered intravascular ultrasound (IVUS) signal analysis has been the subject of extensive study for the past several years. A number of algorithms to analyze IVUS images and underlying RF signals to delineate the composition of atherosclerotic plaque have been reported. In this paper, we present several realistic challenges one faces throughout the process of developing such algorithms to characterize tissue type. The basic tenet of ultrasound tissue characterization is that different tissue types imprint their own "signature" on the backscattered echo returning to the transducer. Tissue characterization is possible to the extent that these echo signals can be received, the signatures read, and uniquely attributed to a tissue type. The principal difficulty in doing tissue characterization is that backscattered RF signals originating as echoes from different groups of cells of the same tissue type exhibit no obvious commonality in appearance in the time domain. This happens even in carefully controlled laboratory experiments. We describe the method of acquisition and digitization of ultrasound radiofrequency (RF) signals from left anterior descending and left circumflex coronary arteries. The challenge of obtaining corresponding histology images to match to specific regions-of-interest on the images is discussed. A tissue characterization technique based on seven features is compared to a full spectrum based approach. The same RF and histology data sets were used to evaluate the performances of these two techniques.
Characterization of the missed spectrum-access opportunities under dynamic spectrum sharing (2016)

The radio frequency (RF) spectrum has been observed to be underutilized in the space, time, and frequency dimensions. To improve its utilization and meet growing demand, dynamic spectrum-sharing models are being investigated. In order to maximize the use of spectrum, we study how much of the spectrum can be potentially shared and how much is actually shared under the constraints defined by a typical spectrum-sharing model. We characterize and quantify the recovered spectrum using statically defined constraints on the secondary-user (SU) transceivers of minimum primary-user (PU) detection sensitivity and maximum SU transmit power. Simulation experiments reveal the impact of conservative worst-case RF-environment assumptions on missed spectrum-access opportunities.
Flexible Capacity Partitioning in Many-Core Tiled CMPs (2013)

Chip Multi-Processors (CMP) have become a mainstream computing platform. As transistor density shrinks and the number of cores increases, more scalable CMP architectures will emerge. Recently, tiled architectures have shown such scalable characteristics and been used in many industry chips. The memory hierarchy in tiled architectures presents interesting design challenges. One major challenge is the organization of the Last Level Cache (LLC). Shared but distributed LLCs are preferred over private LLCs due to better utilization of the aggregate cache capacity. However, such architectures suffer from high on-chip hit latency. Breaking down the the shared LLC into smaller domains called clusters where each cluster is associated with one processor VM can reduce the on-chip hit latency significantly. However, having static cluster sizes may not be the best option as some processes may need more cache capacity than others. In this paper, we propose a novel inter-cluster capacity partitioning scheme called Flexible TiledCMP Capacity Partitioning (FlexTCP). FlexTCP maintains the small hit latency of cluster caches while at the same time enables flexible capacity partitioning across clusters such that clusters with high cache demand can steal capacity from underutilized clusters. FlexTCP proposes multiple ways of shrinking/expanding the cluster size. When applied to a 64-coretiled-CMP running a mix of SPEC CPU2006 and Parsec 2.1 workloads, FlexTCP achieves an average of 21% and 18% improvement in Weighted Speedup over two rival schemes.
Development of low-temperature drop shock resistant solder alloys for handheld devices (2013)

As handheld devices become increasingly smaller and complex, there is a shift in reliability requirements of solder pastes. Considering that thermal management and drop resistance of such devices become more challenging, improved thermal fatigue and mechanical shock properties grow into must have requirements. Additionally, multi-step assembly process and a surge in use of temperature sensitive components bring additional challenges that necessitate the use of low temperature alloys. Here we present the findings of our Alloy Development Program on the next generation of low temperature alloys that can be used in reflow soldering temperatures from 170 to 200°C. By using micro-additives we have created low temperature alloys with superior mechanical properties, higher drop shock resistance and improved fatigue life.
Raman imaging of human macular pigments (2003)

We have expanded our efforts to generate high spatial resolution images showing the distibution of carotenoid macular pigments in the human retina using Raman spectroscopy. A low level of macular pigments is associated with an increased risk of developing age-related macular degeneration, a leading cause of irreversible blindness. Using excised human eyecups and resonant excitation of the pigment molecules with narrow bandwidth blue light from a filtered arc lamp, we record Raman images originating from the carbon-carbon double bond stretch vibrations of lutein and zeaxanthin, the carotenoids comprising human macular pigments. Our Raman images reveal significnt differences among subjects, both in regard to absolute levels ss well as spatial distribution within the macula. Since the light levels used to obtain these images are well below established ssafety limits, this technique holds promise for developing a rapid screening diagnostic in large populations at risk for vision loss from age-realted macular degeneration.
Rapid Dry Etching Of Photoresists Without Toxic Gases (1991)

Experimental dry etching technique strips photoresists from semiconductor wafers without damaging semiconductor materials. Makes use of afterglow existing downstream from plasma generated by radio-frequency electric field. Constituents of afterglow react with sacrificial polymer to make reactive gases that quickly etch-away photoresist. Strips quickly at room temperature; not necessary to heat substrates. No hazardous or toxic chemicals used.
EgoSampling: Wide View Hyperlapse from Single and Multiple Egocentric Videos. (2016)

The possibility of sharing one's point of view makes use of wearable cameras compelling. These videos are often long, boring and coupled with extreme shake as the camera is worn on a moving person. Fast forwarding (i.e. frame sampling) is a natural choice for faster video browsing. However, this accentuates the shake caused by natural head motion in an egocentric video, making the fast forwarded video useless. We propose EgoSampling, an adaptive frame sampling that gives more stable, fast forwarded, hyperlapse videos. Adaptive frame sampling is formulated as energy minimization, whose optimal solution can be found in polynomial time. We further turn the camera shake from a drawback into a feature, enabling the increase of the field-of-view. This is obtained when each output frame is mosaiced from several input frames. Stitching multiple frames also enables the generation of a single hyperlapse video from multiple egocentric videos, allowing even faster video consumption.
Minimally invasive alveolar ridge augmentation procedure (tunneling technique) using rhPDGF-BB in combination with three matrices: a case series. (2009)

This study investigated a minimally invasive surgical procedure for alveolar ridge augmentation that combined recombinant human platelet-derived growth factor BB (rhPDGF-BB) and three different matrices. The minimally invasive tunneling ridge augmentation procedure was applied to 12 patients randomized into three groups: rhPDGF-BB (0.3 mg/mL) was combined with freeze-dried bone allograft (FDBA; group A), anorganic bovine bone graft (ABBG; group B), or anorganic bovine bone graft/mineralized collagen bone substitute (ABBG/MCBS; group C). Computed tomography (CT) scans were obtained presurgically and prior to 14-week re-entry surgery. Clinical reentry revealed adequate bone volume to place implants in all patients in groups A and B and two of four patients in group C. Trephine core biopsies were obtained and evaluated by microCT, backscatter scanning electron microscopy (BE-SEM), and light microscopy. New bone formation was consistently observed with BE-SEM and histologic analysis for group A and B specimens. Newly formed woven and lamellar bone were in close contact with graft particles. The ABBG/MCBS specimens (group C) had more variable results, with fibrous encapsulation of graft particles and limited histologic evidence of new bone formation. Within the limits of this study, the FDBA and ABBG carriers appear to be appropriate scaffolds to deliver rhPDGF-BB for ridge augmentation via minimally invasive surgical techniques.
Interferometer Measures Broardband Surface Acoustic Waves (1985)

Dual differential interferometer uses two pairs of orthogonallypolarized optical beams to measure amplitude and orientation of broadband ultrasonic surface acoustic waves. Instrument modular, and sensitivity limited only by optical detector used.
Interpreting azimuthal Fourier coefficients for anisotropic and fracture parameters (2015)

Abstract Amplitude variation with offset and azimuth (AVOAz) analysis can be separated into two separate parts: amplitude variation with offset (AVO) analysis and amplitude versus azimuth (AVAz) analysis. Useful information about fractures and anisotropy can be obtained just by examining the AVAz. The AVAz can be described as a sum of sinusoids of different periodicities, each characterized by its magnitude and phase. This sum is mathematically equivalent to a Fourier series, and hence the coefficients describing the AVAz response are azimuthal Fourier coefficients (FCs). This FC parameterization is purely descriptive. The aim of this paper is to help the interpreter understand what these coefficients mean in terms of anisotropic and fracture parameters for the case of P-wave reflectivity using a linearized approximation. The FC representation is valid for general anisotropy. However, to gain insight into the significance of FCs, more restrictive assumptions about the anisotropy or facture system must be assumed. In the case of transverse anisotropic media with a horizontal axis of symmetry, the P-wave reflectivity linearized approximation may be rewritten in terms of azimuthal FCs with the magnitude and phase of the different FCs corresponding to traditional AVAz attributes. Linear slip theory is used to show that the FCs can be interpreted similarly for the cases of a single set of parallel vertical fractures in isotropic media and in transverse anisotropic media with a vertical axis of symmetry (VTI). The magnitude of the FCs depends on the fracture weakness parameters and the background media. For the case of vertical fractures in a VTI background, the AVOAz inverse problem is underdetermined, so extra information must be incorporated to determine how the weights are modified due to this background anisotropy. We evaluated this on a 3D data set from northwest Louisiana for which the main target was the Haynesville shale.
Stereo reconstruction from multiperspective panoramas (1999)

The paper presents a new approach to computing depth maps from a large collection of images where the camera motion has been constrained to planar concentric circles. We resample the resulting collection of regular perspective images into a set of multiperspective panoramas, and then compute depth maps directly from these resampled images. Only a small number of multiperspective panoramas is needed to obtain a dense and accurate 3D reconstruction, since our panoramas sample uniformly in three dimensions: rotation angle, inverse radial distance, and vertical elevation. Using multiperspective panoramas avoids the limited overlap between the original input images that causes problems in conventional multi-baseline stereo. Our approach differs from stereo matching of panoramic images taken from different locations, where the epipolar constraints are sine curves. For our multiperspective panoramas, the epipolar geometry to first order consists of horizontal lines. Therefore, any traditional stereo algorithm can be applied to multiperspective panoramas without modification. Experimental results show that our approach generates good depth maps that can be used for image based rendering tasks such as view interpolation and extrapolation.