gebhart/patrepeval huggingface dataset:
Controlled Encapsidation of Gold Nanoparticles by a Viral Protein Shell (2006)

Icosahedral virus capsids demonstrate a high degree of selectivity in packaging cognate nucleic acid components during assembly. This packaging specificity, when integrated as part of a nanotechnological protocol, has the potential to encapsidate a wide array of foreign materials for delivery of therapeutics or biosensors into target cells. Red clover necrotic mosaic virus (RCNMV) exclusively packages two genomic ssRNAs initiated by a specific protein:RNA interaction between the RCNMV coat protein (CP) and the viral RNA origin of assembly (OAS) element. In the present work, an oligonucleotide mimic of the RCNMV OAS sequences is attached to Au nanoparticles as a recognition signal to initiate the virion-like assembly by RCNMV CP. Covalent linkage of the OAS to Au functions as a trigger for specific encapsidation and demonstrates that foreign cargo can be packaged into RCNMV virions.
Ordering Policy for Planned Maintenance with Salvage Value (2006)

A spare ordering policy is considered for planned maintenance. Introducing the ordering, uptime, downtime, inventory costs and salvage value, we derive the expected cost effectiveness. The problem is to determine jointly the ordering time for a spare and the preventive replacement time for the operating unit which maximize the expected cost effectiveness. Some properties regarding the optimal policy are derived, and a numerical example is included to explain the proposed model.
Effectiveness of Natalizumab in Patients with Highly Active Relapsing Remitting Multiple Sclerosis (2015)

Natalizumab is effective in patients with HA-RRMS. Baseline EDSS ≤3.0 increases the probability of remaining disease-free in HA-RRMS treated with natalizumab.
An ~4.35 Ga Ar-Ar Age for GRA 8 and the Complex Chronology of Its Parent Body (2010)

Introduction: GRA06128 and GRA06129 (hereafter GRA 8 and GRA 9) are partial melts of a parent body of approximately chondritic composition [1-3]. We [4,5] reported a conventional Sm-Nd isochron age of 4.559±0.096 Ga and a Sm-Nd model age of 4.549±0.036 for combined data for the two rocks. Plagioclase plus whole rock and leachate (~phosphate) samples gave a secondary Sm-Nd age of 3.4±0.4 Ga [5]. An Ar-Ar age of 4.460±0.028 Ga [3,6] was interpreted by [3] as dating metamorphism in GRA 9. We report Ar-Ar ages in the range ~4344-4366 Ma for GRA 8, establishing similar but different Ar-Ar ages for the two rocks, consistent with their different Sr-istopic systematics [5], and discuss these ages in the context of the complex sequence of events that affected these samples (cf. [3]). Ar-Ar Stepped Ar-Release Ages for GRA 8: We did a stepped-temperature Ar extraction (49 steps) of a plagioclase separate of GRA 8 (12.7 mg) of low magnetic susceptibility (Fig. 1). Small age variations occurred among “phases” with different K/Ca at low, intermediate, and high extraction temperatures, and the summed age is 4354 Ma. Partitioned according to the fraction of Ar released, the calculated ages varied from 4326±18 to 4344±14 to 4362±18 Ma (1 ) for 4-14%, 14-47%, and 52-96% Ar released, resp. A single temperature step for 47-52% of the Ar release appeared to mark a transition in the gas release mechanism as also seen in an Arrhenius plot constructed from the data (Fig. 2).
Properties of Slow Oscillation during Slow-Wave Sleep and Anesthesia in Cats (2011)

Deep anesthesia is commonly used as a model of slow-wave sleep (SWS). Ketamine-xylazine anesthesia reproduces the main features of sleep slow oscillation: slow, large-amplitude waves in field potential, which are generated by the alternation of hyperpolarized and depolarized states of cortical neurons. However, direct quantitative comparison of field potential and membrane potential fluctuations during natural sleep and anesthesia is lacking, so it remains unclear how well the properties of sleep slow oscillation are reproduced by the ketamine-xylazine anesthesia model. Here, we used field potential and intracellular recordings in different cortical areas in the cat to directly compare properties of slow oscillation during natural sleep and ketamine-xylazine anesthesia. During SWS cortical activity showed higher power in the slow/delta (0.1-4 Hz) and spindle (8-14 Hz) frequency range, whereas under anesthesia the power in the gamma band (30-100 Hz) was higher. During anesthesia, slow waves were more rhythmic and more synchronous across the cortex. Intracellular recordings revealed that silent states were longer and the amplitude of membrane potential around transition between active and silent states was bigger under anesthesia. Slow waves were mostly uniform across cortical areas under anesthesia, but in SWS, they were most pronounced in associative and visual areas but smaller and less regular in somatosensory and motor cortices. We conclude that, although the main features of the slow oscillation in sleep and anesthesia appear similar, multiple cellular and network features are differently expressed during natural SWS compared with ketamine-xylazine anesthesia.
ABROGATION OF THE IMMUNOSUPPRESSIVE EFFECT OF DONOR SPLEEN CELLS ON RENAL ALLOGRAFTS IN THE RAT BY IRRADIATION OR HEAT TREATMENT (1986)

In the donor-recipient strain combination Lewis (RT1l) to Dark Agouti (RT1a), indefinite renal allograft survival (MST greater than 100 days) was induced by pretreating recipient animals i.v. with 10(6) to 10(8) viable spleen lymphocytes, seven days before transplantation. Pretreatment with 10(4) or 10(5) cells was ineffective (MST 10 days). However when 10(7) live, but heat-treated (55 degrees C for 10 min) or irradiated (1000 rads) cells were used, all the animals rejected the allograft in a normal fashion (MST 10 and 11 days, respectively). Median survival time of third-party controls was 10 days. The relative amount of cell surface major histocompatibility antigens (class I and class II) expressed by the three spleen cell preparations was investigated using monoclonal antibodies and fluorescence activated cell sorter analysis and found to be similar. After 24 hr in culture, only 1% of heat-treated and 10% of irradiated cells were viable, in contrast to 75% of untreated splenocytes. Trafficking of these lymphocytes in recipient animals was investigated by 51chromium labeling of the cells: 30% of lymphocytes had localized in the liver within 3 hr with little difference in localization among the different cell preparations. But, although 20% of normal and irradiated cells localized in the spleen within 3 hr, at no stage were more than 5% of the heat-treated cells found in the spleen. It is suggested that the length of time viable donor lymphocytes remain in the recipient circulation is important in the induction of specific immunosuppression by spleen lymphocytes.
Loss of Methylthioadenosine Phosphorylase and Elevated Ornithine Decarboxylase Is Common in Pancreatic Cancer (2004)

MTAP activity is frequently lost, and ODC activity is frequently elevated in both pancreatic adenocarcinoma and neuroendocrine tumors. Inhibition of ODC activity caused decreased cell growth and increased apoptosis in pancreatic tumor-derived cell lines. These findings suggest that MTAP and polyamine metabolism could be potential therapeutic targets in the treatment of pancreatic cancer.
Combined Tetanus, Diphtheria, and 5-Component Pertussis Vaccine for Use in Adolescents and Adults (2005)

This Tdap vaccine elicited robust immune responses in adolescents and adults to pertussis, tetanus, and diphtheria antigens, while exhibiting an overall safety profile similar to that of a licensed Td vaccine. These data support the potential routine use of this Tdap vaccine in adolescents and adults.
[The quality of washed autotransfused erythrocytes. The elimination of plasma hemoglobin, osmotic fragility and survival rate of retransfused erythrocytes]. (1986)

Intraoperative transfusion has until recently been understood to mean full retransfusion of the blood removed by a suction pump without significant changes due to external influences, which considerably limited its utilization. Intraoperative transfusion can only be performed without decisive disadvantages when the blood can be suctionally removed in large amounts and immediately retransfused. In recent years, the Cell Saver has provided a system which can also prepare soiled blood for retransfusion. Extensive orthopedic surgery entails large blood losses due to oozing from expanded wound areas; only rarely does acute bleeding occur. Because of intensive tissue contact, the suctioned blood has been soiled with activated clotting factors, lytic enzymes, free haemoglobin from damaged red cells, cleaning solutions, and other undesired elements. With the Cell Saver system, it is possible to remove the plasma and recover 70-80% of the intact red cells sufficiently freed from stroma and free haemoglobin. The osmotic fragility of these cells served as a measure of integrity and membrane stability. They were compared to red cells withdrawn preoperatively and showed an identical osmotic relationship. Determining the survival rate of the retransfused cells in vivo shows that they provide a high-quality and in most cases, a sufficient replacement of blood loss. Even after 6 days, over 70% were found in the circulating blood. Premature, disproportionate elimination, which could be dangerous for the patient, does not occur.
Surface properties of styrene–ethylene oxide block copolymers (1976)

Abstract Hydrophobic–hydrophilic block copolymers were prepared by “living” anionic polymerization. They consist of polystyrene and poly(ethylene oxide) blocks, and are soluble in water. Their interfacial properties were investigated, employing aqueous solutions. The block copolymers lowered the surface tension of water in analogy with the low molecular weight surfactants such as sodium lauryl sulfate and heptaethylene oxide n ‐dodecyl ether. Their aqueous solutions exhibited solubilization properties differing from those of polyethylene glycol. Therefore, it is thought that the polystyrene blocks produce solubilization phenomena. In samples of the same styrene content, the precipitation temperature of a high molecular weight copolymer in water was lower than that of a low molecular weight copolymer at the same concentration in the same solvent. The surface tension and precipitation temperature of aqueous solutions seem to be influenced by molecular weight and composition.
Anonymity: A Formalization of Privacy - '-Diversity (2013)

Anonymization of published microdata has become a very important topic nowadays. The major diculty is to publish data of individuals in a manner that the released table both provides enough information to the public and prevents disclosure of sensitive information. Therefore, several authors proposed definitions of privacy to get anonymous microdata. One definition is called k-Anonymity and states that every individual in one generalized block is indistinguishable from at least k - 1 other individuals. ‘-Diversity uses a stronger privacy definition and claims that every generalized block has to contain at least ‘ dierent sensitive values. Another definition is called t-Closeness. It demands that the distribution of one sensitive value of a generalized block is close to its distribution in the entire table. This paper mainly deals with the principle and notion of ‘Diversity. Therefore, two methods called Homogeneity and Background-Knowledge Attack are discussed to break the privacy constraints of k-Anonymity. Then a model to reason about privacy in microdata, namely Bayes-Optimal Privacy, is introduced. Based on k-Anonymity and Bayes-Optimal Privacy the principle and several instantiations of ‘-Diversity are discussed. At the end ‘-Diversity is applied to a real database gathered from several Android devices.
Identification of Critical Amino Acids within the Nucleoprotein of Tacaribe Virus Important for Anti-interferon Activity (2013)

The arenavirus nucleoprotein (NP) can suppress induction of type I interferon (IFN). This anti-IFN activity is thought to be shared by all arenaviruses with the exception of Tacaribe virus (TCRV). To identify the TCRV NP amino acid residues that prevent its IFN-countering ability, we created a series of NP chimeras between residues of TCRV NP and Pichinde virus (PICV) NP, an arenavirus NP with potent anti-IFN function. Chimera NP analysis revealed that a minimal four amino acid stretch derived from PICV NP could impart efficient anti-IFN activity to TCRV NP. Strikingly, the TCRV NP gene cloned and sequenced from viral stocks obtained through National Institutes of Health Biodefense and Emerging Infections (BEI) resources deviated from the reference sequence at this particular four-amino acid region, GPPT (GenBank KC329849) versus DLQL (GenBank NC004293), respectively at residues 389-392. When efficiently expressed in cells through codon-optimization, TCRV NP containing the GPPT residues rescued the antagonistic IFN function. Consistent with cell expression results, TCRV infection did not stimulate an IFNβ response early in infection in multiple cells types (e.g. A549, P388D1), and IRF-3 was not translocated to the nucleus in TCRV-infected A549 cells. Collectively, these data suggest that certain TCRV strain variants contain the important NP amino acids necessary for anti-IFN activity.
Fabrication of digital sinusoidal gratings and precisely controlled diffusive flats and their application to highly accurate projected fringe profilometry (2003)

Fabrication of digital sinusoidal gratings and precisely controlled diffusive flats and their application to calibration-based highly accurate phase-shifting projected fringe profilometry are presented. The main advantages of using digital sinusoidal gratings are (1) high geometrical accuracy (< 1 μm); (2) high contrast ratio; and (3) very low high-order harmonic distortion. In addition, a high-quality diffusive flat with precisely controlled lateral correlation length, fabricated by VLSI processes, offers a good calibration standard. It is found that, by applying these two components to the calibration-based phase-shifting projected fringe profilometry, absolute 3-D surface profile measurement accuracy on the order of microns can be achieved.
Two African Viruses Serologically and Morphologically Related to Rabies Virus (1970)

Lagos bat virus and an isolate from shrews (IbAn 27377), both from Nigeria, were found to be bullet-shaped and to mature intracytoplasmically in association with a distinct matrix. They were related to, but readily distinguishable from, rabies virus and each other by complement fixation and neutralization tests. The three viruses, including rabies, form a subgrouping within the rhabdoviruses.
A Collection of Robust Organic Synthesis Reactions for <i>In Silico</i> Molecule Design (2011)

A focused collection of organic synthesis reactions for computer-based molecule construction is presented. It is inspired by real-world chemistry and has been compiled in close collaboration with medicinal chemists to achieve high practical relevance. Virtual molecules assembled from existing starting material connected by these reactions are supposed to have an enhanced chance to be amenable to real chemical synthesis. About 50% of the reactions in the dataset are ring-forming reactions, which fosters the assembly of novel ring systems and innovative chemotypes. A comparison with a recent survey of the reactions used in early drug discovery revealed considerable overlaps with the collection presented here. The dataset is available encoded as computer-readable Reaction SMARTS expressions from the Supporting Information presented for this paper.
The Herpesvirus Proteases as Targets for Antiviral Chemotherapy (2000)

Viruses of the family Herpesviridae are responsible for a diverse set of human diseases. The available treatments are largely ineffective, with the exception of a few drugs for treatment of herpes simplex virus (HSV) infections. For several members of this DNA virus family, advances have been made recently in the biochemistry and structural biology of the essential viral protease, revealing common features that may be possible to exploit in the development of a new class of anti-herpesvirus agents. The herpesvirus proteases have been identified as belonging to a unique class of serine protease, with a Ser-His-His catalytic triad. A new, single domain protein fold has been determined by X-ray crystallography for the proteases of at least three different herpesviruses. Also unique for serine proteases, dimerization has been shown to be required for activity of the cytomegalovirus and HSV proteases. The dimerization requirement seriously impacts methods needed for productive, functional analysis and inhibitor discovery. The conserved functional and catalytic properties of the herpesvirus proteases lead to common considerations for this group of proteases in the early phases of inhibitor discovery. In general, classical serine protease inhibitors that react with active site residues do not readily inactivate the herpesvirus proteases. There has been progress however, with activated carbonyls that exploit the selective nucleophilicity of the active site serine. In addition, screening of chemical libraries has yielded novel structures as starting points for drug development. Recent crystal structures of the herpesvirus proteases now allow more direct interpretation of ligand structure-activity relationships. This review first describes basic functional aspects of herpesvirus protease biology and enzymology. Then we discuss inhibitors identified to date and the prospects for their future development.
Understanding and detecting performance and security bugs in IOT OSes (2016)

Operating system (OS) plays an important role in the efficiency and security of service in Internet of Things (IOT). Considering the limited storage resources and power utilization mechanism in IOT OS, we explore the performance bugs and security bugs of three open source IOT OS (Contiki, TinyOS and RIOT OS), including the features of bugs cause, bugs mitigation, bugs detection rules and bugs fixing in them. We present Rulede, a tool built on LLVM compiler framework to find bugs. Experimental results show that Rulede can effectively detect performance bugs and security bugs in target IOT OSes.
Modelling of nonideal active devices in continuous-time OTA-C filters (1989)

Linear and nonlinear modelling of the operational transconductance amplifier (OTA) are presented, allowing the significant device imperfections to be identified under various bias conditions. Their effects are quantified for bandpass filter examples and have close agreement with SPICE-evaluated and measured results. Stability and dynamic range are also discussed. >
Insulin-Like Growth Factor-1 Enhances Inflammatory Responses in Endothelial Cells (2002)

Insulin-like growth factor (IGF)-1 and the type I IGF-1 receptor are important regulators of vascular function that may contribute to cardiovascular disease. We hypothesized that IGF-1 causes endothelial cell dysfunction and expression of neutrophil and monocyte adhesion molecules by enhancing pro-inflammatory cytokine signal transduction. Long-term IGF-1 treatment of endothelial cells potentiated c-Jun and nuclear factor NF-kappaB activation by tumor necrosis factor (TNF)-alpha and enhanced TNF-alpha-mediated adhesion molecule expression. In response to IGF-1 treatment, the expression of kinases in the c-Jun/c-Jun NH(2)-terminal kinase signaling pathway (MEKK1, MEK4, and JNK1/2) was unchanged, but expressions of insulin receptor substrate-1 and Grb2-associated binder-1 (Gab1) were significantly decreased. Because Gab1 is involved in both c-Jun and NF-kappaB activation by TNF-alpha, we focused on Gab1-dependent signaling. Gab1 inhibited c-Jun and NF-kappaB transcriptional activation by TNF-alpha. Interestingly, Gab1 inhibited c-Jun transcriptional activity induced by MEKK3 but not MEKK1 and MEK4. Gab1 associated with MEKK3, and a catalytically inactive form of MEKK3 inhibited TNF-alpha-induced c-Jun and NF-kappaB transcriptional activation, suggesting a critical role for Gab1 and MEKK3 in TNF-alpha signaling. These data demonstrate that Gab1 and MEKK3 play important roles in endothelial cell inflammation via regulating the activation of c-Jun and NF-kappaB. Furthermore, the IGF-1-mediated downregulation of Gab1 expression represents a novel mechanism to promote vascular inflammation and atherosclerosis.
Synthesis, Crystal Structure, Stacking Effect and Antibacterial Studies of a Novel Quaternary Copper (II) Complex with Quinolone (2003)

The structural properties of a new copper (II) complex [Cu2(cip)2(bpy)2(pip)]·6H2O (bpy=2,2’-bipyridyl, cip=1-cyclopropyl-6-4-oxo-1,4-dihydroquinoline-3-carboxylic acid, pip= piperazinyl anion), obtained during the synthesis of the copper complex with ciprofloxacin (cpf), has been investigated. The complex crystallizes in the triclinic system, space group P-1. The cell dimensions are: a=6.874(2) Å, b= 10.761(3) Å, c= 17.969(5) Å, α =80.071(6)°, β= 85.253(6)°, γ=79.109(6)°，V=1284.5(6) Å3, and Z=2. The Cu (II) ion displays a five-coordinate square pyramidal coordination with two nitrogen donors from bpy, the 4-keto and 3-carboxylate oxygen donors of cip, and the third nitrogen atom of the pip anion occupying the fifth site. There is a stack effect between cip ring and bpy ring from another molecule, where the stacking distance is about 3.5 Å. The results of elemental analysis and FT-IR measurement are also included. Both ligand and complex were assayed against gram-positive and gram-negative bacteria by the doubling dilutions method. The complex shows the same minimal inhibitory concentration (MIC) against S. Aureus and E. Coli bacteria as the corresponding ligand.
New .kappa.-receptor agonists based upon a 2-[(alkylamino)methyl]piperidine nucleus (1992)

The syntheses of some 1-[(3,4-dichlorophenyl)acetyl]-2- [(alkylamino)methyl]piperidines and their activities as kappa-opioid receptor agonists are described. Selected structural modifications are made to the basic moiety and at the 2-, 3-, 4-, 5-, and 6-positions on the piperidine nucleus to enable structure-activity relationships to be delineated. As a result, some highly potent and selective kappa-receptor agonists have been identified. In particular, this has been achieved by introduction of oxygen-containing functionality into the 4-position of the piperidine nucleus or the 3-position of the pyrrolidinylmethyl side chain. Thus, 1-[(3,4-dichlorophenyl)acetyl]- 2-[[1-(3-oxopyrrolidinyl)]methyl]piperidine (10) possesses high activity in the rabbit vas deferens (LVD, kappa-specific tissue) (IC50 = 0.20 nM) and is a potent antinociceptive agent, as determined by the mouse acetylcholine-induced abdominal constriction test (MAC) (ED50 = 0.06 mg/kg, sc). The spirocyclic analogue 8-[(3,4-dichlorophenyl)acetyl]-7-(1-pyrrolidinylmethyl)-1,4-dio xa-8- azaspirol4.5]decane (39) showed exceptionally potent activity: LVD, IC50 = 0.10 nM; MAC, ED50 = 0.001 mg/kg, sc. Both 10 and 39 displayed high selectivity for kappa-opioid receptors over both mu- and delta-opioid receptor subtypes.
Arabidopsis R-SNARE Proteins VAMP721 and VAMP722 Are Required for Cell Plate Formation (2011)

These observations suggest that VAMP721 and VAMP722 are involved in secretory trafficking to the plasma membrane via TGN/early endosomal compartment, which contributes substantially to cell plate formation during plant cytokinesis.