gebhart/patrepeval huggingface dataset:
Origins and evolution of isoprenoid lipid biosynthesis in archaea (2004)

A characteristic feature of the domain archaea are the lipids forming the hydrophobic core of their cell membrane. These unique lipids are composed of isoprenoid side-chains stereospecifically ether linked to sn-glycerol-1-phosphate. Recently, considerable progress has been made in characterizing the enzymes responsible for the synthesis of archaeal lipids. However, little is known about their evolution. To better understand how this unique biosynthetic apparatus came to be, large-scale database surveys and phylogenetic analyses were performed. All characterized enzymes involved in the biosynthesis of isoprenoid side-chains and the glycerol phosphate backbone along with their assembly in ether lipids were included in these analyses. The sequence data available in public databases was complemented by an in-depth sampling of isoprenoid lipid biosynthesis genes from multiple genera of the archaeal order Halobacteriales, allowing us to look at the evolution of these enzymes on a smaller phylogenetic scale. This investigation of the isoprenoid biosynthesis apparatus of archaea on small and large phylogenetic scales reveals that it evolved through a combination of evolutionary processes, including the co-option of ancestral enzymes, modification of enzymatic specificity, orthologous and non-orthologous gene displacement, integration of components from eukaryotes and bacteria and lateral gene transfer within and between archaeal orders.
Conjugated Polyelectrolyte Based Fluorescence Turn-On Assay for Real-Time Monitoring of Protease Activity (2010)

A fluorescence "turn-on" assay for monitoring protease activity is developed on the basis of a water-soluble carboxylated polyfluorene derivative, PFP-CO₂Na, and its different fluorescence response toward cytochrome c (cyt c) and its fragments. PFP-CO₂Na is synthesized via Suzuki coupling polymerization between 2,7-dibromo-9,9-bis(3'-tert-butyl propanoate)fluorene and 1,4-bis(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-benzene, followed by treatment with trifluoroacetic acid and Na₂CO₃. The fluorescence of PFP-CO₂Na can be significantly quenched by cyt c due to complexation-mediated electron transfer between the polymer and protein. Using the complex of PFP-CO₂Na/cyt c as a substrate, a real-time fluorescence turn-on assay for trypsin activity study has been developed. Addition of trypsin to the substrate solution induces gradual recovery of the fluorescence intensity for PFP-CO₂Na due to trypsin-catalyzed hydrolysis of cyt c, which dissociates the heme moiety from the polymer vicinity. The time-dependent fluorescence intensity increase of PFP-CO₂Na in the presence of trypsin allows us to derive the initial reaction rates and k(cat)/K(m) (5350 M⁻¹ s⁻¹) for trypsin-catalyzed hydrolysis. Addition of trypsin inhibitor efficiently inhibits trypsin-catalyzed hydrolysis reaction of cyt c, which leads to a decreased fluorescence turn-on response of PFP-CO₂Na.
Gemcitabine with paclitaxel therapy against mesocolic leiomyosarcoma: a case report. (2013)

A 65-year-old man complained of lower right abdominal pain, and an intra-abdominal mass was identified. An intra-abdominal hemorrhage was discovered during a thorough examination and emergency surgery was performed. The tumor was ruptured and was fragile, making it difficult to perform extirpation; thus, an ileocecal resection was performed. The histopathological diagnosis of the tumor was leiomyosarcoma, and recurrence was observed during the early postoperative period. The patient underwent surgery twice; each time there was a recurrence, but complete resection could not be obtained, and paclitaxel and gemcitabine chemotherapy was performed. A temporary effect was observed, and control of disease progression lasted approximately five months. Standard chemotherapy for leiomyosarcoma has not been established, but this method could become a therapeutic strategy for leiomyosarcoma.
The first GPS satellite radio optimized for automatic vehicle location (2003)

A GPS (Global Positioning System) radio designed to serve the needs of the automatic vehicle location (AVL) market is discussed. Market research revealed several key demands for an AVL GPS radio: (i) minimization of urban building blockage; (ii) easy programmability to minimize mobile data transmission costs; (iii) high accuracy for streetmap level coordination; (iv) interface capability with nondigital specialized mobile radios; and (v) selling price close to that of alternatives such as Signposts and Loran-C. The developed system operates at high accuracy in an urban environment and is plug-compatible with nearly all vehicle radios. Among the engineering and production breakthroughs described are a unique approach to satellite tracking, enabling up to 8 GPS satellites to be used for position determination with a two-channel receiver, and a receiver-in-a-microdome design. A powerful application-specific integrated circuit has enabled MARCO to bring GPS within the easy reach of millions of AVL users such as buses, taxis, and delivery vehicle fleets.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cell-to-Cell and Phloem-Mediated Transport of Potato Virus X: The Role of Virions (1998)

Movement-deficient potato virus X (PVX) mutants tagged with the green fluorescent protein were used to investigate the role of the coat protein (CP) and triple gene block (TGB) proteins in virus movement. Mutants lacking either a functional CP or TGB were restricted to single epidermal cells. Microinjection of dextran probes into cells infected with the mutants showed that an increase in the plasmodesmal size exclusion limit was dependent on one or more of the TGB proteins and was independent of CP. Fluorescently labeled CP that was injected into epidermal cells was confined to the injected cells, showing that the CP lacks an intrinsic transport function. In additional experiments, transgenic plants expressing the PVX CP were used as rootstocks and grafted with nontransformed scions. Inoculation of the PVX CP mutants to the transgenic rootstocks resulted in cell-to-cell and systemic movement within the transgenic tissue. Translocation of the CP mutants into sink leaves of the nontransgenic scions was also observed, but infection was restricted to cells close to major veins. These results indicate that the PVX CP is transported through the phloem, unloads into the vascular tissue, and subsequently is transported between cells during the course of infection. Evidence is presented that PVX uses a novel strategy for cell-to-cell movement involving the transport of filamentous virions through plasmodesmata.
Analysis of a reset-free polarization controller for fast automatic polarization stabilization in fiber-optic transmission systems (1994)

We analyze the operation of a reset-free polarization controller comprising three endlessly rotatable wave plates: a first quarter-wave plate followed by a half-wave plate and a second quarter-wave plate, which is rotated synchronously with the first quarter-wave plate. We show that for any arbitrary angular offset between the two quarter-wave plates; the controller allows continuous, reset-free transformations from any varying general input state of polarization into any general output state. An integrated-optic realization of this scheme on z-propagation LiNbO/sub 3/ offers control speeds that well exceed the speed of natural polarization fluctuations in standard single-mode fibers, thus allowing fast automatic polarization stabilization in fiber-optic transmission systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Acid Hydrolysis of Erythropoietin. (1958)

Purified erythropoietin has been subjected to mild acid hydrolysis. This mucoprotein thus has been further characterized and shown to lose erythropoietic activity upon hydrolytic removal of neuraminic acid.
Additional human β2‐microglobulin curbs HLA–B27 misfolding and promotes arthritis and spondylitis without colitis in male HLA–B27–transgenic rats (2006)

These results suggest that B27 misfolding is associated with intestinal inflammation, but that neither B27 misfolding nor intestinal inflammation is critical to the development of B27-associated arthropathy.
A humanized antibody specific for the platelet integrin gpIIb/IIIa. (1994)

C4G1, a murine mAb reactive with the platelet gpIIb/IIIa integrin, was humanized for potential treatment of thrombosis-related disorders. The variable regions of light- and heavy-chain cDNAs from the C4G1 hybridoma were first cloned and sequenced. Humanized C4G1 Ab of the IgG1 isotype was constructed by combining the complementarity-determining regions of C4G1 with human framework and constant regions. The human framework was chosen to maximize homology with the C4G1 variable region sequence, and a computer model of C4G1 was used to aid design of the final framework sequence. Genetic constructs were also developed to produce Fab and F(ab')2 fragments of the humanized C4G1 Ab. The humanized IgG1 Ab as well as the Fab and F(ab')2 fragments showed equivalent binding affinities to their murine counterparts, indicating no loss in binding affinity during the humanization process. The humanized Ab and its fragments were also shown to inhibit platelet aggregation and to inhibit binding of fibrinogen to gpIIb/IIIa in vitro.
The N-terminus and C-terminus of IFN-gamma are binding domains for cloned soluble IFN-gamma receptor (1992)

The mechanism of binding of murine IFN-gamma to its receptor has not been determined. We have studied this mechanism by examining the binding of overlapping synthetic peptides of IFN-gamma to cloned soluble murine IFN-gamma R. IFN-gamma (1-39) and IFN-gamma (95-133) were able to compete with [125I]IFN-gamma for binding to cloned soluble receptor. Peptides corresponding to the inner region of IFN-gamma--IFN-gamma (36-60), IFN-gamma (54-91), and IFN-gamma (78-107)--showed a markedly reduced ability to compete with [125I]IFN-gamma for receptor binding relative to the N-terminal and C-terminal peptides. In direct binding studies, the binding of [125I]-IFN-gamma (1-39) to soluble receptor could only be competed by IFN-gamma (1-39) and IFN-gamma and not by any of the other peptides including IFN-gamma (95-133). This suggests that the N- and C-termini of IFN-gamma bind to different regions of the receptor. These data in conjunction with previous structure/function studies and x-ray crystallographic data have allowed us to formulate a "velcro-key" model of IFN-gamma binding to receptor that involves both the N- and C-terminal domains. The N-terminus binds in the classical "lock-and-key" manner characterized by specific ligand-receptor binding. The hydrophilic C-terminus binds to a region of the receptor distinct from the N-terminus likely through the polycationic region, which is conserved across species barriers. Binding of this type would exhibit high affinity and low specificity similar to a piece of velcro. This interaction becomes specific when the C-terminus is in the context of the whole IFN-gamma molecule and may act to increase the affinity of receptor binding and/or facilitate signal transduction.
Microwave annealing of Mg-implanted and in situ Be-doped GaN (2010)

An ultrafast microwave annealing method, different from conventional thermal annealing, is used to activate Mg-implants in GaN layer. The x-ray diffraction measurements indicated complete disappearance of the defect sublattice peak, introduced by the implantation process for single-energy Mg-implantation, when the annealing was performed at ≥1400 °C for 15 s. An increase in the intensity of Mg-acceptor related luminescence peak (at 3.26 eV) in the photoluminescence spectra confirms the Mg-acceptor activation in single-energy Mg-implanted GaN. In case of multiple-energy implantation, the implant generated defects persisted even after 1500 °C/15 s annealing, resulting in no net Mg-acceptor activation of the Mg-implant. The Mg-implant is relatively thermally stable and the sample surface roughness is 6 nm after 1500 °C/15 s annealing, using a 600 nm thick AlN cap. In situ Be-doped GaN films, after 1300 °C/5 s annealing have shown Be out-diffusion into the AlN layer and also in-diffusion toward the GaN/SiC interface. The in-diffusion and out-diffusion of the Be increased with increasing annealing temperature. In fact, after 1500 °C/5 s annealing, only a small fraction of in situ doped Be remained in the GaN layer, revealing the inadequateness of using Be-implantation for forming p-type doped layers in the GaN.
Synthesis and Biological Evaluation of Naphthyldesferrithiocin Iron Chelators (1996)

The synthesis and iron-clearing properties of the naphthyldesferrithiocins 2-(2'-hydroxynaphth-1'-yl)-delta2-thiazoline-(4R)-carboxylic acid, 2-(2'-hydroxynaphth-1'-yl)-delta2-thiazoline-(4S)-carboxylic acid, 2-(3'-hydroxynaphth-2'-yl)-delta2-thiazoline-(4R)-carboxylic acid, and 2-(3'-hydroxynaphth-2'-yl)-delta2-thiazoline-(4S)-carboxylic acid are described. While the bile duct-cannulated rat model clearly demonstrates that the 3'-hydroxynaphthyl-2'-yl compounds are orally active iron-clearing agents and the corresponding 2'-hydroxynaphthyl-1'-yl compounds are not, in the primate model none of the benz-fused desazadesferrithiocin analogues are active. Oral versus subcutaneous administration of these ligands strongly suggests that metabolism is a key issue in their iron-clearing properties and that these benz-fused desferrithiocins are not good candidates for orally active iron-clearing drugs.
Enzymatic transfer of a preassembled trisaccharide antigen to cell surfaces using a fucosyltransferase. (1992)

The Lewis alpha (1-->3/4)-fucosyltransferase (Le-FucT) is known to fucosylate both Type I (beta Gal(1-->3) beta GlcNAc) and Type II (beta Gal(1-->4) beta GlcNAc) sequences even when these are sialylated at OH-3 or fucosylated at OH-2 of the terminal Gal residues. These acceptor sequences are ubiquitous on mammalian cell-surface glycoproteins and glycolipids. The Le-FucT enzyme is therefore a potential candidate as a universal reagent for the modification of cell surfaces. We have found that a readily accessible, partially purified Le-FucT from human milk, which normally uses GDP-fucose (a 6-deoxy sugar) as the donor for the transfer of a single fucose residue, will also transfer a fucose residue substituted on C-6 by a very large sterically demanding structure, in this instance, a synthetic blood group antigen. As a demonstration of the ability of the Le-FucT to modify glycoconjugates in a mild and specific manner, we chemically synthesized the complex sugar-nucleotide alpha Gal(1-->3) [alpha Fuc(1-->2)]-beta Gal-O-(CH2)8COHN(6)-beta-L-fucose-GDP (13) which is a GDP-fucose analog where the human blood group B trisaccharide antigen is covalently linked to C-6 of fucose through an amino group. It is shown that, in enzyme-linked immunosorbent assays, the Le-FucT uses both immobilized beta Gal(1-->3) beta GlcNAc-bovine serum albumin conjugates and fetuin as acceptor substrates and renders them blood group B-active as detected by a monoclonal anti-B blood-grouping antibody. The fucose residue to which the B-trisaccharide is linked therefore becomes covalently attached to the acceptor oligosaccharide chains of those glycoproteins. Incubation of type "O" erythrocytes with the Le-FucT and complex donor 13 results in the covalent transfer of alpha Gal(1-->3) [alpha Fuc(1-->2)] beta Gal-O-(CH2)8COHN(6)-beta-L-Fuc to cell-surface acceptors since the cells become phenotypically "B" and are agglutinated by the same antibody. It is proposed that the Le-FucT represents a powerful new tool with the ability to label animal cell surfaces with preassembled oligosaccharide and possibly also other complex recognition markers.
A Reinforcement Learning Framework for Spiking Networks with Dynamic Synapses (2011)

An integration of both the Hebbian-based and reinforcement learning (RL) rules is presented for dynamic synapses. The proposed framework permits the Hebbian rule to update the hidden synaptic model parameters regulating the synaptic response rather than the synaptic weights. This is performed using both the value and the sign of the temporal difference in the reward signal after each trial. Applying this framework, a spiking network with spike-timing-dependent synapses is tested to learn the exclusive-OR computation on a temporally coded basis. Reward values are calculated with the distance between the output spike train of the network and a reference target one. Results show that the network is able to capture the required dynamics and that the proposed framework can reveal indeed an integrated version of Hebbian and RL. The proposed framework is tractable and less computationally expensive. The framework is applicable to a wide class of synaptic models and is not restricted to the used neural representation. This generality, along with the reported results, supports adopting the introduced approach to benefit from the biologically plausible synaptic models in a wide range of intuitive signal processing.
Expression of human immunodeficiency virus type 1 reverse transcriptase in trans during virion release and after infection (1996)

The normal reverse transcription of retroviral RNA is a complex process which depends on the orchestration of several steps throughout the virus life cycle. During the assembly of retroviruses, reverse transcriptase (RT) is directed into the virion as a component of the Gag-Pol polyprotein. In the maturation of the Gag-Pol polyprotein of human immunodeficiency virus type 1 (HIV-1), cleavage by the viral protease occurs during viral budding. After infection, reverse transcription of viral RNA into double-stranded DNA is completed in the cytoplasm of the infected cell. In this study, the processing and reverse transcription of HIV-1 have been examined by separate expression of mature HIV-1 RT and proviral molecules bearing RT mutations. The effects of RT expression in trans during virion release and after viral entry were investigated. Constitutive expression of HIV-1 RT was established in CD4- and non-CD4-expressing cells via the coexpression of its individual subunits, and three HIV-1 RT mutant constructs were generated. The results indicate that a bona fide RT trans complementation does not occur during virion release or after infection. However, after infection of an RT-expressing cell with a high titer RT-defective virus, intracellular reverse transcription can be detected.
Protein Adsorption onto Auto-Assembled Polyelectrolyte Films (2001)

We investigate the adsorption processes of a series of positively and negatively charged proteins onto the surface of polyelectrolyte multilayers. We find that proteins strongly interact with the polyelectrolyte film whatever the sign of the charge of both the multilayer and the protein. When the charges of the multilayer and the protein are similar, one usually observes the formation of protein monolayers which can become dense. We also show that when the protein and the multilayer become oppositely charged, the adsorbed amounts are usually larger and the formation of thick protein layers extending up to several times the largest dimension of the protein can be observed. Finally, we find that proteins are mainly adsorbed in a strong way on polyelectrolyte multilayers and protein surface diffusion is strongly suggested. Our results confirm that electrostatic interactions play an important role in polyelectrolyte multilayer/protein interactions.
Methods of reconstruction for bone defect after tumor excision: a review of alternatives. (2008)

Bone defect is a common problem encountered in the treatment of musculoskeletal tumor surgery. Allograft is a commonly used technique to reconstruct a large osseous defect following tumor excision in the United States and some European countries, and relatively good results have been reported because of its biologic nature. However, with the use of an allograft, there are concerns of transmission of infectious diseases, immunological reactions, and social or religious refusal in some regions in the world. Under these circumstances, vascularized autogenous fibular or iliac bone grafts are commonly used techniques and bone lengthening techniques using external fixation have been reported recently. These procedures utilize viable bone. In addition to these procedures, some biological reconstructive techniques utilizing nonviable bone have been performed as surgical alternatives for allografts using treated recycling bone including irradiated or pasteurized resected bone graft and reconstruction using an autograft containing tumor treated by liquid nitrogen. Although each technique has its proper advantages and disadvantages, the clinical results are similar to the allograft, and numerous techniques are now available as reasonable alternatives for allografts.
Inhibition of Angiogenesis by the Antifungal Drug Itraconazole (2007)

Angiogenesis, the formation of new blood vessels, is implicated in a number of important human diseases, including cancer, diabetic retinopathy, and rheumatoid arthritis. To identify clinically useful angiogenesis inhibitors, we assembled and screened a library of mostly Food and Drug Administration-approved drugs for inhibitors of human endothelial cell proliferation. One of the most promising and unexpected hits was itraconazole, a known antifungal drug. Itraconazole inhibits endothelial cell cycle progression at the G1 phase in vitro and blocks vascular endothelial growth factor/basic fibroblast growth factor-dependent angiogenesis in vivo. In attempts to delineate the mechanism of action of itraconazole, we found that human lanosterol 14alpha-demethylase (14DM) is essential for endothelial cell proliferation and may partially mediate the inhibition of endothelial cells by itraconazole. Together, these findings suggest that itraconazole has the potential to serve as an antiangiogenic drug and that lanosterol 14DM is a promising new target for discovering new angiogenesis inhibitors.
High- and Low-Risk Profiles for the Development of Multiple Sclerosis Within 10 Years After Optic Neuritis (2003)

The 10-year risk of multiple sclerosis following an initial episode of acute optic neuritis is significantly higher if there is a single brain MRI lesion; higher numbers of lesions do not appreciably increase that risk. However, even when brain lesions are seen on MRI, more than 40% of the patients will not develop clinical multiple sclerosis after 10 years. In the absence of MRI lesions, certain demographic and clinical features seem to predict a very low likelihood of developing multiple sclerosis. This natural history information is a critical input for estimating a patient's 10-year multiple sclerosis risk and for weighing the benefit of initiating prophylactic treatment at the time of optic neuritis or other initial demyelinating events in the central nervous system.