gebhart/patrepeval huggingface dataset:
Targeting EB3–IP3R3 Interface with Cognate Peptide Protects from Acute Respiratory Distress Syndrome (2023)

Acute respiratory distress syndrome (ARDS) is a lung disease characterized by acute onset of noncardiogenic pulmonary edema, hypoxemia, and respiratory insufficiency. The current treatment for ARDS is mainly supportive in nature, providing a critical need for targeted pharmacological management. We addressed this medical problem by developing a pharmacological treatment for pulmonary vascular leakage, a culprit of alveolar damage and lung inflammation. Our novel therapeutic target is the microtubule accessory factor EB3 (end binding protein 3), which contributes to pulmonary vascular leakage by amplifying pathological calcium signaling in endothelial cells in response to inflammatory stimuli. EB3 interacts with IP<sub>3</sub>R3 (inositol 1,4,5-trisphosphate receptor 3) and orchestrates calcium release from endoplasmic reticulum stores. Here, we designed and tested the therapeutic benefits of a 14-aa peptide named CIPRI (cognate IP3 receptor inhibitor), which disrupted EB3-IP<sub>3</sub>R3 interaction <i>in vitro</i> and in lungs of mice challenged with endotoxin. Treatment with CIPRI or depletion of IP<sub>3</sub>R3 in lung microvascular endothelial monolayers mitigated calcium release from endoplasmic reticulum stores and prevented a disassembly of vascular endothelial cadherin junctions in response to the proinflammatory mediator α-thrombin. Furthermore, intravenous administration of CIPRI in mice mitigated inflammation-induced lung injury, blocked pulmonary microvascular leakage, prevented activation of NFAT (nuclear factor of activated T cells) signaling, and reduced production of proinflammatory cytokines in the lung tissue. CIPRI also improved survival of mice from endotoxemia and polymicrobial sepsis. Together, these data demonstrate that targeting EB3-IP<sub>3</sub>R3 interaction with a cognate peptide is a promising strategy to address hyperpermeability of microvessels in inflammatory lung diseases.
Flexible and modular 3D‐printed peptide models (2019)

A flexible and modular peptide modeling set was designed using freely available software tools. The set consists of space-filling models of all 20 naturally occurring amino acid side chains and a modular kit for constructing peptides employing C-alpha carbons and amide bond groups. Connectors that allow free rotation about phi and psi angles on the peptide, together with explicit representation of peptide backbone hydrogen bond donor and acceptors allows for the construction of a wide range of protein secondary structure motifs. The space-filling side chain models highlight the steric, acid-base, and polarity of these groups. These models were printed using relatively affordable commercially available fused filament fabrication printers with minimal postprinting processing. Use of these models in student group activities focused on amino acids and protein secondary structural features is described. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):432-437, 2019.
Comparative Effects of Selective Cyclooxygenase 1 and Cyclooxygenase 2 Inhibitors on Myeloperoxidase and 3α-Hydroxysteroid Dehydrogenase (1996)

The clinical efficacy of non-steroidal anti-inflammatory drugs (NSAIDs) is believed to result from the ability of these compounds to inhibit the inducible isoform of the enzyme cyclooxygenase, COX2. The gastrointestinal and renal side effects of these drugs, in contrast, are thought to relate to their ability to inhibit the constitutive isozyme, COX1. There is structural and pharmacological evidence that suggests that NSAIDs may also inhibit two unrelated enzymes, myeloperoxidase (MP) and 3 alpha-hydroxysteroid dehydrogenase (3 alpha-HSD), potentially with untoward consequences for the patient. Our laboratories have been investigating a new structural class of potential COX inhibitors, the tri-cyclic aromatics. In this study we have examined the inhibitory potency of selected compounds for the enzymes human COX1, human COX2, human MP, and rat liver 3 alpha-HSD. The compounds selected span a range of COX isoform selectivities, from specific for COX2 to selective for COX1 only, and include three representative tri-cyclic aromatics. We found that compounds within the tri-cyclic aromatic class do not act as potent inhibitors of either myeloperoxidase or 3 alpha-HSD. These results demonstrate the unique inhibitor selectivity that can be achieved with the tri-cyclic aromatics. Examples of COX1 selective, and COX2 selective inhibitors within this structural class are presented.
Light‐Addressable Nanocomposite Hydrogels Allow Plasmonic Actuation and In Situ Temperature Monitoring in 3D Cell Matrices (2021)

Abstract This paper reports a multifunctional platform based on a nanocomposite hydrogel combining poly(ethylene glycol), with rhodamine B‐containing silica nanoparticles (RhB@SiO 2 ), as temperature sensors, and gold nanorods (AuNRs) as plasmonic heaters. This composite material acts as a light‐addressable cellular matrix able to induce 3D temperature gradients locally and dynamically using the localized surface plasmon resonance (LSPR) of AuNRs under near‐infrared (NIR) laser illumination. At the same time, the temperature changes are probed locally by monitoring changes of the RhB@SiO 2 NPs fluorescence. As a result of plasmonic heating, and, depending on the preparation protocol, the light‐addressable hydrogel also deforms controllably and reversibly, allowing mechanical and thermal cellular stimulation in a 3D matrix. The hydrogel deformation is quantified by means of inline holographic microscopy. This approach makes it possible to accurately and locally control and simultaneously measure temperature gradients and deformation in soft, 3D deformable materials and will enable novel platforms for studying cellular thermo‐ and mechanobiology.
Preparation, Antigenicity, and Immunogenicity of Synthetic Ribosylribitol Phosphate Oligomer-Protein Conjugates and Their Potential Use for Vaccination against Haemophilus influenzae Type b Disease (1992)

Synthetically prepared ribosylribitol phosphate dimer and trimer analogous to fragments of the capsular polysaccharide of Haemophilus influenzae type b, containing either an amino- or a (masked) thiol-functionalized spacer, were conjugated to protein by two different methods. The thiol-containing carbohydrates were conjugated to tetanus toxoid or H. influenzae outer membrane protein using N-succinimidyl 3-(2-pyridyldithio)propionate. Glutaric dialdehyde was used to conjugate the amino-containing carbohydrates with tetanus toxoid. All conjugates were able to bind antibodies raised against the native bacterial polysaccharide, as determined by competition ELISA. The glutaric dialdehyde conjugate prepared from ribosylribitol phosphate trimer and tetanus toxoid induced a strong polysaccharide-specific antibody response in mice and rabbits.
Das Individuum als Konstrukt – Zum Stand der psychoanalytischen Gruppenarbeit am PSZ (2004)

Interview mit Georg Hess (He), Susanna Kretschmann (Kr) (beide SGAZ), Thomas von Salis (vSa), Andreas Sidler (Si) (beide AGOG)
Disparate effect of clomiphene and tamoxifen on pituitary gonadotropin release in vitro (1981)

The direct effects of clomiphene citrate (Clomid), tamoxifen, and estradiol (E2) on the gonadotropin-releasing hormone (GnRH)-stimulated release of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) were studied in cultured anterior pituitary cells obtained from adult ovariectomized rats. Treatment of pituitary cells with Clomid or enclomid (10(-8) M) in vitro for 2 days resulted in a marked sensitization of the gonadotroph to GnRH as reflected by a 6.5-fold decrease in the ED50 of GnRH in terms of LH release from 2.2 x 10(-9) M in untreated cells to 3.6 x 10(-10) M. Treatment with E2 or Clomid also increased the sensitivity of the gonadotroph to GnRH in terms of FSH release by 4.3- and 3.3-fold respectively. Tamoxifen, a related antiestrogen, comparable to Clomid in terms of its ability to compete with E2 for pituitary estrogen receptors, was without effect on the GnRH-stimulated LH release at a concentration of 10(-7) M. Furthermore, tamoxifen, unlike Clomid, caused an apparent but not statistically significant inhibition of the sensitizing effect of E2 on the GnRH-stimulated release of LH. Our findings suggest that Clomid and its Enclomid isomer, unlike tamoxifen, exert a direct estrogenic rather than an antiestrogenic effect on cultured pituitary cells by enhancing the GnRH-stimulated release of gonadotropin.
ChemInform Abstract: Synthesis of N‐Arylated Oxazolidinones via a Palladium‐Catalyzed Cross‐Coupling Reaction. Application to the Synthesis of the Antibacterial Agent Dup‐721. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Isolation and sequence analysis of a cDNA clone encoding a type‐1 protein phosphatase catalytic subunit: Homology with protein phosphatase 2A (1987)

A 1.5 kb clone containing the full-length coding sequence of a type-1 protein phosphatase catalytic subunit has been isolated from a rabbit skeletal muscle cDNA library constructed in lambda gt10. The protein sequence deduced from the cDNA contains 311 residues and has a molecular mass of 35.4 kDa. A single mRNA species at 1.6 kb was visualized by Northern blotting. The type-1 protein phosphatase was strikingly homologous to protein phosphatase 2A, 49% of the amino acids between residues 11 and 280 being identical. The first 10 and last 31 residues were dissimilar. Residues 1-101 of the type-1 protein phosphatase also showed 21% sequence identity with a region of mammalian alkaline phosphatases.
Effect of continuous infusion of pentagastrin on lower esophageal sphincter pressure and gastric acid secretion in normal subjects. (1975)

Bolus injections of gastrin or pentagastrin (PG) cause a marked elevation in lower esophageal sphincter pressure (LESP), and it has been suggested that serum gastrin concentration is the main physiological and pathophysiological regulator of LESP. We evaluated this hypothesis by measuring LESP and gastric acid secretion simultaneously in normal subjects during continuous infusion of PG (0.004-12 mjg/kg per h), since continuous infusion of a hormone probably simulates physiological hormone release better than bolus injection. In groups of 8-13 subjects there was no statistically significant increase in average LESP with any of seven PG infusion rates. However, a bolus of PG superimposed on the continuous infusion of PG resulted in a 20-mm Hg increase in LESP. Examination of results in individual subjects suggested that PG by infusion might be stimulating LESP in some subjects and inhibiting it in others. Therefore, individual dose-response studies were performed in two normal subjects. These revealed that 0.9 mug/kg per h PG by infusion elevated LESP by 10-12 mm Hg. This dose of PG also elicited maximal rates of gastric acid secretion. In one of the subjects an infusion of PG calculated to give one-half maximal acid secretion (D50) elevated LESP by 8 mm Hg; in the other the PG-D50 for acid secretion had no effect on sphincter pressure. Infusion of smaller amounts of PG had no effect on LESP, even though gastric acid secretion was stimulated submaximally. Thus, the parietal cells are more sensitive than the lower esophageal sphincter to the effect of PG by infusion. We conclude that PG by continuous infusion elevates LESP to only a modest degree (compared with the contraction that occurs after bolus injections of PG) and that the contraction occurs only within a narrow dose range between the D50 and D100 for acid secretion. Higher doses cause transient relaxation of LESP. Additional studies showed that basal LESP varied between 16 and 71 mm Hg in two subjects studied on 29 separate occasions, but there was no correlation with basal acid secretion. This suggests that the wide day-to-day fluctuations in basal LESP are not due to changing concentrations of gastrin in serum. The results of these experiments cast doubt on the hypothesis that serum gastrin concentration is the major determinant of LESP.
Modeling bacterial contamination of fuel ethanol fermentation (2009)

The emergence of antibiotic-resistant bacteria may limit the effectiveness of antibiotics to treat bacterial contamination in fuel ethanol plants, and therefore, new antibacterial intervention methods and tools to test their application are needed. Using shake-flask cultures of Saccharomyces cerevisiae grown on saccharified corn mash and strains of lactic acid bacteria isolated from a dry-grind ethanol facility, a simple model to simulate bacterial contamination and infection was developed. Challenging the model with 10(8) CFU/mL Lactobacillus fermentum decreased ethanol yield by 27% and increased residual glucose from 6.2 to 45.5 g/L. The magnitude of the effect was proportional to the initial bacterial load, with 10(5) CFU/mL L. fermentum still producing an 8% decrease in ethanol and a 3.2-fold increase in residual glucose. Infection was also dependent on the bacterial species used to challenge the fermentation, as neither L. delbrueckii ATCC 4797 nor L. amylovorus 0315-7B produced a significant decrease in ethanol when inoculated at a density of 10(8) CFU/mL. In the shake-flask model, treatment with 2 microg/mL virginiamycin mitigated the infection when challenged with a susceptible strain of L. fermentum (MIC for virginiamycin < or =2 ppm), but treatment was ineffective at treating infection by a resistant strain of L. fermentum (MIC = 16 ppm). The model may find application in developing new antibacterial agents and management practices for use in controlling contamination in the fuel ethanol industry.
The Effect of Tip Leakage Vortex for Operating Range Enhancement of Centrifugal Compressor (2013)

Recently, the application of turbochargers is increasing because they are effective in improving fuel consumption of engines. One of the most important turbocharger characteristics is compressor operating range, since it has been used in various driving patterns with the advent of variable geometry turbochargers. Owing to the complicated phenomena, such as rotating stall occurring at low flow rate condition, flow analysis is very difficult and details of flow structure have not been fully understood for a long time since the early 1970s. In this study, two compressors with different operating range width were investigated with experimental and computational flow analysis. In the compressor with narrow operating range, the amplitude of blade passing pressure fluctuation decreases rapidly and rotating stall occurs near surging. On the other hand, in the compressor with wide operating range, the blockage by the tip leakage vortex breakdown play a role in stabilizing the flow field and keeping up a high performance even at low flow rates.
ChemInform Abstract: Selective Protection of the C7 and C10 Hydroxyl Groups in 10‐Deacetyl Baccatin III (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
5.4.2 Quantification of Benzene in Groundwater Using SH-Surface Acoustic Wave Sensors (2012)

A need exists for compact sensor systems capable of in-situ monitoring of groundwater for fuel and oil contamination. The work reported here addresses this need using shear horizontal surface acoustic wave (SH-SAW) sensors, which function effectively in the liquid phase. To achieve enhanced sensitivity and partial selectivity for hydrocarbons, the devices are coated with thin chemically sensitive polymer films. Various polymer materials are investigated with the goal of identifying a set of coatings suitable for a sensor array. The system is tested with compounds indicative of fuel and oil contamination, in particular, BTEX (benzene, toluene, ethylbenzene and xylenes), at relatively low concentrations. Of particular importance is benzene, a known carcinogen. Using responses of the SHSAW sensor devices coated with three different polymer materials, benzene was quantified in the aqueous phase in the presence of other aromatic interferents. It is shown that various concentrations of BTEX in water can be identified and quantified by evaluation of both steady-state and transient response information.
Underwater optical communications with a modulating retro-reflector (2009)

Optical communication links using retro-reflectors underwater are investigated. In the retro-reflector geometry, backscattered light from turbid waters can interfere with the retro-reflected information signal. Presented here are polarization techniques to reduce the contribution of backscatter, as well as an evaluation on the impact of communication link range and reliability.
Low and high coverage determinations of the rate of carbon monoxide adsorption and desorption from Pt(110) (1980)

The adsorption probability of CO on Pt(110) was determined to be 0.7 by modulated beam (MBRS) and thermal desorption over a temperature range of 195 to 625 K. By MBRS the desorption rate constant, kd, was measured to be 6×1014 exp{−35.3 (kcal mol−1)/RT s−1} in the low coverage limit. This high value for the desorption pre-exponential factor was explained utilizing transition state theory. The low coverage value of kd was employed to calculate the thermal desorption spectrum, describing the adsorbed state by a one-dimensional Ising model. The repulsive interaction parameter which yielded the best fit was ω=1.5+2.5ϑ kcal mol−1.
Fourier Transforms Using Mathematica (2020)

"The Fourier transform is a ubiquitous tool used in most areas of engineering and physical sciences. The purposes of this book are two-fold: (1) to introduce the reader to the properties of Fourier transforms and their uses, and (2) to introduce the reader to the program Mathematica and demonstrate its use in Fourier analysis. Unlike many other introductory treatments of the Fourier transform, this treatment will focus from the start on both one-dimensional and two-dimensional transforms, the latter of which play an important role in optics and digital image processing, as well as in many other applications. It is hoped that by the time the reader has completed this book, he or she will have a basic understanding of Fourier analysis and Mathematica"--
InAs/GaAs quantum dot lasers on exact GaP/Si (001) and other templates (2017)

We demonstrate InAs quantum dot (QD) laser diodes epitaxially grown on exact (001) Si substrates by molecular beam epitaxy. Intentional 4-6 ° offcut substrates have been traditionally employed to avoid formations that stem from the interface between III-V and Si. However, offcut substrates are not fully compatible with the standard CMOS processing. In this work, we employed on-axis GaP/Si and V-groove Si substrates to enable high performance QD laser diodes with output power of more than ∼100 mW and continuous wave (CW) threshold current of ∼30 mA at room temperature (RT).
Hybrid dispersion compensating Raman amplifier module employing highly nonlinear fiber (2004)

Dispersion compensating Raman amplifier with reduced power consumption has been demonstrated employing a hybrid configuration comprising DCF and highly nonlinear fiber.
ChemInform Abstract: 1‐(TRIFLUOROMETHYL)ETHENYL PHENYL SELENIDE AND 1‐(TRIFLUOROMETHYL)ETHENYL PHENYL SULFIDE (1980)

Abstract Phenylselenyl‐ (Ia) und Phenylsulfenyl‐chlorid (Ib) reagieren mit dem Trifluormethylethylen (II) zu Addukten (III), die mit KOH die Olefine (IV) liefern.
“S-shaped” Photoluminescence Emission Shift in Cu(In, Ga)Se2 Thin Films (2012)

We have utilized photoluminescence (PL) measurement to investigate carrier recombination mechanism in Cu(In,Ga)Se2 thin films and observed an S-shaped emission shift revealed from the corresponding PL peak of near band edge transition.
Modeling users' mobility among WiFi access points (2005)

Modeling movements of users is important for simulating wireless networks, but current models often do not reflect real movements. Using real mobility traces, we can build a mobility model that reflects reality. In building a mobility model, it is important to note that while the number of handheld wireless devices is constantly increasing, laptops are still the majority in most cases. As a laptop is often disconnected from the network while a user is moving, it is not feasible to extract the exact path of the user from network messages. Thus, instead of modeling individual user's movements, we model movements in terms of the influx and outflux of users between access points (APs). We first counted the hourly visits to APs in the syslog messages recorded at APs. We found that the number of hourly visits has a periodic repetition of 24 hours. Based on this observation, we aggregated multiple days into a single day by adding the number of visits of the same hour in different days. We then clustered APs based on the different peak hour of visits. We found that this approach of clustering is effective; we ended up with four distinct clusters and a cluster of stable APs. We then computed the average arrival rate and the distribution of the daily arrivals for each cluster. Using a standard method (such as thinning) for generating non-homogeneous Poisson processes, synthetic traces can be generated from our model.
Strategies for Evaluation of Signaling Pathways and Transcription Factors Altered in Aging (2000)

Aging is characterized by an accumulation of oxidative injury to DNA, RNA, proteins, lipids, and carbohydrates. In addition to damage, oxidative stress can initiate cell signaling cascades that modulate cell function, growth, and death. Aging and two common age-related diseases, diabetes mellitus and atherosclerosis, may share common oxidant-related signaling pathways that lead to abnormal transcription factor activation and ultimately to cellular dysfunction, degeneration, or death. This review will focus on approaches to evaluate key redox-sensitive signaling pathways and the transcription factors altered by diabetes, atherosclerosis, and aging.
Inversion recovery cross-polarization NMR in solid semicrystalline polymers (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInversion recovery cross-polarization NMR in solid semicrystalline polymersD. G. Cory and W. M. RitcheyCite this: Macromolecules 1989, 22, 4, 1611–1615Publication Date (Print):April 1, 1989Publication History Published online1 May 2002Published inissue 1 April 1989https://pubs.acs.org/doi/10.1021/ma00194a018https://doi.org/10.1021/ma00194a018research-articleACS PublicationsRequest reuse permissionsArticle Views388Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts