gebhart/patrepeval huggingface dataset:
Antigenic characterization of the P6 protein of nontypable Haemophilus influenzae (1986)

The purpose of this study was to characterize the degree of antigenic heterogeneity or conservation of a 16,600-dalton outer membrane protein (P6) among strains of nontypable Haemophilus influenzae. Immunization of rabbits with P6 isolated from individual strains resulted in antibody to P6 of all 25 strains tested. The titers of antibody in the sera were similar among the strains. Whole organisms of two strains were used to immunize rabbits, and antibodies were produced to P6 of all strains tested. Monoclonal antibodies developed to P6 from mice immunized with whole cells of three different strains recognized determinants on P6 of all 25 strains tested. Finally, pooled normal human serum contained antibodies to P6 of all 25 strains assayed. These studies indicate that P6 is a highly conserved antigen on the outer membrane of nontypable H. influenzae.
Use of Magnetic Induction to Activate a “Touchless” Shape Memory Alloy Implantable Penile Prosthesis (2019)

A shape memory penile prosthesis is a promising alternative to hydraulic-based penile prostheses and can be activated safely and efficiently using magnetic induction in our models of the human penis. Le BV, McVary KT, McKenna K, et al. Use of Magnetic Induction to Activate a "Touchless" Shape Memory Alloy Implantable Penile Prosthesis. J Sex Med 2019;16:596-601.
Right-side cardiac output determined with a newly developed catheter-tip resistivity probe using saline indicator. (1984)

Right-heart cardiac output was determined in 10 dogs using a newly developed, highly accurate catheter-tip resistivity probe. A saline indicator was injected into the right atrium and the blood resistivity was monitored at the catheter tip in the pulmonary artery. The resulting dilution curves were calibrated electrically according to the manner in which blood resistivity changes with saline concentration and cardiac output values were calculated. Cardiac output values determined simultaneously by the direct Fick method were used as a reference.
Conversion of antigen-specific effector/memory T cells into Foxp3-expressing T <sub>reg</sub> cells by inhibition of CDK8/19 (2019)

A promising way to restrain hazardous immune responses, such as autoimmune disease and allergy, is to convert disease-mediating T cells into immunosuppressive regulatory T (T<sub>reg</sub>) cells. Here, we show that chemical inhibition of the cyclin-dependent kinase 8 (CDK8) and CDK19, or knockdown/knockout of the CDK8 or CDK19 gene, is able to induce Foxp3, a key transcription factor controlling T<sub>reg</sub> cell function, in antigen-stimulated effector/memory as well as naïve CD4<sup>+</sup> and CD8<sup>+</sup> T cells. The induction was associated with STAT5 activation, independent of TGF-β action, and not affected by inflammatory cytokines. Furthermore, in vivo administration of a newly developed CDK8/19 inhibitor along with antigen immunization generated functionally stable antigen-specific Foxp3<sup>+</sup> T<sub>reg</sub> cells, which effectively suppressed skin contact hypersensitivity and autoimmune disease in animal models. The results indicate that CDK8/19 is physiologically repressing Foxp3 expression in activated conventional T cells and that its pharmacological inhibition enables conversion of antigen-specific effector/memory T cells into Foxp3<sup>+</sup> T<sub>reg</sub> cells for the treatment of various immunological diseases.
Outer-Membrane-Vesicle–Associated O Antigen, a Crucial Component for Protecting Against Bordetella parapertussis Infection (2018)

<i>Bordetella parapertussis</i> is a respiratory-disease pathogen producing symptomatology similar to that of pertussis but of underestimated incidence and with no specific vaccine existing. We recently designed a vaccine candidate from <i>B. parapertussis</i> outer-membrane vesicles (OMVs) that proved to be safe and protective in a murine-infection model. Based on protection recently reported for the <i>B. parapertussis</i> O antigen in aqueous solution, we assessed here whether the <i>B. parapertussis</i> O-antigen-containing lipopolysaccharide (BppLPS-O<sup>+</sup>) embedded in the membranes, as present in <i>B. parapertussis</i>-derived OMVs (OMVs(Bpp-LPS-O<sup>+</sup>)), was the component responsible for that previously observed protection by OMVs. By performing a comparative study with OMVs from a human strain with undetectable O antigen (OMVs(Bpp-LPS-O<sup>-</sup>)), we demonstrated that the OMVs(Bpp-LPS-O<sup>+</sup>), but not the OMVs(Bpp-LPS-O<sup>-</sup>), protected mice against sublethal <i>B. parapertussis</i> infections. Indeed, the <i>B. parapertussis</i> loads were significantly reduced in the lungs of OMVs(Bpp-LPS-O<sup>+</sup>) -vaccinated animals, with the CFUs recovered being decreased by 4 log units below those detected in the non-immunized animals or in the animals treated with the OMVs(Bpp-LPS-O<sup>-</sup>), (<i>p</i> < 0.001). We detected that the OMVs(Bpp-LPS-O<sup>+</sup>) induced IgG antibodies against <i>B. parapertussis</i> whole-cell lysates, which immunocomponents recognized, among others, the O antigen and accordingly conferred protection against <i>B. parapertussis</i> infection, as observed in <i>in-vivo</i>-passive-transfer experiments. Of interest was that the OMVs(Bpp-LPS-O<sup>+</sup>) -generated sera had opsonophagocytic and bactericidal capabilities that were not detected with the OMVs(Bpp-LPS-O<sup>-</sup>)-induced sera, suggesting that those activities were involved in the clearance of <i>B. parapertussis</i>. Though stimulation of cultured spleen cells from immunized mice with formulations containing the O antigen resulted in gamma interferon (IFN-γ) and interleukin-17 production, spleen cells from OMVs(Bpp-LPS-O<sup>+</sup>) -immunized mice did not significantly contribute to the observed protection against <i>B. parapertussis</i> infection. The protective capability of the <i>B. parapertussis</i> O antigen was also detected in formulations containing both the OMVs derived from <i>B. pertussis</i> and purified BppLPS-O<sup>+</sup>. This combined formulation protected mice against <i>B. pertussis</i> along with <i>B. parapertussis</i>.
Mesencephalic Astrocyte–Derived Neurotrophic Factor as a Urine Biomarker for Endoplasmic Reticulum Stress–Related Kidney Diseases (2016)

Endoplasmic reticulum (ER) stress and disrupted proteostasis contribute to the pathogenesis of a variety of glomerular and tubular diseases. Thus, it is imperative to develop noninvasive biomarkers for detecting ER stress in podocytes or tubular cells in the incipient stage of disease, when a kidney biopsy is not yet clinically indicated. Mesencephalic astrocyte-derived neurotrophic factor (MANF) localizes to the ER lumen and is secreted in response to ER stress in several cell types. Here, using mouse models of human nephrotic syndrome caused by mutant laminin β2 protein-induced podocyte ER stress and AKI triggered by tunicamycin- or ischemia-reperfusion-induced tubular ER stress, we examined MANF as a potential urine biomarker for detecting ER stress in podocytes or renal tubular cells. ER stress upregulated MANF expression in podocytes and tubular cells. Notably, urinary MANF excretion concurrent with podocyte or tubular cell ER stress preceded clinical or histologic manifestations of the corresponding disease. Thus, MANF can potentially serve as a urine diagnostic or prognostic biomarker in ER stress-related kidney diseases to help stratify disease risk, predict disease progression, monitor treatment response, and identify subgroups of patients who can be treated with ER stress modulators in a highly targeted manner.
Tissue plasminogen activator and urokinase mediate the binding of Glu-plasminogen to plasma fibrin I. Evidence for new binding sites in plasmin-degraded fibrin I. (1985)

The effect of tissue plasminogen activator (TPA) or urokinase on the specific binding of human Glu-plasminogen to fibrin I formed in plasma by clotting with Reptilase was studied using 125I-plasminogen and 131I-fibrinogen. In the absence of TPA, small amounts of plasminogen were bound to fibrin I. TPA induced binding of plasminogen to plasma fibrin I that was dependent upon the concentrations of TPA and plasminogen as well as upon the time of incubation. Plasminogen binding occurred in association with fibrin clot lysis and the formation in the clot supernatant of alpha 2-plasmin inhibitor-plasmin complexes. Urokinase also induced binding of plasminogen to plasma fibrin I that was concentration- and time-dependent. The molecular form of plasminogen bound to the fibrin I plasma clot was identified as Glu-plasminogen by dodecyl sulfate-polyacrylamide gel electrophoresis and by fast performance liquid chromatography. Further studies demonstrated that fibrin I formed from fibrinogen that had been progressively degraded by plasmin-bound Glu-plasminogen. The mole ratio of plasminogen bound increased with the time of plasmin digestion. Glu-plasminogen did not bind to fibrin I formed from fibrinogen progressively digested by human leukocyte elastase, thereby demonstrating the specificity of plasmin. These studies demonstrate that plasminogen activators regulate the binding of Glu-plasminogen to fibrin I by catalyzing plasmin-mediated modifications in the fibrin substrate.
A single donor is sufficient to produce a highly functional in vitro antibody library (2021)

Antibody complementarity determining region diversity has been considered to be the most important metric for the production of a functional antibody library. Generally, the greater the antibody library diversity, the greater the probability of selecting a diverse array of high affinity leads. According to this paradigm, the primary means of elevating library diversity has been by increasing the number of donors. In the present study we explored the possibility of creating an in vitro antibody library from a single healthy individual, showing that the number of lymphocytes, rather than the number of donors, is the key criterion in the production of a diverse and functional antibody library. We describe the construction of a high-quality phage display library comprising 5 × 10<sup>9</sup> human antibodies by applying an efficient B cell extraction protocol from a single donor and a targeted V-gene amplification strategy favoring specific antibody families for their improved developability profiles. Each step of the library generation process was followed and validated by next generation sequencing to monitor the library quality and diversity. The functionality of the library was tested using several therapeutically relevant targets for which a vast number of different antibodies with desired biophysical properties were obtained.
3D Printed Pellets (Miniprintlets): A Novel, Multi-Drug, Controlled Release Platform Technology (2019)

Selective laser sintering (SLS) is a single-step three-dimensional printing (3DP) process that can be leveraged to engineer a wide array of drug delivery systems. The aim of this work was to utilise SLS 3DP, for the first time, to produce small oral dosage forms with modified release properties. As such, paracetamol-loaded 3D printed multiparticulates, termed miniprintlets, were fabricated in 1 mm and 2 mm diameters. Despite their large surface area compared with a conventional monolithic tablet, the ethyl cellulose-based miniprintlets exhibited prolonged drug release patterns. The possibility of producing miniprintlets combining two drugs, namely paracetamol and ibuprofen, was also investigated. By varying the polymer, the dual miniprintlets were programmed to achieve customised drug release patterns, whereby one drug was released immediately from a Kollicoat Instant Release matrix, whilst the effect of the second drug was sustained over an extended time span using ethyl cellulose. Herein, this work has highlighted the versatility of SLS 3DP to fabricate small and intricate formulations containing multiple active pharmaceutical ingredients with distinct release properties.
Code Shift Keying Impulse Modulation for UWB Communications (2008)

In this paper, the system performance of M-ary code shift keying (MCSK) impulse modulation is studied in detail and compared to M-ary pulse position modulation (MPPM) under single- and multi-user scenarios. For that, bounds on the semi- analytic symbol-error rate (SER) expressions are derived and simulation studies are conducted. When practical implementations of MCSK and MPPM are considered, it is shown that MCSK can provide about 2 dB performance gain over MPPM as it reduces the effects of multipath delays on the decision variables by randomizing locations of the transmit pulse.
Detection of SARS Coronavirus in Patients with Severe Acute Respiratory Syndrome by Conventional and Real-Time Quantitative Reverse Transcription-PCR Assays (2004)

NPA and stool samples can be used for early diagnosis of SARS. The real-time quantitative RT-PCR assay for SARS CoV is potentially useful for early detection of SARS CoV. Our results suggest that genomic RNA is the predominant viral RNA species in clinical samples.
Nox3 Regulation by NOXO1, p47 , and p67 (2004)

gp91(phox) (Nox2), the catalytic subunit of the superoxide-generating respiratory burst oxidase, is regulated by subunits p47(phox) and p67(phox). Nox1, a homolog of gp91(phox), is regulated by NOXO1 and NOXA1, homologs of p47(phox) and p67(phox), respectively. For both Nox1 and gp91(phox), an organizer protein (NOXO1 or p47(phox)) cooperates with an activator protein (NOXA1 or p67(phox)) to regulate the catalytic subunit. Herein, we investigate the subunit regulation of Nox3 compared with that of other Nox enzymes. Nox3, like gp91(phox), was activated by p47(phox) plus p67(phox). Whereas gp91(phox) activity required the protein kinase C activator phorbol myristate acetate (PMA), Nox3 activity was already high without PMA, but was further stimulated approximately 30% by PMA. gp91(phox) was also activated by NOXO1/NOXA1 and required PMA for high activity. gp91(phox) regulation required an intact activation domain in the activator protein, as neither p67(phox)(V204A) nor NOXA1(V205A) were effective. In contrast, p67(phox)(V204A) was effective (along with p47(phox)) in activating Nox3. Unexpectedly, Nox3 was strongly activated by NOXO1 in the absence of NOXA1 or p67(phox). Nox3 activity was regulated by PMA only when p47(phox) but not NOXO1 was present, consistent with the phosphorylation-regulated autoinhibitory region in p47(phox) but not in NOXO1. Deletion of the autoinhibitory region from p47(phox) rendered this subunit highly active in the absence of PMA toward both gp91(phox) and Nox3, and high activity required an activator subunit. The unique regulation of Nox3 supports a model in which multiple interactions with regulatory subunits stabilize an active conformation of the catalytic subunit.
Optical Design and Validation of an Infrared Transmissive Spectrum Splitting Concentrator Photovoltaic Module (2017)

A new modular, hybrid solar power system is designed to generate both electrical and thermal energy by utilizing the full solar spectrum. The key element, an infrared-transparent concentrator photovoltaic (CPV) module, acts as a spectrum splitter, dividing solar radiation into two parts. The ultraviolet and visible light (“in-band”) are converted to electricity with high efficiency in CPV cells, while the infrared light (“out-of-band”) is transmitted directly to a thermal receiver, where thermal power may be converted to electricity by a suitable heat engine or used directly for industrial process heat applications whenever needed. Here, we describe the optical design, modeling, fabrication, and performance validation of this novel spectrum splitting CPV module. A transfer matrix style approach, cumulative transmission model, is built to study the reflection, absorption, and transmission in each layer of the CPV module. To optimize the optical performance, different materials for module superstrate/substrate, encapsulant, cell substrate, and cooling fluids are compared in order to enhance the transmission of out-of-band light through the CPV module by minimizing absorption. Six antireflection coatings along with front and backside electrical contact grids are designed to maximize transmittance of in-band light to the cell and out-of-band light to the thermal receiver. The final design, currently being prototyped, predicts out-of-band light transmission to the thermal receiver of 74.1% (for the passively cooled version) and 65.3% (for the actively cooled version). When epitaxial liftoff technology is applied, the transmission will change to 80.8% (passively cooled) and 71.9% (actively cooled). Experimental prototypes show good agreement with modeled optical performance.
Feature-based watermark localization in digital capture systems (2014)

The “Internet of Things” is an appealing concept aiming to assign digital identity to both physical and digital everyday objects. One way of achieving this goal is to embed the identity in the object itself by using digital watermarking. In the case of printed physical objects, such as consumer packages, this identity can be later read from a digital image of the watermarked object taken by a camera. In many cases, the object might occupy only a small portion of the the image and an attempt to read the watermark payload from the whole image can lead to unnecessary processing. This paper proposes a statistical learning-based algorithm for localizing watermarked physical objects taken by a digital camera. The algorithm is specifically designed and tested on watermarked consumer packages read by an off-the-shelf barcode imaging scanner. By employing simple noise-sensitive features borrowed from blind image steganalysis and a linear classifier, we are able to estimate probabilities of watermark presence in every part of the image significantly faster than running a watermark detector. These probabilities are used to pinpoint areas that are recommended for further processing. We compare our adaptive approach with a system designed to read watermarks from a set of fixed locations and achieve significant savings in processing time while improving overall detector robustness.
ELECTROCHEMICAL MONITORING OF PSEUDOMONAS AERUGINOSA BIOFILMS IN MICROFLUIDIC CHANNELS (2014)

Polydimethylsiloxane microfluidic channels were irreversibly plasma bonded to microfabricated electrochemical sensors to monitor the presence of Pseudomonas aeruginosa biofilms. Channels were electrochemically monitored via square wave voltammetry to detect the presence of redox molecules produced by wild type strain PA14 biofilms growing inside the channels.
33.1: <i>Invited Paper</i> : Technology of Wide Color Gamut Backlight with RGB Light‐Emitting Diode for Liquid Crystal Display Television (2007)

Abstract A mercury free Light‐Emitting Diode (LED) backlight making possible a wide color gamut has become active in Liquid Crystal Display (LCD) industry. The development report such as a direct illumination and guided light illumination were being active. Actual commercial product has been waited under this active situation. Sony Corporation launched an LED‐backlit LCD TV. This product offers a very wide color reproduction range, delivering a color gamut of 150% of what conventional televisions typically achieve. This paper presents the background to the development of the LED backlight system and discusses the technologies used to realize the wide color gamut. The main subjects to solve for the commercialization were how to reduce the luminance/color non‐uniformity of the back light and how to treat heat generation from the LED. The combination of the LED backlit LCD TV and the standardization of wide color space definition xvYCC format will make more vivid and correct color expression, and we forecast that will extend to the market in the future.
Antibody–Drug Conjugates with Pyrrole‐Based KSP Inhibitors as the Payload Class (2018)

The number of cytotoxic payload classes successfully employed in antibody-drug conjugates (ADCs) is still rather limited. The identification of ADC payloads with a novel mode of action will increase therapeutic options and potentially increase the therapeutic window. Herein, we describe the utilization of kinesin spindle protein inhibitors (KSPi) as a novel payload class providing highly potent ADCs against different targets, for instance HER-2 or TWEAKR/Fn14. Aspects of technical optimization include the development of different linker attachment sites, the stabilization of ADC linkage to avoid payload deconjugation and finally, the tailor-made design of active metabolites with a long lasting intracellular exposure in the tumor matching the mode of action of KSP inhibition. These KSPi-ADCs are highly potent and selective in vitro and demonstrate in vivo efficacy in a broad panel of tumor models including complete regressions in a patient-derived urothelial cancer model.
Effects of Active Immunization with Inhibin α Subunit on Reproductive Characteristics of Turkey Hens1 (2001)

The hypothesis for the present study is that the active immunization of female turkeys with inhibin (INH) would neutralize endogenous INH, and increase levels of circulating follicle stimulating hormone (FSH) and the number of preovulatory follicles, and subsequently enhance egg production. Two experiments were conducted with female turkeys in their first (30 wk of age) and second (62 wk of age) laying cycles. Treatment groups included control turkeys immunized with keyhole limpet hemocyanine (KLH) and experimental turkeys immunized with recombinant turkey inhibin alpha conjugated to KLH (rtINH), vasoactive intestinal peptide (VIP) conjugated to KLH or rtINH+VIP. Egg production increased (P < 0.05) in VIP and rtINH+VIP immunized birds, but not in rtINH immunized hens in comparison with a control group. A similar number of ovarian follicles, arranged in the follicular hierarchy of laying hens, was observed in all experimental groups. However, there was a larger number of nongraded yellow follicles in rtINH-immunized (62.5%) and rtINH+VIP-immunized (73.5%) groups compared with that of controls, suggesting overstimulation by FSH. Anterior pituitary FSH beta subunit, LH beta subunit, and prolactin (PRL) mRNA contents were determined by Northern blot analysis and reverse transcriptase-polymerase chain reaction (RT-PCR) in laying hens at the end of the experimental period. Hens immunized with rtINH showed increased FSH beta subunit mRNA content, but no change in the content of LH beta subunit or PRL mRNA. Hens immunized with VIP or rtINH+VIP had significant increases in both pituitary LH beta subunit and FSH beta subunit mRNA contents, accompanied by a decline in PRL mRNA abundance. The magnitude of the increase in FSH beta subunit to INH immunoneutralization was greater in first-cycle hens than in second-cycle hens. These data suggest that active immunization of female turkeys with INH neutralizes endogenous INH and increases both circulating FSH and the number of preovulatory follicles. However, no significant increase in egg production was observed in INH-immunized hens. The data confirm previous reports that VIP immunoneutralization increases egg production in turkey hens and shows for the first time that it also increases FSH beta subunit and LH beta subunit gene expression.
Supplementary Information from PF-06804103, A Site-specific Anti-HER2 Antibody–Drug Conjugate for the Treatment of HER2-expressing Breast, Gastric, and Lung Cancers (2023)

<p>Includes Supplementary Materials and Methods, Data and Figure Legends</p>
Catalytic asymmetric hydrogenation (1972)

W. S. Knowles, M. J. Sabacky and B. D. Vineyard, J. Chem. Soc., Chem. Commun., 1972, 10 DOI: 10.1039/C39720000010