gebhart/patrepeval huggingface dataset:
Cooperation of innate and adaptive immunity in the pathogenesis of biliary atresia (2009)

Biliary atresia is a neonatal obstructive cholangiopathy that progresses to end-stage liver disease. Although the etiology is unknown, a neonatal adaptive immune signature has been mechanistically linked to obstruction of the extrahepatic bile ducts. Here, we investigated the role of the innate immune response in the pathogenesis of biliary atresia. Analysis of livers of infants at diagnosis revealed that NK cells populate the vicinity of intrahepatic bile ducts and overexpress several genes involved in cytotoxicity. Using a model of rotavirus-induced biliary atresia in newborn mice, we found that activated NK cells also populated murine livers and were the most abundant cells in extrahepatic bile ducts at the time of obstruction. Rotavirus-primed hepatic NK cells lysed cholangiocytes in a contact- and Nkg2d-dependent fashion. Depletion of NK cells and blockade of Nkg2d each prevented injury of the duct epithelium after rotavirus infection, maintained continuity of duct lumen between the liver and duodenum, and enabled bile flow, despite the presence of virus in the tissue and the overexpression of proinflammatory cytokines. These findings identify NK cells as key initiators of cholangiocyte injury via Nkg2d and demonstrate that injury to the duct epithelium drives the phenotype of experimental biliary atresia.
A new multimodal indicator design integrating standard monitoring and electroencephalographic data for quantification of depth of anesthesia (2012)

Electroencephalographic (EEG) monitoring of the hypnotic component of anesthesia has been suggested as a monitoring technique supplementing standard monitoring to prevent intraoperative awareness. While the EEG reflects brain activity, standard monitoring of anesthesia is based on cardiovascular and respiratory parameters providing indirect information on the effects of anesthetics. The present investigation evaluates the ability of a new multimodal indicator linking EEG and standard monitoring parameters to one index quantifying “anesthetic depth” from wakefulness to deep anesthesia.
Localization in a wide range of industrial environments using relative 3D ceiling features (2008)

This paper presents a localization system for mobile robots that are able to navigate autonomously in industrial environments like factory and exhibition halls. Previous approaches show that ceiling structures like beams, pipes and lighting installation are well-suited for self-localization in large halls. With this paper we describe how to use ceiling structures, measured with a 3D laser range sensor, as natural landmarks. Due to the novel relative representation of 3D ceiling features this method can be used in a wide range of industrial halls with sloped, stepped and even curved ceiling structures. In addition to this new algorithm the paper presents experimental results with an autonomous fork lift working without the need for artificial landmarks or extra infrastructure.
High Density Display of an Anti-Angiogenic Peptide on Micelle Surfaces Enhances Their Inhibition of αvβ3 Integrin-Mediated Neovascularization In Vitro (2020)

Diabetic retinopathy (DR), Retinopathy of Pre-maturity (ROP), and Age-related Macular Degeneration (AMD) are multifactorial manifestations associated with abnormal growth of blood vessels in the retina. These three diseases account for 5% of the total blindness and vision impairment in the US alone. The current treatment options involve heavily invasive techniques such as frequent intravitreal administration of anti-VEGF (vascular endothelial growth factor) antibodies, which pose serious risks of endophthalmitis, retinal detachment and a multitude of adverse effects stemming from the diverse physiological processes that involve VEGF. To overcome these limitations, this current study utilizes a micellar delivery vehicle (MC) decorated with an anti-angiogenic peptide (aANGP) that inhibits αvβ3 mediated neovascularization using primary endothelial cells (HUVEC). Stable incorporation of the peptide into the micelles (aANGP-MCs) for high valency surface display was achieved with a lipidated peptide construct. After 24 h of treatment, aANGP-MCs showed significantly higher inhibition of proliferation and migration compared to free from aANGP peptide. A tube formation assay clearly demonstrated a dose-dependent angiogenic inhibitory effect of aANGP-MCs with a maximum inhibition at 4 μg/mL, a 1000-fold lower concentration than that required for free from aANGP to display a biological effect. These results demonstrate valency-dependent enhancement in the therapeutic efficacy of a bioactive peptide following conjugation to nanoparticle surfaces and present a possible treatment alternative to anti-VEGF antibody therapy with decreased side effects and more versatile options for controlled delivery.
Accommodative Movements of the Vitreous Membrane, Choroid, and Sclera in Young and Presbyopic Human and Nonhuman Primate Eyes (2013)

The monkey anterior hyaloid bends posteriorly during accommodation in proportion to accommodative amplitude and the sclera bows inward with increasing age in both species. Future descriptions of the accommodative mechanism, and approaches to presbyopia therapy, may need to incorporate these findings.
Compression of light pulses by stimulated Raman scattering without a frequency shift (1989)

A system for compressing light pulses without altering the frequency of the original laser radiation is proposed and implemented. Such a system allows further amplification of laser radiation. The conversion in the system occurs in two stages: stimulated Raman scattering conversion of a pulse under counterpropagating amplification conditions and conversion of a compressed Stokes pulse into anti-Stokes radiation of frequency equal to the initial pump frequency. A report is given of the use of stimulated Raman scattering in compressed methane in such a system to shorten pulses of the second harmonic of an Nd laser (λ = 0.528 μm) from 3 ns to 100 ps.
Characterization of Bio-Inspired Electro-Conductive Soy Protein Films (2021)

Protein-based conductive materials are gaining attention as alternative components of electronic devices for value-added applications. In this regard, soy protein isolate (SPI) was processed by extrusion in order to obtain SPI pellets, subsequently molded into SPI films by hot pressing, resulting in homogeneous and transparent films, as shown by scanning electron microscopy and UV-vis spectroscopy analyses, respectively. During processing, SPI denatured and refolded through intermolecular interactions with glycerol, causing a major exposition of tryptophan residues and fluorescence emission, affecting charge distribution and electron transport properties. Regarding electrical conductivity, the value found (9.889 × 10<sup>-4</sup> S/m) is characteristic of electrical semiconductors, such as silicon, and higher than that found for other natural polymers. Additionally, the behavior of the films in contact with water was analyzed, indicating a controlled swelling and a hydrolytic surface, which is of great relevance for cell adhesion and spreading. In fact, cytotoxicity studies showed that the developed SPI films were biocompatible, according to the guidelines for the biological evaluation of medical devices. Therefore, these SPI films are uniquely suited as bioelectronics because they conduct both ionic and electronic currents, which is not accessible for the traditional metallic conductors.
Staphylococcus aureus RnpA Inhibitors: Computational-Guided Design, Synthesis and Initial Biological Evaluation (2021)

Antibiotic resistance is spreading worldwide and it has become one of the most important issues in modern medicine. In this context, the bacterial RNA degradation and processing machinery are essential processes for bacterial viability that may be exploited for antimicrobial therapy. In <i>Staphylococcus aureus</i>, RnpA has been hypothesized to be one of the main players in these mechanisms. <i>S. aureus</i> RnpA is able to modulate mRNA degradation and complex with a ribozyme (<i>rnpB</i>), facilitating ptRNA maturation. Corresponding small molecule screening campaigns have recently identified a few classes of RnpA inhibitors, and their structure activity relationship (SAR) has only been partially explored. Accordingly, in the present work, using computational modeling of <i>S. aureus</i> RnpA we identified putative crucial interactions of known RnpA inhibitors, and we used this information to design, synthesize, and biologically assess new potential RnpA inhibitors. The present results may be beneficial for the overall knowledge about RnpA inhibitors belonging to both RNPA2000-like thiosemicarbazides and JC-like piperidine carboxamides molecular classes. We evaluated the importance of the different key moieties, such as the dichlorophenyl and the piperidine of JC2, and the semithiocarbazide, the furan, and the <i>i</i>-propylphenyl ring of RNPA2000. Our efforts could provide a foundation for further computational-guided investigations.
Zebrafish brain proteomics reveals central proteins involved in neurodegeneration (2013)

Understanding the complex biology of the brain requires analyzing its structural and functional complexity at the protein level. The large-scale analysis of the brain proteome, coupled with characterization of central brain proteins, provides insight into fundamental brain processes and processes linked to neurodegenerative diseases. Here we provide a map of the zebrafish brain proteome by using two-dimensional gel electrophoresis (2DE), followed by the identification of 95 brain proteins using mass spectrometry (LC-ESI MS/MS). Our data show extensive phosphorylation of brain proteins but less prominent glycosylation. Furthermore, ~51% of the identified proteins are predicted to have one or more ubiquitination sites whereas ~90% are predicted to have one or more SUMOylation sites. Our findings provide a valuable proteome map of the zebrafish brain and associated posttranslational modifications demonstrating that zebrafish proteomic approaches can aid in our understanding of proteins central to important neuronal processes and those associated with neurodegenerative disorders.
Small printed magnetic dipole (2007)

Abstract A very compact antenna with magnetic dipole radiation properties is presented. It is horizontally polarized HP with low cross polarization level XPR, it has omnidirectional radiation with a very low ripple in the azimuth cut plane. With a compact design (quarter wavelength square) it is suitable for integration into small WLAN devices. When combined with other radiating elements, this antenna offers new opportunities for diversity system deployment. This antenna can be equally used for propagation channel characterization as a reference for horizontally polarized waves. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 49: 1862–1864, 2007; Published online in Wiley Inter‐Science (www.interscience.wiley.com). DOI 10.1002/mop.22617
Kinetic Consequences of the Removal of a Disulfide Bridge on the Folding of Hen Lysozyme (1994)

Quenched-flow hydrogen exchange labeling, monitored by 1H NMR and electrospray ionization mass spectrometry (ESI-MS), has been employed in conjunction with stopped-flow circular dichroism and fluorescence to study the kinetic refolding from guanidinium chloride of a derivative of hen lysozyme in which one of the four disulfide linkages (Cys6-Cys127) has been selectively chemically reduced and carboxymethylated (CM6,127-lysozyme). Removal of this disulfide bridge has little effect on the structure and activity of the native enzyme, and the overall kinetics of refolding are very similar to those of the unmodified protein. A substantial amount of secondary structure is formed within 2 ms of the initiation of folding, followed by the slower formation of tertiary interactions characteristic of the native state, which are attained with a time constant (tau) of ca. 200 ms. There is clear evidence for fast and slow refolding populations, as in the intact protein. Folding of the three-disulfide derivative does, however, exhibit a major difference from that of the intact protein under the same final refolding conditions, in that the transient intermediate on the major refolding pathway of the intact protein, having persistent structure in the alpha-helical domain of the protein, is not detected by hydrogen exchange labeling during folding of the three-disulfide derivative. This suggests that the disulfide bond linking the N- and C-terminal regions of the protein is crucial for stabilization of the partially folded intermediate. In addition, the overshoot in the far-UV CD and the fluorescence minimum, both of which are attributed to non-native interactions, is not observed in the folding of CM6,127-lysozyme. That the lack of a detectable stable intermediate in the folding of CM6,127-lysozyme does not significantly affect the rate of attainment of the native state of the protein supports the proposed independent nature of the two folding domains and, as the Cys6-Cys127 disulfide bond is located in the alpha-domain, indicates that the rate-limiting step in folding of the intact protein, as well as of the three-disulfide derivative, involves stabilization of the beta-domain. The role of disulfide bridges in the formation and maintenance of the three-dimensional fold of proteins and in facilitating the observation of marginally stable intermediate species is discussed.
Targeted Disruption of Glycogen Synthase Kinase 3a (Gsk3a) in Mice Affects Sperm Motility Resulting in Male Infertility1 (2015)

The signaling enzyme glycogen synthase kinase 3 (GSK3) exists as two isoforms-GSK3A and GSK3B. Protein phosphorylation by GSK3 has important signaling roles in several cells. In our past work, we found that both isoforms of GSK3 are present in mouse sperm and that catalytic GSK3 activity correlates with motility of sperm from several species. Here, we examined the role of Gsk3a in male fertility using a targeted gene knockout (KO) approach. The mutant mice are viable, but have a male infertility phenotype, while female fertility is unaffected. Testis weights of Gsk3a(-/-) mice are normal and sperm are produced in normal numbers. Although spermatogenesis is apparently unimpaired, sperm motility parameters in vitro are impaired. In addition, the flagellar waveform appears abnormal, characterized by low amplitude of flagellar beat. Sperm ATP levels were lower in Gsk3a(-/-) mice compared to wild-type animals. Protein phosphatase PP1 gamma2 protein levels were unaltered, but its catalytic activity was elevated in KO sperm. Remarkably, tyrosine phosphorylation of hexokinase and capacitation-associated changes in tyrosine phosphorylation of proteins are absent or significantly lower in Gsk3a(-/-) sperm. The GSK3B isoform was present and unaltered in testis and sperm of Gsk3a(-/-) mice, showing the inability of GSK3B to substitute for GSK3A in this context. Our studies show that sperm GSK3A is essential for male fertility. In addition, the GSK3A isoform, with its highly conserved glycine-rich N terminus in mammals, may have an isoform-specific role in its requirement for normal sperm motility and fertility.
Non-peptide angiotensin II receptor antagonists. 2. Design, synthesis, and biological activity of N-substituted (phenylamino)phenylacetic acids and acyl sulfonamides (1993)

The design, synthesis, and biological activity of a new class of highly potent non-peptide AII receptor antagonists derived from N-substituted (phenylamino)phenylacetic acids and acyl sulfonamides which exhibit a high selectivity for the AT1 receptor are described. A series of N-substituted (phenylamino)phenylacetic acids (9) and acyl sulfonamides (16) and a tetrazole derivative (19) were synthesized and evaluated in the in vitro AT1 (rabbit aorta) and AT2 (rat midbrain) binding assay. The (phenylamino)phenylacetic acids 9c (AT1 IC50 = 4 nM, AT2 IC50 = 0.74 microM), 9d (AT1 IC50 = 5.3 nM, AT2 IC50 = 0.49 microM), and 9e (AT1 IC50 = 5.3 nM, AT2 IC50 = 0.56 microM) were found to be the most potent AT1-selective AII antagonists in the acid series. Incorporation of various substituents in the central and bottom phenyl rings led to a decrease in the AT1 and AT2 binding affinity of the resulting compounds. Replacement of the carboxylic acid (CO2H) in 9c, 9d, and 9e with the bioisostere acyl sulfonamide (CONHSO2Ph) resulted in a (5-7)-fold increase in the AT1 potency of 16a (AT1 IC50 = 0.9 nM, AT2 IC50 = 0.2 microM), 16b (AT1 IC50 = 1 nM, AT2 IC50 = 2.9 microM), and 16c (AT1 IC50 = 0.8 nM, AT2 IC50 = 0.42 microM) and yielded acyl sulfonamides with subnanomolar AT1 activity. Incorporation of the acyl sulfonamide (CONHSO2Ph) for the CO2H of 9c not only enhanced the AT1 potency but also effected a marked increase in the AT2 potency of 16a (AT2 IC50 = 0.74 microM of 9c vs 0.2 microM of 16a) and made it the most potent AT2 antagonist in this study. Replacement of the CO2H of 9b with the bioisostere tetrazole resulted in 19 (AT1 IC50 = 15 nM) with a 2-fold loss in the AT1 and a complete loss in the AT2 binding affinity. (Phenylamino)phenylacetic acid 9c demonstrated good oral activity in AII-infused conscious normotensive rats at an oral dose of 1.0 mg/kg by inhibiting the pressor response for > 6 h. Acyl sulfonamides 16a-c displayed excellent in vivo activity by blocking the AII-induced pressor response for > 6 h after oral administration in conscious rats at a 3.0 mg/kg dose level. Both acyl sulfonamides 16a and 16c exhibited superior in vivo activity in rats compared to that of (phenylamino)phenylacetic acid 9c.
Clostridium Difficile Infection in the Hematopoietic Unit: A Meta-Analysis of Published Studies (2014)

Hematopoietic stem cell transplant (HSCT) recipients are at high risk of contracting Clostridium difficile infection (CDI). We systematically searched the PubMed and EMBASE databases through March 2014 and performed a random-effects meta-analysis to estimate the prevalence and trends of CDI over time. Among 48 eligible articles that included 12,025 patients at risk, we estimated that 7.9% (95% confidence interval [CI], 6.5% to 9.5%) of HSCT patients are diagnosed with CDI during the peri-transplantation and late post-transplantation periods, an estimation that is relatively consistent across studies (τ(2) = .032). Prevalence of CDI is significantly higher among the 5120 allogeneic patients (9.3% [95% CI, 7.0% to 11.9%]), compared with the 4665 autologous patients (5.2% [95% CI, 3.8% to 6.9%]) (P = .02), and as many as 1 of 10 allogeneic transplant recipients are expected to be diagnosed with CDI compared with 1 of 20 autologous transplantation patients. However, this difference did not reach statistical significance when stratified data from the same centers were examined (P = .11). Importantly, we found an increasing trend of CDI diagnosis both worldwide (P = .02) and across studies conducted in North America (P = .03) over the last 34 years. Notably, studies with a follow-up period that extended through the late post-transplantation period (after day +100) had a similar prevalence of CDI as those that followed patients only during the peri-transplantation period (up to day +100) (P = .94). In summary, CDI is common in the hematopoietic transplantation setting and the majority of infections occur in the peri-transplantation period. The prevalence is almost 9-times higher than that reported among all hospital stays, with an increasing trend over time.
A Low-Cost and Light-Weight Motion Tracking Suit (2013)

His work presents the design and implementation of a low-cost motion tracker system including a network of wired microelectromechanical systems (MEMS) based Inertial Measurement Units (IMUs) which fits into a suit for feasible capturing of human body motions. Using miniaturized IMUs and textile cables, the system is designed to be light-weight and easy to use providing maximal movement flexibility for the user. In order to make a long-term data capturing possible a low-power micro computer is deployed and a new data acquisition approach from multiple sensors is proposed which reduces the CPU load and the wiring complexity. While the complete system including hardware, software and methods for calibration and motion estimation is described, the contribution is mainly in the development of the sensory suit and data acquisition methods providing a novel low-cost, energy-efficient and convenient capturing platform for diverse applications.
Efficiency Analysis of the Secondary-side Buck-boost Type Converter for Inductive Power Transfer System (2016)

An inductive power transfer (IPT) system is sometimes applied to the battery charger of electric vehicles. A DC-DC converter with a diode bridge rectifier (secondary-side converter) is connected to the secondary side of the resonant circuit in order to regulate the current and voltage of a battery. In an IPT system, the secondary-side voltage of the resonant circuit changes significantly depending on the coupling coefficient between the primary coil and the secondary coil. In addition, the voltage changes depending on the load condition. Therefore, a buck-boost converter is suitable for the secondary-side converter because the output voltage range is wider than the other converters, and the IPT system with the buck-boost converter is more efficient than the IPT system with the buck converter. In order to develop a high-efficiency IPT system, a theoretical analysis that considers the characteristics of the IPT system is required. Thus, in this paper, the relationship between the coupling coefficient of the coils and the loss of the secondary-side converter is investigated in order to develop a high-efficiency IPT system with theoretical analysis and experiments that consider the coupling coefficient of the coils. In addition, the circuit parameter selection guideline that makes the secondary-side converter more efficient is shown on the basis of the results of theoretical analysis and experiments. As a result, it was confirmed that the tendency of the characteristics obtained with the experiments is similar as that of theoretical analysis. Thus, it was indicated that theoretical analysis in this paper is useful in analysis of the efficiency and loss of the whole IPT system including secondary-side converter.
Hermetically Sealed Inductor-Capacitor (LC) Resonator for Remote Pressure Monitoring (1998)

This paper reports an integrated inductor-capacitor (LC) resonator structure fabricated using bulk micromachining and anodic bonding technologies. In this resonator structure, pressure change monitored by a capacitive pressure sensor results in the change of resonance frequency. The resonance frequency shift is detected by inductive coupling from an external transmission coil; therefore, pressure can be monitored remotely using the passive LC resonator. The fabricated device size measures 3 mm×3 mm×0.6 mm, and pressure responsivity has been estimated to be 2 MHz/mmHg. This micromachined, hermetically sealed structure is suitable for biomedical applications such as intraocular, cardiovascular and brain pressure monitoring.
A High Data-Rate Kiosk Application circularly polarized fractal antenna for mm-wave band radio with 0.18µm CMOS technology (2016)

A mm-wave circularly polarized (CP) fractal antenna has been designed and simulated using standard 0.18 urn CMOS with six metal-layer structure. The proposed design consists of a wideband circularly polarized multi-segment circular fractal antenna with circular polarization at the top layer M6. The proposed CFA has a small size of 25×25× 1mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> and operates over the frequency band between 49.8- and 64.5-GHz with VSWR <; 2. The multi segment circular fractal structure is employed for antenna design because the circular segments can excites two orthogonal E vectors current to achieve circular polarized radiation. The proposed CMOS antenna can offer a simulated peak gain of -1.71 dBi and a simulated axial ratio bandwidth to cover over operating band from 50 to 64.5 GHz.