gebhart/patrepeval huggingface dataset:
The effect of oxidation on the electronic structure of the green fluorescent protein chromophore (2010)

Electronic structure calculations of the singly and doubly ionized states of deprotonated 4(')-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI anion) are presented. One-electron oxidation produces a doublet radical that has blueshifted absorption, whereas the detachment of two electrons yields a closed-shell cation with strongly redshifted (by about 0.6 eV) absorption relative to the HBDI anion. The results suggest that the doubly oxidized species may be responsible for oxidative redding of green fluorescent protein. The proposed mechanism involves two-step oxidation via electronically excited states and is consistent with the available experimental information [A. M. Bogdanov, A. S. Mishin, I. V. Yampolsky, et al., Nat. Chem. Biol. 5, 459 (2009)]. The spectroscopic signatures of the ionization-induced structural changes in the chromophore are also discussed.
3-Substituted 1,4-benzodiazepin-2-ones (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT3-Substituted 1,4-benzodiazepin-2-onesStanley C. Bell, Ronald J. McCaully, Carl Gochman, Scott J. Childress, and Melvyn I. GluckmanCite this: J. Med. Chem. 1968, 11, 3, 457–461Publication Date (Print):May 1, 1968Publication History Published online1 May 2002Published inissue 1 May 1968https://pubs.acs.org/doi/10.1021/jm00309a010https://doi.org/10.1021/jm00309a010research-articleACS PublicationsRequest reuse permissionsArticle Views435Altmetric-Citations72LEARN 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
Mammalian neurotrophin-4: structure, chromosomal localization, tissue distribution, and receptor specificity. (1992)

Nerve growth factor, brain-derived neurotrophic factor, and neurotrophin-3 (NT-3) are the three members of the neurotrophin family known to exist in mammals. Recently, a fourth neurotrophin (designated neurotrophin-4 or NT-4), which shares all of the features found in the mammalian neurotrophins, has been identified in Xenopus and viper. We used sequences specific to the Xenopus/viper NT-4 to isolate a neurotrophin from both human and rat genomic DNA that appears to represent the mammalian counterpart of Xenopus/viper NT-4. Human NT-4 as well as a human NT-4 pseudogene colocalize to chromosome 19 band q13.3. Mammalian NT-4 has many unusual features compared to the previously identified neurotrophins and is less conserved evolutionarily than the other neurotrophins. However, mammalian NT-4 displays bioactivity and trk receptor specificity similar to that of Xenopus NT-4.
Controlled release of insulin-like growth factor-1 and bone marrow stromal cell function of bone-like mineral layer-coated poly(lactic-co-glycolic acid) scaffolds (2008)

Controlled release of growth factors or drugs provides great therapeutic advantages for bone defects which do not heal with normal therapeutic treatments. We have accelerated the deposition of bone-like mineral (BLM) on the surface of three-dimensional (3D) poly(lactic-co-glycolic acid) (PLGA) porous scaffolds to 36-48 h by modifying the biomimetic process parameters and applying surface treatments onto PLGA scaffolds. We used simulated body fluid containing insulin-like growth factor-1 (IGF-1; 1 microg/ml) to mineralize the PLGA scaffolds for 48 h. IGF-1 was co-precipitated with mineral on the surface of the PLGA scaffolds. IGF-1-incorporated mineralized scaffolds demonstrated slow controlled release over a 30 day period when they were incubated in phosphate-buffered saline (PBS) at 37 degrees C. Bone marrow stromal cell (BMSC) function on three different types of scaffolds, such as control (non-mineralized) scaffolds, mineralized scaffolds, and IGF-1-incorporated mineralized scaffolds was also investigated. BMSC attachment and proliferation was enhanced for IGF-1-incorporated mineralized scaffolds compared with controls during the culture period. BMSC differentiation was not changed during the culture period among the three groups of scaffolds, as assessed by alkaline phosphatase activity and osteocalcin assay. According to findings from this study, BLM has great potential to be used as a carrier for biological molecules for localized release applications as well as bone tissue-engineering applications.
Human brain carboxypeptidase B, which cleaves β‐amyloid peptides in vitro, is expressed in the endoplasmic reticulum of neurons (2001)

Intracellular localization of novel human brain carboxypeptidase B (HBCPB) was investigated in human hippocampus, using immunohistochemistry by confocal laser microscopy and biochemical purification of the homogenate by density gradient ultracentrifugation. The former revealed that the majority of HBCPB was expressed in the endoplasmic reticulum, in which the HBCPB-specific C14-module immunoreactivity was colocalized with GRP78 immunoreactivity, a stress 70 heat shock protein specifically expressed in the endoplasmic reticulum. The latter showed that anti-C14-module immunoreactivity and prepro-HBCPB immunoreactivity were both enriched in the microsome fraction, especially in that of the endoplasmic reticulum-density fraction of normal human hippocampal homogenates from various sources. However, HBCPB prepared from human hippocampus showed exopeptidase activity for synthetic beta-amyloid 1-42 peptide, in which Abeta X-42 C-terminus immunoreactivity was decreased in a fashion dose-dependent of the amount of the protease added. These findings indicate that HBCPB, which is expressed in the endoplasmic reticulum of a group of neuronal perikarya, may play an important physiological role in degradation of beta-amyloid 1-42, which is specifically generated in the endoplasmic reticulum of human and rodent neurons and is also regarded as the most pathogenic and aggregatable species among all beta-amyloid peptides.
Efficient content-based detection of zero-day worms (2005)

Recent cybersecurity incidents suggest that Internet worms can spread so fast that in-time human-mediated reaction is not possible, and therefore initial response to cyberattacks has to be automated. The first step towards combating new unknown worms is to be able to detect and identify them at the first stages of their spread. In this paper, we present a novel method for detecting new worms based on identifying similar packet contents directed to multiple destination hosts. We evaluate our method using real traffic traces that contain real worms. Our results suggest that our approach is able to identify novel worms while at the same time the generated false alarms reach as low as zero percent.
Clinical Applications of DNA Probes in the Diagnosis of Genetic Diseases (1987)

Currently, advances in molecular technology involving recombinant DNA have led to dramatic breakthroughs in genetic diseases, cancer research, and identification of foreign DNA. Of particular interest is the impact these tools have made and will make on the clinical laboratory. We describe the techniques and their effects on clinical testing in the chemistry laboratory by using selected examples of available applications. Specific examples include carrier detections and prenatal diagnosis in cystic fibrosis and hemophilia, and sickle cell anemia.
A kidney-selective biopolymer for targeted drug delivery (2016)

Improving drug delivery to the kidney using renal-targeted therapeutics is a promising but underdeveloped area. We aimed to develop a kidney-targeting construct for renal-specific drug delivery. Elastin-like polypeptides (ELPs) are nonimmunogenic protein-based carriers that can stabilize attached small-molecule and peptide therapeutics. We modified ELP at its NH<sub>2</sub>-terminus with a cyclic, seven-amino acid kidney-targeting peptide (KTP) and at its COOH-terminus with a cysteine residue for tracer conjugation. Comparative in vivo pharmacokinetics and biodistribution in rat and swine models and in vitro cell binding studies using human renal cells were performed. KTP-ELP had a longer plasma half-life than ELP in both animal models and was similarly accumulated in kidneys at levels fivefold higher than untargeted ELP, showing renal levels 15- to over 150-fold higher than in other major organs. Renal fluorescence histology demonstrated high accumulation of KTP-ELP in proximal tubules and vascular endothelium. Furthermore, a 14-day infusion of a high dose of ELP or KTP-ELP did not affect body weight, glomerular filtration rate, or albuminuria, or induce renal tissue damage compared with saline-treated controls. In vitro experiments showed higher binding of KTP-ELP to human podocytes, proximal tubule epithelial, and glomerular microvascular endothelial cells than untargeted ELP. These results show the high renal selectivity of KTP-ELP, support the notion that the construct is not species specific, and demonstrate that it does not induce acute renal toxicity. The plasticity of ELP for attachment of any class of therapeutics unlocks the possibility of applying ELP technology for targeted treatment of renal disease in future studies.
Spacecraft Trajectory Planning with Avoidance Constraints Using Mixed-Integer Linear Programming (2002)

Amethod for e nding fuel-optimal trajectoriesfor spacecraft subjected to avoidancerequirements is introduced. These include avoidance of collisions with obstacles or other vehicles and prevention of thruster plumes from one spacecraft impinging on another spacecraft. The necessary logical constraints for avoidance are appended to a fuel-optimizinglinearprogramby includingbinaryvariablesin theoptimization.Theresulting problem isa mixedintegerlinearprogram (MILP)thatcan besolved using availablesoftware. Thelogical constraints can also beused to express the cone guration requirements for maneuvers where only the e nal relative alignment of the vehicles is important and the assignment of spacecraft within the e eet is not specie ed. The collision avoidance, trajectory optimization, and e eet assignment problems can be combined into a single MILP to obtain the optimal solution for these maneuvers. The MILP problem formulation, including these various avoidance constraints, is presented, and then several examples of their application to spacecraft maneuvers, including recone guration of a satellite formation and close inspection of the International Space Station by a microsatellite, are shown. These examples clearly showthat the trajectory design methods presented areparticularly wellsuited to proposed formation e ying missions that involve multiple vehicles operating in close proximity. Nomenclature G = number of global cone gurations available for end states M = large number for logical constraints N = number of dimensions P = plume length T = number of time steps u = control input V = number of vehicles W = plume width x = vehicle state Subscripts g = global cone guration for e nal states i = time step l = obstacle n, m = axes in some orthogonal coordinate frame p, q = vehicles r = position within e nal cone guration
Color-matched and fluorescence-labeled esophagus phantom and its applications (2013)

We developed a stable, reproducible three-dimensional optical phantom for the evaluation of a wide-field endoscopic molecular imaging system. This phantom mimicked a human esophagus structure with flexibility to demonstrate body movements. At the same time, realistic visual appearance and diffuse spectral reflectance properties of the tissue were simulated by a color matching methodology. A photostable dye-in-polymer technology was applied to represent biomarker probed "hot-spot" locations. Furthermore, fluorescent target quantification of the phantom was demonstrated using a 1.2 mm ultrathin scanning fiber endoscope with concurrent fluorescence-reflectance imaging.
Decision tree with better ranking (2003)

AUC (Area Under the Curve) of ROC (Receiver Operating Characteristics) has been recently used as a measure for ranking performance of learning algorithms. In this paper, we present a novel probability estimation algorithm that improves the AUC value of decision trees. Instead of estimating the probability at the single leaf where the example falls into, our method averages probability estimates from all leaves of the tree. The contribution
Type 2 alveolar cells are stem cells in adult lung (2013)

Gas exchange in the lung occurs within alveoli, air-filled sacs composed of type 2 and type 1 epithelial cells (AEC2s and AEC1s), capillaries, and various resident mesenchymal cells. Here, we use a combination of in vivo clonal lineage analysis, different injury/repair systems, and in vitro culture of purified cell populations to obtain new information about the contribution of AEC2s to alveolar maintenance and repair. Genetic lineage-tracing experiments showed that surfactant protein C-positive (SFTPC-positive) AEC2s self renew and differentiate over about a year, consistent with the population containing long-term alveolar stem cells. Moreover, if many AEC2s were specifically ablated, high-resolution imaging of intact lungs showed that individual survivors undergo rapid clonal expansion and daughter cell dispersal. Individual lineage-labeled AEC2s placed into 3D culture gave rise to self-renewing "alveolospheres," which contained both AEC2s and cells expressing multiple AEC1 markers, including HOPX, a new marker for AEC1s. Growth and differentiation of the alveolospheres occurred most readily when cocultured with primary PDGFRα⁺ lung stromal cells. This population included lipofibroblasts that normally reside close to AEC2s and may therefore contribute to a stem cell niche in the murine lung. Results suggest that a similar dynamic exists between AEC2s and mesenchymal cells in the human lung.
Correlation of liquid slug velocity and frequency in horizontal cocurrent gas‐liquid slug flow (1969)

Abstract No Abstracts.
Fibroblast growth factor stimulates the proliferation and differentiation of neural precursor cells in vitro (1990)

We have developed an in vitro culture system to study the regulation of proliferation and differentiation of neural precursor cells contained within the neuroepithelium of embryonic day 10 mice. A number of soluble growth factors have been tested for their ability to regulate these early events and, of these factors, we have found that the fibroblast growth factors [FGFs] can directly stimulate the proliferation and survival of the neuroepithelial cells. At least 50% of the neuroepithelial cells divide in the presence of FGF whereas in the absence of FGF all of the cells die within 6 days of culture. At higher concentrations of FGF, the cells change from being nonadherent round cells in tight clusters into a more flattened cell type which adheres to the substratum. This morphological change is accompanied by the expression of both neurofilament and GFAP, which are definitive markers of the two major cell types in the central nervous system: neurons and glia. In addition a neuroepithelial cell line, which does not rely on FGF for survival or proliferation, expresses both of these markers in response to FGF. These results indicate that FGF is stimulating the differentiation of the neuroepithelial cells into mature neurons and glia.
Microshell®-Tipped Optical Fibers As Sensors Of High-Pressure Pulses In Adverse Environments (1984)

We have developed and used an optical-fiber sensor for detecting the arrival of strong pressure pulses. The sensor consists of an optical fiber, tipped with a gas-filled microballoon. They have been used successfully in adverse environments including explosives, ballistics and electromagnetic pulses (EMP). The sensor produces a bright optical pulse caused by the rapid shock-heating of a gas, typically argon or xenon, which is con-fined in the spherical glass or plastic microballoon. The light pulse is transmitted via the optical fiber to a photo detector, usually a streak camera or photomultiplier tube. The microballoon optical sensor (called an optical &quot;pin&quot; by analogy to standard electri-cal &quot;pins&quot;), was originally developed for diagnosing an explosive, pulsed-power generator. Optical pins are required due to the EMP. The optical pins are economical arrival-time indicators because many channels can be recorded by one streak camera. The generator tests and related experiments, involving projectile velocities and detonation velocities of several kilometers per sec have demonstrated the usefulness of the sensors in explosives and ballistics applications. We have also measured the sensitivity of the optical pins to slowly-moving projectiles and found that a 200 m/sec projectile impacting the microballoon sensor produces a flash having a risetime less than 100 ns and a pulse duration (FWHM) of less than 300 ns. The technical and cost advantages of this optical pin make it potentially useful for many electromagnetic, explosive, and ballistics applications.
Characterization of orally efficacious influenza drug with high resistance barrier in ferrets and human airway epithelia (2019)

Influenza viruses constitute a major health threat and economic burden globally, frequently exacerbated by preexisting or rapidly emerging resistance to antiviral therapeutics. To address the unmet need of improved influenza therapy, we have created EIDD-2801, an isopropylester prodrug of the ribonucleoside analog <i>N</i> <sup>4</sup>-hydroxycytidine (NHC, EIDD-1931) that has shown broad anti-influenza virus activity in cultured cells and mice. Pharmacokinetic profiling demonstrated that EIDD-2801 was orally bioavailable in ferrets and nonhuman primates. Therapeutic oral dosing of influenza virus-infected ferrets reduced group pandemic 1 and group 2 seasonal influenza A shed virus load by multiple orders of magnitude and alleviated fever, airway epithelium histopathology, and inflammation, whereas postexposure prophylactic dosing was sterilizing. Deep sequencing highlighted lethal viral mutagenesis as the underlying mechanism of activity and revealed a prohibitive barrier to the development of viral resistance. Inhibitory concentrations were low nanomolar against influenza A and B viruses in disease-relevant well-differentiated human air-liquid interface airway epithelia. Correlating antiviral efficacy and cytotoxicity thresholds with pharmacokinetic profiles in human airway epithelium models revealed a therapeutic window >1713 and established dosing parameters required for efficacious human therapy. These data recommend EIDD-2801 as a clinical candidate with high potential for monotherapy of seasonal and pandemic influenza virus infections. Our results inform EIDD-2801 clinical trial design and drug exposure targets.
Real-Time Face and Facial Feature Tracking and Applications. (1998)

A human face provides a variety of different communicative functions. In this paper, we present approaches for real-time face/facial feature tracking and their applications. First, we present techniques of tracking human faces. It is revealed that human skincolor can be used as a major feature for tracking human faces. An adaptive stochastic model has been developed to characterize the skin-color distributions. Based on the maximum likelihood method, the model parameters can be adapted for different people and different lighting conditions. The feasibility of the model has been demonstrated by the development of a realtime face tracker. We then present a top-down approach for tracking facial features such as eyes, nostrils, and lip corners. These real-time tracking techniques have been successfully applied to many applications such as eye-gaze monitoring, head pose tracking, and lip-reading. 1. Introduction Many applications in human computer interaction require tracking a human face...
186 The interaction of HMG-box proteins with the four-way DNA junction (1997)

Conference Article| November 01 1997 186 The interaction of HMG-box proteins with the four-way DNA junction J. RICHARD G. PÖHLER; J. RICHARD G. PÖHLER 1C.R.C. Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DD1 4HN Search for other works by this author on: This Site PubMed Google Scholar DAVID M.J. LILLEY DAVID M.J. LILLEY 1C.R.C. Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DD1 4HN Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1997) 25 (4): S647. https://doi.org/10.1042/bst025s647 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation J. RICHARD G. PÖHLER, DAVID M.J. LILLEY; 186 The interaction of HMG-box proteins with the four-way DNA junction. Biochem Soc Trans 1 November 1997; 25 (4): S647. doi: https://doi.org/10.1042/bst025s647 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1997 Biochemical Society1997 Article PDF first page preview Close Modal You do not currently have access to this content.
EML4-ALK Fusion Gene and Efficacy of an ALK Kinase Inhibitor in Lung Cancer (2008)

EML4-ALK is found in the minority of NSCLC. ALK kinase inhibitors alone or in combination may nevertheless be clinically effective treatments for NSCLC patients whose tumors contain EML4-ALK.
Sagnac Effect in Coupled-Resonator Slow-Light Waveguide Structures (2006)

We study the effect of rotation on the propagation of electromagnetic waves in slow-light waveguide structures consisting of coupled microring resonators. We show that such configurations exhibit a new type of Sagnac effect which can be used for the realization of highly compact integrated rotation sensors and gyroscopes.