gebhart/patrepeval huggingface dataset:
Engineering Transgenic Eggplant (Solanum melongena L.) Resistant to the Colorado Potato Beetle (Leptinotarsa decemlineata Say) (1996)

A chimeric construct, containing the synthetic cryIIIA (Btt) gene, the NPTII selectable marker and the uidA reporter gene, was incorporated via Agrobacterium tumefaciens into eggplant, variety Hibush. The synthetic cryIIIA gene, altered at the nucleotide level without changing the amino acids of the toxic protein by J. Kemp of New Mexico State Univ., Las Cruces, is adapted for high expression in plant cells. To verify the transgenic status, GUS assays were performed on over 300 plants, from which 185 were confirmed to be transgenic. Physical incorporation of the chimeric construct was further confirmed by Southern analysis of about 30 transgenic plants; both single and multiple site incorporation of the Btt gene were found. Resistance to Colorado potato beetle (CPB) was assessed by: a) placing egg masses of CPB on leaves of plants grown in the growth chamber; b) placing first-instar larvae on detached leaves; c) observing 173 transgenic plants under field conditions. About 60% of the transgenic plants displayed a very high level of resistance to CPB. No larvae survived on the resistant plants longer than 50–60 hours after hatching. Upon selfing, the transgenic plants with a single construct segregate in the S 1 generation in a Mendelian fashion.
Synthesis of 5,6-Dihydroxyindole: A Novel Reductive Cyclization of (E)-4,5-Dihydroxy-2,β-Dinitrostyrene (1985)

Abstract A unique catalytic reductive cyclization of (E)-4,5-dihydroxy-2,β-dinitrostyrene (1) to 5,6-dihydroxyindole (2) is reported. Compound 1 is obtained either by one-step CF3CO2H deprotection of 4,5-dibenzyloxy-2,β-dinitrostyrene (7), or by an improved two-step demethylenation of 6-nitropiperonal (5), followed by condensation with CH3NO2.
Growth Conditions of and Emetic Toxin Production by <i>Bacillus cereus</i> in a Defined Medium with Amino Acids (1999)

The growth and emetic toxin (cereulide) production of Bacillus cereus strains in defined culture media were studied. We found that a fully synthetic medium (CADM) allowed the production of emetic toxin and the addition of glucose enhanced it. By subtracting each amino acid from CADM, we found that only three amino acids, valine, leucine and threonine, were essential for growth and toxin production by B. cereus. The addition of high levels (50 mM) of leucine, isoleucine and glutamic acid decreased the toxin production. Other amino acids had no effect at this concentration.
Potent and selective activation of abscisic acid receptors in vivo by mutational stabilization of their agonist-bound conformation (2011)

Pyrabactin resistance (PYR) 1 and its relatives belong to a family of soluble abscisic acid (ABA) receptors that inhibit type 2C protein phosphatases (PP2C) when in their agonist-stabilized conformation. Given their switch-like properties, we envisioned that mutations that stabilize their agonist-bound conformation could be used to activate signaling in vivo. To identify such mutations, we subjected PYR1 to site-saturation mutagenesis at 39 highly conserved residues that participate in ABA or PP2C contacts. All 741 possible single amino acid substitutions at these sites were tested to identify variants that increase basal PYR1-PP2C interactions, which uncovered activating mutations in 10 residues that preferentially cluster in PYR1's gate loop and C-terminal helix. The mutations cause measurable but incomplete receptor activation in vitro; however, specific triple and quadruple mutant combinations were constructed that promote an agonist-bound conformation, as measured by heteronuclear single quantum coherence NMR, and lead to full receptor activation. Moreover, these mutations retain functionality when introduced into divergent family members, and can therefore be used to dissect individual receptor function in vivo, which has been problematic because of redundancy and family size. Expression of activated PYL2 in Arabidopsis seeds activates ABA signaling by a number of measures: modulation of ABA-regulated gene expression, induction of hyperdormancy, and suppression of ABA deficiency phenotypes in the aba2-1 mutant. Our results set the stage for systematic gain-of-function studies of PYR1 and related ABA receptors and reveal that, despite the large number of receptors, activation of a single receptor is sufficient to activate signaling in planta.
Shear wave viscoelasticity imaging using local system identification (2017)

Tissue elasticity is an important parameter which relates to the pathological state of soft tissue. Fibrotic lesions or malignant tumors are known to be notoriously stiff compared to benign tissue. Shear wave elastography can provide a fully quantitative measure of lesion stiffness by estimating the speed at which acoustically induced shear waves propagate through the material. This speed is in turn related to the Young's modulus. In soft tissue, elasticity is generally accompanied by viscosity, leading to dispersion of the shear wave. For the detection and characterization of malignant lesions, viscosity has in fact diagnostic value. Here, we describe a new method that enables imaging not only elasticity but also viscosity from shear wave elastography by local model-based system identification. We show that the proposed method can be applied effectively to standard shear wave acquisitions, and is able to generate high-resolution parametric maps of the viscoelastic material properties in an in-vitro setting.
Deliverable navigation for multicriteria IMRT treatment planning by combining shared and individual apertures (2013)

We consider the problem of deliverable Pareto surface navigation for step-and-shoot intensity-modulated radiation therapy. This problem amounts to calculation of a collection of treatment plans with the property that convex combinations of plans are directly deliverable. Previous methods for deliverable navigation impose restrictions on the number of apertures of the individual plans, or require that all treatment plans have identical apertures. We introduce simultaneous direct step-and-shoot optimization of multiple plans subject to constraints that some of the apertures must be identical across all plans. This method generalizes previous methods for deliverable navigation to allow for treatment plans with some apertures from a collective pool and some apertures that are individual. The method can also be used as a post-processing step to previous methods for deliverable navigation in order to improve upon their plans. By applying the method to subsets of plans in the collection representing the Pareto set, we show how it can enable convergence toward the unrestricted (non-navigable) Pareto set where all apertures are individual.
Efficient Gene Transfer via Retrograde Transport in Rodent and Primate Brains Using a Human Immunodeficiency Virus Type 1-Based Vector Pseudotyped with Rabies Virus Glycoprotein (2007)

The primate lentiviral vector system based on human immunodeficiency virus type 1 (HIV-1) has been used for a wide range of gene therapy trials in animal models. Axonal transport in the retrograde direction, which is observed with some viral vectors, confers a considerable advantage to gene transfer into neuronal cell bodies that are localized in regions remote from the injection site of the vectors. However, retrograde axonal transport of the HIV-1-based lentiviral vector pseudotyped with vesicular stomatitis virus glycoprotein is reported to be inefficient. In the present study, we developed an efficient gene transfer system through retrograde transport in the brain with the HIV-1-based vector pseudotyped with rabies virus glycoprotein (RV-G). Injection of the RV-G-pseudotyped HIV-1 vector into the dorsal striatum of mice yielded an increase in gene transfer into neuronal populations in the cerebral cortex, thalamus, and ventral midbrain, each of which innervates the striatum. In addition, injection of the RV-G-pseudotyped vector into the monkey striatum (putamen) resulted in highly efficient transfer into neurons in the ventral midbrain (nigrostriatal dopamine neurons). Our results indicate that pseudotyping of the HIV-1 vector with RV-G enhances the efficiency of gene transfer through retrograde axonal transport in both mouse and monkey brains. This primate lentiviral vector system will provide a powerful approach to gene therapy for neurological and neurodegenerative diseases by means of enhanced retrograde transport.
Development of PCSA-Targeted Minibodies for Imaging of Prostate Cancer (2009)

Abstract : The humanized antibody to prostate stem cell antigen (PSCA), a cell surface marker on prostate cancer cells, combined with PET scanning was developed to image prostate tumor. The antibody was successful in preclinical model, although humanization caused a loss of affinity relative to the parental monoclonal antibody. To improve the imaging agent, multiple versions of humanized PSCA antibody fragments were created and subsequently tested for their abilities to image in vivo using micro-PET, with the goal to eventually detect distant metastases. Both the engineered minibodies and diabodies were able to successfully detect tumor, and the affinity that was decreased upon humanization was improved. Experiments are ongoing to characterize the affinity matured variant of the minibodies, therefore a lead agent has not been chosen, but this is expected to happen in the next year. On the other hand, a human PSCA knockin mouse model was generated, verified and maintained. This genetically engineered murine line is being expanded and will be used to cross to a known model of mouse prostate cancer in the next year.
Abstract TP255: Calcium Release-activated Calcium Channel Inhibition Protects Against Inflammation in Ischemic Stroke (2018)

Purpose: Inflammatory responses after ischemic stroke contribute to worsening of ischemic brain injury. Calcium release-activated calcium (CRAC) channels are known to be involved in the activation of immune responses in microglia, and have been studied indirectly through non-specific calcineurin inhibitors such as cyclosporine and FK506. Since these compounds have many off-target effects and unacceptable side effects, we studied a novel CRAC channel inhibitor which is specific to the CRAC channel and appears safe in preclinical studies in anticipation of human clinical trials for other indications. We explored whether this inhibitor might improve outcome in experimental stroke by inhibiting microglial activation. Subjects and Methods: 2-3 month old C57/BL6 male mice, were exposed to transient middle cerebral artery occlusion (tMCAO, filament model) for 2h followed by reperfusion. Some were treated with the CRAC channel inhibitor (CM-EX-137, 5mg/kg IP; tMCAO-CM) or vehicle control (tMCAO) daily beginning immediately after occlusion and the following two days. Brains were collected 3d post-stroke. Neurological function was evaluated using a Bederson score, elevated body swing test, adhesive removal test, and corner test at baseline, at 3, 24 and 72 h. Relative cerebral blood flow (rCBF) was studied in some mice using laser Doppler flowmetry. Ischemic lesion size was evaluated by 2,3,5-triphenyl tetrazolium chloride (TTC) staining. Microglial/monocyte activation was assessed by isolectin B4 histochemistry. Results: A total of 18 mice were studied (tMCAO-CM: 8; tMCAO: 8, sham:2). rCBF was no different between experimental groups, and is consistent with the notion that the compound should not alter blood flow. Neurological function at 1 & 3d after ischemia was significantly improved in tMCAO-CM group compared to tMCAO (p<0.001). The CM compound also significantly reduced infarct volume by ~60% (p<0.05). Isolectin B4 staining was markedly reduced in the tMCAO-CM group compared to tMCAO 3d post ischemia (p<0.01). Conclusion: CRAC channel inhibition protects against experimental stroke by decreasing lesion size, improving neurological outcomes and decreasing microglial activation.
Positive Interaction between 5-FU and FdUMP[10] in the Inhibition of Human Colorectal Tumor Cell Proliferation (1999)

Interaction between 5-fluorouracil (5-FU) and FdUMP[10], a novel pro-drug formulation of the thymidylate synthase (TS) inhibitory nucleotide 5-fluoro-2'-deoxyuridine-5'-O-monophosphate (FdUMP), was investigated to evaluate the feasibility of using these two forms of fluorinated pyrimidine in combination chemotherapy regimens. 5-FU and FdUMP[10] are expected to differ in their relative intracellular distribution of active metabolites, and their combined administration may result in either a positive or a negative interactive effect. The dose-response behaviors of 5-FU and FdUMP[10] toward H630 and H630-10 (human colorectal tumor) cells were first investigated separately. Effects on cell viability were measured using an assay for 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), while cytotoxicity and apoptosis were investigated using clonogenic and TUNEL assays, respectively. Exposure of H630 cells to concentrations of FdUMP[10] insufficient to inhibit cell proliferation as a single agent markedly increased the cytotoxicity of 5-FU. The results indicate that 5-FU and FdUMP[10] interact in a positive manner, and that combining these two forms of fluorinated pyrimidine may be clinically beneficial.
<title>Controlled continuous tuning of an adaptively tunable vibration absorber incorporating shape memory alloys</title> (2000)

Controlled continuous tuning of the stiffness of shape memory alloy (SMA) spring elements of an adaptively tunable vibration absorber (ATVA) is a novel concept for adaptive-passive vibration control. Minimization of the vibration of a primary system is achieved indirectly via stiffness control of the SMA structural elements supporting a secondary mass. Stiffness control is further achieved via the heating of the SMA elements. In this paper a control law to achieve phase- tracking by controlling the heating of the SMA elements is developed and implemented. Successful analytical and experimental results demonstrate the feasibility of continuous control of the SMA ATVA. Performance of the SMA ATVA is compared to the performance of comparable passive tuned vibration absorbers (TVA). The comparison shows that substantial improvements in vibration attenuation can be achieved through the implementation of the SMA ATVA.
Accurate calibration of the four-detector photopolarimeter with imperfect polarizing optical elements (1989)

The first three columns of the instrument matrix A of the four-detector photopolarimeter (FDP) are determined by Fourier analysis of the output current vector I(P) as a function of the azimuth angle P of the incident linearly polarized light. Therefore 12 of the 16 elements of A are measured free of the imperfections of the (absent) quarter-wave retarder (QWR). The effect of angular beam deviation by the polarizer is compensated for by taking the average, (1/2) [I(P) + I(P + 180°)], of the FDP output at 180°-apart, optically equivalent, angular positions of the polarizer. The remaining fourth column of A is determined by the FDP’s response to the right- and left-handed circular polarization states. Because these states are impossible to generate with an imperfect QWR, a novel procedure is developed. In particular, the response of the FDP to the unattainable right- or left-handed circular polarization state is found by taking the average of the responses of the FDP to an elliptical near-circular state and that state rotated in azimuth by 90°. This calibration scheme is applied to measure A of our prototype FDP of four Si detectors at λ = 632.8 nm. A is determined, in external and internal reference frames, free of imperfections in the polarizing optical elements. The FDP, with its uncontaminated A matrix, is used subsequently to evaluate the imperfections of the QWR with the help of an appropriate model.
Perforated pzt-polymer composites for piezoelectric transducer applications (1982)

Abstract Composites of PZT and polymer with 3-1 and 3-2 connectivity patterns have been fabricated by drilling holes in sintered PZT blocks and filling the holes with epoxy. The influence of hole size and volume fraction PZT on the hydrostatic properties of the composite was evaluated. By decoupling the piezoelectric [dbar]33 and [dbar]31 coefficients in the composite, the hydrostatic coefficients are greatly enhanced. On samples optimized for hydrophone performance, the dielectric constants of 3-1 and 3-2 composites are 600 and 300 respectively. The piezoelectric coefficients [dbar]h, [gbar]h, and [dbar]hdh for 3-1 composites are 230 (pCN−1), 34 (x10−3 VmN−1), and 7800 (10−15 m2N−1) respectively, and the corresponding values for 3-2 composites are 372 (pCN−1), 123 (10−3 VmN−1), and 45000 (10−15 m2N−1).
InGaAs/AlGaAs strained quantum-well diode lasers (1993)

The OMVPE growth and performance of graded-index separate-confinement heterostructure strained quantum-well InGaAs-AlGaAs diode lasers are reviewed. Broad-stripe lasers have exhibited J<SUB>th</SUB> as low as 60 A cm<SUP>-2</SUP> for a cavity length L equals 1500 micrometers and differential quantum efficiency (eta) <SUB>d</SUB> as high as 90% for L equals 300 micrometers . Similar heterostructures have been used to fabricate traveling wave amplifiers with a laterally tapered gain region that emit over 1 W cw in a nearly diffraction-limited spatial lobe at 0.98 micrometers , linear arrays of 200-micrometers -long uncoated ridge-waveguide lasers with average threshold currents of 4 mA and (eta) <SUB>d</SUB> approximately 90%, and high-power broad-stripe lasers with power conversion efficiency exceeding 50% at 75 degree(s)C.
A novel biomimetic treatment for an improved osteointegration of titanium. (2012)

Direct osteointegration of titanium and titanium alloys implants is one of the main goals of biomaterials research for dental and orthopedic applications. Chemical, mechanical or biological treatments are investigated searching for fast and durable implant to bone bonding. The aim of the present work is to assess the in vitro mineralisation capabilities and to investigate the mechanical and physico-chemical properties of a new biomimetic treatment on titanium. The new surface treatment was obtained using Anodic Spark Deposition technique, and consists of a first ASD treatment performed in solutions containing phosphate ions followed by a second ASD treatment in a solution rich in calcium ions. The resulting surface is finally treated by alkali etching. The physio-chemical and mechanical properties of this material are analyzed and the mineralization potential is considered by surface analysis after soaking it in different solutions of simulated body fluid (SBF). The developed biomimetic treatment was then compared to other treatments from the literature. The proposed treatment was found to possess a very high mineralization capaci-ty, that makes its application very interesting in terms of speed and strength of direct implant osteointegration. (Journal of Ap-plied Biomaterials & Biomechanics 2003; 1: 33-42).
System calibration unit for magnetic particle imaging: System matrix (2013)

Magnetic particle imaging (MPI) has the potential to deliver images at high time resolution and submillimetre spatial resolution. In order to reconstruct the images from the measured data one needs to obtain a so called system matrix. A system matrix can be measured by physically moving a voxel sized sample and measuring the signal at each position within the imaging volume of the scanner. A system calibration unit (SCU) provides a fast and efficient method to measure a system matrix. The physical movement of the sample can be replaced by the use of homogeneous focus fields. This resulted in time saving of a factor of 2-3. In this paper, the use of sensitive dedicated receive coils is described that provide a further improvement by up to an order of magnitude in sensitivity.
Circulating and tumor-associated caspase-4: a novel diagnostic and prognostic biomarker for non-small cell lung cancer (2018)

Late diagnosis limits therapeutic options and survival rate of non-small cell lung cancer (NSCLC) patients. Therefore the identification of biomarkers represents an emerging medical need. A highly sensitive and specific test was developed to identify/quantify a novel/selective diagnostic biomarker for NSCLC patients, caspase-4. This test was validated by using i) plasma from 125 NSCLC patients and 79 healthy (non-pathological) subjects, ii) plasma from 139 smokers and iii) from 70 chronic-obstructive pulmonary disease (COPD) patients. Caspase-4 quantification was also assessed in the lung tumor mass of 98 paired NSCLC patients compared to 10 non-tumor lung tissues (i.e. tuberculosis). Circulating caspase-4 was detected in both healthy and NSCLC patients; however at different range values: 2.603-3.372 ng/ml for NSCLC patients (95% CI) compared to 0.3994-0.6219 ng/ml for healthy subjects (95% CI). The sensitivity of the test ranged from 97.07% to 100%; the specificity was 88.1% with a positive predictive value of 92.54%, accuracy of 95.19% and AUC of 0.971. Smokers (95% CI, 0.3947-0.6197 ng/ml) and COPD patients (95% CI, 1.703-2.995 ng/ml) showed intermediate values of circulating caspase-4. Tissue levels of caspase-4 in the tumor mass showed that 72 (72.7%) out of 99 patients were positive. More importantly, higher levels (cut-off value = 0.307 ng/ml) of caspase-4 in the tumor mass were associated to reduced overall survival (median 0.92 years) compared to NSCLC patients with lower levels (median 3.02 years). We report for the first time caspase-4 as a novel diagnostic and prognostic biomarker, opening new therapeutic perspectives for NSCLC patients.
A DCT-Based Video Object Segmentation Algorithm for Rainy Situation Using Change Detection (2006)

This paper proposes a DCT-based moving object extraction algorithm which is focused on rainy condition by change detection method. The DCT kchniqzle is used to decrease the rainy efect in order to construct a reliable background model. Then, we use change detection to classzfj, pixeb in video frame into the foregro~lnd region or background region so as to acquire an initial object mask. Besides, reflection eflect can be removed from initial object mask through edge detection and bounding box match. Finally, a post-processing is used lo refine the boundary of moving object by connect component labeling and morphological operation. Experimental results show lhat the proposed algorithm can provide a safisfactory segmentation resztlt in rainy situations.