gebhart/patrepeval huggingface dataset:
<title>Diffuse reflectance spectroscopy to quantify inflammation of the oral epithelium <emph type="1">In Vivo</emph></title> (2002)

Recent studies suggest that inflammatory cell products may contribute to the evolution of particular cancers leading to new chemoprevention trials exploring the benefit of anti-inflammatory drugs such as aspirin and related products. As part of a prospective trial evaluating this anti-inflammatory strategy for oral cancer, we evaluated a non-invasive optical system to determine if we could use an indirect measure of oral inflammation, mucosal thickness, as a monitoring parameter to evaluate the effectiveness of anti-inflammatory drug therapy. Diffuse reflectance spectroscopy has the potential for probing near-surface structures, however, traditional methods for accounting for scattering of photons are generally invalid for typical epithelial thicknesses. Monte Carlo simulations have shown that, with proper scaling, a simple photon model may be used to predict photon behavior under these conditions. A differential measure, which is very sensitive to small changes, has been shown to have the potential to quantify epithelial thickness. A simple prototype device has been brought from desk, to bench and bedside in a rapid manner to fill a need for a non-invasive measure of oral inflammation. From the theory, a simple feature has been identified that corresponds to patient oral inflammation. Preliminary results from this work are presented and indicate that further development of the approach to enable quantification of epithelial thickness in vivo is warranted.
Spline Interface for Intuitive Skinning Weight Editing (2018)

Despite the recent advances in automatic methods for computing skinning weights, manual intervention is still indispensable to produce high-quality character deformation. However, current modeling software does not provide efficient tools for the manual definition of skinning weights. Widely used paint-based interfaces give users high degrees of freedom, but at the expense of significant efforts and time. This article presents a novel interface for editing skinning weights based on splines, which represent the isolines of skinning weights on a mesh. When a user drags a small number of spline anchor points, our method updates the shape of the isolines and smoothly interpolates or propagates the weights while respecting the given iso-value on the spline. We introduce several techniques to enable the interface to run in real-time and propose a particular combination of functions that generates appropriate skinning weight over the surface. Users can create skinning weights from scratch by using our method. In addition, we present the spline and the gradient fitting methods that closely approximate initial given weights, so that a user can modify the weights with our spline interface. We show the effectiveness of our spline-based interface through a number of test cases.
A vessel length-based method to compute coronary fractional flow reserve from optical coherence tomography images (2017)

A novel formulation for the total resistance of LPM is introduced to accurately simulate a 3D CFD model of the ROI. The simulated FFR values compared well with clinically measured ones, showing the accuracy of the method. Moreover, the present method is fast in terms of computational time, enabling clinicians to provide solutions handled within the hospital.
Impact of Water Softening on Chemical Enhanced Oil Recovery Project Economics (2014)

Abstract Chemical enhanced oil recovery (EOR) provides the means to increase oil production through manipulation of the chemical and fluid properties within a given reservoir. The number of chemical EOR projects being developed, pilot tested, and commercially implemented is on the rise as a function of the relative decrease in chemical costs, advancements in chemical performance, more precise subsurface modeling, and recent stable oil pricing. The amount of calcium and magnesium (hardness) in the injection water plays a critical role in determining the type and dosage of alkali, surfactant, co-solvents and/or polymer (ASCP) used in a chemical EOR flood. The hardness dictates whether alkali can be used and affects the surfactant adsorption, achievable viscosity at specific polymer dosages, polymer stability, polymer choice as a function of thermal stability, as well as emulsion stability in the produced water. The ability to remove hardness and thereby use soft injection water with chemical EOR is a game changer, in that it can enable chemical floods that are otherwise uneconomic, infeasible or that are considered too risky. Soft water, invariably, comes at a cost related to treating the source water to remove calcium and magnesium. Source water for a chemical EOR flood is dictated by availability and environmental constraints and is usually limited to produced water, seawater or brine from deep aquifers. Occasionally, a surface water source is available. This paper reports on representative chemical EOR project case studies in seawater, brackish water and produced water applications at various sites and capacities. The cost of water softening is weighed against the reservoir and production benefits, culminating in a side-by-side economic analysis for each case study based on cost per incremental barrel of oil. The results can be used to guide the development of new chemical EOR projects in determining facility needs as a function of economics.
Adapting ISFETs for Epigenetics: An Overview (2018)

This paper gives an overview of how CMOS design methods can be applied to ion-sensitive field effect transistor (ISFETs) for pH-based DNA methylation and miRNA detection. Design specifications are fundamentally defined by the choice of analysis. As such, the focus for DNA methylation was on developing front-end analogue circuits to carry out Methylation-specific PCR (MSP) for Point-of-Care applications, and sequencing for detailed analysis. The use of MSP prompted the design of an ISFET weak inversion current mirror topology for differential sensing and reduction of drift and temperature sensitivities. The primary limitation in ion-semiconductor sequencing is base calling of repeated nucleotides known as homopolymers. Implementation of a switched current integrator can potentially increase both accuracy and window for detection, within the frequency region of DNA reactions. For quantifying miRNAs, digital back-end processing circuits were considered toward a fully portable platform that can carry out real-time monitoring of DNA amplification reactions. Two systems to evaluate threshold cycles were developed, based on the Derivative method and a new proposed 3-point exponential evaluation aim to reduce detection time simultaneously. Both implementations were tested with datasets from fluorescent qPCR reactions, as well as pH-LAMP experiments that have been optimized for on-chip amplifications. All designs were fabricated in unmodified CMOS with performance assessed based on functionality as well as pH-resolution required in practice.
Effect of soluble epoxide hydrolase polymorphism on substrate and inhibitor selectivity and dimer formation (2014)

Epoxy FAs (EpFAs) are important lipid mediators that are mainly metabolized by soluble epoxide hydrolase (sEH). Thus, sEH inhibition is a promising therapeutic target to treat numerous ailments. Several sEH polymorphisms result in amino acid substitutions and alter enzyme activity. K55R and R287Q are associated with inflammatory, cardiovascular, and metabolic diseases. R287Q seems to affect sEH activity through reducing formation of a catalytically active dimer. Thus, understanding how these SNPs affect the selectivity of sEH for substrates and inhibitors is of potential clinical importance. We investigated the selectivity of four sEH SNPs toward a series of EpFAs and inhibitors. We found that the SNPs alter the catalytic activity of the enzyme but do not alter the relative substrate and inhibitor selectivity. We also determined their dimer/monomer constants (KD/M). The WT sEH formed a very tight dimer, with a KD/M in the low picomolar range. Only R287Q resulted in a large change of the KD/M However, human tissue concentrations of sEH suggest that it is always in its dimer form independently of the SNP. These results suggest that the different biologies associated with K55R and R287Q are not explained by alteration in dimer formation or substrate selectivity.
The Effect of Urethane Acrylate Structure on the Fracture Toughness and Puncture Resistance of Optical Fiber Coatings (2006)

Optical fibers are typically coated with a dual layer acrylate coating system, the main purpose of which is to protect the glass fiber from optical, environmental and mechanical failure modes. The coating system consists of a soft inner coating, commonly referred to as the ﬁinner primaryﬂ or ﬁprimaryﬂ coating, and a hard outer coating, commonly referred to as the ﬁouter primaryﬂ or ﬁsecondaryﬂ coating. The properties and dimensions of the coating system are designed to minimize microbend induced attenuation losses
An Improved SCFlip Decoder for Polar Codes (2016)

This paper focuses on the recently introduced Successive Cancellation Flip (SCFlip) decoder of polar codes. Our contribution is twofold. First, we propose the use of an optimized metric to determine the flipping positions within the SCFlip decoder, which improves its ability to find the first error that occurred during the initial SC decoding attempt. We also show that the proposed metric allows closely approaching the performance of an ideal SCFlip decoder. Second, we introduce a generalisation of the SCFlip decoder to a number of ω nested flips, denoted by SCFlip-ω, using a similar optimized metric to determine the positions of the nested flips. We show that the SCFlip-2 decoder yields significant gains in terms of decoding performance and competes with the performance of the CRC-aided SC-List decoder with list size L=4, while having an average decoding complexity similar to that of the standard SC decoding, at medium to high signal to noise ratio.
Low temperature metal-organic chemical vapor deposition of tungsten nitride as diffusion barrier for copper metallization (1999)

A metal-organic chemical vapor deposition process has been developed for the growth of amorphous tungsten nitride thin films for barrier layer applications in ultralarge scale integration copper interconnect schemes. The process employs tungsten hexacarbonyl, [W(CO)6] and ammonia (NH3) as, respectively, the tungsten and nitrogen sources. Tungsten nitride films were produced within a wide process window, including a substrate temperature of 200–350 °C, W(CO)6 flow rate of 1–20 sccm, reactor pressure of 0.2–0.5 Torr, and NH3 flow rates of 100–500 sccm. The films were analyzed by x-ray photoelectron spectroscopy, cross-section scanning electron microscopy, x-ray diffraction, transmission electron microscopy, four-point resistivity probe, and Rutherford backscattering spectrometry. These studies indicated that the films consisted predominantly of a W2N phase. Films were grown with carbon and oxygen concentrations ⩽5 at. %, even at the lowest processing temperature investigated, where precursor dissociation would be expected to be the least efficient given the reduced thermal budget available to the decomposition reaction. Films deposited below 275 °C were amorphous, while those deposited between 275 and 350 °C were polycrystalline. Resistivities as low as 123 μΩ cm were achieved for 50-nm-thick films, with corresponding step coverage better than 90% in nominal 0.25 μm trench structures with aspect ratio of 4:1.
A protein associated with frost hardiness of western white pine is up-regulated by infection in the white pine blister rust pathosystem (1998)

A 19-kDa protein, Pin m III, was recently shown to be associated with overwintering and frost hardiness of western white pine (Pinus monticola Dougl. ex D. Don) seedlings. Here, we report that this protein is up-regulated by the fungus Cronartium ribicola Fisch, the causal agent of white pine blister rust in western white pine trees. Between 1991 and 1994, bark samples of mature western white pine trees (resistant with no stem cankers and susceptible with stem cankers) were collected in winter, spring, and fall. Proteins were extracted and analyzed by Western immunoblot utilizing specific rabbit polyclonal anti-Pin l I (a homologue of Pin m III) antibodies. During all collection dates, but particularly in the spring, susceptible trees had more Pin m III than resistant trees. In July 1995, 43 previously inoculated 7-year-old white pine seedlings were also analyzed. In all susceptible seedlings (cankered) tested, cankered tissue had high levels of Pin m III, and samples collected from the outside edge of the canker margin had low levels of Pin m III; this protein was also detected in some healthy bark of cankered trees. Since the level of Pin m III in healthy white pine trees is normally lowest in summer months, the high level Pin m III in summer samples of infected tissues is a consequence of the fungal infection.
Natural light-gated anion channels: A family of microbial rhodopsins for advanced optogenetics (2015)

Light-gated rhodopsin cation channels from chlorophyte algae have transformed neuroscience research through their use as membrane-depolarizing optogenetic tools for targeted photoactivation of neuron firing. Photosuppression of neuronal action potentials has been limited by the lack of equally efficient tools for membrane hyperpolarization. We describe anion channel rhodopsins (ACRs), a family of light-gated anion channels from cryptophyte algae that provide highly sensitive and efficient membrane hyperpolarization and neuronal silencing through light-gated chloride conduction. ACRs strictly conducted anions, completely excluding protons and larger cations, and hyperpolarized the membrane of cultured animal cells with much faster kinetics at less than one-thousandth of the light intensity required by the most efficient currently available optogenetic proteins. Natural ACRs provide optogenetic inhibition tools with unprecedented light sensitivity and temporal precision.
Towards a comprehensive CT image segmentation for thoracic organ radiation dose estimation and reporting (2014)

Administered dose of ionizing radiation during medical imaging is an issue of increasing concern for the patient, for the clinical community, and for respective regulatory bodies. CT radiation dose is currently estimated based on a set of very simplifying assumptions which do not take the actual body geometry and organ specific doses into account. This makes it very difficult to accurately report imaging related administered dose and to track it for different organs over the life of the patient. In this paper this deficit is addressed in a two-fold way. In a first step, the absorbed radiation dose in each image voxel is estimated based on a Monte-Carlo simulation of X-ray absorption and scattering. In a second step, the image is segmented into tissue types with different radio sensitivity. In combination this allows to calculate the effective dose as a weighted sum of the individual organ doses. The main purpose of this paper is to assess the feasibility of automatic organ specific dose estimation. With respect to a commercially applicable solution and respective robustness and efficiency requirements, we investigated the effect of dose sampling rather than integration over the organ volume. We focused on the thoracic anatomy as the exemplary body region, imaged frequently by CT. For image segmentation we applied a set of available approaches which allowed us to cover the main thoracic radio-sensitive tissue types. We applied the dose estimation approach to 10 thoracic CT datasets and evaluated segmentation accuracy and administered dose and could show that organ specific dose estimation can be achieved.
Stretchable multichannel antennas in soft wireless optoelectronic implants for optogenetics (2016)

Optogenetic methods to modulate cells and signaling pathways via targeted expression and activation of light-sensitive proteins have greatly accelerated the process of mapping complex neural circuits and defining their roles in physiological and pathological contexts. Recently demonstrated technologies based on injectable, microscale inorganic light-emitting diodes (μ-ILEDs) with wireless control and power delivery strategies offer important functionality in such experiments, by eliminating the external tethers associated with traditional fiber optic approaches. Existing wireless μ-ILED embodiments allow, however, illumination only at a single targeted region of the brain with a single optical wavelength and over spatial ranges of operation that are constrained by the radio frequency power transmission hardware. Here we report stretchable, multiresonance antennas and battery-free schemes for multichannel wireless operation of independently addressable, multicolor μ-ILEDs with fully implantable, miniaturized platforms. This advance, as demonstrated through in vitro and in vivo studies using thin, mechanically soft systems that separately control as many as three different μ-ILEDs, relies on specially designed stretchable antennas in which parallel capacitive coupling circuits yield several independent, well-separated operating frequencies, as verified through experimental and modeling results. When used in combination with active motion-tracking antenna arrays, these devices enable multichannel optogenetic research on complex behavioral responses in groups of animals over large areas at low levels of radio frequency power (<1 W). Studies of the regions of the brain that are involved in sleep arousal (locus coeruleus) and preference/aversion (nucleus accumbens) demonstrate the unique capabilities of these technologies.
Liquid Phase Growth of HgCdTe Epitaxial Layers (1980)

Epitaxial layers of mercury cadmium telluride with Cd composition ( value) from 0.17 to 1.0 have been grown in Te solution by a liquid phase epitaxial (LPE) technique. The layers are grown on substrates with (100), (110), (111)Cd, and (111)Te orientations. The best surface is obtained on the (111)Cd surface. Typical hole concentration of layers with Cd composition of 0.2 is on the order of with a Hall mobility of 400 cm2/Vsec at 77°K. X‐ray topographic analysis indicates that these epilayers have as good a crystalline structure as that of the substrates.
Innate–adaptive IFN cross-talk reprograms myeloid and T cells for antitumor immunity with a second-generation recombinant MVA (2022)

SUMMARY Resistance to immune checkpoint blockade (ICB) remains a major obstacle in cancer immunotherapy. We rationally engineered a second-generation recombinant Modified Vaccinia virus Ankara (MQ833) by deleting viral immune-evasion genes ( E3L , E5R , WR199 ) and incorporating Flt3L , OX40L , and matrix-anchored IL12 . Intratumoral MQ833 elicited robust tumor regressions across multiple models, including ICB-resistant and MHC-I–deficient tumors. Single-cell RNA sequencing revealed extensive remodeling of the tumor microenvironment, characterized by neutrophil and monocyte recruitment and activation, M2 macrophage depletion, M1 polarization, and effector T-cell differentiation and proliferation. Conditional Ifnar1 knockout mice demonstrated that MQ833 efficacy requires type I interferon signaling in neutrophils, macrophages/monocytes, and T cells. Moreover, Nos2 deficiency impaired therapeutic efficacy, confirming iNOS⁺ myeloid cells as key effectors. Together, these findings show that MQ833 activates innate–adaptive IFN cross-talk to reprogram myeloid and T cells, defining a rationally designed viral immunotherapy capable of overcoming ICB resistance. GRAPHIC ABSTRACT
Listen, look, and gotcha (2013)

Mobile video is quickly becoming a mass consumer phenomenon. More and more people are using their smartphones to search and browse video content while on the move. In this paper, we have developed an innovative instant mobile video search system through which users can discover videos by simply pointing their phones at a screen to capture a very few seconds of what they are watching. The system is able to index large-scale video data using a new layered audio-video indexing approach in the cloud, as well as extract light-weight joint audio-video signatures in real time and perform progressive search on mobile devices. Unlike most existing mobile video search applications that simply send the original video query to the cloud, the proposed mobile system is one of the first attempts at instant and progressive video search leveraging the light-weight computing capacity of mobile devices. The system is characterized by four unique properties: 1) a joint audio-video signature to deal with the large aural and visual variances associated with the query video captured by the mobile phone, 2) layered audio-video indexing to holistically exploit the complementary nature of audio and video signals, 3) light-weight fingerprinting to comply with mobile processing capacity, and 4) a progressive query process to significantly reduce computational costs and improve the user experience---the search process can stop anytime once a confident result is achieved. We have collected 1,400 query videos captured by 25 mobile users from a dataset of 600 hours of video. The experiments show that our system outperforms state-of-the-art methods by achieving 90.79% precision when the query video is less than 10 seconds and 70.07% even when the query video is less than 5 seconds.
The Swiss Army smartphone (2011)

A smartphone can be configured to look like any Universal Serial Bus (USB) peripheral and can be managed remotely through its wireless data connection. By virtue of these features, smartphones are ideal vehicles for the delivery of a variety of brand-new, USB-powered services that support the management and troubleshooting of mobile laptops. We provide examples of such USB services and describe a general architecture for their implementation. The services are easy to deploy, because they can be extended to remote laptops without prior installation of new software, and well-suited for delivery through virtualization in a cloud infrastructure. While our examples target mostly the enterprise, USB services, especially virtualized ones, can easily be tailored to suit a broad set of consumer applications.
Biological Studies of Turmeric Oil, Part 1: Selective <i>in vitro</i> Anticancer Activity of Turmeric Oil (TO) and TO-Paclitaxel Combination (2013)

The oil from turmeric (Curcuma longa) contains several sesquiterpenes with medicinal properties. The oil fractions were purified by repeated high vacuum distillations to constant boiling points and by column chromatography. The major components in the oil fractions were identified as α,β and ar-turmerones. The purified turmeric oil (TO) fractions had growth inhibitory activity against breast (SKBR-3), pancreatic (PANC-1), and prostate (PC-3) cancers, and reduced activity against a non-cancerous cell line, WI-38. A combination of the distillation fraction of turmeric oil and paclitaxel showed substantial increase in growth inhibitory activity against the three cancer cell lines compared with paclitaxel alone, while having reduced activity against the non-cancerous cell line. Percent inhibition may be related to the structural parameters of the turmerones. These results suggest that components in turmeric oil fractions have anticancer activity against breast, pancreatic and prostate cancer and a strong positive effect on the activity of paclitaxel.
A novel series of milbemycin antibiotics from Streptomyces strain E225. II. Isolation, characterization, structure elucidation and solution conformations. (1990)

A novel series of milbemycin antibiotics were isolated from the fermentation broth of a Streptomyces species designated E225. The structures of the four main metabolites VM 44857 (1), VM 44864 (2), VM 44865 (3) and VM 44866 (4) were determined by NMR techniques. In addition we describe the solution conformations of the major metabolite VM 44857 (1).