gebhart/patrepeval huggingface dataset:
Signaling Mechanisms Regulating Self-Renewal and Differentiation of Pluripotent Embryonic Stem Cells (1999)

An ability to propagate pluripotent embryonic cells in culture is the foundation both for defined germline modification in experimental rodents and for future possibilities for broad-based cellular transplantation therapies in humans. Yet, the molecular basis of the self-renewing pluripotent phenotype remains ill-defined. The relationship between factors that influence embryonic stem cell propagation in vitro and mechanisms of stem cell regulation operative in the embryo is also uncertain. In this article we discuss the role of intracellular signalling pathways in the maintenance of pluripotency and induction of differentiation in embryonic stem cell cultures and the mammalian embryo.
Presence of NMDA Receptor Subunits in the Male Lower Urogenital Tract (2000)

Some sexual responses in the male rat, specifically penile erection, are controlled by neural circuits in the brain and spine that are stimulated by the binding of excitatory amino acids (EAAs) to the postsynaptic N-methyl-D-aspartate receptor (NMDAR). In the hypothalamus, EAA/NMDAR interaction triggers the activation of neuronal nitric oxide synthase (nNOS) to produce nitric oxide (NO). The local synthesis of this neurotransmitter in the penile nerve terminals causes corpora cavernosal relaxation and erection. During sexual activity, NO is assumed to participate in seminal emission and ejaculation in the prostate and to inhibit voiding reflexes in the bladder. This study aimed to determine in vitro whether NMDAR is present in these organs and whether it affects the tone of tissue strips through an NO-dependent mechanism. We obtained penile, urinary bladder, and ventral prostate tissues from adult male rats and homologous surgical tissues from human male patients. We detected the NMDAR protein by Western blot and determined the binding of the NMDA antagonist, 3H-CGP. The NMDAR messenger ribonucleic acid (mRNA) was detected by reverse transcription/polymerase chain reaction and identified by cloning and sequencing. The in vitro response to NMDAR antagonists was measured in tissue strips that were precontracted with bethanechol or electrical field stimulation (in rat and human bladder), phenylephrine (in human corpora cavernosa), or norepinephrine (in human prostate). The NMDAR2B protein; ligand-binding activity; and NMDAR1, 2A, and 2B mRNAs were detected in all tissues studied. We found an NMDAR1 variant in rat prostate and penis and in human prostate that is larger than its cerebellar counterpart, but it encodes a 767-amino acid truncated protein (NMDAR1-T). The in vitro contraction of tissue strips was inhibited by NMDAR antagonists against the following sites: polyamine (with ifenprodil); ion channnel high affinity (with dizocilpine); ion channel low affinity (with memantidine, dextrometorphan, and ketamine); and, in an NO-independent, nonadrenergic-noncholinergic pathway that was only partially affected by EAAs. We conclude that, in vitro, all the essential NMDAR subunits are present in the lower urogenital tract, a novel variant of subunit 1 is expressed, the tissues bind an NMDAR ligand, and the NMDAR antagonists induce relaxation of tissue strips. Further work is necessary to determine whether the NMDAR subunits form a fully active receptor and participate in the control of organ tone that is relevant to male sexual activity.
Integrating Software-Defined Metasurfaces into Wireless Communication Systems: Design and Prototype Evaluation (2022)

Software-Defined Metasurfaces (SDMs) have ad-vanced from basic theoretical ideas to a key enabler for next generation wireless systems. When massively deployed in a wireless environment, they can realize precise, software-defined propagation of signals and wireless channel customizations. A plethora of studies have thoroughly investigated the physical design of the SDMs and their wireless channel engineering capa-bilities. This work introduces a novel architecture and associated processes for integrating SDMs into existing networked wireless systems. First, the integration architecture and the according complex underlying physics of the SDMs are presented. Then the software abstractions are proposed that enable the interaction of the surfaces in a physics-agnostic manner. These software abstractions require an SDM profile to operate in real-time, i.e., a database that accurately describes the capabilities of a given metasurface. Thus, the manufacturing time workflows are suggested to produce such a profile. The proposed solutions are evaluated in an actual physical setup/testbed.
Acoustically tuned optical filters and switches for WDM systems (1995)

Wavelength-division multiplexing (WDM) can greatly increase the connectivity of a fiber-optic network because information can be aggregated and routed on a wavelength-by-wavelength basis, by using wavelength-selective passive or active switches. In particular, the acousto-optic switch (AOS), an electronically controlled integrated-optic device for directing traffic in multiwavelength systems, is a compelling candidate for wavelength routing in all-optical networks.1 The AOS is a polarization-independent configuration of the acousto-optic tunable filter that directs incoming light to either of two output ports on a wavelength-band-by-wavelength-band basis, performing wavelength sorting by narrowband TE-TM interconversion. Polarization flipping is restricted to those phase-matched wavelength bands for which the polarization beat length Lb = λ/Δn equals the period of a collinearly propagating surface acoustic wave.
Protection against sepsis-induced lung injury by selective inhibition of protein kinase C-δ (δ-PKC) (2010)

Inflammation and proinflammatory mediators are activators of δ-PKC. In vitro, δ-PKC regulates proinflammatory signaling in neutrophils and endothelial and epithelial cells, cells that can contribute to lung tissue damage associated with inflammation. In this study, a specific δ-PKC TAT peptide inhibitor was used to test the hypothesis that inhibition of δ-PKC would attenuate lung injury in an animal model of ARDS. Experimental ARDS was induced in rats via 2CLP, a model of polymicrobial sepsis. Following 2CLP surgery, the δ-PKC TAT inhibitory peptide (2CLP+δ-PKC TAT in PBS) or PBS (2CLP+PBS) was administered intratracheally. Controls consisted of SO, where animals underwent a laparotomy without 2CLP. Twenty-four hours after SO or 2CLP, blood, BALF, and lung tissue were collected. 2CLP induced δ-PKC phosphorylation in the lung within 24 h. Treatment with the δ-PKC TAT inhibitory peptide significantly decreased pulmonary δ-PKC phosphorylation, indicating effective inhibition of δ-PKC activation. Plasma and BALF levels of the chemokines CINC-1 and MIP-2 were elevated in 2CLP + PBS rats as compared with SO rats. Treatment with δ-PKC TAT reduced 2CLP-induced elevations in chemokine levels in BALF and plasma, suggesting that δ-PKC modulated chemokine expression. Most importantly, intratracheal administration of δ-PKC TAT peptide significantly attenuated inflammatory cell infiltration, disruption of lung architecture, and pulmonary edema associated with 2CLP. Thus, δ-PKC is an important regulator of proinflammatory events in the lung. Targeted inhibition of δ-PKC exerted a lung-protective effect 24 h after 2CLP.
Engineering Glucose Responsiveness Into Insulin (2017)

Insulin has a narrow therapeutic index, reflected in a small margin between a dose that achieves good glycemic control and one that causes hypoglycemia. Once injected, the clearance of exogenous insulin is invariant regardless of blood glucose, aggravating the potential to cause hypoglycemia. We sought to create a "smart" insulin, one that can alter insulin clearance and hence insulin action in response to blood glucose, mitigating risk for hypoglycemia. The approach added saccharide units to insulin to create insulin analogs with affinity for both the insulin receptor (IR) and mannose receptor C-type 1 (MR), which functions to clear endogenous mannosylated proteins, a principle used to endow insulin analogs with glucose responsivity. Iteration of these efforts culminated in the discovery of MK-2640, and its in vitro and in vivo preclinical properties are detailed in this report. In glucose clamp experiments conducted in healthy dogs, as plasma glucose was lowered stepwise from 280 mg/dL to 80 mg/dL, progressively more MK-2640 was cleared via MR, reducing by ∼30% its availability for binding to the IR. In dose escalations studies in diabetic minipigs, a higher therapeutic index for MK-2640 (threefold) was observed versus regular insulin (1.3-fold).
From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions (1999)

A database of functional sites for proteins with known structures, SITE, is constructed and used in conjunction with a simple pattern matching program SiteMatch to evaluate possible function conservation in a recently constructed database of fold predictions for Escherichia coli proteins (Rychlewski L et al., 1999, Protein Sci 8:614-624). In this and other prediction databases, fold predictions are based on algorithms that can recognize weak sequence similarities and putatively assign new proteins into already characterized protein families. It is not clear whether such sequence similarities arise from distant homologies or general similarity of physicochemical features along the sequence. Leaving aside the important question of nature of relations within fold superfamilies, it is possible to assess possible function conservation by looking at the pattern of conservation of crucial functional residues. SITE consists of a multilevel function description based on structure annotations and structure analyses. In particular, active site residues, ligand binding residues, and patterns of hydrophobic residues on the protein surface are used to describe different functional features. SiteMatch, a simple pattern matching program, is designed to check the conservation of residues involved in protein activity in alignments generated by any alignment method. Here, this procedure is used to study conservation of functional features in alignments between protein sequences from the E. coli genome and their optimal structural templates. The optimal templates were identified and alignments taken from the database of genomic structural predictions was described in a previous publication (Rychlewski L et al., 1999, Protein Sci 8:614-624). An automated assessment of function conservation is used to analyze the relation between fold and function similarity for a large number of fold predictions. For instance, it is shown that identifying low significance predictions with a high level of functional residue conservations can be used to extend the prediction sensitivity for fold prediction methods. Over 100 new fold/function predictions in this class were obtained in the E. coli genome. At the same time, about 30% of our previous fold predictions are not confirmed as function predictions, further highlighting the problem of function divergence in fold superfamilies.
Flexible Parylene-based Microelectrode Technology for Intraocular Retinal Prostheses (2006)

We present the first single metal layer flexible microelectrode arrays designed for intraocular implantation that utilize parylene C as their primary structural and insulating material. These electrodes are fabricated as a key component of an intraocular retinal prosthesis comprising a radio-frequency coil for power and data transfer, a packaged high lead-count telemetry-recovery and driving application-specific integrated circuit (ASIC), and a high-density epiretinal stimulating microelectrode array for the treatment of retinal degenerative blindness in humans. Electrochemical tests have demonstrated that these thin-film platinum electrodes perform as necessary for neuronal stimulation. A novel bioconformal MEMS geometry for a complete intraocular system with capsular retaining-wings that enables all the components of the system to be implanted and retained within the lens capsule and vitreous cavity of the eye is also presented. The efficacy of this geometry when compared with a previous model without capsular retaining-wings has been verified by surgical implantation in animal models.
Precision-guided, Personalized Intrapleural Fibrinolytic Therapy for Empyema and Complicated Parapneumonic Pleural Effusions: The Case for The Fibrinolytic Potential (2017)

Complicated pleural effusions and empyema with loculation and failed drainage are common clinical problems. In adults, intrapleural fibrinolytic therapy is commonly used with variable results and therapy remains empiric. Despite the intrapleural use of various plasminogen activators; fibrinolysins, for about sixty years, there is no clear consensus about which agent is most effective. Emerging evidence demonstrates that intrapleural administration of plasminogen activators is subject to rapid inhibition by plasminogen activator inhibitor-1 and that processing of fibrinolysins is importantly influenced by other factors including the levels and quality of pleural fluid DNA. Current therapy for loculation that accompanies pleural infections also includes surgery, which is invasive and for which patient selection can be problematic. Most of the clinical literature published to date has used flat dosing of intrapleural fibrinolytic therapy in all subjects but little is known about how that strategy influences the processing of the administered fibrinolysin or how this influences outcomes. We developed a new test of pleural fluids <i>ex vivo</i>, which is called the Fibrinolytic Potential or FP, in which a dose of a fibrinolysin is added to pleural fluids <i>ex vivo</i> after which the fibrinolytic activity is measured and normalized to baseline levels. Testing in preclinical and clinical empyema fluids reveals a wide range of responses, indicating that individual patients will likely respond differently to flat dosing of fibrinolysins. The test remains under development but is envisioned as a guide for dosing of these agents, representing a novel candidate approach to personalization of intrapleural fibrinolytic therapy.
Adaptive generalized rake reception in DS-CDMA systems - [transactions papers] (2009)

Direct-sequence code-division multiple-access (DSCDMA) cellular systems, such as wideband CDMA (WCDMA), are limited in performance by interference. Linear equalization, such as generalized Rake (G-Rake) receivers and transversal chip equalizers, can theoretically provide significant gains in performance by suppressing interference. In this paper, an adaptive G-Rake receiver is developed, employing practical algorithms for finger placement and weight computation. Finger placement is determined by selecting delays from a candidate set using a "maximal-weight" criterion. Weight computation includes estimation of an impairment covariance matrix using a parametric approach. While described in the context of the downlink, these algorithms can be used in the uplink as well. Both single-antenna and dual-antenna receivers are considered. Link and system performance are evaluated for the downlink, showing significant gains in high-rate coverage.
Fouling measurement using a thermal-based microsystem (2009)

In : 20th workshop on Micromachining, Micromechanics and Microsystems (MME 09), Paper ID : 127, Main topic : physical sensors, Toulouse, France, 20-22 September 2009<br/>In : 20th workshop on Micromachining, Micromechanics and Microsystems (MME 09), Paper ID : 127, Main topic : physical sensors, Toulouse, France, 20-22 September 2009
Subsurface damage and polishing compound affect the 355-nm laser damage threshold of fused silica surfaces (1998)

Subsurface damage, namely grinding and polishing fractures or scratches hidden by the polishing redeposition layer, may lower laser damage threshold by reducing fracture strength, providing sites for absorbing contaminants, and modulating the electromagnetic field. Polishing compound may affect 355-nm laser damage by absorption and scratching. Fused silica surfaces were finished with different grinding and polishing removal depths to leave different extents of subsurface damage from grinding. Three surfaces were polished with ceria and three with zirconia. The surfaces were 355-nm laser damage tested using an automated 'R- on-1' protocol, and also characterized for surface roughness, subsurface damage as revealed by etching, and total internal reflectance microscopy (TIRM). The zirconia polishing produced the highest laser thresholds, especially when the surface was free of polishing and grinding damage. The zirconia polishing was prone to damaging the surface, which significantly reduced laser thresholds at some sites. the ceria polishing left very little polishing damage, and showed uniform damage thresholds when there was no subsurface damage from grinding present. Residual Blanchard fractures lowered thresholds dramatically. Subsurface fractures from fine loose grinding sometimes reduced threshold dramatically and sometimes very little. TIRM images correlate fairly well with microphotographs of subsurface damage revealed by etching.
A multi-anode photomultiplier tube based wavelength-shifting-fiber detector for neutron diffraction (2012)

Wavelength-shifting (WLS) fiber scintillator neutron detectors were developed for two time-of-flight (TOF) neutron powder diffractometers (POWGEN, VULCAN) at Spallation Neutron Source (SNS). In a recent module (v3.0), however, there are 32 1-inch-diameter photomultiplier tubes (PMTs), which are bulky and expensive. We built a new detector module (v3.1) based on four multi-anode (MA) PMTs, and tested its performance including detection efficiency, count rate capability, spatial resolution, ghosting properties, and gamma-ray sensitivity. The v3.1 module was compared with two prior v3.0 modules, and <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> He tube detectors.
Expression and secretion of Mirabilis antiviral protein in Escherichia coli and its inhibition of in vitro eukaryotic and prokaryotic protein synthesis. (1990)

Mirabilis antiviral protein (MAP), a ribosome-inactivating protein, exhibits inhibitory effects on both plant virus infection and protein synthesis. To study these functions by site-specific mutagenesis, the total synthetic gene of MAP was constructed and expressed in Escherichia coli. However, the growth of the host was inhibited by the products, and the yield of MAP was very low. To improve the system for expressing MAP, an expression vector, pSH7, was constructed. This vector is based on the high copy number plasmid pUC19 and includes PL promoter and temperature-sensitive cI857 repressor. The plasmid also contains the ompA signal sequence and the total synthetic MAP gene. The MAP gene was expressed and its product was secreted into the culture medium after E. coli transformants were cultivated at 30 degrees C and the temperature was raised to 42 degrees C. The secreted MAP was then purified and characterized. This protein was identical to native MAP as determined by its mobility in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the amino acid sequence at the NH2 terminus, and its inhibitory effect on in vitro protein synthesis. MAP was found to inhibit the in vitro protein synthesis of rabbit reticulocyte and wheat germ. It further showed an IC50 concentration of approximately 200 nM in an E. coli in vitro translation system in contrast to ricin A-chain, a well known ribosome-inactivating protein.
Bright-blood and dark-blood phase sensitive inversion recovery late gadolinium enhancement and T1 and T2 maps in a single free-breathing scan: an all-in-one approach (2021)

A single free-breathing acquisition using multi-parametric SASHA provides T1 and T2 maps and calculated BB and DB PSIR LGE images for comprehensive tissue characterization.
Deposition factors and band gap of zinc-blende AlN (2001)

Successful deposition of zinc-blende AlN films with thickness up to 1000 Å was performed with plasma source molecular beam epitaxy. The films were epitaxial to the Si(001) substrate. The formation of a thin 3C-SiC layer on the Si(001) surface is one of the important factors for the formation of zinc-blende AlN. Evidence for the presence of 3C-SiC is provided by an Auger electron spectroscopy depth profile and a high-resolution transmission electron microscopy plot profile. Spectroscopic ellipsometry was used to determine the optical constants of zinc-blende AlN in the range from 1.85 to 6.5 eV. The extinction coefficient data indicates that zinc-blende AlN is an indirect semiconductor with a band gap of ∼5.34 eV.
Influences of Target Configurations on the Trigger Characteristics of Laser-Triggered Vacuum Switch (2019)

Working performances of laser-triggered vacuum switch (LTVS) mainly rely on the interactions of laser with target materials. Influences from target configuration, which is one of key factors in the interactions, are neglected so far. The trigger performances of LTVS with different target configurations are studied in this paper. Relevant influence factors about target configurations are discussed briefly based on theoretical analysis about the trigger process. The test prototype is established based on detachable vacuum chamber. The trigger characteristics of LTVS with different target structures, target depths, and laser focal positions are compared. The relationships between target configurations and trigger performances of LTVS are analyzed and discussed. The preferred targets in LTVS are suggested while considering its lifetime. The test results prove that the conical target shows the best trigger performances compared to other targets. Due to the enlarged laser irradiated area and shortened plasma moving distance, the delay time of LTVS reduces with the decrease in conical target angle and the increase in target depth, while the delay time is controlled within 32 ns. Benefited from laser reflection and plasma collision, the trigger performances of conical targets can be enhanced by focusing laser on the target side surface. In particular, the 90° conical target with 1.5 mm depth is suggested to be employed in LTVS products.
Direct‐Drive Acoustic Amplification Using a Tympanostomy Tube (2013)

Objectives: Determine whether a tympanostomy tube with a ferromagnetic cap can be actuated to deliver sound to the cochlea. Methods: A ferromagnetic mixture of nickel powder and epoxy was glued to the outer flange of an Armstrong V Grommet tympanostomy tube. The tube was then placed into the pars tensa portion of a cadaveric temporal bone. The Direct‐Drive Hearing Device (DHD), a completely‐in‐the‐canal hearing aid prototype developed in our lab, was coupled to the nickel‐epoxy flange and fixed inside the ear canal. The displacements of the posterior crus of the stapes were then measured using a Laser Doppler Vibrometer. The range of displacements induced by the device was compared to those of natural sound. Results: A 200 mV input to the device produced a range of displacements equivalent to those of sound at 70 dB sound pressure level (SPL; mean 0.44 nm; range 0.01‐2.80). A 400 mV input produced a range of displacements equivalent to those of sound at 80 dB SPL (mean 1.34 nm; range 0.02‐8.87). Conclusions: DHD, a small completely‐in‐the‐canal hearing aid prototype, is capable of actuating the TM through a ferromagnetic tympanostomy tube and producing range of displacements equivalent to moderate to severe levels of hearing loss.