gebhart/patrepeval huggingface dataset:
CMOS Imaging of Pin-Printed Xerogel-Based Luminescent Sensor Microarrays (2010)

We present the design and implementation of a luminescence-based miniaturized multisensor system using pin-printed xerogel materials which act as host media for chemical recognition elements. We developed a CMOS imager integrated circuit (IC) to image the luminescence response of the xerogel-based sensor array. The imager IC uses a 26 × 20 (520 elements) array of active pixel sensors and each active pixel includes a high-gain phototransistor to convert the detected optical signals into electrical currents. The imager includes a correlated double sampling circuit and pixel address/digital control circuit; the image data is read-out as coded serial signal. The sensor system uses a light-emitting diode (LED) to excite the target analyte responsive luminophores doped within discrete xerogel-based sensor elements. As a prototype, we developed a 4 × 4 (16 elements) array of oxygen (O<sub>2</sub>) sensors. Each group of 4 sensor elements in the array (arranged in a row) is designed to provide a different and specific sensitivity to the target gaseous O<sub>2</sub> concentration. This property of multiple sensitivities is achieved by using a strategic mix of two oxygen sensitive luminophores ([Ru(dpp)<sub>3</sub>]<sup>2+</sup> and ([Ru(bpy)<sub>3</sub>]<sup>2+</sup>) in each pin-printed xerogel sensor element. The CMOS imager consumes an average power of 8 mW operating at 1 kHz sampling frequency driven at 5 V. The developed prototype system demonstrates a low cost and miniaturized luminescence multisensor system.
A high gain strategy with positive-feedback gain enhancement technique (2002)

Several new CMOS very high DC-gain amplifiers that use internal positive-feedback techniques are presented. These amplifiers have a controllable gain and don't require perfect matching of transistors to achieve the high DC gain. An implementation of a sample and hold circuit constructed using one of the proposed amplifiers is described. Simulation results predict a DC gain larger than 100 dB is possible without limiting the speed of the amplifier.
Aberrant methylation of <i>Reprimo</i> correlates with genetic instability and predicts poor prognosis in pancreatic ductal adenocarcinoma (2006)

These results suggest that aberrant methylation of Reprimo is a common event in pancreatic carcinogenesis and is associated with genetic instability and unfavorable outcome after surgical resection.
Two <i>C. elegans</i> genes control the programmed deaths of specific cells in the pharynx (1991)

The genes ces-1 and ces-2 control the decisions of two cells in the nematode Caenorhabditis elegans to undergo programmed cell death. Mutations that cause a gain of ces-1 function or a reduction of ces-2 function prevent these cells, the sisters of the two pharyngeal NSM neurons, from dying. These mutations do not affect most other cell deaths. Genetic studies indicate that ces-1 and ces-2 affect the fates of the NSM sisters by regulating the genes required for all programmed cell deaths to occur.
Formation Damage Induced by Various Water-Based Fluids Used to Drill HP/HT Wells (2008)

Abstract Drilling Unayzah-B reservoir (shale and sandstone) in Saudi Arabia requires high mud density (± 95 pcf) to mechanically stabilize the shale and balance the reservoir pressure. Two fluids are used to drill this reservoir: KCl/ BaSO4/ CaCO3 whereas the second is potassium formate/CaCO3. Barite is added with CaCO3 to reduce the amount of solids needed to formulate the drill-in fluid. However, BaSO4 is insoluble in acids and requires chelating agents to remove it from the formation. Formate drill-in fluids with low solid content can then be used, but they are expensive and corrosive at pH values less than 7-8. To overcome some of the problems associated with these two systems Saudi Aramco developed water-based drill-in fluids using Mn3O4. No similar formulations were developed before to the best of the authors' knowledge. The objective of this study is to determine formation damage induced by KCl/Mn3O4 mud at 95 pcf. A mini-flow loop was used to assess formation damage induced by the three the drill-in fluids. The experiments were conducted using reservoir cores at bottom hole conditions. Another set of experiments were conducted using a dynamic HPHT cell to determine the thickness and composition of the filter cake filter cake, spurt loss and chemical analysis of filtrate. Compatibility tests between mud filtrate and produced water were performed at 300 °F and 500 psi using see through cells. The KCl/Mn3O4 showed the least formation damage compared to the other two fluids. The return permeability was significantly higher than those obtained with potassium formate/CaCO3 or BaSO4/CaCO3 mud systems. Potassium formate filtrate was not compatible with Unayzah-b formation brine, which resulted in its low return permeability (42%) in spite of its low solids content. Unlike formate based fluids, mud filtrate of KCl/Mn3O4 was compatible with the formation brine. BaSO4/CaCO3 drill-in fluid resulted in 40% because the barite solids were trapped inside the core. KCl/Mn3O4 drill-in fluid resulted in 70% return permeability. The main reason for this high result is the spherical shape and small size of Mn3O4 particles, which allowed them to be removed by flow of hydrocarbons.
Direct imaging of surface plasmon excitation with radially polarized beam (2009)

When a radially polarized beam is focused onto a metal-dielectric interface, the entire beam is TM polarized with respect to the interface. Consequently surface plasmons can be excited at all directions. These surface plasmons will propagate to the geometric center, constructively interfere with each other and generate a strongly focused evanescent nondiffracting Bessel beam. In this paper, we report the experimental results on the direct imaging of such plasmonic focusing. Radially polarized beam is tightly focused onto a silver-glass interface with a high numerical aperture oil immersion objective lens. The intensity distribution at the back focal plane of the objective lens after reflection is captured with a CCD camera. A dark ring corresponding to surface plasmon resonance excitation by a focused radially polarized beam is observed. A collection mode near field scanning optical microscope is applied to map the two-dimensional intensity distributions at different distances from the sample to verify the non-spreading and decaying natures of the evanescent Bessel beam.
DNA molecule provides a computing machine with both data and fuel (2003)

The unique properties of DNA make it a fundamental building block in the fields of supramolecular chemistry, nanotechnology, nano-circuits, molecular switches, molecular devices, and molecular computing. In our recently introduced autonomous molecular automaton, DNA molecules serve as input, output, and software, and the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA stores energy, available on hybridization of complementary strands or hydrolysis of its phosphodiester backbone. Here we show that a single DNA molecule can provide both the input data and all of the necessary fuel for a molecular automaton. Each computational step of the automaton consists of a reversible software molecule input molecule hybridization followed by an irreversible software-directed cleavage of the input molecule, which drives the computation forward by increasing entropy and releasing heat. The cleavage uses a hitherto unknown capability of the restriction enzyme FokI, which serves as the hardware, to operate on a noncovalent software input hybrid. In the previous automaton, software input ligation consumed one software molecule and two ATP molecules per step. As ligation is not performed in this automaton, a fixed amount of software and hardware molecules can, in principle, process any input molecule of any length without external energy supply. Our experiments demonstrate 3 x 10(12) automata per microl performing 6.6 x 10(10) transitions per second per microl with transition fidelity of 99.9%, dissipating about 5 x 10(-9) W microl as heat at ambient temperature.
Determination of Total Dietary Fiber of Intact Cereal Food Products by Near-Infrared Reflectance (2000)

Near-infrared reflectance spectra of cereal food products were acquired with a commercial dual-diode-array (Si, InGaAs) spectrometer customized to allow rapid acquisition of scans of intact breakfast cereals, snack foods, whole grains, and milled products. Substantial gains in the performance of multivariate calibration models generated from these data were obtained by a computational strategy that systematically analyzed the performance of various spectral windows. The calibration model based on 137 cereal food products determined the total dietary fiber (TDF) content of a test set of 45 intact diverse cereal food products with root-mean-squared error of cross-validation of between 1.8 and 2.0% TDF, relative to the laborious enzymatic-gravimetric reference method. The calibration performance is adequate to estimate TDF over the range of values found in diverse types of cereal food products (0.7-50.1%). The method requires no sample preparation and is relatively unaffected by specimen moisture content.
New ruthenium-based catalysts for Z-selective metathesis of hindered olefins (2014)

A series of new ruthenium-based metathesis catalysts with varying N-heterocyclic carbene (NHC) substituents and their reactivity toward hindered olefins are reported. Through systematic variation of the sterics and electronics of the NHC substituents, metathesis activity and Z-selectivity are related to structure, resulting in catalysts that perform cross metathesis of a wide variety of allylic-substituted olefins in high yield and excellent Z-selectivity. Further insights into reactivity are obtained from the solid-state structures and soln. dynamics of the catalysts.
Pressure-induced high-density amorphous ice in protein crystals (2008)

Crystal cryocooling has been used in X-ray protein crystallography to mitigate radiation damage during diffraction data collection. However, cryocooling typically increases crystal mosaicity and often requires a time-consuming search for cryoprotectants. A recently developed high-pressure cryocooling method reduces crystal damage relative to traditional cryocooling procedures and eases or eliminates the need to screen for cryoprotectants. It has been proposed that the formation of high-density amorphous (HDA) ice within the protein crystal is responsible for the excellent diffraction quality of the high-pressure cryocooled crystals. This paper reports X-ray data that confirm the presence of HDA ice in the high-pressure cryocooled protein crystallization solution and protein crystals analyzed at ambient pressure. Diffuse scattering with a spacing characteristic of HDA ice is seen at low temperatures. This scattering then becomes characteristic successively to low-density amorphous, cubic and hexagonal ice phases as the temperature is gradually raised from 80 to 230 K, and seems to be highly correlated with the diffraction quality of crystals.
Direct Synthesis of (+)‐Erogorgiaene through a Kinetic Enantiodifferentiating Step (2005)

Die Kombination einer C-H-Aktivierung mit einer Cope-Umlagerung erwies sich als effiziente Methode zum Aufbau der drei Stereozentren (rot im Schema) des Diterpens Erogorgiaen (1). Katalysiert wird die Sequenz durch den Rhodium-Katalysator [Rh2(R-dosp)4] (dosp=(N-Dodecylbenzolsulfonyl)prolinat). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2005/z462227_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Memory Management in Successive-Cancellation based Decoders for Multi-Kernel Polar Codes (2018)

Multi-kernel polar codes have recently been proposed to construct polar codes of lengths different from powers of two. Decoder implementations for multi-kernel polar codes need to account for this feature, that becomes critical in memory management. We propose an efficient, generalized memory management framework for implementation of successive-cancellation decoding of multi-kernel polar codes. It can be used on many types of hardware architectures and different flavors of SC decoding algorithms. We illustrate the proposed solution for small kernel sizes, and give complexity estimates for various kernel combinations and code lengths.
Indexing and production of virus-free chrysanthemums (2005)

Chrysanthemum morifolium cv. Regol Time plants were found to be infected with Chrysanthemum B carlavirus (CVB). They were made CVB-free by using meristem tip culture, chemotherapy and thermotherapy. The plants were indexed by biological assay, double antibody sandwitch enzyme linked immunosorbent assay (DAS-ELISA) and reverse transcriptase polymerase chain reaction (RT-PCR). The maximum number of virus-free plants (26.7 %, as indexed by RT-PCR) was obtained with 2-thiouracil at 0.04 g dm-3 concentration. Only 12 % plants were found to be virus-free, after being kept at 38 Â°C for 30 d. For indexing CVB in chrysanthemums, RT-PCR was found to be the most reliable method.
Characterization of a <i>Porphyromonas gingivalis</i> gene <i>prtK</i> that encodes a lysine‐specific cysteine proteinase and three sequence‐related adhesins (1999)

Porphyromonas gingivalis extracellular arginine- and lysine-specific proteinases have been implicated as major virulence factors in the development of adult periodontitis. We have previously purified a 48-kDa lysine-specific cysteine proteinase, designated PrtK48, from a P. gingivalis W50 cell-associated multiprotein complex. PrtK48 was non-covalently associated with three sequence-related adhesins designated PrtK39, PrtK15 and PrtK44 in the multiprotein complex. In this study we cloned and characterized the gene, designated prtK, that encodes a polyprotein that is post-translationally processed to yield the Lys-specific proteinase PrtK48 and the three sequence-related adhesins PrtK39, PrtK15 and PrtK44.
Soft magnetic properties of bulk Fe-based amorphous alloys prepared by copper mold casting (1996)

Fe-based amorphous alloys in Fe-(Al,Ga)-(P,B,C,Si) system were found to exhibit a wide supercooled liquid region exceeding 50 K before crystallization. The high stability of the supercooled liquid enabled the production of cylindrical bulk amorphous alloys with diameters up to 2 mm by copper mold casting. The Fe-based bulk amorphous alloys exhibit ferromagnetism with the Curie temperature of about 600 K. The saturation magnetization (Bs), coercivity (Hc) and permeability (/spl mu//sub c/) at 1 kHz in as-quenched state are 1.07 T, 12.7 A/m and 3600, respectively, for Fe/sub 73/Al/sub 5/Ga/sub 2/P/sub 11/C/sub 5/B/sub 4/ and 1.14 T, 0.5 A/m and 3200, respectively for Fe/sub 72/Al/sub 5/Ga/sub 2/P/sub 10/C/sub 6/B/sub 4/Si/sub 1/. Besides, the use of the Fe-based amorphous alloys enabled the production of thick amorphous ribbons above 100 /spl mu/m in thickness and the thick samples also exhibit good soft magnetic properties. The success of synthesizing the bulk Fe-based amorphous alloys with good soft magnetic properties is promising for future development as a new type of soft magnetic materials.
Discovery of VU0467485/AZ13713945: An M<sub>4</sub> PAM Evaluated as a Preclinical Candidate for the Treatment of Schizophrenia (2016)

Herein, we report the structure-activity relationships within a series of potent, selective, and orally bioavailable muscarinic acetylcholine receptor 4 (M<sub>4</sub>) positive allosteric modulators (PAMs). Compound <b>6c</b> (VU0467485) possesses robust <i>in vitro</i> M<sub>4</sub> PAM potency across species and <i>in vivo</i> efficacy in preclinical models of schizophrenia. Coupled with an attractive DMPK profile and suitable predicted human PK, <b>6c</b> (VU0467485) was evaluated as a preclinical development candidate.
In vivo generation of human dendritic cell subsets by Flt3 ligand (2000)

Abstract Dendritic cells (DCs) represent a family of ontogenically distinct leukocytes involved in immune response regulation. The ability of DCs to stimulate T-cell immunity has led to their use as vectors for immunotherapy vaccines. However, it is unclear whether and to what degree in vitro–generated DCs are representative of DCs that develop in vivo. Treatment of mice with human Flt3 ligand (FL) dramatically increases the number of DCs. We report here that administration of FL to healthy human volunteers increased the number of circulating CD11c+ IL-3Rlow DC (mean 44-fold) and CD11c− IL-3Rhigh DC precursors (mean 12-fold). Moreover, the CD11c+ DCs were efficient stimulators of T cells in vitro. Thus, FL can expand the number of circulating, functionally competent human DCs in vivo.
Recombinant soluble CD14 mediates the activation of endothelial cells by lipopolysaccharide. (1993)

Recent studies have suggested that soluble CD14 found in serum is involved in the LPS-induced activation of endothelial cells (EC). To more fully investigate the relevance of sCD14 to LPS-induced activation of EC, we have used recombinant soluble CD14 (rsCD14) and have examined, under serum-free conditions, its role in the LPS-induced EC response in the presence of LPS alone as well as in the presence of LPS-binding protein. Our studies show that EC can be activated by high concentrations of LPS in the presence of rsCD14 alone. However, at low concentrations of LPS (5 and 10 ng/ml), the rsCD14-stimulated activation is strongly enhanced by LPS-binding protein. In addition, we show that LPS binds to rsCD14 directly; in the presence of low concentrations of LPS this binding is enhanced by the presence of LPS-binding protein. These results show that while the membrane form of CD14 can function as a receptor, its soluble form can function as a co-ligand with LPS in the EC-LPS response.
Holographic recording aspects of high-resolution Bayfol HX photopolymer (2011)

We have been developing a new class of recording materials for volume holography, offering the advantages of full color recording and depth tuning without any chemical or thermal processing, combined with low shrinkage and detuning. These photopolymers are based on the two-chemistry concept in which the writing chemistry is dissolved in a preformed polymeric network. This network gives the necessary mechanical stability to the material prior to recording. In this paper we describe several aspects of holographic recording into Bayfol® HX which are beneficial for its effective use and discuss them within a more elaborate reaction-diffusion model. Inhibition phenomena and the influence of precure are studied within this model and are investigated experimentally for single hologram recording and angular multiplexed hologram recordings. Also the dark reaction after the exposure period and the minimum allowable waiting time for full hologram formation are addressed. The proper understanding of these phenomena is important for the optimal usage of these new materials, in for example step-and-repeat mass production of holograms.
Intra‐arc binary collimation with dynamic axes trajectory optimization for the SRS treatment of multiple metastases with multiple prescriptions (2022)

CODA-iABC is a novel planning technique that has been developed to automatically generate patient-specific multi-axis trajectories for multiple metastases cranial SRS/SRT. This work has demonstrated the feasibility of planning with this novel method. The 1-arc CODA-iABC planning technique is slightly dosimetric inferior to VMAT. With an increased sampling of a three-dimensional CODA cube by using a 3-arc CODA-iABC technique, there was improved total dose sparing to all the OARs and increased MU efficiency, but with a cost in target conformity, when compared to VMAT.
Emerging pharmacologic treatment options for fragile X syndrome (2015)

Fragile X syndrome (FXS) is the most common single gene cause of intellectual disability and autism spectrum disorder. Caused by a silenced fragile X mental retardation 1 gene and the subsequent deficiency in fragile X mental retardation protein, patients with FXS experience a range of physical, behavioral, and intellectual debilitations. The FXS field, as a whole, has recently met with some challenges, as several targeted clinical trials with high expectations of success have failed to elucidate significant improvements in a variety of symptom domains. As new clinical trials in FXS are planned, there has been much discussion about the use of the commonly used clinical outcome measures, as well as study design considerations, patient stratification, and optimal age range for treatment. The evidence that modification of these drug targets and use of these failed compounds would prove to be efficacious in human clinical study were rooted in years of basic and translational research. There are questions arising as to the use of the mouse models for studying FXS treatment development. This issue is twofold: many of the symptom domains and molecular and biochemical changes assessed and indicative of efficacy in mouse model study are not easily amenable to clinical trials in people with FXS because of the intolerability of the testing paradigm or a lack of noninvasive techniques (prepulse inhibition, sensory hypersensitivity, startle reactivity, or electrophysiologic, biochemical, or structural changes in the brain); and capturing subtle yet meaningful changes in symptom domains such as sociability, anxiety, and hyperactivity in human FXS clinical trials is challenging with the currently used measures (typically parent/caregiver rating scales). Clinicians, researchers, and the pharmaceutical industry have all had to take a step back and critically evaluate the way we think about how to best optimize future investigations into pharmacologic FXS treatments. As new clinical trials are coming down the drug discovery pipeline, it is clear that the field is moving in a direction that values the development of molecular biomarkers, less subjective quantitative measures of symptom improvement, and rating scales developed specifically for use in FXS in conjunction with drug safety. While summarizing preclinical evidence, where applicable, and discussing challenges in FXS treatment development, this review details both completed clinical trials for the targeted and symptomatic treatment of FXS and introduces novel projects on the cusp of clinical trial investigation.
Crowdsourcing Translation by Leveraging Tournament Selection and Lattice-Based String Alignment (2013)

Crowdsourcing translation tasks typically face issues due to poor quality and spam translations. We propose a novel method for generating large multilingual text corpora leveraging Tournament Selection and Lattice-Based String Alignment without requiring expert involvement or Gold data. We use crowdsourcing for gathering a set of candidate translations of a given source sentence. A crowd sourced Tournament Selection allows to prune this set and keep an n-best list. Finally, a lattice-based string alignment allows to compose parts of these n-best translations to generate a consensus translation. As a work-in-progress, the evaluation is still ongoing, but we are confident in the potential for this method to generate translations of good quality.