gebhart/patrepeval huggingface dataset:
Immunocytochemical localisation of tenascin during the development of scleral papillae and scleral ossicles in the embryonic chick. (1988)

We have used a polyclonal antibody against tenascin (a 240 kDa extracellular matrix glycoprotein) and indirect immunofluorescence to investigate the distribution of tenascin in cryostat sections of the chick sclera during the six stages of scleral papilla development (Murray, 1943) and formation of membrane bone anlagen (mesenchymal condensations between 6-12 days of incubation - HH Stage 29-37). At Stages 1 and 2, when the papilla was a slight thickening in the conjunctival epithelium and mesenchymal condensation formation was initiated, tenascin was sparse in the sclera. At Stage 3, when the papilla had an epithelial mass intruding into the mesenchyme, there was an accumulation of tenascin fibrils along the subsurface of the papilla with fibrils extending from this region into the mesenchymal condensation. Interestingly, tenascin was sparse between papillae and between mesenchymal condensations. The Stage 4 papilla had a similar localisation of tenascin fibrils and in addition fine arborizing fibrils of tenascin were observed within the basal epithelia of the papilla adjacent to the epithelial-mesenchymal interface (which suggested that the fibrils infiltrated through the basement membrane region). The Stage 5 and 6 papillae had a column of vertical tenascin fibrils extending from the subsurface of the papilla to the interior mesenchyme corresponding exactly to the location of the mesenchymal condensation which was then forming the anlage of the ossicle in a flat bed about 100 microns from the conjunctival surface. The column of tenascin disappeared as the osteoid appeared in the ossicular bed on the 12th day of incubation but a dense accumulation of tenascin remained along the subsurface of the papilla. With the exception of tenascin fluorescence in the basal region of the Stage 4 papilla, tenascin fibrils were not observed in the other stages of papilla development in the epithelium covering areas between the mesenchymal condensation. This restricted distribution of tenascin may be important in the morphogenesis of scleral papillae and scleral ossicles.
Quantitative characterization of postnatal growth trends in proximal pulmonary arteries in rats by phase-contrast magnetic resonance imaging (2011)

Malformations of the pulmonary arteries can increase right heart workload and result in morbidity, heart failure, and death. With the increased use of murine models to study these malformations, there is a pressing need for an accurate and noninvasive experimental technique that is capable of characterizing pulmonary arterial hemodynamics in these animals. We describe the growth trends of pulmonary arteries in 13 male Sprague-Dawley rats at 20, 36, 52, 100, and 160 days of age with the introduction of phase-contrast MRI as such a technique. PCMRI results correlated closely with cardiac output measurements by ultrasound echocardiography and with fluorescent microspheres in right-left lung flow split (flow partition). Mean flow, average cross-sectional area, distensibility, and shear rates for the right and left pulmonary arteries (RPA and LPA) were calculated. The RPA was larger and received more flow at all times than the LPA (P < 0.0001). Right-left flow split did not change significantly with age, and arterial distensibility was not significantly different between RPA and LPA, except at 160 days (P < 0.01). Shear rates were much higher for the LPA than the RPA (P < 0.0001) throughout development. The RPA and LPA showed different structure-function relationships but obeyed similar allometric scaling laws, with scaling exponents comparable to those of the main pulmonary artery. This study is the first to quantitatively describe changes in RPA and LPA flows and sizes with development and to apply phase-contrast MRI techniques to pulmonary arteries in rats.
A distributed sensor system for detection of toxic and hazardous gases (2010)

This paper presents a distributed sensor system for the detection of toxic and hazardous gases like carbon monooxide (CO) and hydrogen (H<sub>2</sub>), respectively. The system is based on AlGaN/GaN heterostructures with floating gates as the catalytic absorption surfaces for the target gases. Due to the presence of 2-dimensional electron gas (2-DEG) at the heterointerface, AlGaN/GaN based High Electron Mobility Transistor (HEMT) and Metal- Oxide-Semiconductor HEMT (MOS-HEMT) is highly sensitive to any changes in the surface charge conditions. The individual sensor is made selective towards a specific target by the design of different gate structures. From the simulation results, it has been found that this type of high mobility field-effect devices can be applied to detect very low concentrations of gases with widely linear sensor characteristics. The modeled AlGaN/GaN HEMT with the Pt floating gate can detect hydrogen gas with the least concentrations at the sub-ppb level and with the linear current variations for ~ ppb to 100 ppm level of hydrogen. For the MOSHEMT structure, we simulated sub-ppm detection of CO with the linearity of responses near 1000 ppm.
Synthesis and Evaluation of Novel Radioligands for Positron Emission Tomography Imaging of Metabotropic Glutamate Receptor Subtype 1 (mGluR1) in Rodent Brain (2012)

We designed three novel positron emission tomography ligands, N-(4-(6-(isopropylamino)pyrimidin-4-yl)-1,3-thiazol-2-yl)-4-[(11)C]methoxy-N-methylbenzamide ([(11)C]6), 4-[(18)F]fluoroethoxy-N-[4-[6-(isopropylamino)pyrimidin-4-yl]-1,3-thiazol-2-yl]-N-methylbenzamide ([(18)F]7), and 4-[(18)F]fluoropropoxy-N-[4-[6-(isopropylamino)pyrimidin-4-yl]-1,3-thiazol-2-yl]-N-methylbenzamide ([(18)F]8), for imaging metabotropic glutamate receptor type 1 (mGluR1) in rodent brain. Unlabeled compound 6 was synthesized by benzoylation of 4-pyrimidinyl-2-methylaminothiazole 10, followed by reaction with isopropylamine. Removal of the methyl group in 6 gave phenol precursor 12 for radiosynthesis. Two fluoroalkoxy analogues 7 and 8 were prepared by reacting 12 with tosylates 13 and 14. Radioligands [(11)C]6, [(18)F]7, and [(18)F]8 were synthesized by O-[(11)C]methylation or [(18)F]fluoroalkylation of 12. Compound 6 showed high in vitro binding affinity for mGluR1, whereas 7 and 8 had weak affinity. Autoradiography using rat brain sections showed that [(11)C]6 binding is aligned with the reported distribution of mGluR1 with high specific binding in the cerebellum and thalamus. PET study with [(11)C]6 in rats showed high brain uptake and a similar distribution pattern to that in autoradiography, indicating the usefulness of [(11)C]6 for imaging brain mGluR1.
Phonon-tuned bright single-photon source (2014)

Pure and bright single photon sources have recently been obtained by inserting solid-state emitters in photonic nanowires or microcavities. The cavity approach presents the attractive possibility to greatly increase the source operation frequency. However, it is perceived as technologically demanding because the emitter resonance must match the cavity resonance. Here we show that the spectral matching requirement is actually strongly lifted by the intrinsic coupling of the emitter to its environment. A single photon source consisting of a single InGaAs quantum dot inserted in a micropillar cavity is studied. Phonon coupling results in a large Purcell effect even when the quantum dot is detuned from the cavity resonance. The phonon-assisted cavity enhanced emission is shown to be a good single-photon source, with a brightness exceeding $40$ \% for a detuning range covering 15 cavity linewidths.
Interaction of 5-bromocamphor with cytochrome P-450 cam. Production of 5-ketocamphor from a mixed spin state hemoprotein. (1981)

Camphor is stereospecifically hydroxylated by the soil bacterium Pseudomonas putida at the 5-exo position by a cytochrome P-450 mixed function oxidase system consisting of a flavoprotein reductase; putidaredoxin, an iron-sulfur oxidation-reduction transport-effector protein; and the P-450 hemoprotein. We have studied the interaction of a substrate analog of camphor, 5-exo-bromocamphor, with this cytochrome P-450 mixed function oxidase system in order to probe the molecular mechanisms of electron transport and catalytic substrate oxygenation. 5-exo-Bromocamphor was found to bind tightly in a 1:1 complex with P-450 with a dissociation constant of 2.9 microM, very near that for the normal camphor substrate. Contrary to camphor, however, the 5-exo-bromocamphor-bound material exhibits only a 46% population of the high spin form of the macromolecule. Measurement of the oxidation-reduction potential of the bromocamphor-P-450 complex yields a value of E0' = -246 mV, intermediate between that of substrate-free (-300 mV) and camphor-bound (-173 mV) cytochrome. These data are interpreted in terms of a thermodynamic linkage model relating spin, substrate, and oxidation-reduction equilibria in the P-450 monoxygenase system. 5-exo-Bromocamphor is readily metabolized by the P-450cam mixed function oxidase to 5-ketocamphor at rates and yields similar to that of the normal substrate, camphor, suggesting abstraction of the endo-hydrogen of 5-exo-bromocamphor and oxygen addition to produce a transient 5-bromo-5-hydroxycamphor intermediate. Implications of these chemical findings for the chemical mechanisms of P-450-catalyzed oxygenations and the flexibility of substrates at the active site of the macromolecule are discussed.
Transplantation of Neural Progenitor Cells Expressing Glial Cell Line-Derived Neurotrophic Factor into the Motor Cortex as a Strategy to Treat Amyotrophic Lateral Sclerosis (2018)

Early dysfunction of cortical motor neurons may underlie the initiation of amyotrophic lateral sclerosis (ALS). As such, the cortex represents a critical area of ALS research and a promising therapeutic target. In the current study, human cortical-derived neural progenitor cells engineered to secrete glial cell line-derived neurotrophic factor (GDNF) were transplanted into the SOD1<sup>G93A</sup> ALS rat cortex, where they migrated, matured into astrocytes, and released GDNF. This protected motor neurons, delayed disease pathology and extended survival of the animals. These same cells injected into the cortex of cynomolgus macaques survived and showed robust GDNF expression without adverse effects. Together this data suggests that introducing cortical astrocytes releasing GDNF represents a novel promising approach to treating ALS. Stem Cells 2018;36:1122-1131.
Persister Cells Form in the Plant Pathogen Xanthomonas citri subsp. citri under Different Stress Conditions (2021)

Citrus canker disease, caused by the bacterium <i>Xanthomonas citri</i> subsp. <i>citri</i> is a constant threat to citrus-producing areas. Since it has no cure, agricultural practices to restrain its dissemination are essential to reduce the economic damage. Hence, increased knowledge of the basic aspects of <i>X. citri</i> biology could lead to more efficient management practices that can eliminate dormant bacteria in the field. The dormant cells, also referred to as persisters, are phenotypic variants with lowered metabolism, which in turn leads to tolerance to antimicrobials and undermines existing control approaches. We show here that <i>X. citri</i> forms persisters, identifying triggers for this phenotype, including antibiotics, high temperature, and metals (copper and zinc), which increase persistence rates by 10-100 times. The antioxidant N-acetylcysteine reduced copper and zinc-induced persisters, but not those induced by tetracycline, indicating that oxidative stress may be an important inducer of <i>X. citri</i> persistence. In addition, we found that metabolism-independent drugs like cisplatin and mitomycin C are able to eliminate <i>X. citri</i> persistent cells, as well as copper, at high concentrations. Specific amino acids like proline and isoleucine interfered with the physiological balance of the dormancy in <i>X. citri</i>, stimulating or preventing persister resuscitation. Taken together, we discover chemicals that can induce, wake, and kill <i>X. citri</i> persister cells; these results provide insights that should be considered for more efficient integrated control management in the field.
L-NAC reverses of the adverse effects of fentanyl infusion on ventilation and blood-gas chemistry (2022)

There is an urgent need for development of drugs that are able to reverse the adverse effects of opioids on breathing and arterial blood-gas (ABG) chemistry while preserving opioid analgesia. The present study describes the effects of bolus injections of N-acetyl-L-cysteine (L-NAC, 500 μmol/kg, IV) on ventilatory parameters, ABG chemistry, Alveolar-arterial (A-a) gradient, sedation (righting reflex) and analgesia status (tail-flick latency assay) in unanesthetized adult male Sprague Dawley rats receiving a continuous infusion of fentanyl (1 μg/kg/min, IV). Fentanyl infusion elicited pronounced disturbances in (1) ventilatory parameters (e.g., decreases in frequency of breathing, tidal volume and minute ventilation), (2) ABG chemistry (decreases in pH, pO<sub>2</sub>, sO<sub>2</sub> with increases in pCO<sub>2</sub>), (3) A-a gradient (increases that were consistent with reduced alveolar gas exchange), and (4) sedation and analgesia. Bolus injections of L-NAC given 60 and 90 min after start of fentanyl infusion elicited rapid and sustained reversal of the deleterious effects of fentanyl infusion on ventilatory parameters and ABG chemistry, whereas they did not affect the sedative or analgesic effects of fentanyl. Systemic L-NAC is approved for human use, and thus our findings raise the possibility that this biologically active thiol may be an effective compound to combat opioid-induced respiratory depression in human subjects.
Supplementary Data Figure 4 from Functional Silencing of <i>HSD17B2</i> in Prostate Cancer Promotes Disease Progression (2023)

&lt;p&gt;Androgen stimulation has limited effect on HSD17B2 mRNA level.&lt;/p&gt;
Functional Expression of P‐Glycoprotein in an Immortalised Cell Line of Rat Brain Endothelial Cells, RBE4 (1996)

The presence of P-glycoprotein in the cell plasma membrane limits the penetration of many cytotoxic substances into cells that express the gene product. There is considerable evidence also to indicate that P-glycoprotein is expressed as part of the normal blood-brain barrier in the luminal membranes of the cerebral capillary endothelial cells, where it presumably performs a protective function for the brain. This report describes the functional expression of P-glycoprotein in an immortalised cell line, RBE4, derived from rat cerebral capillary endothelial cells. The expression of P-glycoprotein is demonstrated by western immunoblotting and by immunogold and fluorescent staining with monoclonal antibodies. The cellular accumulation of [3H]colchicine and [3H]-vinblastine is investigated and shown to be enhanced by the presence of azidothymidine, chlorpromazine, verapamil, cyclosporin A, and PSC 833 ([3'-keto-Bmt1]-[Val2]-cyclosporin) at 50 or 100 microM concentration. It is concluded that the RBE4 cell line is a valuable tool for investigating the mechanisms of P-glycoprotein activity both in the blood-brain barrier and in multidrug resistance in general.
Protein secondary structure and solvent accessibility of proteins in decellularized heart valve scaffolds (2012)

Decellularized heart valve scaffolds can be used for pulmonary heart valve replacements in heart surgery. In order to assess quality parameters of heart valves prior to implantation into patients various techniques can be applied, including ultrastructural evaluation and biomechanical testing. Fourier transform infrared spectroscopy (FTIR) was used here to study protein secondary structure and solvent accessibility in decellularized heart valve matrices. FTIR was used to study proteins in the three main types of structures in decellularized heart valves: leaflet, pulmonary artery wall and heart muscle. The amide-I band region was used to reveal differences in the overall protein secondary structure amongst tissues. Leaflet material contains a relatively high contribution of α-helical structures, whereas artery matrix contains a relatively high content of triple-helix and β-sheet structures. Solvent accessibility of tissue proteins was studied by exposing material to D 2 O. The exchange of hydrogen of the NH amide-II bond for deuterium originating from D 2 O was visible as an increase in the area of the amide-II band (1500–1400 cm −1 ). The amide-I band also depicted changes in shape and position during incubation in D 2 O: a low frequency band at around 1625 cm −1 increased as a function of time. Remarkable differences in hydrogen-to-deuterium exchange kinetics and protein solvent accessibility were observed among the three types of heart valve matrices: proteins in artery matrix are highly accessible to solvent, whereas proteins in leaflet and heart muscle structures are relatively inaccessible to solvent and show slow hydrogen/deuterium exchange. The differences in protein solvent accessibility in the different types of matrices likely reflect differences in scaffold porosity.
Combined Effect of Salt Water and High‐Temperature Exposure on the Strength Retention of Nextel ™ 720 Fibers and Nextel ™ 720‐Aluminosilicate Composites (2006)

The relative contribution of fiber strength loss to reported degradation in the mechanical behavior of Nextel ™ 720‐aluminosilicate composites after exposure to salt fog (ASTM B117) was explored. Single filament tension tests were performed on Nextel ™ 720 (3M, Inc., Minneapolis, MN) fibers after immersion in NaCl solutions followed by high‐temperature exposure in air. The results were compared with the behavior of control specimens which received high‐temperature exposure but were not immersed in NaCl solution. There was no degradation in fiber strengths for NaCl solutions below 1 wt%. However, significant degradation was observed at 5 wt% NaCl upon exposure to temperatures between 900° and 1150°C, while no degradation was observed upon an exposure to 1200°C. The relative contribution of fiber strength loss to composite degradation was estimated as nearly 50%, indicating that both fibers and matrix/interface degrade from exposure to salt water. X‐ray diffraction and transmission electron microscopy of the exposed fibers and composites were conducted to help rationalize the observations. Microstructure of degraded fibers showed presence of Na at grain boundaries near the surface, without any evidence of a crystalline phase, indicating weakening from segregation or formation of an amorphous phase. The degraded composites showed that matrix and fiber/matrix interfaces had Na rich regions/phases.
AIMS-45 image validation of contact hole patterns after inverse lithography at NA 1.35 (2008)

The AIMS<sup>TM</sup>-45, when used in scanner mode, can emulate image intensity as seen in resist on the wafer at scanner illumination conditions. We show that this feature makes AIMS<sup>TM</sup>-45 well-suited to analyze patterns treated with inverse lithography. We have used an inverse lithography technique by Mentor Graphics, to treat a random contact hole layout (drawn at minimal pitch 115nm) for imaging at NA 1.35. The combination of the dense 115nm pitch and available NA of 1.35 makes Quasar illumination necessary, and the inverse lithography treatment automatically generated optimal (model-based) Assist Features (AF) for all geometries in the design. The mask, after inverse lithography treatment, has CH patterns with numerous AF of different sizes and orientations, and is a challenge for both mask making and mask qualification. We have analyzed the inverse lithography masks with the model-based AF using an AIMS<sup>TM</sup>-45 aerial image measurement tool, and compare the results of the AIMS<sup>TM</sup>-45 to wafer data obtained after exposure on an ASML XT:1900i. A first benefit of AIM<sup>TM</sup>-45 is that the most meaningful quantity (image in resist) is generated without the intermediate steps of doing multiple reticle SEM measurements followed by extensive simulation. A second point of interest is that the AIMS<sup>TM</sup>-45 generates image intensities, which allows a direct validation of the intensity-driven inverse litho conversion. Both features prove the value of the AIMS<sup>TM</sup>-45 for analyzing inverse litho masks and geometries.
Scaling Anomaly Detection Service Using Serverless Technology (2021)

This poster paper presents an efficient design of deploying anomaly detection service using serverless technology. Our design is motivated by the fact that the workload originating from the service calls are adhoc and reserving the infrastructure upfront is not advisable. To address this, we utilized the emerging serverless platform for executing the incoming training request. Our extensive experimental analysis demonstrate the usefulness of the proposed idea.
Severe head injury in the United Kingdom and Ireland (1996)

We conclude that there are wide variations in the management of the severely head-injured patient in the UK and Ireland. Some of the therapies employed are not supported by available research findings. Rationalization (using rational management, i.e., based on good evidence) of the intensive care management of severe head injury with the development of widely accepted guidelines may result in an improvement in the quality of care of the head-injured patient.
56-Gb/s Silicon Optical Receiver Using a Low-Noise Fully-Differential Transimpedance Amplifier in SiGe SiCMOS (2018)

We present a silicon optical receiver consisting of a low-noise fully-differential transimpedance amplifier with on-chip biasing for a SiPh Ge PD. Error-free 56Gb/s NRZ operation is demonstrated with a record OMA sensitivity of -10.2dBm at 170mW.
Host Proteins Identified in Extracellular Viral Particles as Targets for Broad-Spectrum Antiviral Inhibitors (2018)

Liquid chromatography mass spectrometry (LCMS) proteomic analyses have revealed that host proteins are often captured in extracellular virions. These proteins may play a role in viral replication or infectivity and can represent targets for broad-spectrum antiviral agent development. We utilized LCMS to determine the host protein composition of Lassa virus-like particles (LASV VLPs). Multiple host proteins incorporated in LASV VLPs are also incorporated in unrelated viruses, notably ribosomal proteins. We assembled a data set of host proteins incorporated into extracellular viral particles. The frequent incorporation of specific host proteins into viruses of diverse families suggests that interactions of these proteins with viral factors may be important for effective viral replication. Drugs that target virion-associated host proteins could affect the protein in the extracellular virion or the host cell. Compounds that target proteins incorporated into virions with high frequency, but with no known antiviral activity, were assayed in a scalable viral screening platform, and hits were tested in competent viral systems. One of these molecules, GAPDH modulating small molecule CGP 3466B maleate (Omigapil), exhibited a dose-dependent inhibition of HIV, dengue virus, and Zika virus.