gebhart/patrepeval huggingface dataset:
An Inexpensive, Point‐of‐Care Urine Test for Bladder Cancer in Patients Undergoing Hematuria Evaluation (2017)

Although hematuria (blood in urine) is the most common symptom of bladder cancer, 70-98% of hematuria cases are benign. These hematuria patients unnecessarily undergo costly, invasive, and expensive evaluation for bladder cancer. Therefore, there remains a need for noninvasive office-based tests that can rapidly and reliably rule out bladder cancer in patients undergoing hematuria evaluation. Herein, a clinical assay for matrix metalloproteinases ("Ammps") is presented, which generates a visual signal based on the collagenase activity (in urine of patients) on the Ammps substrates. Ammps substrates are generated by crosslinking gelatin with Fe(II) chelated alginate nanoparticles, which precipitate in urine samples. The cleavage of gelatin-conjugated alginate (Fe(II)) nanoparticles by collagenases generates free-floating alginate (Fe(II)) nanoparticles that participate in Fenton's reaction to generate a visual signal. In a pilot study of 88 patients, Ammps had 100% sensitivity, 85% specificity, and a negative predictive value (NPV) of 100% for diagnosing bladder cancer. This high NPV can be useful in ruling out bladder cancer in patients referred for hematuria evaluation.
Characterization of superhydrophobic surfaces for drag reduction in turbulent flow (2018)

A significant amount of the fuel consumed by marine vehicles is expended to overcome skin-friction drag resulting from turbulent boundary layer flows. Hence, a substantial reduction in this frictional drag would notably reduce cost and environmental impact. Superhydrophobic surfaces (SHSs), which entrap a layer of air underwater, have shown promise in reducing drag in small-scale applications and/or in laminar flow conditions. Recently, the efficacy of these surfaces in reducing drag resulting from turbulent flows has been shown. In this work we examine four different, mechanically durable, large-scale SHSs. When evaluated in fully developed turbulent flow, in the height-based Reynolds number range of 10 000 to 30 000, significant drag reduction was observed on some of the surfaces, dependent on their exact morphology. We then discuss how neither the roughness of the SHSs, nor the conventional contact angle goniometry method of evaluating the non-wettability of SHSs at ambient pressure, can predict their drag reduction under turbulent flow conditions. Instead, we propose a new characterization parameter, based on the contact angle hysteresis at higher pressure, which aids in the rational design of randomly rough, friction-reducing SHSs. Overall, we find that both the contact angle hysteresis at higher pressure, and the non-dimensionalized surface roughness, must be minimized to achieve meaningful turbulent drag reduction. Further, we show that even SHSs that are considered hydrodynamically smooth can cause significant drag increase if these two parameters are not sufficiently minimized.
Soil Texture From Tdr Waveform Analysis (2007)

The dispersive electromagnetic (EM) behavior of soils is strongly related to the mineralogy, soil structure, and pore fluid characteristics. However, time domain reflectometry (TDR) measurements (TDR waveforms) are predominantly used for soil water content and dry density estimation. These two parameters are calculated based on empirical equations that relate them to the soil dielectric permittivity (Ka) and the bulk electric conductivity (ECb). Ka and ECb are obtained in the time domain from few data points of the TDR waveform, disregarding most of the acquired data (usually 2048 data points) that reflects the EM response of the material over a broad frequency range. The complexity of the soil-water interaction in the presence of a time-varying EM field, and the presence of a non-transverse propagation mode in the TDR system limit the characterization of soils by dielectric spectroscopy. This paper presents a semi-empirical method for soil texture identification based on an integrated numerical and experimental analysis of the effect of the EM soil dispersive behavior on TDR waveforms. Evaluation of TDR tests conducted at 20°C on sands, silts, and clays using tap water at different water contents and dry densities shows that a simple time-domain signal processing of the first reflection from the probe section captures the effects of the EM soil-water interaction. Considering that the coefficients of the TDR empirical equations for soil water content and dry density estimation are<br>soil-type dependent, the developed method allows self-calibrating the TDR system. The result of this work provides the basis for making the TDR technique a tool not only for water content and dry density estimation, but also for soil characterization.
Expression of an Androgenic Gland-Specific Insulin-Like Peptide during the Course of Prawn Sexual and Morphotypic Differentiation (2011)

The crustacean male-specific androgenic gland (AG) regulates sexual differentiation. In the prawn Macrobrachium rosenbergii, silencing an AG-specific insulin-like encoding transcript (Mr-IAG) inhibited the development of male sexual characters, suggesting that Mr-IAG is a key androgenic hormone. We used recombinant pro-Mr-IAG peptide to generate antibodies that recognized the peptide in AG cells and extracts, as verified by mass spectrometry. We revealed the temporal expression pattern of Mr-IAG and studied its relevance to the timetable of sex differentiation processes in juveniles and after puberty. Mr-IAG was expressed from as early as 20 days after metamorphosis, prior to the appearance of external male sexual characters. Mr-IAG expression was lower in the less reproductively active orange-clawed males than in both the dominant blue-clawed males and the actively sneak mating small males. These results suggest a role for Mr-IAG both in the timing of male sexual differentiation and in regulating reproductive strategies.
Structure−Activity Studies for a Novel Series of Bicyclic Substituted Hexahydrobenz[<i>e</i>]isoindole α<sub>1A</sub> Adrenoceptor Antagonists as Potential Agents for the Symptomatic Treatment of Benign Prostatic Hyperplasia (2001)

In search of a uroselective agent that exhibits a high level of selectivity for the alpha(1A) receptor, a novel series of tricyclic hexahydrobenz[e]isoindoles was synthesized. A generic pharmacophoric model was developed requiring the presence of a basic amine core and a fused heterocyclic side chain separated by an alkyl chain. It was shown that the 6-OMe substitution with R, R stereochemistry of the ring junction of the benz[e]isoindole and a two-carbon spacer chain were optimal. In contrast to the highly specific requirements for the benz[e]isoindole portion and linker chain, a wide variety of tricyclic fused heterocyclic attachments were tolerated with retention of potency and selectivity. In vitro functional assays for the alpha(1) adrenoceptor subtypes were used to further characterize these compounds, and in vivo models of vascular vs prostatic tone were used to assess uroselectivity.
Detecting O-GlcNAc using in vitro sulfation (2014)

O-linked β-N-acetylglucosamine (O-GlcNAc) glycosylation, the covalent attachment of N-acetylglucosamine to serine and threonine residues of proteins, is a post-translational modification that shares many features with protein phosphorylation. O-GlcNAc is essential for cell survival and plays important role in many biological processes (e.g. transcription, translation, cell division) and human diseases (e.g. diabetes, Alzheimer's disease, cancer). However, detection of O-GlcNAc is challenging. Here, a method for O-GlcNAc detection using in vitro sulfation with two N-acetylglucosamine (GlcNAc)-specific sulfotransferases, carbohydrate sulfotransferase 2 and carbohydrate sulfotransferase 4, and the radioisotope (35)S is described. Sulfation on free GlcNAc is first demonstrated, and then on O-GlcNAc residues of peptides as well as nuclear and cytoplasmic proteins. It is also demonstrated that the sulfation on O-GlcNAc is sensitive to OGT and O-β-N-acetylglucosaminidase treatment. The labeled samples are separated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and visualized by autoradiography. Overall, the method is sensitive, specific and convenient.
Control of Splicing Efficiency by the Mouse Histone H2a Element in a Murine Leukemia Virus–based Retroviral Vector (2006)

While using various human complementary DNA (cDNA) sequences in the context of the murine leukemia virus (MLV)-based retroviral vector, it was found that a retroviral vector containing some human cDNA sequences produces unusually low viral titer. One of those sequences is that for the human IL-1 receptor antagonist protein (IL1RN). The RNA analysis showed that a cryptic splice acceptor sequence is present in the middle of its coding region, resulting in the deletion of the packaging signal sequence and the removal of some coding sequences that lead to low viral titer and a low level of the transgene product. We tested whether the mouse Hist2h2aa1 element (mH2aE), previously shown to suppress the splicing function, could inhibit the cryptic splicing in the context of MLV-based retroviral vectors. It was found that the mH2aE could efficiently suppress such unwanted splicing event, thus increasing the amount of unspliced transcript, which eventually led to the increase in the level of IL1RN expression and viral titer. The mH2aE could also be used to control unusually high splicing activity. Our data suggested that the mH2aE could be used for the fine-tuning of the splicing process, thus improving the level of gene expression and viral titer in the context of retroviral vectors.
Clinicopathological Characteristics and Molecular Analyses of Multifocal Intraductal Papillary Mucinous Neoplasms of the Pancreas (2011)

The majority of multifocal IPMNs arise independently and exhibit a gastric-foveolar subtype, with low to intermediate dysplasia. These findings underscore the importance of life-long follow-up after resection for an IPMN.
In vivo diagnosis of cervical precancer using Raman spectroscopy and genetic algorithm techniques (2011)

This study aimed to evaluate the clinical utility of applying near-infrared (NIR) Raman spectroscopy and genetic algorithm-partial least squares-discriminant analysis (GA-PLS-DA) to identify biomolecular changes of cervical tissues associated with dysplastic transformation during colposcopic examination. A total of 105 in vivo Raman spectra were measured from 57 cervical sites (35 normal and 22 precancer sites) of 29 patients recruited, in which 65 spectra were from normal sites, while 40 spectra were from cervical precancerous lesions (i.e., 7 low-grade CIN and 33 high-grade CIN). The GA feature selection technique incorporated with PLS was utilized to study the significant biochemical Raman bands for differentiation between normal and precancer cervical tissues. The GA-PLS-DA algorithm with double cross-validation (dCV) identified seven diagnostically significant Raman bands in the ranges of 925-935, 979-999, 1080-1090, 1240-1260, 1320-1340, 1400-1420, and 1625-1645 cm(-1) related to proteins, nucleic acids and lipids in tissue, and yielded a diagnostic accuracy of 82.9% (sensitivity of 72.5% (29/40) and specificity of 89.2% (58/65)) for precancer detection. The results of this exploratory study suggest that Raman spectroscopy in conjunction with GA-PLS-DA and dCV methods has the potential to provide clinically significant discrimination between normal and precancer cervical tissues at the molecular level.
Low voltage tunable liquid crystal lens (2013)

In this Letter, we report a method to prepare a liquid crystal (LC) lens based on a variable pretilt angle of a photoalignment (PA) layer. With precise control of the irradiance, such PA provides good control on the pretilt angle that can be tuned in the range of 1°-89°. Therefore, the precise control of the irradiance generates a spatially varying pretilt angle with any desired pretilt angle profile. Thus, the tunable LC lenses have been fabricated and characterized. With low voltage operations, easy fabrication, and relatively high switching speed, such lenses can be applied in many modern optical and photonic devices.
Induction-Motor Rotor Temperature Estimation Using Superheterodyne Receivers (2012)

A rotor temperature estimator is proposed in this paper for grid-connected squirrel-cage induction motors during dynamic or steady-state operations. The method utilizes a pipelined architecture with two superheterodyne receivers that operate on a common complex current vector input. The first superheterodyne receiver detects motor speed by extracting an instantaneous rotor-slot-harmonic frequency from the complex current vector. The second superheterodyne receiver extracts a complex fundamental current vector from the same complex current vector. Given a few known motor parameters and a complex voltage vector, a model-reference adaptive system then produces an estimate of the rotor time constant from the superheterodyne receivers' outputs. Finally, the rotor temperature is derived from the estimated rotor time constant via a correlation between the rotor temperature and its resistance. Experimental results demonstrate that the proposed method is capable of estimating induction-motor rotor temperature on a sample-by-sample basis without using temperature or speed sensors.
A Quantitative High-Throughput <i>In Vitro</i> Splicing Assay Identifies Inhibitors of Spliceosome Catalysis (2012)

Despite intensive research, there are very few reagents with which to modulate and dissect the mRNA splicing pathway. Here, we describe a novel approach to identify such tools, based on detection of the exon junction complex (EJC), a unique molecular signature that splicing leaves on mRNAs. We developed a high-throughput, splicing-dependent EJC immunoprecipitation (EJIPT) assay to quantitate mRNAs spliced from biotin-tagged pre-mRNAs in cell extracts, using antibodies to EJC components Y14 and eukaryotic translation initiation factor 4aIII (eIF4AIII). Deploying EJIPT we performed high-throughput screening (HTS) in conjunction with secondary assays to identify splicing inhibitors. We describe the identification of 1,4-naphthoquinones and 1,4-heterocyclic quinones with known anticancer activity as potent and selective splicing inhibitors. Interestingly, and unlike previously described small molecules, most of which target early steps, our inhibitors represented by the benzothiazole-4,7-dione, BN82685, block the second of two trans-esterification reactions in splicing, preventing the release of intron lariat and ligation of exons. We show that BN82685 inhibits activated spliceosomes' elaborate structural rearrangements that are required for second-step catalysis, allowing definition of spliceosomes stalled in midcatalysis. EJIPT provides a platform for characterization and discovery of splicing and EJC modulators.
Evaluating Foam Stability using Tailored Water Chemistry for Gas Mobility Control Applications (2019)

Abstract Generating in-situ foam is regarded as one of the most promising techniques to overcome gas mobility issues and improve sweep efficiency in both miscible and immiscible gas injection enhanced oil recovery (EOR) processes. Gravity override, viscous fingering and channeling through permeable zones are the major limiting factors that can impair the efficiency of gas floods, mainly due to low density and viscosity of the gas relative to reservoir fluids. Generating strong and stable foam while injecting gas is one way to achieve in-depth conformance improvement in the reservoir. In this study, a tailored water chemistry (formulated low salinity water) has been evaluated in comparison to using typical high salinity injection water (i.e. seawater) and deionized water in surfactant solutions to determine its overall effect on the produced foam. Using bulk foam tests, foam rheology apparatus and microfluidics device, the foam stabilization factors were analyzed and quantified by measuring the foam-life over time of different surfactants in varying salinity water solutions. In addition, the foam rheological properties were measured under high pressure. The microfluidics device was also used to examine the generated foam strength in porous media. The results from laboratory experiments clearly demonstrated that the use of tailored water chemistry can improve the stability of produced foam when compared to both high salinity water and deionized water. Low salinity tailored water chemistry solutions resulted in a longer lasting foam, by almost 1.8-3.0 times depending on the surfactant type. The foam rheology results showed that the produced foams with the tailored low salinity water are of higher apparent viscosity when compared to those obtained with deionized water. Both longer foam-life and higher apparent viscosity are indicative of better, stronger and more stable foam. The higher resistance to gas flow was observed in porous media with foams generated using the low salinity tailored water chemistry solutions when compared to those foams obtained with deionized water and high salinity water. This experimental study, for the first time, demonstrated substantial improvements in the foam stability by using a tailored water chemistry aqueous solution. Such huge foam stabilization improvements obtained with tailored water chemistry has the promising potential to increase the apparent viscosity of injected gas and subsequently more effectively mitigate gas mobility issues encountered in EOR applications.
Cell‐free metabolic engineering: Biomanufacturing beyond the cell (2014)

Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility.
Design of an electron projection system with slider lenses and multiple beams (2002)

The commercial applicability of electron beam projection lithography systems may be limited at high resolution because of low throughput. The main limitations to the throughput are: (i) Beam current. The Coulomb interaction between electrons result in an image blue. Therefore less beam current can be allowed at higher resolution, impacting the illuminate time of the wafer. (ii) Exposure field size. Early attempts to improve throughput with 'full chip' electron beam projection systems failed, because the system suffered from large off-axis aberrations of the electron optics, which severely restricted the useful field size. This has impact on the overhead time. A new type of projection optics will be proposed in this paper to overcome both limits. A slider lens is proposed that allows an effective field that is much larger than schemes proposed by SCALPEL and PREVAIL. The full width of the die can be exposed without mechanical scanning by sliding the beam through the slit-like bore of the lens. Locally, at the beam position, a 'round'-lens field is created with a combination of a rectangular magnetic field and quadruples that are positioned inside the lens. A die can now be exposed during a single mechanical scan as in state-of-the-art light optical tools. The total beam current can be improved without impact on the Coulomb interaction blur by combining several beams in a single lithography system if these beams do not interfere with each other. Several optical layouts have been proposed that combined up to 5 beams in a projection system consisting of a doublet of slider lenses. This type of projection optics has a potential throughput of 50 WPH at 45 nm with a resist sensitivity of 6 (mu) C/cm<SUP>2</SUP>.
Architectural Support for Software-Defined Metadata Processing (2015)

Optimized hardware for propagating and checking software-programmable metadata tags can achieve low runtime overhead. We generalize prior work on hardware tagging by considering a generic architecture that supports software-defined policies over metadata of arbitrary size and complexity; we introduce several novel microarchitectural optimizations that keep the overhead of this rich processing low. Our model thus achieves the efficiency of previous hardware-based approaches with the flexibility of the software-based ones. We demonstrate this by using it to enforce four diverse safety and security policies---spatial and temporal memory safety, taint tracking, control-flow integrity, and code and data separation---plus a composite policy that enforces all of them simultaneously. Experiments on SPEC CPU2006 benchmarks with a PUMP-enhanced RISC processor show modest impact on runtime (typically under 10%) and power ceiling (less than 10%), in return for some increase in energy usage (typically under 60%) and area for on-chip memory structures (110%).
Magnetizable concrete composite materials for road-embedded wireless power transfer pads (2017)

In this paper, MAGnetizable CONcrete (MagCon) composite materials are introduced and studied thoroughly. MagCon material is obtained by mixing cement with a magnetic material, for example, powdered ferrite or magnetite with different aggregate ratios and sizes, and optionally adding other aggregates to the mixture. Effective relative permeability (μ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r, eff</sub> ) of MagCon is evaluated as a function of volumetric ratio of the magnetic material in the mixture. Furthermore, the effect of aggregate size of the magnetic materials is examined and the core losses of MagCon are analyzed. Compressive strength of the new material is also discussed. MagCon can be used in the core structure of road-embedded Wireless Power Transfer (WPT) pads for Electric Vehicle (EV) charging applications. MagCon has the benefit of significant design flexibility and reduced cost. This paper investigates how to take advantage of the characteristics of the new composite material to design new pad structures for WPT systems. 3D finite element analysis (FEA) approach is used to simulate and compare the proposed pad design with a properly selected reference pad. The mutual inductance between the aligned primary and secondary coils is adopted as the figure of merit in order to maximize the power transfer capability of WPT pads. Considering the fact that magnetite is significantly less expensive than the ferrite tiles or bars, MagCon with magnetite could be a very cost-effective solution. On the other hand, using MagCon in the road creates a more durable structure comparing with the junction of ferrite bars or tiles in regular concrete. This is important for road-embedded implementation of WPT coils where the pad is permanently under the mechanical stress due to heavy vehicles passing over it.