gebhart/patrepeval huggingface dataset:
Abstract 879: New serum biomarkers for prostate cancer diagnosis (2014)

Abstract Prostate-specific antigen (PSA) is currently used as a biomarker for the early diagnosis and management of prostate cancer (CaP). However, PSA generally lacks the sensitivity and specificity desired of an effective diagnostic biomarker. The goal of this study was to identify an additional biomarker or a panel of biomarkers that is more sensitive and specific than PSA in differentiating benign vs. malignant prostate disease and/or localized CaP vs. metastatic CaP. Concurrent measurements of circulating IL-8, TNF-alpha (TNF-α) and sTNFR1 were obtained from four groups of men: (1) controls (2) men with elevated PSA with a negative prostate biopsy (eIPSA_negBx) (3) men with clinically localized CaP and (4) men with castration resistant CaP (CRPC). TNF-α (AUC=0.93) and sTNFR1 (AUC=0.97) were strong predictors of elPSA_negBx vs CaP). The best predictor of elPSA_negBx vs prostate cancer was sTNFR1 and IL8 combined (AUC=0.997). The strongest single predictors of localized versus metastatic CaP were TNF-α (AUC=0.992) and PSA (AUC=0.963) levels. Conclusions: The specificity and sensitivity of a PSA-based CaP diagnosis can be significantly enhanced by concurrent serum measurements of IL-8, TNF-α and sTNFR1. In view of the concerns about the ability of PSA to distinguish clinically relevant CaP from indolent disease, assessment of these biomarkers in larger cohort consisting of Caucasians and African Americans is warranted. Citation Format: Kailash C. Chadha, Austin Miller, Bindukumar B. Nair, Stanley A. Schwartz, Donald L. Trump, Willie Underwood. New serum biomarkers for prostate cancer diagnosis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 879. doi:10.1158/1538-7445.AM2014-879
Early Immunomodulatory Effects of Implanted Human Perivascular Stromal Cells During Bone Formation (2017)

Human perivascular stem/stromal cells (PSC) are a multipotent mesodermal progenitor cell population defined by their perivascular residence. PSC are most commonly derived from subcutaneous adipose tissue, and recent studies have demonstrated the high potential for clinical translation of this fluorescence-activated cell sorting-derived cell population for bone tissue engineering. Specifically, purified PSC induce greater bone formation than unpurified stroma taken from the same patient sample. In this study, we examined the differences in early innate immune response to human PSC or unpurified stroma (stromal vascular fraction [SVF]) during the in vivo process of bone formation. Briefly, SVF or PSC from the same patient sample were implanted intramuscularly in the hindlimb of severe combined immunodeficient (SCID) mice using an osteoinductive demineralized bone matrix carrier. Histological examination of early inflammatory infiltrates was examined by hematoxylin and eosin and immunohistochemical staining (Ly-6G, F4/80). Results showed significantly greater neutrophilic and macrophage infiltrates within and around SVF in comparison to PSC-laden implants. Differences in early postoperative inflammation among SVF-laden implants were associated with reduced osteogenic differentiation and bone formation. Similar findings were recapitulated with PSC implantation in immunocompetent mice. Exaggerated postoperative inflammation was associated with increased IL-1α, IL-1β, IFN-γ, and TNF-α gene expression among SVF samples, and conversely increased IL-6 and IL-10 expression among PSC samples. These data document a robust immunomodulatory effect of implanted PSC, and an inverse correlation between host inflammatory cell infiltration and stromal progenitor cell-mediated ossification.
Adjustable-Frequency Spectrophone Laser Stabilization (1985)

Gas laser frequency stabilizing system includes sensitive spectrophone that senses dither modulation of frequency of laser beam, producing Lorentzian, Voigt, or Doppler spectral tuning response.
Polarization mode basis functions for modeling insulator-coated through-silicon via (TSV) interconnections (2009)

For the design of high-density 3-D integration, this paper presents a method to model through-silicon via (TSV) interconnections. Focusing on the modeling of annular insulator coating around the TSV, this paper proposes a new type of modal basis functions that describe polarization current density distribution in insulator. The equivalent network including modal excess capacitance from the basis functions provides accurate electrical characteristics, compared with analytic and EM simulation results.
Atomic description of the immune complex involved in heparin-induced thrombocytopenia (2015)

Heparin-induced thrombocytopenia (HIT) is an autoimmune thrombotic disorder caused by immune complexes containing platelet factor 4 (PF4), antibodies to PF4 and heparin or cellular glycosaminoglycans (GAGs). Here we solve the crystal structures of the: (1) PF4 tetramer/fondaparinux complex, (2) PF4 tetramer/KKO-Fab complex (a murine monoclonal HIT-like antibody) and (3) PF4 monomer/RTO-Fab complex (a non-HIT anti-PF4 monoclonal antibody). Fondaparinux binds to the 'closed' end of the PF4 tetramer and stabilizes its conformation. This interaction in turn stabilizes the epitope for KKO on the 'open' end of the tetramer. Fondaparinux and KKO thereby collaborate to 'stabilize' the ternary pathogenic immune complex. Binding of RTO to PF4 monomers prevents PF4 tetramerization and inhibits KKO and human HIT IgG-induced platelet activation and platelet aggregation in vitro, and thrombus progression in vivo. The atomic structures provide a basis to develop new diagnostics and non-anticoagulant therapeutics for HIT.
[Methods of obtaining and formation mechanisms of polymer nanoparticles]. (2001)

Severals processes exist today for manufacturing colloidal systems of nanospheres or nanocapsules. These nanoparticles have applications in various industrial fields such as cosmetic, pharmacy, food industry, agrochemicals.... The formation of nanoparticles allows the protection of an active molecule by a polymeric coating and the release of this product following a perfectly defined profile, which depends on the nature of the polymer, the type of particle and the field of use. The purpose of this article is to expose the different methods of preparation of nanoparticular systems. These methods are classified in two mains categories. The first gathers most of the methods which are based on polymerization reactions, the second presents the use of preformed polymers (of natural or synthetic origin). A thorough study is devoted to the mechanisms of formation, in order to find the advantages and the disadvantages of each technique to support the development of manufactoring processes.
Non-Equilibrium Plasma Methods for Tailoring Surface Properties of Polyvinylidene Fluoride: Review and Challenges (2021)

Modification and functionalization of polymer surface properties is desired in numerous applications, and a standard technique is a treatment with non-equilibrium gaseous plasma. Fluorinated polymers exhibit specific properties and are regarded as difficult to functionalize with polar functional groups. Plasma methods for functionalization of polyvinylidene fluoride (PVDF) are reviewed and different mechanisms involved in the surface modification are presented and explained by the interaction of various reactive species and far ultraviolet radiation. Most authors used argon plasma but reported various results. The discrepancy between the reported results is explained by peculiarities of the experimental systems and illustrated by three mechanisms. More versatile reaction mechanisms were reported by authors who used oxygen plasma for surface modification of PVDF, while plasma sustained in other gases was rarely used. The results reported by various authors are analyzed, and correlations are drawn where feasible. The processing parameters reported by different authors were the gas pressure and purity, the discharge configuration and power, while the surface finish was predominantly determined by X-ray photoelectron spectroscopy (XPS) and static water contact angle (WCA). A reasonably good correlation was found between the surface wettability as probed by WCA and the oxygen concentration as probed by XPS, but there is hardly any correlation between the discharge parameters and the wettability.
Home-based mobile fetal/maternal electrocardiogram acquisition and extraction with cloud assistance (2019)

Electrocardiogram (ECG) monitoring of the fetus during pregnancy, before and during labor, can provide crucial information for the assessment of fetal well-being and development, as well as labor progress. An out-of-clinics fetal ECG monitoring system may pave the way for instant diagnosis, suggesting immediate intervention, which could help reduce the fetal mortality rate. In this paper, we present an unobtrusive fetal maternal ECG monitoring system which can operate in the home setting. The acquisition of the mother's abdominal ECG is done using the non-contact electrode approach. The extraction of the fetal ECG from the combined fetal/maternal ECG signal is investigated using both Fast Independent Component Analysis (FastICA) and RobustICA algorithms. An accelerometer is integrated for motion artifact detection which would help reduce interferences due to movement. The device also is connected to a cloud server, allowing doctors to access the data in real time.
Preclinical Characterization of Immunogenicity and Efficacy against Diarrhea from MecVax, a Multivalent Enterotoxigenic E. coli Vaccine Candidate (2021)

There are no vaccines licensed for enterotoxigenic Escherichia coli (ETEC), a leading cause of diarrhea for children in developing countries and international travelers. Virulence heterogeneity among strains and difficulties identifying safe antigens for protective antibodies against STa, a potent but poorly immunogenic heat-stable toxin which plays a key role in ETEC diarrhea, are challenges in ETEC vaccine development. To overcome these challenges, we applied a toxoid fusion strategy and a novel epitope- and structure-based multiepitope fusion antigen (MEFA) vaccinology platform to construct two chimeric multivalent proteins, toxoid fusion 3xSTa<sub>N12S</sub>-mnLT<sub>R192G/L211A</sub> and adhesin CFA/I/II/IV MEFA, and demonstrated that the proteins induced protective antibodies against STa and heat-labile toxin (LT) produced by all ETEC strains or the seven most important ETEC adhesins (CFA/I and CS1 to CS6) expressed by the ETEC strains causing 60 to 70% of diarrheal cases and moderate to severe cases. Combining two proteins, we prepared a protein-based multivalent ETEC vaccine, MecVax. MecVax was broadly immunogenic; mice and pigs intramuscularly immunized with MecVax developed no apparent adverse effects but had robust antibody responses to the target toxins and adhesins. Importantly, MecVax-induced antibodies were broadly protective, demonstrated by significant adherence inhibition against E. coli bacteria producing any of the seven adhesins and neutralization of STa and cholera toxin (CT) enterotoxicity. Moreover, MecVax protected against watery diarrhea and provided over 70% and 90% protection against any diarrhea from an STa-positive or an LT-positive ETEC strain in a pig challenge model. These results indicated that MecVax induces broadly protective antibodies and prevents diarrhea preclinically, signifying that MecVax is potentially an effective injectable vaccine for ETEC. <b>IMPORTANCE</b> Enterotoxigenic Escherichia coli (ETEC) bacteria are a top cause of children's diarrhea and travelers' diarrhea and are responsible for over 220 million diarrheal cases and more than 100,000 deaths annually. A safe and effective ETEC vaccine can significantly improve public health, particularly in developing countries. Data from this preclinical study showed that MecVax induces broadly protective antiadhesin and antitoxin antibodies, becoming the first ETEC vaccine candidate to induce protective antibodies inhibiting adherence of the seven most important ETEC adhesins and neutralizing the enterotoxicity of not only LT but also STa toxin. More importantly, MecVax is shown to protect against clinical diarrhea from STa-positive or LT-positive ETEC infection in a pig challenge model, recording protection from antibodies induced by the protein-based, injectable, subunit vaccine MecVax against ETEC diarrhea and perhaps the possibility of intramuscularly administered protein vaccines for protection against intestinal mucosal infection.
Nanoparticle Liquids for Surface Modification and Lubrication of MEMS Switch Contacts (2008)

Contact failures in microelectromechanical system (MEMS) switches, particularly during hot switching, prevent their widespread use. In this paper, a nanoparticle liquid (NPL) lubricant is synthesized and deposited on MEMS switch contacts as a nanotechnology-based lubricant. NPLs are monolithic hybrid materials comprised of an inorganic nanosized metallic core and an organic low viscosity corona. The NPL used here utilizes either Au or Pt nanoparticles as the core and a mercaptoethanesulfonate ionic liquid as the corona. Performance, reliability, and chemical/physical processes on hot-switched NPL-lubricated contact surfaces were investigated at high (1 mA) and low (10 ) currents using a micro/nanoadhesion apparatus as a MEMS switch simulator with in situ monitoring of contact resistance and adhesion force. This was coupled with ex-situ analyses of the contacts using scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, and scanning Auger spectroscopy. NPLs exhibited improved electrical performance and durability (orders of magnitude improvement) as compared to uncoated and self-assembled monolayer-coated switch contacts. Improved performance and reliability results from the following: 1) controlled nanoscale surface roughness that spreads current through multiple nanocontacts; 2) restricted size melting regions and termination of nanowire growth (prevents shorting) during contact opening; 3) enhanced thermal and electrical conductivity that reduces lubricant degradation; and 4) lubricant self-healing (flow to damaged areas) as confirmed with physical and chemical analyses. Based on these results, NPLs show excellent potential as surface modifiers/lubricants for MEMS switch contacts.
Optimal design of a superconducting transmon qubit with tapered wiring (2021)

Analytical formulas are presented for simplified but useful qubit geometries that predict surface dielectric loss when its thickness is much less than the metal thickness, the limiting case needed for real devices. These formulas can thus be used to precisely predict loss and optimize the qubit layout. Surprisingly, a significant fraction of surface loss comes from the small wire that connects the Josephson junction to the qubit capacitor. Tapering this wire is shown to significantly lower its loss. Also predicted are the size and density of the two-level state (TLS) spectrum from individual surface dissipation sites.
High‐throughput microplate technique for enzymatic hydrolysis of lignocellulosic biomass (2008)

Several factors will influence the viability of a biochemical platform for manufacturing lignocellulosic based fuels and chemicals, for example, genetically engineering energy crops, reducing pre-treatment severity, and minimizing enzyme loading. Past research on biomass conversion has focused largely on acid based pre-treatment technologies that fractionate lignin and hemicellulose from cellulose. However, for alkaline based (e.g., AFEX) and other lower severity pre-treatments it becomes critical to co-hydrolyze cellulose and hemicellulose using an optimized enzyme cocktail. Lignocellulosics are appropriate substrates to assess hydrolytic activity of enzyme mixtures compared to conventional unrealistic substrates (e.g., filter paper, chromogenic, and fluorigenic compounds) for studying synergistic hydrolysis. However, there are few, if any, high-throughput lignocellulosic digestibility analytical platforms for optimizing biomass conversion. The 96-well Biomass Conversion Research Lab (BCRL) microplate method is a high-throughput assay to study digestibility of lignocellulosic biomass as a function of biomass composition, pre-treatment severity, and enzyme composition. The most suitable method for delivering milled biomass to the microplate was through multi-pipetting slurry suspensions. A rapid bio-enzymatic, spectrophotometric assay was used to determine fermentable sugars. The entire procedure was automated using a robotic pipetting workstation. Several parameters that affect hydrolysis in the microplate were studied and optimized (i.e., particle size reduction, slurry solids concentration, glucan loading, mass transfer issues, and time period for hydrolysis). The microplate method was optimized for crystalline cellulose (Avicel) and ammonia fiber expansion (AFEX) pre-treated corn stover.
Manipulating DNA Conformation Using Intertwined Conducting Polymer Chains (2001)

In the field of inherently conducting polymers, polyaniline (Pani) has elicited tremendous interest due to its promising electrical properties and unique redox tunability. Synthetic routes involving the use of polyelectrolytes have significantly improved the processability of polyaniline. Recently, a template guided synthesis catalyzed by an enzyme, horseradish peroxidase (HRP), has provided a means of polymerizing aniline under milder pH conditions (pH 4.3) and subsequently widened the choice of templates to more delicate biological macromolecules. Here we report a strategy that exploits the inherent molecular order as well as the polyelectrolyte behavior of DNA to enzymatically synthesize and biologically assemble conducting polyaniline. This “wrapping” of polyaniline on DNA has been found to induce reversible changes in the secondary structure of DNA, leading to the formation of an over-wound polymorph. The polyaniline synthesized on the DNA also exhibited a template-induced macroasymmetry. This unique polyaniline/DNA intertwined complex has been used to “probe” and control the conformation of the DNA double helix.
Design, fabrication, and performance analysis of GaN vertical electron transistors with a buried p/n junction (2015)

The Current Aperture Vertical Electron Transistor (CAVET) combines the high conductivity of the two dimensional electron gas channel at the AlGaN/GaN heterojunction with better field distribution offered by a vertical design. In this work, CAVETs with buried, conductive p-GaN layers as the current blocking layer are reported. The p-GaN layer was regrown by metalorganic chemical vapor deposition and the subsequent channel regrowth was done by ammonia molecular beam epitaxy to maintain the p-GaN conductivity. Transistors with high ON current (10.9 kA/cm2) and low ON-resistance (0.4 mΩ cm2) are demonstrated. Non-planar selective area regrowth is identified as the limiting factor to transistor breakdown, using planar and non-planar n/p/n structures. Planar n/p/n structures recorded an estimated electric field of 3.1 MV/cm, while non-planar structures showed a much lower breakdown voltage. Lowering the p-GaN regrowth temperature improved breakdown in the non-planar n/p/n structure. Combining high breakdown voltage with high current will enable GaN vertical transistors with high power densities.
Simple template-based method to produce bradbury-nielsen gates (2007)

A Bradbury-Nielsen gate (BNG) consists of two interleaved and electrically isolated sets of wires and can transmit or deflect charged particles by applying a varying voltage difference across the two wire sets. We present a simple template-based method to fabricate BNGs with wire spacings as small as 50 microm with minimal use of a microscope. The small wire spacing allows modulation rates at tens of megahertz. Using this method, we have fabricated four BNGs with wire spacings of 500, 200, 100, and 50 microm using 10 microm gold-coated tungsten wires. The performance of the four BNGs is characterized using an imaging detector and compared with theoretical predictions.
Polarization rotator based on silicon wire waveguides (2008)

We describe a polarization rotator based on an off-axis double-core structure consisting of a silicon wire waveguide and a silicon-oxinitride waveguide. The rotator can be made by planar fabrication technology and do not require complex processes, such as three-dimensional structure formation. A rotator with 35-microm long provides the polarization rotation angle of 72 degrees and the polarization extinction ratio of 11 dB with the excess loss of about 1 dB. Our polarization rotator represents a significant step towards accomplishing an optical circuit with polarization diversity based on silicon wire waveguides.
A new method for long-term home monitoring of fetal movement by pregnant women themselves (2011)

Fetal movement is one index of fetal well-being. We designed and built a new recorder based on fetal movement acceleration measurement (FMAM). The FMAM recorder has a newly developed, capacitive acceleration sensor that can detect the oscillations of the maternal abdominal wall caused by fetal movements. In this study, the recorder was examined for its suitability for long-term home monitoring of fetal movement by pregnant women themselves. Experiment I: Fourteen pregnant women underwent 45 examinations in the laboratory at gestational 20-39 weeks. We simultaneously recorded fetal movement as detected by the recorder, ultrasonography, and maternal perception, and then calculated agreement among the three methods. We evaluated agreement using prevalence-adjusted bias-adjusted kappa (PABAK). Agreement for gross fetal movement as detected by FMAM and ultrasonography was substantial or almost perfect, while agreement between maternal perception and ultrasonography was moderate or substantial. Experiment II: Six pregnant women undertook 53 experiments at home by themselves. Fetal movement during maternal nocturnal sleep was successfully recorded 50 out of 53 times at home. In conclusion, there was high agreement for gross fetal movement between FMAM and ultrasonography. The recorder is promising for objective, accurate, and long-term home monitoring of gross fetal movement by pregnant women themselves.