gebhart/patrepeval huggingface dataset:
Supplementary Figures 1-3 from Fecal Bacteria Act as Novel Biomarkers for Noninvasive Diagnosis of Colorectal Cancer (2023)

<p>Supplementary Figure S1. Good consistency in quantification of nusG/F. nucleatum (Fn) was achieved by two experimenters using our convenient platform. Two samples with outlier highlevels of Fn were further excluded so as to show more clearly the good consistency even in samples with relatively low levels of Fn. Abundances of Fn were shown in arbitrary unit; Supplementary Figure S2. Contaminant human DNA had little effect on the new qPCR platform. (A) A representative example of qPCR evaluation of the internal control on a mixture of 10 randomly selected fecal samples added with different concentrations of human DNA. (B) A representative example of duplex qPCR evaluation of the internal control and F. nucleatum on a randomly selected fecal sample added with different concentrations of human DNA; Supplementary Figure S3. Metagenome sequencing data showed that combination with other markers improved the diagnostic ability of Fusobacterium nucleatum (Fn) for colorectal cancer. ROC curves for Fn alone and simple linear combination of all the five selected bacterial marker candidates including Fn, Bacteroides clarus (Bc), Clostridium hathewayi (Ch), one undefined species (labeled as m7), and Roseburia intestinalis (Ri). The best cutoff values that maximize sensitivity and specificity were determined for Fn and 5-markers individually in the metagenome sequencing cohort with 74 CRC patients and 54 controls. AUROC, area under the receiver operating characteristic curve; PPV, positive predictive value; NPV, negative predictive value.</p>
Electrostatic Discharge (ESD) and Failure Analysis (2003)

Failure analysis is fundamental to the design and development methodology of electrostatic discharge (ESD) devices and ESD robust circuits. The role of failure analysis (FA) in the models, methodology, band mechanisms evaluation for improving ESD robustness of semiconductor products in CMOS, silicon-on-insulator (SOI) and silicon germanium (SiGe) technologies will be reviewed.
An Emerging Screening Method for Interrogating Human Brain Function: Tutorial (Preprint) (2022)

<sec> <title>UNSTRUCTURED</title> Cognitive decline can be observed due to a myriad of causes. Clinicians would benefit from a noninvasive quantitative tool to screen and monitor brain function based on direct measures of neural features. In this study, we used neuroimaging data from magnetoencephalography (with a whole-head Elekta Neuromag 306 sensor system) to derive a set of features that strongly correlate with brain function. We propose that simple signal characteristics related to peak variability, timing, and abundance can be used by clinicians as a screening tool to investigate cognitive function in at-risk individuals. Using a minimalistic set of features, we were able to perfectly distinguish between participants with normative and nonnormative brain function, and we were also able to successfully predict participants’ Mini-Mental Test score (<i>r</i>=0.99; <i>P</i>&lt;.001; mean absolute error=0.413). This set of features can be easily visualized in an analog fashion, providing clinicians with several graded measurements (in comparison to a single binary diagnostic tool) that can be used for screening and monitoring cognitive decline. </sec>
Monitoring external beam radiotherapy using real‐time beam visualization (2014)

The RT-BV system is capable of localizing radiation therapy beams with sub-millimeter precision and tracking beam movement at video-rate exposure.
Management of work in progress in relational information systems (1998)

In many complex applications, there is a need to manage work-in-progress. Typically, this requires that each user has a private and non-volatile workspace, in which multiple pieces of work are finished and stored before it is appropriate for these data changes to be made globally accessible to other users. These requirements reflect current work practices in paper-based systems, which ensure security, persistence, privacy and accountability for work-in-progress. This paper describes a technique for implementing work-in-progress that requires no extensions to existing relational database management systems. The semantics of private workspace and work-in-progress are implemented by augmenting the database schema and modifying query and update operations against this augmented schema.
Shaft-Less Energy Storage Flywheel (2015)

This paper provides an overview of a 100 kw flywheel capable of 100 kW-Hr energy storage that is being built by Vibration Control and Electromechanical Lab (VCEL) at Texas A&M University and Calnetix Technologies. The novel design has a potential of nearly doubling the energy density of conventional steel flywheels. Applications include renewable energy source energy storage, frequency regulation at power plants, regenerative braking on vehicles and cranes and backup power at data centers and hospitals. The design and construction of this Department of Energy sponsored flywheel will be presented.
Unraveling <i>Brucella</i> Genomics and Pathogenesis in Immunocompromised IRF‐1<sup>−/−</sup> Mice (2005)

Genomic islands contribute to Brucella pathogenicity. Biophotonic imaging suggests that Brucella dissemination in mice parallels acute and chronic infections of humans.
Fabrication of a novel C-scan photoacoustic imaging camera (2015)

Our objective is to provide researchers with an inexpensive and fast photoacoustic imaging (PAI) device for exvivo studies. We implement this using an acoustic lens based focusing idea together with photoacoustic technology, resulting in a prototype imaging system. A complete photoacoustic imaging system simulation modeling is presented. The system resolution is evaluated through simulation and experiment. Imaging capability with the prototype system is demonstrated.
Studies on the coagulation of soymilk-protein by commercial proteinases. (1987)

A coagulation test of soymilk-protein was carried out with various commercial proteinases originating from microorganisms, plants and animals. The soymilk-protein was coagulated by the following proteinases: Bacillus amyloliquefaciens, Bacillus subtilis, Bacillus polymyxa, Streptomyces griseus, Streptomyces caespitosus, Aspergillus oryzae, Aspergillus sojae, Endothia parasitica, Rhizopus sp., Mucor miehei, bromelain, papain and trypsin. However, such proteinases as Aspergillus saitoi, rennin and pepsin did not coagulate the protein. The coagulability of enzymes decreased as the pH of the soymilk was increased from 5.9 to 6.7. The optimum temperature for soymilk-clotting activity varied widely with the enzyme origin; for example, 55°C in the case of proteinases of Bacillus polymyxa and Rhizopus sp., 65°C in that of Aspergillus oryzae, Aspergillus sojae and trypsin, 75°C in that of Bacillus amyloliquefaciens, Streptomyces griseus, Streptomyces caespitosus and Endothia paracitica, and 85°C in that of Bacillus subtilis and Bacillus thermoproteolyticus. The coagulum made with the enzyme was separated into soymilk-curd and whey in a volume ratio of 1 to 1 by centrifugation at about 1600 × g. The moisture content of the curd was about 87%.
Atomic layer deposition process with TiF_4 as a precursor for depositing metal fluoride thin films (2008)

A novel atomic layer deposition process for the preparation of fluoride thin films in a temperature range of 225 degrees C-400 degrees C is introduced. The crystallinity, morphology, composition, thicknesses, refractive indices, and transmittance of the films are analyzed. Low impurity levels are obtained at 350 degrees C-400 degrees C with good stoichiometry. Refractive indices of 1.34-1.42 for MgF(2), 1.43 for CaF(2), and 1.57-1.61 for LaF(3) films are obtained.
Hybrid Image Registration based on Configural Matching of Scale-Invariant Salient Region Features (2005)

We present a novel method for aligning images under arbitrary poses, based on finding correspondences between image region features. In contrast with using purely feature-based or intensity-based methods, we adopt a hybrid method that integrates the merits of both approaches. Our method uses a small number of automatically extracted scale-invariant salient region features, whose interior intensities can be matched using robust similarity measures. While previous techniques have primarily focused on finding correspondences between individual features, we emphasize the importance of geometric configural constraints in preserving global consistency of individual matches and thus eliminating false feature matches. Our matching algorithm consists of two steps: region component matching (RCPM) and region configural matching (RCFM), respectively. The first step finds correspondences between individual region features. The second step detects a joint correspondence between multiple pairs of salient region features using a generalized Expectation-Maximization framework. The resulting joint correspondence is then used to recover the optimal transformation parameters. We applied our method to registering a pair of aerial images and several pairs of single and multiple modality medical images with promising results. The preliminary results, in particular, showed that the proposed method has excellent robustness to image noise, intensity change and inhomogeneity, appearance and disappearance of structures, as well as partial matching.
Creating discrete cylindrical vector beams using coherently combined fiber arrays (2010)

A novel method is presented for beam shaping far field intensity distributions using coherently combined fiber arrays. Traditionally, coherent arrays have been composed of linearly polarized elements having their polarization vector along a common axis. In this novel method, the fibers are arranged uniformly on the perimeter of a circle, and the linearly polarized beams are oriented with their polarization vectors arranged in a cylindrical fashion such that each subsequent vector is rotated by 2π/N where N is the number of elements on the circle. The elements each have the same Gaussian intensity distribution and power. The ensemble yields a far field intensity pattern that is a good approximation to a cylindrical vector (CV) beam which is characterized by a nonuniform polarization distribution and a null in the center of the beam. These synthetically created CV beams, or discrete cylindrical vector (DCV) beams, can be represented in a closed form solution to predict the far field intensity distributions. This solution is shown to agree with experimental results where several values of N, the number of elements, were tested. In addition, some more complex geometries such as nested geometries, fractal geometries, and some nonuniform geometries have been simulated, all of which also have a central null in the beam and have a nonuniform polarization distribution. These results are in contrast to linearly polarized beams, where the intensity peaks on axis, and from traditional cylindrical vector beams, which are generated by a single laser cavity.
Determination of Total Styrene in Styrene/Butadiene Block Copolymers by Process NMR and Chemometrics Modeling (2001)

A new method involving the use of chemometric techniques was developed on a process nuclear magnetic resonance (NMR) spectrometer for measurement of total styrene in styrene/butadiene (Sty/BD) block copolymers. The method uses partial least-squares (PLS) regression to correlate the total styrene data produced by solutions H-1 NMR to the data produced by process NMR. The new method has comparable accuracy and precision to the solution NMR method, but it is much faster and easier to perform. It also has the additional capability of being selective for a specific process and/or polymer. The NMR method and chemometrics models are discussed, and results for validation of the models and prediction of the total styrene in unknown samples are presented.
A candidate vaccine for hepatitis B containing the complete viral surface protein (1988)

The entire surface protein of hepatitis B virus serotype ayw containing the preS (preS1+preS2) and S domains has been expressed in the yeast Saccharomyces cerevisiae. Yeast containing a recombinant plasmid utilizing a constitutive promoter did not express this gene successfully due to the toxicity of the protein. A plasmid using a regulatable promoter directed expression which initiated late in the exponential phase of growth and resulted in the accumulation of high intracellular levels of the complete surface protein. The purified polypeptide aggregates into a form which, although not comprised of typical 20 nm particles, displays antigenic determinants encoded by the preS1, preS2 and S domains. Immunization of rabbits elicited the formation of antibodies directed against all three domains. This candidate vaccine will be useful for studying the contributions to viral immunity of the host response to the preS1 and preS2 domains.
Preparation of Bispecific Antibodies by Chemical Recombination of Monoclonal Immunoglobulin G <sub>1</sub> Fragments (1985)

Preparation of bispecific antibodies by the chemical reassociation of monovalent fragments derived from monoclonal mouse immunoglobulin G1 is inefficient because of side reactions during reoxidation of the multiple disulfide bonds linking the heavy chains. These side reactions can be avoided by using specific dithiol complexing agents such as arsenite and effecting disulfide formation with a thiol activating agent such as 5,5'-dithiobis(2-nitrobenzoic acid). In this way bispecific antibodies were obtained in high yield and free of monospecific contaminants from monoclonal mouse immunoglobulin G1 fragments. The bispecific antibodies were used as agents for the selective immobilization of enzymes.
Measurement of bulk mechanical properties of tissue using laser speckle rheology (2011)

In virtually all tissues, disease progression is accompanied by changes in the mechanical properties. Laser speckle rheology (LSR) is a new technique we have developed to measure the mechanical properties of tissue. By illuminating the sample with coherent laser light and calculating the speckle intensity modulations from reflected laser speckle patterns, LSR calculates τ, the decay time constant of intensity decorrelation which is closely associated with tissue mechanical properties. In this paper we validate the use of LSR technology in measuring mechanical properties of tissue. LSR measurements of τ are performed on a variety of phantom and tissue samples and compared with the complex shear modulus G*, measured using a rheometer. In all cases, strong correlation is observed between τ and G* (r=0.95, p < 0.002). These results demonstrate the efficacy of LSR as a non-invasive and non-contact technology for mechanical evaluation of biological samples.
<title>C60-doped silicon dioxide sonogels for optical limiting</title> (1994)

We report the successful preparation of a solid solution of C<SUB>60</SUB> in a silicon dioxide (SiO<SUB>2</SUB>) glass matrix by means of sol-gel chemistry. Raman spectroscopy and x-ray diffraction were used to verify that our synthetic route produced glasses with a homogeneous dispersion of intact fullerenes. The vibrational spectrum of C<SUB>60</SUB> is preserved in the C<SUB>60</SUB>/SiO<SUB>2</SUB> gel glass. Raman and X-ray diffraction data confirm that the C<SUB>60</SUB> is microscopically dispersed, and does not form detectable phase-separated, microcrystalline regions. We report preliminary observations of optical limiting in these gels, with intensity and concentration dependence consistent with that observed for C<SUB>60</SUB> in solution.
Adapting to the Shifting Intent of Search Queries (2010)

Search engines today present results that are often oblivious to abrupt shifts in intent. For example, the query `independence day' usually refers to a US holiday, but the intent of this query abruptly changed during the release of a major film by that name. While no studies exactly quantify the magnitude of intent-shifting traffic, studies suggest that news events, seasonal topics, pop culture, etc account for 50% of all search queries. This paper shows that the signals a search engine receives can be used to both determine that a shift in intent has happened, as well as find a result that is now more relevant. We present a meta-algorithm that marries a classifier with a bandit algorithm to achieve regret that depends logarithmically on the number of query impressions, under certain assumptions. We provide strong evidence that this regret is close to the best achievable. Finally, via a series of experiments, we demonstrate that our algorithm outperforms prior approaches, particularly as the amount of intent-shifting traffic increases.
Sensitivity to the Service-Time Distribution in the Nonstationary Erlang Loss Model (1995)

The stationary Erlang loss model is a classic example of an insensitive queueing system: the steady-state distribution of the number of busy servers depends on the service-time distribution only through its mean. However, when the arrival process is a nonstationary Poisson process, the insensitivity property is lost. We develop a simple, effective numerical algorithm for the M t /PH/s/0 model with two service phases and a nonhomogeneous Poisson arrival process, and apply it to show that the time-dependent blocking probability with nonstationary input can be strongly influenced by the service-time distribution beyond the mean. With sinusoidal arrival rates, the peak blocking probability typically increases as the service-time distribution gets less variable. The influence of the service-time distribution, including this seemingly anomalous behavior, can be understood and predicted from the modified-offered-load and stationary-peakedness approximations, which exploit exact results for related infinite-server models.
Enhancement of absorption and color contrast in ultra-thin highly absorbing optical coatings (2013)

Recently a new class of optical interference coatings was introduced which comprises ultra-thin, highly absorbing dielectric layers on metal substrates. We show that these lossy coatings can be augmented by an additional transparent subwavelength layer. We fabricated a sample comprising a gold substrate, an ultra-thin film of germanium with a thickness gradient, and several alumina films. The experimental reflectivity spectra showed that the additional alumina layer increases the color range that can be obtained, in agreement with calculations. More generally, this transparent layer can be used to enhance optical absorption, protect against erosion, or as a transparent electrode for optoelectronic devices.
Novel wide tunable dual-band reconfigurable chassis-antenna for future mobile terminals (2010)

This paper presents a novel reconfigurable chassis-antenna for use in current and future wireless communication systems. The antenna uses a pair of coupling elements which give independent and versatile dual frequency and bandwidth reconfiguration, using a number of external matching circuits. The matching circuit incorporates a pair of varactors and several fixed inductors. Simulations suggest that the antenna has a total tuning range of 2854 MHz (from 442 MHz to 2896 MHz). The antenna maintains a return loss above 6 dB, when tuning across this range. An equivalent circuit has been developed for the two port chassis-antenna. In the final section of the paper, the external matching circuit is connected to the equivalent circuit and the impedance behaviour is compared with that obtained through the antenna simulation with the matching circuit.
Multi-physics Inversion for Reservoir Monitoring (2016)

Summary In this paper we consider the use of, time-domain electromagnetic, DC electrical and injection-production data in isolation and in combinations in order to investigate their potential for monitoring spatial fluid saturation changes within reservoirs undergoing enhanced oil recovery. We specifically consider two scenarios, a CO2 EOR within a relatively shallow reservoir, and a water flood within a deep carbonate reservoir. The recognition of the signal-enhancing role that electrically high conductivity steel well casings play makes the use of EM data possible in both these scenarios. The work has demonstrated that reservoir fluid saturation changes from EOR processes produce observable changes in surface electric fields when surface-to-borehole (deep reservoirs), and surface-to-surface (shallow reservoirs) configurations are used and the steel well casings are accurately modeled. Coupled flow and TDEM data inversion can significantly improve estimate of fluid saturation levels and location compared to inversion of flow data only. The inversion of surface time-domain electric fields, including DC fields can resolve volumetric and resistivity differences that can distinguish between various water flood scenarios. Coupled flow and DC data can resolve the size and orientation of elongated fracture zones within limits that are considered a significant improvement over estimates made with traditional data.
Ammeline-melamine-formaldehyde resins. Preparation and properties (1996)

Ammeline–melamine–formaldehyde resins (AMF Resins) containing 5–100 mol % of ammeline, were synthesized by polymerization of the preformed sodium salt of ammeline, melamine, and formaldehyde in basic medium by three methods. These resins, when cured, constitute a new class of thermosets. The rate of hydroxymethylation of the amino groups of the ammeline salt with formaldehyde was somewhat larger then that of the amino groups on melamine. At higher pH values ammeline insolubility was not a problem. The AMF resin composition was approximately equal to the mol ratio of the components originally charged. Both ammeline and melamine were consumed over the entire reaction period. Thus, it is possible to make approximately uniform random ammeline-melamine-formaldehyde resins (AMF) with any mol ratio of ammeline salt to melamine. By controlling the pH of the solution from which the resins were isolated, the (SINGLE BOND) O− Na+/(SINGLE BOND) OH ratio could be varied. Resin melting points varied widely with the mol fraction of ammeline and the (SINGLE BOND) O− Na+/(SINGLE BOND) OH ratio. AMF resin solubilities, shelf lives, cloud points, and water tolerance depended upon the method of preparation, pH, and other factors. The sodium salt of ammeline was hydroxymethylated in water more readily than ammeline. More highly methylolated ammeline species were readily formed in solution but upon precipitation only bis-N-hydroxymethylammeline was isolated. © 1996 John Wiley & Sons, Inc.
Synthesis and Characterization of Water-Soluble Starch-Acrylamide Graft Copolymers (1986)

Abstract A series of water-soluble starch-polyacrylamide graft copolymers (ST-g-PAM) were prepared by Ce4+-initiated graft copolym-erizations of acrylamide (AM) onto starch (ST) dissolved in water at 30°C. The copolymers were found to contain 3-33% (wt) of ST. The structure of the copolymers, including the average number of grafts per chain and the efficiency of the initiator, was determined by acid-catalyzed degradation of the ST followed by size exclusion chromatography (SEC) analysis of the PAM chains and was found to be consistent with the presence or absence of free ST in the polymerization product prior to hydrolysis. The average number of grafts per starch molecule was found to be three or less, depending on conditions. The initiator efficiency (6–43%) was shown to decrease with increasing [Ce4+] and decreasing [AM], and this was found to be qualitatively in accord with the proposed mechanism of initiation and polymerization. The low efficiency was shown to be due, in part, to the low rate of reaction of Ce4+ compared to the polymerization rate. The copolymers were characterized by ultra-centrifugation, SEC, and viscometry.