gebhart/patrepeval huggingface dataset:
Abstract LB-217: A gene signature that predicts deficiency of homologous recombination DNA repair. (2013)

Abstract DNA repair pathways play a fundamental role to maintain genomic stability. Defects in specific DNA repair pathways predispose to cancer development, but also provide therapeutic opportunities: for example, poly-ADP ribose polymerase (PARP) inhibitors are synthetically lethal with cancer cells, which are defective in homologous recombination (HR)-mediated DNA repair, such as BRCA1/BRCA2-deficient tumors. However, recent clinical trials of PARP inhibitors have shown rather disappointing results, particularly in the treatment of triple-negative breast cancer (TNBC), which has a molecular phenotype similar to that of BRCA-deficient breast cancer. As a targeted therapy, the clinical success of PARP inhibitors is dependent on identifying cancer cells with HR repair deficiency. Thus the observations of PARP inhibitors from clinical trials raise a key question: Can we identify a molecular signature of HR repair deficiency in cancer cells? To answer this question, we utilized the gene expression profiling approach to measure the cellular transcriptional reprograming in HR-deficient cell lines. By analyzing the molecular changes of transcriptional landscape, we identified an HR-defect gene signature that predicted HR repair deficiency in cells, predicted clinical outcomes of multiple human cancers, and predicted sensitivity of human cancer cells to PARP inhibitors. HR repair deficiency leads to genomic instability and often promotes accumulation of additional mutations. Our gene signature analysis further revealed that combinatorial effects of co-existing genetic changes such as loss of both BRCA1 and PTEN may extensively rewire the HR repair network and confer resistance to PARP inhibitor treatment. Moreover, to combat PARP inhibitor resistance, we successfully used our HR-defect gene signature as a drug discovery tool and found that TTK, mTOR and PI3K inhibitors could induce HR repair deficiency and sensitize cancer cells to PARP inhibitor treatment. Collectively, our findings demonstrate that transcriptional signature can be used to define the functional status of the HR repair network in cells. In summary, our study identifies a gene signature of HR repair deficiency, which provides a novel network view of the DNA repair process. In addition to using our gene signature as a prognostic marker for multiple cancers including breast, ovarian and lung cancer, our findings potentially have a significant impact on predicting responsiveness and overcoming resistance to targeted therapeutic regimens with DNA repair inhibitors such as PARP inhibitors. Citation Format: Guang Peng, Gordon Mills, Shiaw-Yih Lin. A gene signature that predicts deficiency of homologous recombination DNA repair. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-217. doi:10.1158/1538-7445.AM2013-LB-217
Construction of the Bacteriochlorin Macrocycle with Concomitant Nazarov Cyclization To Form the Annulated Isocyclic Ring: Analogues of Bacteriochlorophyll <i>a</i> (2017)

Bacteriochlorophylls contain a bacteriochlorin macrocycle bearing an annulated fifth ring. The fifth ring, termed the isocyclic ring or ring E, is equipped with 13<sup>1</sup>-oxo and 13<sup>2</sup>-carbomethoxy substituents. Herein, a general route to stable, synthetic bacteriochlorophyll analogues is described. Knoevenagel condensation (∼40 mM, rt, CH<sub>2</sub>Cl<sub>2</sub>, piperidine/AcOH/molecular sieves) of a dihydrodipyrrin-carboxaldehyde (AD half) and a dihydrodipyrrin substituted with a β-ketoester (BC half) forms a propenone bearing the two halves (a hydrobilin analogue). Subsequent treatment (0.2 mM) with acid (Yb(OTf)<sub>3</sub>, CH<sub>3</sub>CN, 80 °C) promotes a double ring-closure process: (i) condensation between the α-position of pyrrole ring A and the α-acetal unit attached to pyrroline ring B forms the bacteriochlorin macrocycle, and (ii) Nazarov cyclization of the β-(propenoyl)-substituted ring C forms the isocyclic ring (E). Five new bacteriochlorins bearing various substituents (alkyl/alkyl, aryl, and alkyl/ester) at positions 2 and 3 (β-pyrrole sites, ring A) and 13<sup>2</sup> carboalkoxy groups (R = Me or Et) were constructed in 37-61% yield from the hydrobilin analogues. The BC half and AD half are available in five and eight steps, respectively, from the corresponding pyrrole-2-carboxaldehyde and unsaturated ketone. The bacteriochlorins exhibit absorption spectra typical of bacteriopheophytins (free base bacteriochlorophylls), with a strong near-infrared absorption band (707-751 nm).
Design of a channel drop filter by using a donor-type cavity with high-quality factor in a two-dimensional photonic crystal slab (2003)

We report a design of the surface-emitting-type channel drop filters based on point defect cavities and line defect waveguides in two-dimensional photonic crystal slabs, which aim to improve the filtering resolution and light emission characteristics. Since the filters are passive, the mode volume size of the defects needs not be minimized, but the interaction between the defect cavity and the line defect waveguide must be considered. By adopting a donor-type point defect with three missing holes of linear shape, the quality factor of the filter theoretically increases to values as high as 2900 while it reached only 500 in the previously utilized acceptor-type defect. The results suggest that this donor-type defect is very useful for the development of ultrasmall channel add/drop devices.
The Synthesis of Potential Parasitic Drugs (1989)

Abstract : During the period from 1 April 1988 to 31 March 1989, we submitted to WRAIR 8 target compounds (Table I) and 15 intermediates (Table II). A number of additional syntheses are in progress (Table III). In earlier work, we prepared a series of primaquines with a methyl group at position 4 and a phenylalkoxy group at position 5. These compounds combined low toxicity with a unique dual efficacy against the blood and tissue forms of the malarial parasite. (Tables VI and VII) . In the past year, we have attempted to enhance this series by attaching various substituents to the phenyl portion of the 5-phenylalkoxy group. Screening data for the new compounds are still too sparse for SAR conclusions (Tables IV & V). While awaiting additional data, we have started work on another groups of primaquines. These derivatives will have an alkoxy, phenoxy, or benzyloxy group at position 5, a methyl group at positions 3 or 4 and a methoxy or methyl group at position 2. Keywords: Antiparasitic drugs, Antimalarials, Primaquine, SAR, 8-Aminoquinolines, Blood schizontocides, Tissue schizontocides, Syntheses, RAI.
Improved Modified Pressure Imaging and Software for Egg Micro-Crack Detection and Egg Quality Grading (2012)

Cracks in the egg shell increase the food safety risk. Eggs with very fine, hairline cracks (micro-cracks) are often undetected during the grading process because they are almost impossible to detect visually. A modified pressure imaging system was developed to detect eggs with micro-cracks and regular cracks alike without adversely affecting egg quality. The modified pressure imaging system forces a change in pressure from the atmospheric pressure to the negative pressure (vacuum) in an enclosure to open the cracked shell surface momentarily, while intensity changes in the open shell surface are recorded by a high-resolution digital camera and detected by an image processing algorithm. In this article, modifications and improvements to the system are reported along with application software development. The previous design for 15 eggs was modified to accommodate 20 eggs and improved to add a stepper motor to image the entire surface of eggs automatically and the data management software was added to aid a professional grader in egg grading. In a three-day study with 3,000 eggs in a commercial egg processing plant, a professional grader operated the 20-egg imaging system after a short training on the first day and another professional grader graded the eggs with hand candling. The accuracy in crack detection of both graders and the system itself was compared in order to test the crack-detection performance of the system and to explore the possibility of the use of the system for egg grading by USDA graders. The system automatically detected checked and cracked eggs with 94.53% accuracy with 0.29% of a false positive rate while a hand candler had 83.58% accuracy in crack detection. The grader operating the system had 98.51% accuracy in crack detection without any false positives. Other quality factors were also graded by both graders. The study demonstrated the potential of the system for egg grading in high accuracy.
Speech reconstruction from mel frequency cepstral coefficients and pitch frequency (2002)

This paper presents a novel low complexity, frequency domain algorithm for reconstruction of speech from the mel-frequency cepstral coefficients (MFCC), commonly used by speech recognition systems, and the pitch frequency values. The reconstruction technique is based on the sinusoidal speech representation. A set of sine-wave frequencies is derived using the pitch frequency and voicing decisions, and synthetic phases are then assigned to each respective sine wave. The sine-wave amplitudes are generated by sampling a linear combination of frequency domain basis functions. The basis function gains are determined such that the mel-frequency binned spectrum of the reconstructed speech is similar to the mel-frequency binned spectrum, obtained from the original MFCC vector by IDCT and antilog operations. Natural sounding, good quality intelligible speech is obtained by this procedure.
Olefin polymerization with metallocene catalysts supported on polysiloxane derivatives (1995)

Abstract Three kinds of zirconocene catalysts, supported on polysiloxanes substituted with methylindenyl, methyl‐fluorenyl and two indenyl groups, respectively, were prepared and applied to propene and ethylene polymerizations using methylaluminoxane as cocatalyst. Both the activity and stereospecificity of these catalysts were found to lie between those of corresponding homogeneous and SiO 2 ‐supported catalysts. Surprisingly, all the catalysts gave a mixture of atactic and isotactic poly(propylene), plausible reasons for which are briefly discussed.
Modelling and optimizing two- and four-stroke hybrid pneumatic engines (2008)

Hybrid pneumatic engines, which are designed to follow the downsizing and supercharging paradigm, offer a fuel-saving potential that is almost equal to that of hybrid electric powertrains while inducing much lower additional mass and cost penalties. This paper presents a systematic optimization of the operation of such an engine system. Both two-stroke and four-stroke modes are analysed. The optimized valve and throttle actuation laws for all modes and operating areas lead to generic maps that are independent of the engine size. So far, the pneumatic hybridization of internal combustion engines was thought to require two-stroke operation. This paper presents a novel hybrid pneumatic engine configuration that entails fixed camshafts for both intake and exhaust valves while utilizing variable valve actuation for one charge valve per cylinder only. This configuration is operated entirely in four-stroke modes. Such a configuration requires a careful optimization of its operating strategy to achieve its fuel economy potential. Compared with a full two-stroke operation, only small efficiency losses result from using four-stroke modes with these new operating strategies. Initial measurement results with such an engine system are presented in this paper to confirm the validity of the principles of operation.
Surface Enhanced Raman Spectroscopy for Monitoring Lactate and Glucose (2005)

The development of robust, portable, and simple biomedical device for the monitoring of glucose, lactate and other metabolites of interest is of great practical importance to routine treatment of diabetes and to the evaluation of individuals under high-stress situations, e.g. warfighters and astronauts. Raman spectroscopy is a powerful analytical tool that permits the unambiguous identification of molecules based on their unique vibrational modes. This spectral fingerprinting of molecules is well suited to multi-analyte detection without cumbersome sample preparation or separation. The Surface Enhanced Raman Scattering (SERS) phenomenon increases by up to a trillion fold the Raman signal from molecules near gold and silver nanoscale materials. We have shown that the incorporation of chemically tailored coatings on SERS active surfaces may serve as a partitioning layer, selectively concentrating the molecules of interest near the surface, thus simultaneously increasing target signal and decreasing the noise signal from interferants even with low power (~1mW) lasers. We have successfully developed and tested these SERS active substances in vitro and in vivo in the subcutaneous space of a rat. Work continues in rat models of hyperglycemia and hyperlactatemia.
Magnetic Effects in Oxide Superconductors (1987)

The incorporation of magnetic ions into superconducting materials has historically been an important tool for studying both superconductivity and magnetism. In the oxide superconductors we encounter, for the first time, a situation where the superconducting interactions are much stronger than the magnetic interactions, and this can be expected to lead to unusual and unex pected phenomena. In this paper, the currently available information concerning magnetic effects in the superconducting materials La 1.85 Sr 0.15 CuO 4 (T c ∼40 K) and YBa 2 Cu 3 O 7-β (T c ∼90 K) is reviewed. Substitution of strongly mahnetic rare-earth ions for Y or La gives no effect on T c related to magnetic pair-breaking, although effects exist which seem to be due to electronic and/or structural phenomena. Substitution of transition metal ions for Cu results in magnetic pair-breaking, although the results are again complicated by other effects. In addition, antiferromagnetic ordering is seen on the Cu sublattice in compounds where the stoichiometry has been altered to make the materials non-superconducting.
Smart Chemical Taste Sensor for Determination and Prediction of Taste Qualities Based on a Two-Phase Optimized Radial Basis Function Network (2005)

A novel, smart, chemical taste sensor that realistically mimics the behavior of the human gustatory system is described. The taste sensor consists of an array of electrochemical sensors that represent the gustatory receptors on the human tongue, and a two-phase optimized radial basis function network (RBFN) to represent the human brain, which comprehensively analyzes the gustatory stimulation and judges the overall taste. In the illustrated model, eight electrodes were fabricated to determine the eight major taste-causing substances, Na+, K+, Cl-, H+, sucrose, glucose, glutamate, and caffeine. The detected signals were fed to a two-phase RBFN optimized by the implementation of a basis optimization algorithm and weight decay term for appropriate data processing. The first phase of the two-phase RBFN quantifies the amount of taste-causing substances in food samples from the responses of the electrodes. These results are then fed to the second phase, which correlates the amount of substances with the overall taste. The final output is scored on a scale of 1−5 for each of the five basic tastes sensed by the human gustatory system, which are saltiness, sourness, sweetness, bitterness, and umami. The constructed network estimated the intensity of the basic tastes of 30 drink varieties with an average relative error of 7.0% compared to the human scores. The network could also estimate the variance in the human sensory perception. Moreover, the sensor successfully predicted the interactions of tastes such as suppression of bitterness by sweetness and enhancement of umami by saltiness, which are illusions sensed by the human gustatory system. With these abilities, the novel taste sensor can be considered as a quantitative yet humanlike sensor with a great potential for practical applications.
Spectral Contrast Optical Coherence Tomography Angiography Enables Single-Scan Vessel Imaging (2018)

Abstract Optical coherence tomography angiography relies on motion for contrast and requires at least two data acquisitions per pointwise scanning location. We present a method termed spectral contrast optical coherence tomography angiography using visible light that relies on the spectral signatures of blood for angiography from a single scan using endogenous contrast. We demonstrate the molecular sensitivity of this method, which enables lymphatic vessel, blood, and tissue discrimination.
<title>Science and technology of ultrananocrystalline diamond (UNCD) thin films for multifunctional devices</title> (2001)

MEMS devices are currently fabricated primarily in silicon because of the available surface machining technology. However, Si has poor mechanical and tribological properties, and practical MEMS devices are currently limited primarily to applications involving only bending and flexural motion, such as cantilever accelerometers and vibration sensors. However, because of the poor flexural strength and fracture toughness of Si, and the tendency of Si to adhere to hydrophyllic surfaces, even these simple devices have limited dynamic range. Future MEMS applications that involve significant rolling or sliding contact will require the use of new materials with significantly improved mechanical and tribological properties, and the ability to perform well in harsh environments. Diamond is a superhard material of high mechanical strength, exceptional chemical inertness, and outstanding thermal stability. The brittle fracture strength is 23 times that of Si, and the projected wear life of diamond MEMS moving mechanical assemblies (MEMS-MMAs) is 10,000 times greater than that of Si MMAs. However, as the hardest known material, diamond is notoriously difficult to fabricate. Conventional CVD thin film deposition methods offer an approach to the fabrication of ultra-small diamond structures, but the films have large grain size, high internal stress, poor intergranular adhesion, and very rough surfaces, and are consequently ill-suited for MEMS-MMA applications. A thin film deposition process has been developed that produces phase-pure ultrananocrystalline diamond (UNCD) with morphological and mechanical properties that are ideally suited for MEMS applications in general, and MMA use in particular. We have developed lithographic techniques for the fabrication of diamond microstructures including cantilevers and multi-level devices, acting as precursors to micro-bearings and gears, making UNCD a promising material for the development of high performance MEMS devices.
Cholesterol Reduction in Liquid Egg Yolk using β‐Cyclodextrin (1995)

ABSTRACT A process to reduce cholesterol in liquid egg yolk using β‐cyclodextrin (CD) was optimized by response surface methodology, based on cholesterol reduction and yield. The most important factors influencing cholesterol reduction were dilution of egg yolk to a defined water:solid ratio and CD concentration. In the final process, egg yolk was adjusted to pH 10.5, diluted to a water:solid ratio of 2.9, heated to 50°C, and CD added at a CD:cholesterol molar ratio of 4.0. The slurry was mixed for 6.5 min at 1800 rpm, cooled to 4°C and centrifuged. Cholesterol in the supernatant was reduced by 89.2%. The yield, cholesterol and CD in the final product were adjusted by varying centrifugal force and CD concentration.
Ultrasound-Specific Segmentation via Decorrelation and Statistical Region-Based Active Contours (2006)

Segmentation of ultrasound images is often a very challenging task due to speckle noise that contaminates the image. It is well known that speckle noise exhibits an asymmetric distribution as well as significant spatial correlation. Since these attributes can be difficult to model, many previous ultrasound segmentation methods oversimplify the problem by assuming that the noise is white and/or Gaussian, resulting in generic approaches that are actually more suitable to MR and X-ray segmentation than ultrasound. Unlike these methods, in this paper we present an ultrasound-specific segmentation approach that first decorrelates the image, and then performs segmentation on the whitened result using statistical region-based active contours. In particular, we design a gradient ascent flow that evolves the active contours to maximize a log likelihood functional based on the Fisher-Tippett distribution. We present experimental results that demonstrate the effectiveness of our method.
High-content screening in microfluidic devices (2010)

Microfluidics technology will drive significant advancements and broader usage and applicability of HCS in drug discovery.
Identifying mirror symmetry density with delay in spiking neural networks (Conference Presentation) (2018)

The ability to rapidly identify symmetry and anti-symmetry is an essential attribute of intelligence. Symmetry perception is a central process in human vision and may be key to human 3D visualization. While previous work in understanding neuron symmetry perception has concentrated on the neuron as an integrator, here we show how the coincidence detecting property of the spiking neuron can be used to reveal symmetry density in spatial data. We develop a method for synchronizing symmetry-identifying spiking artificial neural networks to enable layering and feedback in the network. We show a method for building a network capable of identifying symmetry density between sets of data and present a digital logic implementation demonstrating an 8x8 leaky-integrate-and-fire (LIF) symmetry detector in a field programmable gate array. Our results show that the efficiencies of spiking neural networks can be harnessed to rapidly identify symmetry in spatial data with applications in image processing, 3D computer vision, and robotics.In conclusion, we have presented a novel algorithm for finding a scalar field representing the symmetry of points in a multi-dimensional space. We have shown how time synchronization in the input values of spiking neural networks, with the appropriate choice of threshold and spike period, results in the identification of output neurons along points of high symmetry density to the network inputs. We have demonstrated an implementation of the symmetry selective LIF neural network in common hardware with a high speed, 2.8 MHz identification of symmetry points in an 8x8 Manhattan metric space. Our results show that utilizing only the delay and coincidence detecting properties of a single layer of neurons in spiking neural networks naturally lead to effective symmetry identification. A greater understanding of symmetry perception in artificial intelligences will lead to systems with more effective pattern visualization, compression, and goal setting processes.
A Benzopyrane Derivative as a P‐Glycoprotein Stimulator: A Potential Agent to Decrease β‐Amyloid Accumulation in Alzheimer’s Disease (2011)

A simulating interaction: The P-glycoprotein (P-gp) ligand 13 displays high P-gp interacting activity (EC50=2.90 μM) and selectivity in tumor cell lines. Here, this promising compound was further evaluated ex vivo in an everted gut sac assay and found to behave as a P-gp stimulator, making this agent a potential lead for the development of new therapeutics to treat Alzheimer′s disease.