gebhart/patrepeval huggingface dataset:
Cation-independent Mannose 6-Phosphate Receptor (2009)

The 300-kDa cation-independent mannose 6-phosphate receptor (CI-MPR), which contains multiple mannose 6-phosphate (Man-6-P) binding sites that map to domains 3, 5, and 9 within its 15-domain extracytoplasmic region, functions as an efficient carrier of Man-6-P-containing lysosomal enzymes. To determine the types of phosphorylated N-glycans recognized by each of the three carbohydrate binding sites of the CI-MPR, a phosphorylated glycan microarray was probed with truncated forms of the CI-MPR. Surface plasmon resonance analyses using lysosomal enzymes with defined N-glycans were performed to evaluate whether multiple domains are needed to form a stable, high affinity carbohydrate binding pocket. Like domain 3, adjacent domains increase the affinity of domain 5 for phosphomannosyl residues, with domain 5 exhibiting approximately 60-fold higher affinity for lysosomal enzymes containing the phosphodiester Man-P-GlcNAc when in the context of a construct encoding domains 5-9. In contrast, domain 9 does not require additional domains for high affinity binding. The three sites differ in their glycan specificity, with only domain 5 being capable of recognizing Man-P-GlcNAc. In addition, domain 9, unlike domains 1-3, interacts with Man(8)GlcNAc(2) and Man(9)GlcNAc(2) oligosaccharides containing a single phosphomonoester. Together, these data indicate that the assembly of three unique carbohydrate binding sites allows the CI-MPR to interact with the structurally diverse phosphorylated N-glycans it encounters on newly synthesized lysosomal enzymes.
Modeling Residual NAPL in Water-Wet Porous Media (2002)

A model is outlined that predicts NAPL which is held in pore wedges and as films or lenses on solid and water surfaces and contributes negligibly to NAPL advection. This is conceptually referred to as residual NAPL. Since residual NAPL is immobile, it remains in the vadose zone after all free NAPL has drained. Residual NAPL is very important because it is a long-term source for groundwater contamination. Recent laboratory experiments have demonstrated that current models for predicting subsurface NAPL behavior are inadequate because they do not correctly predict residual NAPL. The main reason for the failure is a deficiency in the current constitutive theories for multiphase flow that are used in numerical simulators. Multiphase constitutive theory governs the relations among relative permeability, saturation, and pressure for fluid systems (i.e., air, NAPL, water). In this paper, we outline a model describing relations between fluid saturations and pressures that can be combined with existing multiphase constitutive theory to predict residual NAPL. We test the revised constitutive theory by applying it to a scenario involving NAPL imbibition and drainage, as well as water imbibition and drainage. The results suggest that the revised constitutive theory is able to predict the distribution of residual NAPL in the vadose zone as a function of saturation-path history. The revised model describing relations between fluid saturation and pressures will help toward developing or improving numerical multiphase flow simulators.
Comparison of 17 genome types of adenovirus type 3 identified among strains recovered from six continents (1988)

Restriction endonucleases BamHI, BclI, BglI, BglII, BstEII, EcoRI, HindIII, HpaI, SalI, SmalI, XbalI, and XholI were used to analyze 61 selected strains of adenovirus type 3 (Ad3) isolated from Africa, Asia, Australia, Europe, North America, and South America. It was noted that the use of BamHI, BclI, BglII, HpaI, SalI, and SmaI was sufficient to distinguish 17 genome types; 13 of them were newly identified. All 17 Ad3 genome types could be divided into three genomic clusters. Genome types of Ad3 cluster 1 occurred in Africa, Europe, South America, and North America. Genomic cluster 2 was identified in Africa; genomic cluster 3 was identified in Africa, Asia, Australia, Europe (a few), and North America. This was of interest because 15 identified genome types of Ad7 could also be divided into three genomic clusters. The degree of genetic relatedness between the 17 Ad3 and the 15 Ad7 genome types was analyzed and was expressed in a three-dimensional model.
The GA5 locus of Arabidopsis thaliana encodes a multifunctional gibberellin 20-oxidase: molecular cloning and functional expression. (1995)

The biosynthesis of gibberellins (GAs) after GA12-aldehyde involves a series of oxidative steps that lead to the formation of bioactive GAs. Previously, a cDNA clone encoding a GA 20-oxidase [gibberellin, 2-oxoglutarate:oxygen oxidoreductase (20-hydroxylating, oxidizing), EC 1.14.11.-] was isolated by immunoscreening a cDNA library from liquid endosperm of pumpkin (Cucurbita maxima L.) with antibodies against partially purified GA 20-oxidase. Here, we report isolation of a genomic clone for GA 20-oxidase from a genomic library of the long-day species Arabidopsis thaliana Heynh., strain Columbia, by using the pumpkin cDNA clone as a heterologous probe. This genomic clone contains a GA 20-oxidase gene that consists of three exons and two introns. The three exons are 1131-bp long and encode 377 amino acid residues. A cDNA clone corresponding to the putative GA 20-oxidase genomic sequence was constructed with the reverse transcription-PCR method, and the identity of the cDNA clone was confirmed by analyzing the capability of the fusion protein expressed in Escherichia coli to convert GA53 to GA44 and GA19 to GA20. The Arabidopsis GA 20-oxidase shares 55% identity and > 80% similarity with the pumpkin GA 20-oxidase at the derived amino acid level. Both GA 20-oxidases share high homology with other 2-oxoglutarate-dependent dioxygenases (2-ODDs), but the highest homology was found between the two GA 20-oxidases. Mapping results indicated tight linkage between the cloned GA 20-oxidase and the GA5 locus of Arabidopsis. The ga5 semidwarf mutant contains a G-->A point mutation that inserts a translational stop codon in the protein-coding sequence, thus confirming that the GA5 locus encodes GA 20-oxidase. Expression of the GA5 gene in Ara-bidopsis leaves was enhanced after plants were transferred from short to long days; it was reduced by GA4 treatment, suggesting end-product repression in the GA biosynthetic pathway.
Mapping Large, Urban Environments with GPS-Aided SLAM (2010)

Simultaneous Localization and Mapping (SLAM) has been an active area of research for several decades, and has become a foundation of indoor mobile robotics. However, although the scale and quality of results have improved markedly in that time period, no current technique can e ectively handle city-sized urban areas. <br><br> The Global Positioning System (GPS) is an extraordinarily useful source of localization information. Unfortunately, the noise characteristics of the system are complex, arising from a large number of sources, some of which have large autocorrelation. Incorporation of GPS signals into SLAM algorithms requires using low-level system information and explicit models of the underlying system to make appropriate use of the information. The potential bene ts of combining GPS and SLAM include increased robustness, increased scalability, and improved accuracy of localization. <br><br> This dissertation presents a theoretical background for GPS-SLAM fusion. The presented model balances ease of implementation with correct handling of the highly colored sources of noise in a GPS system.. This utility of the theory is explored and validated in the framework of a simulated Extended Kalman Filter driven by real-world noise. <br><br> The model is then extended to Smoothing and Mapping (SAM), which overcomes the linearization and algorithmic complexity limitations of the EKF formulation. This GPS-SAM model is used to generate a probabilistic landmark-based urban map covering an area an order of magnitude larger than previous work.
Robust and Reverse-Engineering Resilient PUF Authentication and Key-Exchange by Substring Matching (2014)

This paper proposes novel robust and low-overhead physical unclonable function (PUF) authentication and key exchange protocols that are resilient against reverse-engineering attacks. The protocols are executed between a party with access to a physical PUF (prover) and a trusted party who has access to the PUF compact model (verifier). The proposed protocols do not follow the classic paradigm of exposing the full PUF responses or a transformation of them. Instead, random subsets of the PUF response strings are sent to the verifier so the exact position of the subset is obfuscated for the third-party channel observers. Authentication of the responses at the verifier side is done by matching the substring to the available full response string; the index of the matching point is the actual obfuscated secret (or key) and not the response substring itself. We perform a thorough analysis of resiliency of the protocols against various adversarial acts, including machine learning and statistical attacks. The attack analysis guides us in tuning the parameters of the protocol for an efficient and secure implementation. The low overhead and practicality of the protocols are evaluated and confirmed by hardware implementation.
LPS induces NK1.1+ αβ T cells with potent cytotoxicity in the liver of mice via production of IL-12 from Kupffer cells (1996)

We recently reported that systemic administration of IL-12 into mice activates NK1.1+ alpha beta T cells with intermediate TCR (NK1+TCRint) and induces strong MHC-unrestricted cytotoxicity in C57BL/6 mice. In the present report, we examined the effect of LPS on Kupffer cells and NK1+TCRint, cells in C57BL/6 mice. Administration of LPS, as well as synthetic lipid A analogue (ONO-4007), but not detoxified LPS, induces the increase of NK1 expression of NK1+TCRint cells (NKlhighTCRint) and the acquisition of strong MHC-unrestricted cytotoxicity of these cells against NK-sensitive and NK-resistant targets as does IL-12 administration. LPS as well as ONO-4007 induced IL-12 mRNA in hepatic mononuclear cells, mainly in plastic-adherent Kupffer cells. LPS-induced cytotoxicity of hepatic mononuclear cells was greatly reduced by in vivo injections of anti-IL-12 Ab, to a lesser extent by anti-IFN-gamma Ab, but not by anti-IL-1 nor anti-TNF-alpha Ab. Pretreatment of mice with LPS induced inhibition of hepatic metastases of i.v. injected EL4 cells in C57BL/6 euthymic and athymic mice and this antimetastasis was inhibited by injection of anti-IL-12 Ab. This antimetastatic effect of LPS in the liver was also observed in different strains of mice and tumors, In contrast to IL-12, however, LPS was not so effective when administered after tumor inoculation. These results revealed that LPS (lipid A) stimulates NK1+TCRint cells through IL-12 production from Kupffer cells and suggest that bacterial components, probably including those from intestine, are activators of Kupffer cells and NK1+TCRint, cells in the liver. It is also suggested that the host condition as well as LPS-induced cytokines other than IL-12 may affect antitumor effect induced by LPS in the liver.
Intestinal reperfusion injury is mediated by IgM and complement (1999)

Intestinal ischemia-reperfusion injury is dependent on complement. This study examines the role of the alternative and classic pathways of complement and IgM in a murine model of intestinal ischemia-reperfusion. Wild-type animals, mice deficient in complement factor 4 (C4), C3, or Ig, or wild-type mice treated with soluble complement receptor 1 were subjected to 40 min of jejunal ischemia and 3 h of reperfusion. Compared with wild types, knockout and treated mice had significantly reduced intestinal injury, indicated by lowered permeability to radiolabeled albumin. When animals deficient in Ig were reconstituted with IgM, the degree of injury was restored to wild-type levels. Immunohistological staining of intestine for C3 and IgM showed colocalization in the mucosa of wild-type controls and minimal staining for both in the intestine of Ig-deficient and C4-deficient mice. We conclude that intestinal ischemia-reperfusion injury is dependent on the classic complement pathway and IgM.
Development of a Decellularized Lung Bioreactor System for Bioengineering the Lung: The Matrix Reloaded (2010)

We developed a decellularized murine lung matrix bioreactor system that could be used to evaluate the potential of stem cells to regenerate lung tissue. Lungs from 2-3-month-old C57BL/6 female mice were excised en bloc with the trachea and heart, and decellularized with sequential solutions of distilled water, detergents, NaCl, and porcine pancreatic DNase. The remaining matrix was cannulated and suspended in small airway growth medium, attached to a ventilator to simulate normal, murine breathing-induced stretch. After 7 days in an incubator, lung matrices were analyzed histologically. Scanning electron microscopy and histochemical staining demonstrated that the pulmonary matrix was intact and that the geographic placement of the proximal and distal airways, alveoli and vessels, and the basement membrane of these structures all remained intact. Decellularization was confirmed by the absence of nuclear 4',6-diamidino-2-phenylindole staining and negative polymerase chain reaction for genomic DNA. Collagen content was maintained at normal levels. Elastin, laminin, and glycosaminglycans were also present, although at lower levels compared to nondecellularized lungs. The decellularized lung matrix bioreactor was capable of supporting growth of fetal alveolar type II cells. Analysis of day 7 cryosections of fetal-cell-injected lung matrices showed pro-Sp-C, cytokeratin 18, and 4',6-diamidino-2-phenylindole-positive cells lining alveolar areas that appeared to be attached to the matrix. These data illustrate the potential of using decellularized lungs as a natural three-dimensional bioengineering matrix as well as provide a model for the study of lung regeneration from pulmonary stem cells.
Design, synthesis, and photophysical characterization of novel pentacyclic red shifted azine dyes (1999)

Abstract As part of our continuing efforts to develop second generation photodynamic therapeutic agents [1], we synthesized three pentacyclic azine dyes that were designed with the aid of MNDO calculations to absorb visible light having wavelengths longer than 600 nm. Photophysical measurements for the azine dyes 1,4,8,11‐tetraethyl‐1,2,3,4,8,9,10,11,13‐nonahydrodipyrazino[2,3‐ b :2′, 3′‐ i ] phenazinium acetate, 13 , 1,4,8,11‐tetraethyl‐2,3,4,8,9,10,11,12,13‐octahydro‐13‐methyldipyrazino[2,3‐ b :2,3′‐ i ]phenazinium iodide, 14 , and l,4,8,11,13‐pentaethyl‐2,3,4,8,9,10,11,12,13‐octahydrodipyrazino[2,3‐ b :2′,3′‐ i ]phenazinium iodide, 15 , are highlighted by a 35 nm red shift in their absorption spectra and a 5–7 fold increase in their singlet oxygen quantum yield relative to tricyclic model compounds 3,7‐bis(diethylamino)phenazinium chloride, 20 , and 3,7‐bis(diethylamino)‐5‐ethyl‐phenazinium iodide, 21 , which were also synthesized for this study. Incorporation of rigid peripheral tetrahydropyrazino ring systems in the pentacyclic azines 13 , 14 , and 15 are responsible for the improved fluorescence and singlet oxygen quantum yields relative to the tricyclic azines 20 and 21 .
A Convenient Procedure for Esterification of Carboxylic Acids (1978)

Abstract A variety of carboxylic acids including simple acids, sterically hindered acids, thermally unstable acids and N-protected amino acids react with alkyl halides in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in benzene to give esters in good yields. The reaction is simple, affording a general method for esterification of carboxylic acids.
Glass transition temperature as a guide to selection of polymers suitable for PTC materials (1973)

Abstract It has been shown that the only way to predict the size of the PTC effect displayed by a crystalline polymer when filled with conductive particles is through the knowledge of the glass transition point of the polymer. The size of the PTC anomaly is found to decrease sharply with rise in glass transition temperature and for a polymer to be a useful PTC material its glass transition must be below 0°C. It has not been possible to explain this relationship by any of the current theories of the PTC mechanism in filled polymers.
Substitution of the carboxyl-terminal domain of apo AI with apo AII sequences restores the potential of HDL to reduce the progression of atherosclerosis in apo E knockout mice. (1998)

HDL metabolism and atherosclerosis were studied in apo E knockout (KO) mice overexpressing human apo AI, a des- (190-243)-apo AI carboxyl-terminal deletion mutant of human apo AI or an apo AI-(1-189)-apo AII-(12-77) chimera in which the carboxyl-terminal domain of apo AI was substituted with the pair of helices of apo AII. HDL cholesterol levels ranked: apo AI/apo E KO approximately apo AI-(1-189)-apo AII- (12-77)/apo E KO > > des-(190-243)-apo AI/apo E KO > apo E KO mice. Progression of atherosclerosis ranked: apo E KO > des-(190-243)-apo AI/apo E KO > > apo AI-(1-189)- apo AII-(12-77)/apo E KO approximately apo AI/apo E KO mice. Whereas the total capacity to induce cholesterol efflux from lipid-loaded THP-1 macrophages was higher for HDL of mice overexpressing human apo AI or the apo AI/apo AII chimera, the fractional cholesterol efflux rate, expressed in percent cholesterol efflux/microg apolipoprotein/h, for HDL of these mice was similar to that for HDL of mice overexpressing the deletion mutant and for HDL of apo E KO mice. This study demonstrates that the tertiary structure of apo AI, e.g., the number and organization of its helices, and not its amino sequence is essential for protection against atherosclerosis because it determines HDL cholesterol levels and not cholesterol efflux. Amino acid sequences of apo AII, which is considered to be less antiatherogenic, can be used to restore the structure of apo AI and thereby its antiatherogenicity.
Synthesis and Patterning of Gold Nanostructures on InP and GaAs via Galvanic Displacement (2005)

Plugging into III–Vs: Crystalline, sub-100 nm gold nanoparticles are formed via simple galvanic displacement reactions on InP and GaAs surfaces (see images). The reactions require only four ingredients (gold salt, semiconductor, water, and dilute acid) and result in firmly bound gold nanoparticle arrays on the surface. The chemistry can be patterned via AFM-tip-mediated scribing of the sub-5-nm-thick surface oxide to reveal the underlying semiconductor, leading to galvanic displacement only in the exposed areas. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2421/2005/z500121_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
FGFR1-Induced Epithelial to Mesenchymal Transition through MAPK/PLCγ/COX-2-Mediated Mechanisms (2012)

Tumour invasion and metastasis is the most common cause of death from cancer. For epithelial cells to invade surrounding tissues and metastasise, an epithelial-mesenchymal transition (EMT) is required. We have demonstrated that FGFR1 expression is increased in bladder cancer and that activation of FGFR1 induces an EMT in urothelial carcinoma (UC) cell lines. Here, we created an in vitro FGFR1-inducible model of EMT, and used this model to identify regulators of urothelial EMT. FGFR1 activation promoted EMT over a period of 72 hours. Initially a rapid increase in actin stress fibres occurred, followed by an increase in cell size, altered morphology and increased migration and invasion. By using site-directed mutagenesis and small molecule inhibitors we demonstrated that combined activation of the mitogen activated protein kinase (MAPK) and phospholipase C gamma (PLCγ) pathways regulated this EMT. Actin stress fibre formation was regulated by PLCγ activation, and was also important for the increase in cell size, migration and altered morphology. MAPK activation regulated migration and E-cadherin expression, indicating that combined activation of PLCγ and MAPK is required for a full EMT. We used expression microarrays to assess changes in gene expression downstream of these signalling cascades. COX-2 was transcriptionally upregulated by FGFR1 and caused increased intracellular prostaglandin E(2) levels, which promoted migration. In conclusion, we have demonstrated that FGFR1 activation in UC cells lines promotes EMT via coordinated activation of multiple signalling pathways and by promoting activation of prostaglandin synthesis.
Effect of Fiber Content and Chemical Treatment on the Thermal Properties ofSpartium junceumFiber-Reinforced Polypropylene Composites (2008)

The thermal and crystallization behavior of PP/Spartium junceum fiber composites were studied by thermogravimetry (TGA) and differential scanning calorimetry (DSC). The surface modification of Spartium junceum fibers was carried out using silane coupling agents in order to improve the interfacial adhesion between the fiber and the matrix. The effects of fiber content and chemical treatment on thermal properties were evaluated. It was found that Spartium junceum fiber degraded before the PP matrix but the thermal stability of the PP/Spartium junceum fiber composites was higher than those of the fiber and the matrix. DSC measurements showed that the incorporation of Spartium junceum fiber caused an increase in the crystallinity of the matrix. These effects have been attributed to the fact that the surfaces of Spartium junceum fibers act as nucleating agents for the crystallization of the polymer, promoting the growth and the formation of transcrystalline regions around the fibers.
Incidence and Occurrence of Total (First-Ever and Recurrent) Stroke (1999)

We conservatively estimate that there were 750 000 first-ever or recurrent strokes in the United States during 1995. This new figure emphasizes the importance of preventive measures for a disease that has identifiable and modifiable risk factors and for the development of new and improved treatment strategies and infrastructures that can reduce the consequences of stroke.
General Approach to Epipolythiodiketopiperazine Alkaloids: Total Synthesis of (+)-Chaetocins A and C and (+)-12,12′-Dideoxychetracin A (2010)

A highly stereoselective and systematic strategy for the introduction of polysulfides in the synthesis of epipolythiodiketopiperazines is described. We report the first total synthesis of dimeric epitri- and epitetrathiodiketopiperazines.
Synthesis, Calcium Mobilizing, and Physicochemical Properties of d-chiro-Inositol 1,3,4,6-Tetrakisphosphate, a Novel and Potent Ligand at the d-myo-Inositol 1,4,5-Trisphosphate Receptor (1999)

The synthesis of a novel and potent ligand at the D-myo-inositol 1,4, 5-trisphosphate receptor (InsP3R) is described. D-chiro-Inositol 1,3, 4,6-tetrakisphosphate (7) and L-chiro-inositol 1,3,4, 6-tetrakisphosphate (ent-7) have been synthesized from D-2, 5-di-O-benzyl-chiro-inositol and L-2,5-di-O-benzyl-chiro-inositol, respectively. The potency of binding and Ca2+ release of 7 and ent-7 were examined in L15 and Lvec cells. 7 was a full agonist at the InsP3R in both cells, and ent-7 was inactive. The results are compared to those from D-myo-inositol 1,4,5-trisphosphate (1), DL-scyllo-inositol 1,2,4-trisphosphate (2), DL-myo-inositol 1,2,4, 5-tetrakisphosphate (3), scyllo-inositol 1,2,4,5-tetrakisphosphate (4), D-myo-inositol 2,4,5-trisphosphate (5), and D-chiro-inositol 1, 3,4-trisphosphate (6). The protonation processes of 7 have also been investigated by 31P NMR titration experiments.