gebhart/patrepeval huggingface dataset:
Surface association induces cytotoxic alkyl-quinolones in Pseudomonas aeruginosa (2019)

Abstract Surface attachment, an early step in the colonization of multiple host environments, activates the virulence of the human pathogen P. aeruginosa . However, the signaling pathways and downstream toxins specifically induced by surface association to stimulate P. aeruginosa virulence are not fully understood. Here, we demonstrate that alkyl-quinolone (AQ) secondary metabolites are rapidly induced upon surface association and represent a major class of surface-dependent cytotoxins. AQ cytotoxicity is direct and independent of other AQ functions like quorum sensing or PQS-specific activities like iron sequestration. Furthermore, the regulation of AQ production can explain the surface-dependent virulence regulation of the quorum sensing receptor, LasR, and the pilin-associated candidate mechanosensor, PilY1. PilY1 regulates surface-induced AQ production by repressing the AlgR-AlgZ two-component system. AQs also contribute to the known cytotoxicity of secreted outer membrane vesicles. These findings collectively explain previously mysterious aspects of virulence regulation and provide new avenues for the development of anti-infectives.
On-demand rendering of an oblique slice through 3D volumetric data using JPEG2000 client-server framework (2006)

In medical imaging, the popularity of image capture modalities such as multislice CT and MRI is resulting in an exponential increase in the amount of volumetric data that needs to be archived and transmitted. At the same time, the increased data is taxing the interpretation capabilities of radiologists. One of the workflow strategies recommended for radiologists to overcome the data overload is the use of volumetric navigation. This allows the radiologist to seek a series of oblique slices through the data. However, it might be inconvenient for a radiologist to wait until all the slices are transferred from the PACS server to a client, such as a diagnostic workstation. To overcome this problem, we propose a client-server architecture based on JPEG2000 and JPEG2000 Interactive Protocol (JPIP) for rendering oblique slices through 3D volumetric data stored remotely at a server. The client uses the JPIP protocol for obtaining JPEG2000 compressed data from the server on an <i>as needed </i>basis. In JPEG2000, the image pixels are wavelet-transformed and the wavelet coefficients are grouped into precincts. Based on the positioning of the oblique slice, compressed data from only certain precincts is needed to render the slice. The client communicates this information to the server so that the server can transmit only relevant compressed data. We also discuss the use of caching on the client side for further reduction in bandwidth requirements. Finally, we present simulation results to quantify the bandwidth savings for rendering a series of oblique slices.
A Cholecystokinin Receptor Antagonist Halts Nonalcoholic Steatohepatitis and Prevents Hepatocellular Carcinoma (2019)

These results support the novel role of CCK receptors in the pathogenesis of NASH and HCC.
Upconverting reporters: Properties and biomedical applications (2004)

Upconverting reporters are excited in the infrared and emit visible radiation. There are two classes of these materials: upconverting phosphors and upconverting chelates. Significant properties of upconverting reporters include no background from autofluorescence, no photobleaching, and no interference from conventional reporters.
Acoustically Active Lipospheres Containing Paclitaxel (1998)

Acoustically active lipospheres represent a new class of acoustically active drug delivery vehicles. Future studies will assess efficacy of AALs for ultrasound-mediated drug delivery.
Effect of aging on response time of nuclear plant pressure sensors (1989)

A research program was initiated to study the effects of normal aging on the dynamic performance of safety-related pressure transmitters in nuclear power plants. The project began with an experimental assessment of the conventional and new testing methods for measurement of response time of pressure transmitters. This was followed by developing a laboratory set up and performing initial tests to study the aging characteristics of representative transmitters of the type used in power plants. The project also included a search of the LER data base for pressure sensing system, problems and a review of the Regulatory Guide 1.118 and the industry standards on performance testing of pressure transmitters. The work reported herein was a feasibility study performed over a six-month period. As such, the results and conclusions presented herein are preliminary. 15 refs., 44 figs., 25 tabs.
Degradation and biocompatibility of photoembossed PLGA–acrylate blend for improved cell adhesion (2016)

We have shown previously that PMMA-acrylate photopolymers are biocomopatible and can exhibit improved cell adhesion compared to PMMA, due to an increase in negative surface charge caused by UV radiation PLGA has been used widely in soft tissue regeneration due to its high biocompatibility and cell adhesion. This polymer is also biodegradable and can be utilised in the field of vascular regeneration. In this study, PLGA is blended with a triacrylate monomer (TPETA) to create a degradable photopolymer blend. Surface relief structures are formed on this PLGA-TPETA by photoembossing. An optimum height of 950 nm was achieved for a 10 µm pitch with the height of these relief structures being controlled by changing UV intensity, processing temperature and time. Degradation studies of this blend revealed a bulk degradation mechanism with PLGA-TPETA degrading slower compared to pure PLGA. We also evaluated the adhesion of human umbilical vein endothelial cells (HUVECs) on both smooth and textured PLGA-TPETA films. Embossed PLGA-TPETA films showed improved cell adhesion compared to smooth substrates. Furthermore, HUVECs proliferated faster on the embossed surface compared to their smooth counterparts. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 163-171, 2018.
The SARS-CoV-2 Conserved Macrodomain Is a Mono-ADP-Ribosylhydrolase (2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-related CoVs encode 3 tandem macrodomains within nonstructural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated antiviral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Here, we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose. SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) Mac1 domains exhibit similar structural folds, and all 3 proteins bound to ADP-ribose with affinities in the low micromolar range. Importantly, using ADP-ribose-detecting binding reagents in both a gel-based assay and novel enzyme-linked immunosorbent assays (ELISAs), we demonstrated de-MARylating activity for all 3 CoV Mac1 proteins, with the SARS-CoV-2 Mac1 protein leading to a more rapid loss of substrate than the others. In addition, none of these enzymes could hydrolyze poly-ADP-ribose. We conclude that the SARS-CoV-2 and other CoV Mac1 proteins are MAR-hydrolases with similar functions, indicating that compounds targeting CoV Mac1 proteins may have broad anti-CoV activity.<b>IMPORTANCE</b> SARS-CoV-2 has recently emerged into the human population and has led to a worldwide pandemic of COVID-19 that has caused more than 1.2 million deaths worldwide. With no currently approved treatments, novel therapeutic strategies are desperately needed. All coronaviruses encode a highly conserved macrodomain (Mac1) that binds to and removes ADP-ribose adducts from proteins in a dynamic posttranslational process that is increasingly being recognized as an important factor that regulates viral infection. The macrodomain is essential for CoV pathogenesis and may be a novel therapeutic target. Thus, understanding its biochemistry and enzyme activity are critical first steps for these efforts. Here, we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose and describe its ADP-ribose binding and hydrolysis activities in direct comparison to those of SARS-CoV and MERS-CoV Mac1 proteins. These results are an important first step for the design and testing of potential therapies targeting this unique protein domain.
Excited-State Mixed Valence in Transition Metal Complexes (2006)

Mixed valence in the lowest-energy metal-to-ligand charge-transfer excited state of di-(4-acetylpyridine)tetraammineruthenium(II) complexes is defined and analyzed. The excited state has two interchangeably equivalent ligands with different oxidation states. The electronic absorption band energies, selection rules, and bandwidths are analyzed quantitatively in terms of the signs and orientations of the transition dipole moments, sign and magnitude of the coupling, and resonance Raman analysis of displaced normal modes.
Granular cell tumor of colon: Report of a case and review of literature (2004)

Granular cell tumor (GCT) is uncommon in the colon and rectum. Here we report a case of GCT in the transverse colon. A 48-year-old male patient underwent a screening colonoscopy. A yellowish sessile lesion, about 4 mm in diameter, was found in the transverse colon. An endoscopic snare resection was performed without complication. Histological examination revealed the tumor consisted of plump neoplastic cells with abundant granular eosinophilic cytoplasm containing acidophilic periodic acid Schiff-positive, diastase-resistant granules. Immunohistochemical analysis showed the tumor cells expressed S-100 protein and neuron-specific enolase. Thus, the resected tumor was diagnosed as a GCT. Since GCTs are usually benign, endoscopic resection constitutes an easy and safe treatment. Colonoscopists should consider the possibility of GCT in the differential diagnosis of submucosal tumors of the colon.
An innovative course emphasizing real-time digital signal processing applications (1996)

This paper presents an innovative undergraduate real-time digital signal processing (DSP) course, Digital Signal Processors, which emphases hands-on experiments and practical applications. It enables students to experiment with sophisticated DSP applications to augment the theoretical, conceptual, and analytical material provided in their first DSP course, Digital Filter Design. The inclusion of both software and hardware developmental experiences permits undergraduates to undertake a wide range of real-time DSP projects in their required Senior Engineering Design course. This paper briefly introduces representative examples of some challenging DSP applications, such as acoustic echo cancellation, active noise control, and image compression.
EPCO-08. CONSERVED FEATURES OF TERT PROMOTER DUPLICATIONS REVEAL AN ACTIVATION MECHANISM THAT MIMICS HOTSPOT MUTATIONS IN CANCER (2022)

Abstract Mutations in the TERT promoter are the single most common non-coding mutation in cancer and represent the genetic underpinnings of tumor cell immortality. Beyond the two most common point mutations, G228A and G250A, which selectively recruit the ETS factor GABP to activate TERT, the significance of other variants in the TERT promoter are unknown. We identified duplications of wildtype sequence within the core promoter region of TERT in 7 different cancer types that have strikingly similar features including size, insertion position, and inclusion of one of the native ETS motifs. Each duplication activates the TERT promoter to a similar level as G228A and G250A and is critically dependent on the insertion site. The GABP tetramer binds to the TERT duplicated promoter sequence by virtue of the native ETS motif and its duplicated version with precise spacing, and it is necessary for the transcriptional activation by all duplications tested. Spatiotemporal analysis in a multifocal glioblastoma shows the duplication is clonal and its activation of TERT is readily detectable at the single cell level and in bulk tumor tissue. We conclude that recurrent TERT promoter duplications of the native ETS sequence are functionally and mechanistically equivalent to the hotspot mutations that confer tumor cell immortality. The shared mechanism of these divergent somatic genetic alterations suggests a strong selective pressure for recruitment of the GABP tetramer to activate TERT.
Preparation and characterization of Cu(In1−xGax)3Se5 thin films (1995)

Polycrystalline Cu(In1−xGax)3Se5 thin films were prepared by four source evaporation with controlling and shielding of the molecular beams from elemental sources. Ga content x, can be controlled by deposition times of CuIn3Se5 and CuGa3Se5 layers, which form Cu(In1−xGax)3Se5 films through the interdiffusion. X-ray diffraction analyses showed that the films with x≲0.5 have an ordered vacancy chalcopyrite and the films with x≳0.5 have a zinc blende structure. The optical band gap of the films linearly increased from 1.23 eV (x=0) to 1.85 eV (x=1) with increasing Ga content. The conductivity of the films was about 10−6/Ω cm and about 10−7/Ω cm under and above x=0.3, respectively.
Improving light output of blue light-emitting diodes by photonic crystal of epitaxially-grown zinc oxide (2011)

To improve light output in blue light-emitting diode, photonic crystal (PhC) is fabricated by a wet epitaxial growth of zinc oxide (ZnO) rods. The fabricated PhC enhances light output by 1.4 times as designed, indicating that the wet-grown ZnO exhibits the excellent optical and structural quality for PhC.
A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation (2013)

Using meta-analysis of eight independent transplant datasets (236 graft biopsy samples) from four organs, we identified a common rejection module (CRM) consisting of 11 genes that were significantly overexpressed in acute rejection (AR) across all transplanted organs. The CRM genes could diagnose AR with high specificity and sensitivity in three additional independent cohorts (794 samples). In another two independent cohorts (151 renal transplant biopsies), the CRM genes correlated with the extent of graft injury and predicted future injury to a graft using protocol biopsies. Inferred drug mechanisms from the literature suggested that two FDA-approved drugs (atorvastatin and dasatinib), approved for nontransplant indications, could regulate specific CRM genes and reduce the number of graft-infiltrating cells during AR. We treated mice with HLA-mismatched mouse cardiac transplant with atorvastatin and dasatinib and showed reduction of the CRM genes, significant reduction of graft-infiltrating cells, and extended graft survival. We further validated the beneficial effect of atorvastatin on graft survival by retrospective analysis of electronic medical records of a single-center cohort of 2,515 renal transplant patients followed for up to 22 yr. In conclusion, we identified a CRM in transplantation that provides new opportunities for diagnosis, drug repositioning, and rational drug design.
Les villes comme tissu social : fragmentation et intégration. Introduction au débat (2005)

Spire est le dépôt institutionnel de la production scientifique de Sciences Po et contient le texte intégral des articles, ouvrages, chapitres d’ouvrages, working papers et communications dans des conférences de la communauté académique de Sciences Po.
Graduate Biomedical Science Education Needs a New Philosophy (2017)

There is a growing realization that graduate education in the biomedical sciences is successful at teaching students how to conduct research but falls short in preparing them for a diverse job market, communicating with the public, and remaining versatile scientists throughout their careers. Major problems with graduate level education today include overspecialization in a narrow area of science without a proper grounding in essential critical thinking skills. Shortcomings in education may also contribute to some of the problems of the biomedical sciences, such as poor reproducibility, shoddy literature, and the rise in retracted publications. The challenge is to modify graduate programs such that they continue to generate individuals capable of conducting deep research while at the same time producing more broadly trained scientists without lengthening the time to a degree. Here we describe our first experiences at Johns Hopkins and propose a manifesto for reforming graduate science education.
5 450 000 000 and rising (1992)

Journal Article 5 450 000 000 and rising Get access Henry J. Leese Henry J. Leese Department of Biology, University of YorkYork YO1 5DD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Reproduction, Volume 7, Issue 9, 1 October 1992, Page 1185, https://doi.org/10.1093/oxfordjournals.humrep.a137822 Published: 01 October 1992
The Mini-Modified Orbitozygomatic and Supraorbital Approaches Anatomical Comparison (2018)

Seven sides of cadaver heads were used to compare the surgical exposures provided by the mini-modified orbitozygomatic (MOz) and supraorbital (SO) approaches. The Optotrak 3020 computerized tracking system (Northern Digital, Waterloo, ON, Canada) was utilized to evaluate the area of anatomical exposure defined by six points: (1) ipsilateral sphenoid ridge; (2) most distal point of the ipsilateral middle cerebral artery (MCA); (3) most distal point of the ipsilateral posterior cerebral artery (PCA); (4) most distal point of the contralateral PCA; (5) most distal point of the contralateral MCA; and (6) contralateral sphenoid ridge. Additionally, angles of approach for the ipsilateral MCA bifurcation, ipsilateral ICA bifurcation, basilar artery tip, contralateral MCA and ICA bifurcation and anterior communicating artery (AcomA) were evaluated, first for SO and then for MOz. An image guidance system was used to evaluate the limits of surgical exposure. No differences in the area of surgical exposure were noted (p > 0.05). Vertical angles were significantly wider for the ipsilateral and contralateral ICA bifurcation, AcomA, contralateral MCA and basilar tip (p < 0.05) for MOz. No differences in horizontal angles were observed between the approaches for the six targets (p > 0.05). There were no differences in the limits of exposure. MOz affords no additional surgical working space. However, our results demonstrate systematically that vertical exposure is improved. The MOz should be performed while planning an approach to these regions and a wider exposure in the vertical axis is needed.
Purification and characterisation of a new hypothalamic satiety peptide, cocaine and amphetamine regulated transcript (CART), produced in yeast (1998)

Cocaine and amphetamine regulated transcript (CART) is a newly discovered hypothalamic peptide with a potent appetite suppressing activity following intracerebroventricular administration. When the mature rat CART sequence encoding CART(1-102) was inserted in the yeast expression plasmid three CART peptides could be purified from the fermentation broth reflecting processing at dibasic sequences. None of these corresponded to the naturally occurring CART(55-102). In order to obtain CART(55-102) the precursor Glu-Glu-Ile-Asp-CART(55-102) has been produced and CART(55-102) was generated by digestion of the precursor with dipeptidylaminopeptidase-1. All four generated CART peptides have been characterised by N-terminal amino acid sequencing and mass spectrometry. The CART peptides contain six cysteine residues and using the yeast expressed CART(62-102) the disulphide bond configuration was found to be I-III, II-V and IV-VI. When the four CART peptides were intracerebroventricularly injected in fasted mice (0.1 to 2.0 microg) they all produced a dose dependent inhibition of food intake.
Photoinduced Electron and Energy Transfer Processes in a Bichromophoric Pyrene−Perylene Bisimide System (2004)

The synthesis and photophysical properties of a system consisting of a bay-functionalized perylene bisimide, containing four appended pyrene and two coordinating pyridine units, and its reference system are described. A complete study of their photophysical properties was obtained using UV−vis absorption, steady state and time-resolved emission, and femtosecond transient absorption. Analysis of the data, obtained from time-resolved emission and femtosecond transient absorption spectroscopy, showed the presence of both photoinduced electron and energy transfer processes. A high yield (>90%) and fast photoinduced energy transfer (ken ≈ 6.2 × 109 s-1) is followed by efficient electron transfer (70%, ket ≈ 6.6 × 109 s-1) from the pyrene units to the perylene bisimide moiety. The energy donor−acceptor distance, R = 8.6 Å, is calculated from the experimental energy transfer rate using Förster theory. Temperature-dependent time-resolved emission spectroscopy showed an increase of the acceptor emission lifetime with decreasing temperature. It also indicates the presence of different conformations because two different electron transfer barriers (0.08 and 0.42 eV) were found. These barrier values were corroborated by a theoretical analysis of the energetics of the process using Marcus theory, indicating average donor−acceptor distances of 4.5 Å (room temperature) to 11 Å (at low T).
Dimerization of Terminal Alkynes Catalyzed by a Nickel Complex Having a Bulky Phosphine Ligand. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Stereohaptics (2016)

With a recent rise in the availability of affordable head mounted gear sets, various sensory stimulations (e.g., visual, auditory and haptics) are integrated to provide seamlessly embodied virtual experience in areas such as education, entertainment, therapy and social interactions. Currently, there is an abundance of available toolkits and application programming interfaces (APIs) for generating the visual and audio content. However, such richness in hardware technologies and software tools is missing in designing haptic experiences. Current solutions to integrate haptic effects are limited due to: i) a user's rigid adaptation to new hardware and software technologies, ii) limited scalability of the existing tools to incorporate haptic hardware and applications, iii) inflexible authoring capabilities, iv) missing infrastructure for storing, playback and distribution, and v) and unreliable hardware for long term usage.
Elastic Anisotropy from Walkaway VSP and Sonic Data Recorded in the North Sea (2018)

Summary The Hejre oil and gas field is located in the Danish Central Graben, a shallow water part of the central North Sea. The reservoir lies at depths below 5 km in a high-temperature (172°C) and high-pressure (1 kbar) environment. Seismic resolution is relatively poor due to absorption in the overburden, multiples and distortion from a complex structure. Anisotropic depth processing improved the seismic quality but the anisotropy uncertainty remained high. In order to measure elastic anisotropy in-situ, reduce the velocity model uncertainties and allow improvements in anisotropic surface seismic processing, comprehensive Walkaway VSP and modern wireline sonic logging surveys were planned in a new deviated production well drilled in 2016. This project represents a first step in the velocity model calibration workflow and highlights the importance of integrating measurements taken at different scales: cores, sonic, borehole and surface seismic, in order to understand the elastic anisotropy of the rocks drilled and allow reducing the uncertainties in the seismic velocity models used for depth imaging.