gebhart/patrepeval huggingface dataset:
Species-Specific Variation in the B30.2(SPRY) Domain of TRIM5α Determines the Potency of Human Immunodeficiency Virus Restriction (2005)

Retroviruses encounter dominant postentry restrictions in cells of particular species. Human immunodeficiency virus type 1 (HIV-1) is blocked in the cells of Old World monkeys by TRIM5alpha, a tripartite motif (TRIM) protein composed of RING, B-box 2, coiled-coil, and B30.2(SPRY) domains. Rhesus monkey TRIM5alpha (TRIM5alpha(rh)) more potently blocks HIV-1 infection than human TRIM5alpha (TRIM5alpha(hu)). Here, by studying chimeric TRIM5alpha proteins, we demonstrate that the major determinant of anti-HIV-1 potency is the B30.2(SPRY) domain. Analysis of species-specific variation in TRIM5alpha has identified three variable regions (v1, v2, and v3) within the B30.2 domain. The TRIM5alpha proteins of Old World primates exhibit expansion, duplication, and residue variation specifically in the v1 region. Replacement of three amino acids in the N terminus of the TRIM5alpha(hu) B30.2 v1 region with the corresponding TRIM5alpha(rh) residues resulted in a TRIM5alpha molecule that restricted HIV-1 nearly as efficiently as wild-type TRIM5alpha(rh). Surprisingly, a single-amino-acid change in this region of TRIM5alpha(hu) allowed potent restriction of simian immunodeficiency virus, a phenotype not observed for either wild-type TRIM5alpha(hu) or TRIM5alpha(rh). Some of the chimeric TRIM5alpha proteins that are >98% identical to the human protein yet mediate a strong restriction of HIV-1 infection may have therapeutic utility. These observations implicate the v1 variable region of the B30.2(SPRY) domain in TRIM5alpha(rh) antiviral potency.
Real-time 3D scene layout from a single image using Convolutional Neural Networks (2016)

We consider the problem of understanding the 3D layout of indoor corridor scenes from a single image in real time. Identifying obstacles such as walls is essential for robot navigation, but also challenging due to the diversity in structure, appearance and illumination of real-world corridor scenes. Many current single-image methods make Manhattan-world assumptions, and break down in environments that do not meet this mold. They also may require complicated hand-designed features for image segmentation or clear boundaries to form certain building models. In addition, most cannot run in real time. In this paper, we propose to combine machine learning with geometric modelling to build a simplified 3D model from a single image. We first employ a supervised Convolutional Neural Network (CNN) to provide a dense, but coarse, geometric class labelling of the scene. We then refine this labelling with a fully connected Conditional Random Field (CRF). Finally, we fit line segments along wall-ground boundaries and “pop up” a 3D model using geometric constraints. We assemble a dataset of 967 labelled corridor images. Our experiments on this dataset and another publicly available dataset show our method outperforms other single image scene understanding methods in pixelwise accuracy while labelling images at over 15Hz.
Induction of Antitumor Acquired Immunity by Baculovirus <i>Autographa californica</i> Multiple Nuclear Polyhedrosis Virus Infection in Mice (2007)

The baculovirus Autographa californica multiple nuclear polyhedrosis virus (AcMNPV) has been studied as a gene therapy vector. Here, we demonstrated that AcMNPV induces antitumor acquired immunity. These results suggest that AcMNPV has the potential to be an efficient virus or tumor therapy agent which induces innate and acquired immunity.
Protein kinase A regulation of cAMP phosphodiesterase expression in rat skeletal myoblasts. (1994)

We have been studying cAMP signaling in L6 myoblasts because of its potential role in regulating the differentiation of these cells into multinucleate myotubes. Previous studies have shown that treatment of L6 myoblasts with cAMP analogs causes an increase in cAMP phosphodiesterase activity. To assess the role of protein kinase A in this cAMP-mediated increase in cAMP phosphodiesterase activity, L6 myoblasts were transfected with a plasmid containing the cDNA for a mutant regulatory subunit of protein kinase A, which functions as a dominant negative inhibitor of this enzyme. The cDNA was under control of the metallothionein promoter in the construct. Induction of the mutant regulatory subunit with Zn2+ decreased cAMP-dependent protein kinase activity by 90%. Zn2+ treatment was also able to completely block the cAMP-mediated increase in phosphodiesterase activity, showing that this effect is mediated by protein kinase A. The activity of the cAMP-induced phosphodiesterase was inhibited by low concentrations of RO 20-1724, showing that it was a member of the type IV low Km cAMP phosphodiesterase family of enzymes. We used the polymerase chain reaction and consensus primers designed to amplify phosphodiesterase sequences to show that L6 myoblasts also contain mRNA for a type IV low Km cAMP phosphodiesterase designated PDE3.1. The levels of this mRNA were increased greatly by treatment with dibutyryl cAMP or forskolin in L6 myoblasts and also in differentiated L6 myotubes. Run-off transcription assays showed that this increase in PDE mRNA was regulated, at least in part, by an increase in the rate of transcription of the PDE3 gene. The induction of PDE3 message by cAMP was blocked when the L6 transfectants were treated with Zn2+ to induce protein kinase A inhibition. Therefore, some of the cAMP-mediated increase in phosphodiesterase activity seen in L6 myoblasts is due to a protein kinase A-mediated increase in PDE3 mRNA. This pathway may serve as a feedback mechanism to modulate the inhibitory effects of cAMP on myogenesis.
Neochloris oleabundans UTEX #1185: a suitable renewable lipid source for biofuel production (2009)

Energy crises, global warming, and climatic changes call for technological and commercial advances in manufacturing high-quality transportation fuels from unconventional feedstocks. Microalgae is one of the most promising sources of biofuels due to the high yields attained per unit area and because it does not displace food crops. Neochloris oleabundans (Neo) microalga is an important promising microbial source of single-cell oil (SCO). Different experimental growth and lipid production conditions were evaluated and compared by using optical density (540 nm), dry-weight determination, and flow cytometry (FC). Best Neo average biomass productivity was obtained at 30 degrees C under conditions of nitrogen-sufficiency and CO(2) supplementation (N+/30 degrees C/CO(2)), with an average doubling time of 1.4 days. The second and third highest productivities occurred with N-sufficient cultures without CO(2) supplementation at 26 degrees C (N+/26 degrees C) and at 30 degrees C (N+/30 degrees C), with doubling times of 1.7 and 2.2 days, respectively. Microbial lipid production was monitored by flow cytometry using Nile red (NR), a lipophilic fluorochrome that possesses several advantageous characteristics for in situ screening near real time (at line). Results showed maximum lipid content (56%) after 6 days of nitrogen depletion under nitrogen starvation without CO(2) supplementation (N-/30 degrees C), followed by N-/30 degrees C/CO(2) and N-/26 degrees C conditions with 52% lipid content, after 5 and 6 days of N starvation, respectively. The adequate fatty acid profile and iodine value of Neo lipids reinforced this microalga as a good source of SCO, in particular for use as biodiesel.
ChemInform Abstract: Multilevel Selectivity in the Mild and High‐Yielding Chlorosilane‐Induced Cleavage of Carbamates to Isocyanates. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Membrane Proximal Region of the Integrin β Cytoplasmic Domain Can Mediate Oligomerization (1998)

Integrin-ligand binding generates many intracellular signals, including signals to initiate focal contact formation and to regulate cellular decisions concerning growth and differentiation. Oligomerization of the beta subunit cytoplasmic domain appears to be required for many of these events. In order to study these processes, we have generated a novel chimeric protein, consisting of the chicken integrin beta 1 cytoplasmic domain connected to the central rod domain of a neuronal intermediate filament, alpha-internexin. This chimeric protein, when expressed transiently in 293T cells, oligomerizes in a beta cytoplasmic domain-dependent manner. This oligomerization requires the membrane proximal amino acids LLMII of the beta 1 cytoplasmic domain, as demonstrated by deletion analysis. Therefore, the integrin beta cytoplasmic domain in this system contains an oligomerization function, which may provide some insight as to the function of intact integrins in vivo.
Antiherpesviral and anticellular effects of 1-beta-D-arabinofuranosyl-E-5-(2-halogenovinyl) uracils (1981)

1-beta-D-arabinofuranosyl-E-5-(2-bromovinyl) uracil (BV-ara-U) and 1-beta-D-arabinofuranosyl-E-5-(2-chlorovinyl)uracil (CV-ara-U) were tested for their anti-herpesviral activity in virus rating method, a plaque reduction method, and a virus yield reduction method, using human embryonic lung fibroblast (HEL-F) cells, At a concentration as low as 0.1 microgram/ml, both drugs exerted a marked inhibitory effect on the development of cytopathogenic effect induced by herpes simplex virus type 1 (HSV-1) infection and on the multiplication and plaque formation of HSV-1. Neither BV-ara-U nor CV-ara-U was significantly active against HSV type 2 (HSV-2). They scarcely inhibited growth of HEL-F cells, mouse L, and murine leukemia cells. Compared with 1-beta-D-arabinofuranosylthymine and 5-iodo-deoxyuridine, BV-ara-U and CV-ara-U were more than 10 times as active against HSV-1 and much less active against HSV-2. BV-ara-U was as active as E-5-(2-bromovinyl)-2'-deoxyuridine against HSV-1 and less inhibitory to growth of HEL-F cells. Cellular deoxyribonucleic acid synthesis was not significantly influenced by the new derivatives of arabinosyluracil, even at a concentration as high as 300 microgram/ml. The derivatives showed extremely marked inhibition of deoxyribonucleic acid synthesis in HSV-1-infected cells, whereas their inhibitory effect on deoxyribonucleic acid synthesis in HSV-2-infected cells was much lower than that in HSV-1-infected cells. These findings indicate that BV-ara-U and CV-ara-U are selectively inhibitory to HSV-1 multiplication.
Selective binding of looped oligonucleotides to a single-stranded DNA and its influence on replication<i>in vitro</i> (1995)

Complexing of looped and circular oligonucleotides, composed of either 2'-deoxyribo- or 2'-O-methylribonucleoside units, with completely matching or partially mismatching complementary DNA sequences was studied. Melting experiments revealed considerable differences among the stabilities of these hybrid complexes. Maximum stability and selectivity was displayed by oligomers 2 and 5. It was concluded that a linear stretch, attached to 1'-O- of 3'-deoxypsicothymidine unit (Z) increases the selectivity of hybridisation and stability of the complex as a whole. This allows one to aim the target DNA very precisely at its polyadenine part as well as at adjacent sequence simultaneously. Experiments on termination of primer extension catalysed by different DNA-polymerases--Sequenase, Klenow fragment and Tth--have demonstrated that looped oligomer 5, composed of 2'-O-methylribonucleosides appears to be a highly selective and potent inhibitor of replication in vitro. Features of looped oligonucleotides, composed of 2'-O-methylribonucleosides seem to be useful for design of highly specific antigene oligonucleotides.
Meriolins (3-(Pyrimidin-4-yl)-7-azaindoles): Synthesis, Kinase Inhibitory Activity, Cellular Effects, and Structure of a CDK2/Cyclin A/Meriolin Complex (2008)

We report the synthesis and biological characterization of 3-(pyrimidin-4-yl)-7-azaindoles (meriolins), a chemical hybrid between the natural products meridianins and variolins, derived from marine organisms. Meriolins display potent inhibitory activities toward cyclin-dependent kinases (CDKs) and, to a lesser extent, other kinases (GSK-3, DYRK1A). The crystal structures of 1e (meriolin 5) and variolin B (Bettayeb, K.; Tirado, O. M.; Marionneau-Lambert, S.; Ferandin, Y.; Lozach, O.; Morris, J.; Mateo-Lozano, S.; Drückes, P.; Schächtele, C.; Kubbutat, M.; Liger, F.; Marquet, B.; Joseph, B.; Echalier, A.; Endicott, J.; Notario, V.; Meijer, L. Cancer Res. 2007, 67, 8325-8334) in complex with CDK2/cyclin A reveal that the two inhibitors are orientated in very different ways inside the ATP-binding pocket of the kinase. A structure-activity relationship provides further insight into the molecular mechanism of action of this family of kinase inhibitors. Meriolins are also potent antiproliferative and proapoptotic agents in cells cultured either as monolayers or in spheroids. Proapoptotic efficacy of meriolins correlates best with their CDK2 and CDK9 inhibitory activity. Meriolins thus constitute a promising class of pharmacological agents to be further evaluated against the numerous human diseases that imply abnormal regulation of CDKs including cancers, neurodegenerative disorders, and polycystic kidney disease.
Reconfigurable intelligent sensors for health monitoring: a case study of pulse oximeter sensor (2005)

Design of low-cost, miniature, lightweight, ultra low-power, intelligent sensors capable of customization and seamless integration into a body area network for health monitoring applications presents one of the most challenging tasks for system designers. To answer this challenge we propose a reconfigurable intelligent sensor platform featuring a low-power microcontroller, a low-power programmable logic device, a communication interface, and a signal conditioning circuit. The proposed solution promises a cost-effective, flexible platform that allows easy customization, run-time reconfiguration, and energy-efficient computation and communication. The development of a common platform for multiple physical sensors and a repository of both software procedures and soft intellectual property cores for hardware acceleration will increase reuse and alleviate costs of transition to a new generation of sensors. As a case study, we present an implementation of a reconfigurable pulse oximeter sensor.
GaN power device and reliability for automotive applications (2012)

Many power switching devices are used in a hybrid vehicle (HV) and an electric vehicle (EV) systems. For future development of the HV/EV, higher performances than Si power device, for example, low on-resistance, high speed, high operation temperature, are strongly required. GaN power devices are promising candidate for the requirements. Present status of the GaN power device development is presented. Reliability of the GaN power device was also discussed.
Realization of optimized quantum controlled-logic gate based on the orbital angular momentum of light (2016)

We propose and experimentally demonstrate an optimized setup to implement quantum controlled-NOT operation using polarization and orbital angular momentum qubits. This device is more adaptive to inputs with various polarizations, and can work both in classical and quantum single-photon regime. The logic operations performed by such a setup not only possess high stability and polarization-free character, they can also be easily extended to deal with multi-qubit input states. As an example, the experimental implementation of generalized three-qubit Toffoli gate has been presented.
TGF-β2: A Novel Target of CD44-Promoted Breast Cancer Invasion (2013)

We have developed a tetracycline (tet)-off regulated expression of CD44s gene in the breast cancer (BC) cell line MCF-7 (B5 clone) and identified TGF-β2 (Transforming Growth Factor beta-2; 3 fold induction) as a potential CD44-downstream transcriptional target by microarray analysis. To further validate this finding, the same RNA samples, used for microarray analysis and their corresponding protein lysates, collected from the BC cell line MCF-7-B5, were examined for CD44 expression in the presence of HA. Our results showed that TGF-β2 mRNA levels were significantly elevated following the removal of tetracycline at 18, 24, and 48 h post-HA stimulation compared to the parental cells. Furthermore, the TGF-β2 precursor protein increased in a time-dependent pattern upon HA-stimulation and in the absence of tetracycline. More interestingly, inhibition of CD44 gene by RNAi method decreased TGF-β2 expression upon HA-stimulation, and subsequently inhibited BC cell invasion in vitro. In addition to identifying TGF-β2 as a target for HA/CD44 signaling, this data suggests that ATF/CREB might be a potential transcription factor linking HA/CD44 activation to TGF-β2 transcription and additional experiments are required for a better understanding of the molecular mechanisms underpinning the novel function of the CD44/ TGF-β2 signaling pathway in breast cancer metastasis.
Cardiomyocyte Transplantation in a Porcine Myocardial Infarction Model (1998)

Transplantation of cardiomyocytes into the heart is a potential treatment for replacing damaged cardiac muscle. To investigate the feasibility and efficiency of this technique, either a cardiac-derived cell line (HL-1 cells), or normal fetal or neonatal pig cardiomyocytes were grafted into a porcine model of myocardial infarction. The myocardial infarction was created by the placement of an embolization coil in the distal portion of the left anterior descending artery in Yorkshire pigs (n = 9). Four to 5 wk after creation of an infarct, the three preparations of cardiomyocytes were grafted, at 1 × 10 6 cells/20 μL into normal and into the middle of the infarcted myocardium. The hearts were harvested and processed for histologic examinations 4 to 5 wk after the cell grafts. Histologic evaluation of the graft sites demonstrated that HL-1 cells and fetal pig cardiomyocytes formed stable grafts within the normal myocardium without any detrimental effect including arrhythmia. In addition, a marked increase in angiogenesis was observed both within the grafts and adjacent host myocardium. Electron microscopy studies demonstrated that fetal pig cardiomyocytes and the host myocardial cells were coupled with adherens-type junctions and gap junctions. Histologic examination of graft sites from infarct tissue failed to show the presence of grafted HL-1 cells, fetal, or neonatal pig cardiomyocytes. Cardiomyocyte transplantation may provide the potential means for cell-mediated gene therapy for introduction of therapeutic molecules into the heart.
Accurate tuning of mismatched twin-core fiber filters (1998)

We have demonstrated a reproducible and accurate way of tuning the coupling wavelength of a mismatched twin-core filter. This method allows high quality all-fiber filters to be implemented with low loss at any desired wavelength over a range of few hundred nanometers from the same fiber. An ~500-nm tuning range is demonstrated, limited only by the measurement setup and not by the technique itself. Highly accurate control of the filtering wavelength in combination with control of filtering strength by adjustment of the length of the twin-core fibers allows complex filter profiles to be implemented by cascading of several different filters. These filters are also very stable to a change in temperature (~0.26 nm/100 degrees C at 1.55 microm) and strain (less than 0.3 nm/mstrain at 1.55 microm), permitting easy packaging.
Diarrheagenic<i>Escherichia coli</i> (1998)

Escherichia coli is the predominant nonpathogenic facultative flora of the human intestine. Some E. coli strains, however, have developed the ability to cause disease of the gastrointestinal, urinary, or central nervous system in even the most robust human hosts. Diarrheagenic strains of E. coli can be divided into at least six different categories with corresponding distinct pathogenic schemes. Taken together, these organisms probably represent the most common cause of pediatric diarrhea worldwide. Several distinct clinical syndromes accompany infection with diarrheagenic E. coli categories, including traveler's diarrhea (enterotoxigenic E. coli), hemorrhagic colitis and hemolytic-uremic syndrome (enterohemorrhagic E. coli), persistent diarrhea (enteroaggregative E. coli), and watery diarrhea of infants (entero-pathogenic E. coli). This review discusses the current level of understanding of the pathogenesis of the diarrheagenic E. coli strains and describes how their pathogenic schemes underlie the clinical manifestations, diagnostic approach, and epidemiologic investigation of these important pathogens.
Multiple input DC-DC power converter for fuel-cell powered hybrid vehicles (2003)

Customer demands for greater acceleration, performance, and vehicle range in pure EVs plus mandated requirements to further reduce emissions in HEVs increase the appeal for combined on-board energy storage systems and generators. This paper deals with a multiple input DC-DC power converter devoted to combine the power flow of multi-source on-board energy systems. The proposed energy storage arrangement includes fuel cell generator, ultracapacitor tank, and battery system. Possibility of optimization of the output capacitors bank in relation to the RMS value of the current ripple is investigated.