gebhart/patrepeval huggingface dataset:
Hydrophobic interactions at subsite S1′ of human dipeptidyl peptidase IV contribute significantly to the inhibitory effect of tripeptides (2020)

Functional inhibitory peptides of human dipeptidyl peptidase 4 (hDPP4) have been highly anticipated as the active ingredient of functional food for type II diabetes; however, the molecular mechanism of hDPP4 inhibition remains unclear. In this study, we focused on dipeptides and tripeptides, which display structure-function correlations that are relatively easy to analyze, and examined their interactions with hDPP4 on an atomic level using a combination of docking studies and an hDPP4 inhibition assay. First, we performed comprehensive binding mode analysis of the dipeptide library and demonstrated that the formation of a tight interaction with the S1 subsite composing part of the substrate pocket is essential for dipeptides to compete with the substrate and strongly inhibit hDPP4. Next, we synthesized tripeptides by adding various amino acids to the C-terminus of Ile-Pro and Val-Pro, which have especially high inhibitory activity among compounds in the dipeptide library, and measured the hDPP4 inhibitory activity of the tripeptides. When hydrophobic amino acids (Ile, Met, Val, Trp) were added, the inhibitory activity increased several-fold. This phenomenon could be explained as follows: the C-terminal amino acid of the tripeptide formed hydrophobic interactions with Tyr547 and Trp629, which compose the S1' subsite located relatively outside the substrate pocket, thereby stabilizing the hDPP4-peptide binding. The structural information on the interaction between hDPP4 and peptide inhibitors attained in this study is anticipated to be useful in the development of a more potent hDPP4 competitive inhibitor.
A homing CRISPR mouse resource for barcoding and lineage tracing (2018)

Abstract Cellular barcoding using nuclease-induced genetic mutations is an effective approach that is emerging for recording biological information, including developmental lineages. We have previously introduced the homing CRISPR system as a promising methodology for generating such barcodes with scalable diversity and without crosstalk. Here, we present a mouse line (MARC1) with multiple genomically-integrated and heritable homing guide RNAs (hgRNAs). We determine the genomic locations of these hgRNAs, their activity profiles during gestation, and the diversity of their mutants. We apply the line for unique barcoding of mouse embryos and differential barcoding of embryonic tissues. We conclude that this mouse line can address the unique challenges associated with in vivo barcoding in mammalian model organisms and is thus an enabling platform for recording and lineage tracing applications in a mammalian model system.
Viscosity and concentration effects on charge transfer photochemistry. Tris(dibenzyldithiocarbamato)iron(III) (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTViscosity and concentration effects on charge transfer photochemistry. Tris(dibenzyldithiocarbamato)iron(III)Po-Hsin Liu and Jeffrey I. ZinkCite this: J. Am. Chem. Soc. 1977, 99, 7, 2155–2159Publication Date (Print):March 1, 1977Publication History Published online1 May 2002Published inissue 1 March 1977https://pubs.acs.org/doi/10.1021/ja00449a022https://doi.org/10.1021/ja00449a022research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations11LEARN 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
<title>Two-dimensional electron gas charge-coupled devices</title> (1991)

The two-dimensional electron gas charge-coupled device (2DEG-CCD) structure is an outgrowth of recent advances in 2DEG-FET structures for digital logic circuitry and microwave devices. The 2DEG-FET structures, which are known by severalacronyms such as HEMT, SDHT, TEGFET, HIGFET, and MODFET, utilize the abrupt heterointerface between two semiconductor materials and consequent conduction band discontinuity to confine electrons [1]. Due to confinement in the direction perpendicular to the interface, the resultant electron distribution is known as a two-dimensional electron gas. Because of the confinement dimensions and the low electron effective mass usually associated with group 111-V materials, quantum mechanics plays an important role in broadening the spatial electron distribution and defining allowed energy states. However, quantum effects typically play a minor role in understanding device behavior at temperatures above 77 K. 2DEG-FET devices have several attributes which include very high mobility of the channel charge (typically in excess of 5,000 cm2/V-sec at room temperature), high transconductance, and low voltage swing requirements. The 2DEG structure is attractive for CCD applications for several reasons. First, the high low-field mobility and use of a semi-insulating substrate suggest very high speed device operation. Second, the charge-handlin capabilty of the 2DEG-CCD structure is large compared with MESFET-type CCDs, and can exceed 1x101 carriers/cm2. Third, the lattice-matched heterointerface has a potentially lower interface trap density than the intrinsically mismatched silicon-silicon dioxide interface, as well as improved radiation hardness. Finally, the useful operating temperature of the 2DEG-CCD is expected to be lower than that of the silicon CCD. Other features of the 2DEG-CCD include fabrication compatibility with high-performance, low noise 2DEG-FET output circuitry and an anti-blooming gate structure.
Plasma and synovial fluid concentration of doxycycline following low‐dose, low‐frequency administration, and resultant inhibition of matrix metalloproteinase‐13 from interleukin‐stimulated equine synoviocytes (2013)

Low-dose orally administered doxycycline achieves SF concentrations in vivo capable of diminishing MMP-13 expression. This study supports the use of doxycycline as a disease modifying osteoarthritic drug.
Implementing Direct Electron Detection Camera K2 and Dose Fractionation for Near Atomic Resolution Single Particle CryoEM (2013)

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.
Thermal Fabrication of Magnetic Fe3O4 (Nanoparticle)@Carbon Sheets from Waste Resources for the Adsorption of Dyes: Kinetic, Equilibrium, and UV–Visible Spectroscopy Investigations (2023)

Thermal treatment is applied for the direct conversion of palm stalk waste to Fe<sub>3</sub>O<sub>4</sub> (np)@carbon sheets (Fe<sub>3</sub>O<sub>4</sub> (np)@CSs). The effect of conversion temperature was investigated. The TEM examination of the prepared magnetic Fe<sub>3</sub>O<sub>4</sub> (np)@CSs showed the formation of Fe<sub>3</sub>O<sub>4</sub> (np) in a matrix of carbon sheets as a coated layer with surface functional groups including carbonyl and hydroxyl groups. Removal of dyes such as methyl orange, methylene blue, and neutral red was achieved using fabricated Fe<sub>3</sub>O<sub>4</sub> (np)@CSs which were prepared at 250 °C, 400 °C, and 700 °C in a weak acidic medium. By studying the contact time effect for the adsorption of methylene blue, neutral red, and methyl orange, using the fabricated Fe<sub>3</sub>O<sub>4</sub> (np)@CSs which were prepared at 250 °C and 400 °C, equilibrium occurred between 120 min and 180 min. In addition, the first-order and second-order kinetic models were applied to the adsorption data. The results revealed that the adsorption data fit better with the second-order kinetic model. Furthermore, the Freundlich model was found to be more suitable for describing the process of the separation of the dyes onto Fe<sub>3</sub>O<sub>4</sub> (np)@CSs which were prepared at 250 °C and 400 °C, suggesting heterogenous surfaces and multi-layer adsorption.
Effects of the Humanized Anti-Adrenomedullin Antibody Adrecizumab (HAM8101) on Vascular Barrier Function and Survival in Rodent Models of Systemic Inflammation and Sepsis (2018)

Pretreatment with the humanized anti-ADM antibody HAM8101 improved vascular barrier function and survival in rodent models of systemic inflammation and sepsis.
The Swimsuit (2012)

<JATS1:p>The Swimsuit: Fashion from Poolside to Catwalk documents the modern swimsuit's trajectory from men's underwear and circus/performance wear to its unique niche in world fashion. It emphasizes the relationship between fashion, media, celebrity, sport and the cultivation of the modern body.</JATS1:p> <JATS1:p>This fascinating book provides an historical, sociological and cultural context in which to view how the swimsuit - and Australia, the country that significantly influenced its modern form - migrated from the cultural and colonial periphery to the centre of international attention. In addition, the book offers new perspectives on national histories of the swimsuit and investigates how traditional European fashion centers have opened up to new markets and modes of living, bringing together influences from around the globe.</JATS1:p> <JATS1:p>The Swimsuit is essential reading for students, scholars, and the general reader interested in fashion, popular culture, history, media, sport, and gender studies.</JATS1:p>
Experimental studies of photodynamic therapy in a retinoblastoma‐like tumour (1987)

Combination therapy with a purified hematoporphyrin derivative, Photofrin II, and red light (photodynamic therapy) was investigated in a retinoblastoma-like tumour growing in the eyes of rats in vivo and in cell cultures. There was a marked dose-response relationship between Photofrin II and the light energy both in vitro and in vivo. Up to 33% of the tumours could be controlled in vivo. In vivo/in vitro assays indicated Photofrin II uptake in the tumour cells in vivo in relation to the administered doses. Studies of cell death kinetics suggested that the mechanisms of photodynamic therapy were both a primary cell kill effect and a secondary tissue destruction, probably as a consequence of vascular damage.
A convergence scheme for over-erased flash EEPROM's using substrate-bias-enhanced hot electron injection (1995)

A novel convergence scheme using substrate-bias-enhanced hot electron injection is proposed to tighten the cell threshold voltage distribution after erasure for stacked gate flash EEPROM's. By lowering the drain voltage and increasing the magnitude of the negative substrate bias voltage, the substrate current is reduced but the hot electron gate current is enhanced significantly, and the convergence time is shown to be more than a hundred times shorter than the previous scheme. With the convergence operation performed near the ON-OFF transition region of the cells, the total drain current for all the converged cells is reduced and low power consumption is achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The [2,3] Sigmatropic Rearrangement of Sulfilimines from 3-Exomethylenecephams (1991)

-3-Exomethylenecepham sulfides react with phthalimidonitrene and the resulting sulfilimine undergoes a [2,3] sigmatropic rearrangement to give the 1,2,6-thiadiazepine azetidinone ring system
REAL-TIME WALKTHROUGH AURALISATION OF THE ACOUSTICS OF CHRIST CHURCH CATHEDRAL, DUBLIN (2023)

G Kearney Department of Theatre, Film and Television, University of York, United Kingdom M Gorzel Department of Electronic and Electrical Engineering, Trinity College Dublin, Ireland F Boland Department of Electronic and Electrical Engineering, Trinity College Dublin, Ireland F Smyth Urban Institute, University College Dublin, Ireland D Lennon Urban Institute, University College Dublin, Ireland H Rice Department of Mechanical and Manufacturing Engineering, Trinity College Dublin, Ireland
Engineering future light emitting diodes and photovoltaics with inexpensive materials:Integrating ZnO and Si into GaN-based devices (2013)

Indium Gallium Nitride (InGaN) based PV have the best fit to the solar spectrum of any alloy system and emerging LED lighting based on InGaN technology and has the potential to reduce energy consumption by nearly one half while enabling significant carbon emission reduction. However, getting the maximum benefit from GaN diode -based PV and LEDs will require wide-scale adoption. A key bottleneck for this is the device cost, which is currently dominated by the substrate (i.e. sapphire) and the epitaxy (i.e. GaN). This work investigates two schemes for reducing such costs. First, we investigated the integration of Zinc Oxide (ZnO) in InGaN-based diodes. (Successful growth of GaN on ZnO template layers (on sapphire) was illustrated. These templates can then be used as sacrificial release layers for chemical lift-off. Such an approach provides an alternative to laser lift-off for the transfer of GaN to substrates with a superior cost-performance profile, plus an added advantage of reclaiming the expensive single-crystal sapphire. It was also illustrated that substitution of low temperature n-type ZnO for n-GaN layers can combat indium leakage from InGaN quantum well active layers in inverted p-n junction structures. The ZnO overlayers can also double as transparent contacts with a nanostructured surface which enhances light in/out coupling. Thus ZnO was confirmed to be an effective GaN substitute which offers added flexibility in device design and can be used in order to simultaneously reduce the epitaxial cost and boost the device performance. Second, we investigated the use of GaN templates on patterned Silicon (100) substrates for reduced substrate cost LED applications. Controlled local metal organic chemical vapor deposition epitaxy of cubic phase GaN with on-axis Si(100) substrates was illustrated. Scanning electron microscopy and transmission electron microscopy techniques were used to investigate uniformity and examine the defect structure in the GaN. Our results suggest that groove structures are very promising for controlled local epitaxy of cubic phase GaN. Overall, it is concluded that there are significant opportunities for cost reduction in novel hybrid diodes based on ZnO-InGaN-Si hybridization.
Evolution of biogenic gases in peat blocks inferred from noninvasive dielectric permittivity measurements (2007)

Peatlands contain methanogenic archea responsible for generating significant amounts of free‐phase biogenic gases (for example, methane and carbon dioxide), but considerable uncertainty still exists regarding the mechanisms of formation and spatial distribution of these gases within the soil matrix. We demonstrate the effectiveness of a new method to record noninvasively the evolution, spatial distribution, and emission patterns of biogenic gases in a peat soil. A peat block (0.022 m 3 ) was extracted from a large freshwater peatland in Maine. The bulk dielectric permittivity (at 1.2 GHz) for multiple slices of the block was measured noninvasively (1) as temperature was increased 2°C d −1 from 5°C to 21°C, and (2) for a subsequent 2‐month period during which temperature was held constant at 21 ± 1°C. Methane emissions at the surface and peat surface deformation were monitored concurrently using a portable methane detector and a grid of surface elevation rods, respectively. Our results demonstrate that (1) the measurement of electromagnetic wave traveltimes across a peat block offers a unique (and more accurate when compared to surface deformation measurements) way to monitor gasdynamics and spatial gas distribution within a peat block without any disturbance to the natural gas regime; (2) the ebullition under our experimental conditions seems to preferentially occur from the near‐surface peat and shows some correspondence with changes in atmospheric pressure; and (3) the ebullition flux exhibits periodicity, suggesting that it may be predictable and quantifiable, which could assist climate modeling efforts. Our findings are consistent with previous studies based on gasdynamics in peat soils (including gas volumes and fluxes associated with biogenic gas ebullition).
Identification of Quinoline-Based RIP2 Kinase Inhibitors with an Improved Therapeutic Index to the hERG Ion Channel (2018)

RIP2 kinase was recently identified as a therapeutic target for a variety of autoimmune diseases. We have reported previously a selective 4-aminoquinoline-based RIP2 inhibitor <b>GSK583</b> and demonstrated its effectiveness in blocking downstream NOD2 signaling in cellular models, rodent in vivo models, and human ex vivo disease models. While this tool compound was valuable in validating the biological pathway, it suffered from activity at the hERG ion channel and a poor PK/PD profile thereby limiting progression of this analog. Herein, we detail our efforts to improve both this off-target liability as well as the PK/PD profile of this series of inhibitors through modulation of lipophilicity and strengthening hinge binding ability. These efforts have led to inhibitor <b>7</b>, which possesses high binding affinity for the ATP pocket of RIP2 (IC<sub>50</sub> = 1 nM) and inhibition of downstream cytokine production in human whole blood (IC<sub>50</sub> = 10 nM) with reduced hERG activity (14 μM).
Complement Activation and Organ Damage After Trauma—Differential Immune Response Based on Surgical Treatment Strategy (2020)

<b>Background:</b> The complement system is part of the innate immunity, is activated immediately after trauma and is associated with adult respiratory distress syndrome, acute lung injury, multiple organ failure, and with death of multiply injured patients. The aim of the study was to investigate the complement activation in multiply injured pigs as well as its effects on the heart <i>in vivo</i> and <i>in vitro</i>. Moreover, the impact of reamed vs. non-reamed intramedullary nailing was examined with regard to the complement activation after multiple trauma in pigs. <b>Materials and Methods:</b> Male pigs received multiple trauma, followed by femoral nailing with/without prior conventional reaming. Systemic complement hemolytic activity (CH-50 and AH-50) as well as the local cardiac expression of C3a receptor, C5a receptors1/2, and the deposition of the fragments C3b/iC3b/C3c was determined <i>in vivo</i> after trauma. Human cardiomyocytes were exposed to C3a or C5a and analyzed regarding calcium signaling and mitochondrial respiration. <b>Results:</b> Systemic complement activation increased within 6 h after trauma and was mediated via the classical and the alternative pathway. Furthermore, complement activation correlated with invasiveness of fracture treatment. The expression of receptors for complement activation were altered locally <i>in vivo</i> in left ventricles. C3a and C5a acted detrimentally on human cardiomyocytes by affecting their functionality and their mitochondrial respiration <i>in vitro</i>. <b>Conclusion:</b> After multiple trauma, an early activation of the complement system is triggered, affecting the heart <i>in vivo</i> as well as <i>in vitro</i>, leading to complement-induced cardiac dysfunction. The intensity of complement activation after multiple trauma might correlate with the invasiveness of fracture treatment. Reaming of the femoral canal might contribute to an enhanced "second hit" response after trauma. Consequently, the choice of fracture treatment might imply the clinical outcome of the critically injured patients and might be therefore crucial for their survival.
Introduction—The changing view of neurorehabilitation: A new era of optimism (2006)

Stroke is the leading health care problem requiring rehabilitation services today (CDC, 2001; Lee et al., 1996) with the worldwide incidence estimated to be between 300 and 500 per 100,000 people (Sudlow &amp; Warlow, 1997). In most recent years, the rates of mortality are decreasing, resulting in a significant increase in the number of survivors living with the disabilities/handicaps associated with stroke (Thorvaldsen et al., 1997). Not only is stroke a common health problem, but the cognitive disorders that result are common as well (Mayo, 1993; Paolucci et al., 1996).This article is based in part on a Presidential Address by the first author to the Annual meeting of the International Neuropsychological Society in Honolulu, Hawaii in February, 2002.
A critical appraisal of opportunities for wearable medical sensors (2005)

This paper provides an appraisal of the sensor requirements and prospects available for the growing field of wearable medical sensors. The results of a literature survey for various sensor use-models indicate that the design goals for each intended sensor application must focus on task specific criteria for ultimate sensor acceptance. Provided use-models include the examination of the relevant medical problems, the diagnostic utility of the available physiologic signals, and the impact of false alarms on the specific implementation area.
Radiation Exposure During Radiofrequency Catheter Ablation for Atrial Fibrillation (2003)

RF catheter ablation of paroxysmal atrial fibrillation (PAF) is associated with prolonged fluoroscopy. The procedural duration and fluoroscopic exposure to patients and medical staff were recorded and compared among 43 ablation procedures for PAF, 20 for common atrial flutter, and 16 for accessory pathways. Patient radiation exposure was measured by dosimeters placed over the xyphoid, while that of physicians and nurses was measured by dosimeters placed outside and inside the lead apron. The mean fluoroscopy time was 57 +/- 30 minutes for PAF, 20 +/- 10 minutes for common flutter, and 22 +/- 21 minutes for accessory pathway ablation. The patient median radiation exposure was 1110 microSv for PAF, compared with 500 microSv for common flutter and 560 microSv for accessory pathway ablation (P < 0.01). The median radiation exposure to physician and nurse inside the lead apron were, respectively, 2 microSv and 3 microSv for PAF, 1 microSv and 2 microSv for common flutter, and < 0.5 microSv and 3 microSv for accessory pathway ablations. RF catheter ablation for PAF was associated with prolonged fluoroscopy times and a twofold higher radiation exposure to the patient and physician compared with other ablation procedures. Assuming 300 procedures/year, radiation exposure to the medical staff was below the upper recommended annual dose limit.