gebhart/patrepeval huggingface dataset:
Haloperidol-Based Irreversible Inhibitors of the HIV-1 and HIV-2 Proteases (1994)

The proteases expressed by the HIV-1 and HIV-2 viruses process the polyproteins encoded by the viral genomes into the mature proteins required for virion replication and assembly. Eight analogs of haloperidol have been synthesized that cause time-dependent inactivation of the HIV-1 protease and, in six cases, HIV-2 protease. The IC50 values for the analogues are comparable to that of haloperidol itself. Enzyme inactivation is due to the presence of an epoxide in two of the analogues and carbonyl-conjugated double or triple bonds in the others. Irreversible inactivation is confirmed by the failure to recover activity when one of the inhibitors is removed from the medium. At pH 8.0, the agents inactivate the HIV-1 protease 4-80 times more rapidly than the HIV-2 protease. Faster inactivation of the HIV-1 protease is consistent with alkylation of cysteine residues because the HIV-1 protease has four such residues whereas the HIV-2 protease has none. Inactivation of the HIV-2 protease requires modification of non-cysteine residues. The similarities in the rates of inactivation of the HIV-2 protease by six agents that have intrinsically different reactivities toward nucleophiles suggest that the rate-limiting step in the inactivation process is not the alkylation reaction itself. At least five of the agents inhibit polyprotein processing in an ex vivo cell assay system, but they are also toxic to the cells.
Silica gel impregnated with iron(III) salts: A safe humidity indicator (2002)

Silica gel impregnated with iron(III) salts functions as a humidity indicator, turning from a deep amber color when dry, to nearly colorless when humidified. The mechanism is proposed as being the result of the formation of species with Fe-OH-Si bridges. These are thought to be highly colored when dry buy dissociate into pale colored monomeric iron(III) species when exposed to moisture.
Release of Dengue Virus Genome Induced by a Peptide Inhibitor (2012)

Dengue virus infects approximately 100 million people annually, but there is no available therapeutic treatment. The mimetic peptide, DN59, consists of residues corresponding to the membrane interacting, amphipathic stem region of the dengue virus envelope (E) glycoprotein. This peptide is inhibitory to all four serotypes of dengue virus, as well as other flaviviruses. Cryo-electron microscopy image reconstruction of dengue virus particles incubated with DN59 showed that the virus particles were largely empty, concurrent with the formation of holes at the five-fold vertices. The release of RNA from the viral particle following incubation with DN59 was confirmed by increased sensitivity of the RNA genome to exogenous RNase and separation of the genome from the E protein in a tartrate density gradient. DN59 interacted strongly with synthetic lipid vesicles and caused membrane disruptions, but was found to be non-toxic to mammalian and insect cells. Thus DN59 inhibits flavivirus infectivity by interacting directly with virus particles resulting in release of the genomic RNA.
Iridoids from <i>Fraxinus excelsior</i> with Adipocyte Differentiation-Inhibitory and PPARα Activation Activity (2009)

Two new secoiridoid glucosides, excelsides A (1) and B (2), were isolated from the seeds of Fraxinus excelsior. Their structures were elucidated as (2S,4S,3E)-methyl 3-ethylidene-4-(2-methoxy-2-oxoethyl)-2-[(6-O-beta-D-glucopyranosyl-beta-d-glucopyranosyl)oxy]-3,4-dihydro-2H-pyran-5-carboxylate and (2S,4S,3E)-methyl 3-ethylidene-4-{2-[2-(4-hydroxyphenyl)ethyl]oxy-2-oxoethyl}-2-[(6-O-beta-d-glucopyranosyl-beta-d-glucopyranosyl)oxy]-3,4-dihydro-2H-pyran-5-carboxylate, respectively, on the basis of NMR and MS data. Eight known compounds were identified as nuzhenide (3), GI3 (4), GI5 (5), ligstroside (6), oleoside 11-methyl ester (7), oleoside dimethyl ester (8), 1'''-O-beta-D-glucosylformoside (9), and salidroside (10). Compounds 1-9 inhibited adipocyte differentiation in 3T3-L1 cells. Dilutions of the aqueous extract of F. excelsior (1:10,000) as well as compounds 2, 3, 4, 5, and 8 activated the peroxisome proliferator-mediated receptor-alpha (PPARalpha) reporter cell system in the range of 10(-4) M, compared to 10(-7)-10(-8) M for the synthetic PPARalpha activator, WY14,643. Both biological activity profiles support the hypothesis that inhibition of adipocyte differentiation and PPARalpha-mediated mechanisms might be relevant pathways for the antidiabetic activity of F. excelsior extract.
High susceptibility of human c‐Ha‐ras proto‐oncogene transgenic rats to carcinogenesis: A cancer‐prone animal model (2005)

Transgenic animals carrying human c-Ha-ras proto-oncogene, v-Ha-ras transgenic mice, pim-1 transgenic mice and several knockout mice deficient of tumor suppressor genes, such as p53, have been shown to exhibit increased carcinogen susceptibility. As a result, studies into practical application and medium-term screening of environmental carcinogens are under way. Given the advantages of rat models characterized by larger organ size, abundant information regarding preneoplasias and virus-free constitution, we have concentrated on the generation of transgenic rats bearing copies of the human c-Ha-ras proto-oncogene and shown the Hras128 strain to be extremely sensitive to the induction of mammary carcinomas, and to a lesser extent, lesions in the urinary bladder, esophagus and skin. In most, if not all, the mammary cancers mutations of the transgene but not the endogenous H-ras gene are present, appearing to occur early in the process of tumorigenesis, which involves proliferation of cells in TEB and intraductal hyperplasia before carcinomas arise. Preliminary findings suggest that this is independent of endogenous ovarian hormones, although inhibited by soy isoflavones and promoted by atrazine and nonylphenols. Although further studies of the mechanisms are clearly necessary, the model appears to have great potential for screening purposes, not only for modifiers active in the breast, but also other organs where tumors characterized by ras gene mutations develop.
Laser-based molecular identification (2006)

Polarization and phase shaped pulses can now be used for the absolute identification and quantification of mixtures containing isomers and enantiomers. The performance of this methodology will be discussed.
Electrocatalysis of Anodic Oxygen‐Transfer Reactions: The Electrochemical Incineration of Benzoquinone (1995)

The electrochemical performance of several anode materials is compared for the electrochemical incineration ofp‐benzoquinone in acetate buffer media (pH 5). The chemical oxygen demand (COD) estimated for benzoquinone by titration with standard permanganate solution can be decreased to virtually zero by electrolysis at electrodes comprised of Fe(III)‐doped films on Ti substrates. Carbon dioxide is a product of the electrochemical process; however, the possibility of other volatile products cannot be dismissed. Addition of solid benzoquinone to acetate media is followed by slow formation of a brownish black color that is concluded to result from one or more humic compounds produced by condensation of benzoquinone; however, it cannot be concluded whether the condensation reaction is a necessary prerequisite to successful electrochemical incineration of benzoquinone. Optimal operating conditions suggested for electrochemical incineration of benzoquinone in acetate buffer include heating of the anode (e.g., 60°C) to increase the rate of anodic discharge of and, thereby, decrease the anodic overpotential. Evidence also is presented that the rate of electrochemical incineration is enhanced slightly by the addition of a traces of Fe(III) with reduction of dioxygen to hydrogen peroxide at a cooled stainless steel cathode (e.g., 15°C) in an undivided cell.
A long-life catalyst for glycerol dehydration to acrolein (2010)

While the initial catalytic performances of silica-supported silicotungstic acid are high in the glycerol dehydration reaction, they rapidly decrease with time on stream and the acrolein yield quickly decreases.
Pulmonary-specific expression of SP-D corrects pulmonary lipid accumulation in<i>SP-D</i>gene-targeted mice (2000)

Targeted disruption of the surfactant protein (SP) D (SP-D) gene caused a marked pulmonary lipoidosis characterized by increased alveolar lung phospholipids, demonstrating a previously unexpected role for SP-D in surfactant homeostasis. In the present study, we tested whether the local production of SP-D in the lung influenced surfactant content in SP-D-deficient [SP-D(-/-)] and SP-D wild-type [SP-D(+/+)] mice. Rat SP-D (rSP-D) was expressed under control of the human SP-C promoter, producing rSP-D, SP-D(+/+) transgenic mice. SP-D content in bronchoalveolar lavage fluid was increased 30- to 50-fold in the rSP-D, SP-D(+/+) mice compared with the SP-D(+/+) parental strain. Lung morphology, phospholipid content, and surfactant protein mRNAs were unaltered by the increased concentration of SP-D. Likewise, the production of endogenous mouse SP-D mRNA was not perturbed by the SP-D transgene. rSP-D, SP-D(+/+) mice were bred to SP-D(-/-) mice to assess whether lung-selective expression of SP-D might correct lipid homeostasis abnormalities in the SP-D(-/-) mice. Selective expression of SP-D in the respiratory epithelium had no adverse effects on lung function, correcting surfactant phospholipid content and decreasing phosphatidylcholine incorporation significantly. SP-D regulates surfactant lipid homeostasis, functioning locally to inhibit surfactant phospholipid incorporation in the lung parenchyma and maintaining alveolar phospholipid content in the alveolus. Marked increases in biologically active tissue and alveolar SP-D do not alter lung morphology, macrophage abundance or structure, or surfactant accumulation.
Central Blood Pressure Monitoring via a Standard Automatic Arm Cuff (2017)

Current oscillometric devices for monitoring central blood pressure (BP) maintain the cuff pressure at a constant level to acquire a pulse volume plethysmography (PVP) waveform and calibrate it to brachial BP levels estimated with population average methods. A physiologic method was developed to further advance central BP measurement. A patient-specific method was applied to estimate brachial BP levels from a cuff pressure waveform obtained during conventional deflation via a nonlinear arterial compliance model. A physiologically-inspired method was then employed to extract the PVP waveform from the same waveform via ensemble averaging and calibrate it to the brachial BP levels. A method based on a wave reflection model was thereafter employed to define a variable transfer function, which was applied to the calibrated waveform to derive central BP. This method was evaluated against invasive central BP measurements from patients. The method yielded central systolic, diastolic, and pulse pressure bias and precision errors of -0.6 to 2.6 and 6.8 to 9.0 mmHg. The conventional oscillometric method produced similar bias errors but precision errors of 8.2 to 12.5 mmHg (p ≤ 0.01). The new method can derive central BP more reliably than some current non-invasive devices and in the same way as traditional cuff BP.
Low-Temperature Thermoelectric Materials (2017)

Bismuth (Bi), Antimony (Sb), and the Bi–Sb alloys form a complete class of thermoelectric semiconductors that are particularly suited to thermoelectric applications below room temperature. Large thermal conductivity suppression by nanostructuring at low temperature is much more significant than any other nanostructured thermoelectric materials at high temperatures. This chapter discusses the current status of research on low-temperature thermoelectric materials and the thermoelectric properties of some rare earth (RE) alloys that we think will be a good direction for research to bring thermoelectric cryogenic cooling into a reality. More research into other materials may be required, rather than focusing only on heavily doped semiconductor thermoelectric materials. The other research directions points toward Kondo materials. The investigation of RE alloys could be a good direction to bring thermoelectric cryogenic cooling toward reality. These materials need further study and optimization to make them practical for applications.
Dialog state tracking, a machine reading approach using Memory Network (2017)

In an end-to-end dialog system, the aim of dialog state tracking is to accurately estimate a compact representation of the current dialog status from a sequence of noisy observations produced by the speech recognition and the natural language understanding modules. This paper introduces a novel method of dialog state tracking based on the general paradigm of machine reading and proposes to solve it using an End-to-End Memory Network, MemN2N, a memory-enhanced neural network architecture. We evaluate the proposed approach on the second Dialog State Tracking Challenge (DSTC-2) dataset. The corpus has been converted for the occasion in order to frame the hidden state variable inference as a questionanswering task based on a sequence of utterances extracted from a dialog. We show that the proposed tracker gives encouraging results. Then, we propose to extend the DSTC-2 dataset and the definition of this dialog state task with specific reasoning capabilities like counting, list maintenance, yes-no question answering and indefinite knowledge management. Finally, we present encouraging results using our proposed MemN2N based tracking model.
A vaccine to prevent transmission of human malaria: A long way to travel on a dusty and often bumpy road (2007)

The goal for an effective malaria transmission-blocking vaccine (TBV) is to induce immunity against the stages of the parasite that infect mosquitoes so that malaria transmission can be reduced or halted. Malaria transmission is generally spatially confined to an infectious source, thus a TBV used in a community can effectively suppress malaria transmission to others. Antibodies induced by TBVs target antigens on the surface of sexual and mosquito midgut stages of the malaria parasite and antibodies interfere with the development of the parasites in the midgut of the mosquito. Proteins synthesized in the gametocytes (pre-fertilization antigens, in Plasmodium falciparum: Pfs230 and Pfs48/45) and in the zygotes-ookinetes (post-fertilization antigens, in P. falciparum: Pfs25 and Pfs28) represent some of the key target antigens for the development of TBVs. All the four proteins contain multiple cysteine-rich sequences and the epitopes recognized by transmission-blocking antibodies are reduction-sensitive conformational in nature. The inability to express properly folded proteins has frustrated a protein-based TBV development approach and DNA-based vaccine constructs were envisaged to overcome the conformational problem in recombinant proteins. Indeed studies in mice and monkeys have firmly established the value of DNA-based TBV approach. Although immunogenic in larger animals, delivery of DNA-based TBVs needs to be further optimized to elicit a strong and long lasting functional immune response. This DNA vaccine platform can also facilitate evaluation of a cocktail of pre-and post-fertilization antigens in pre-clinical setting prior to the development of an ideal and effective TBV for clinical trials in human volunteers.
Molecular Cytogenetic Characterization of the Human Cerebral Microvessel Endothelial Cell Line hCMEC/D3 (2009)

The immortalized human cerebral microvessel endothelial cell line hCMEC/D3 has been repeatedly used as a model of human blood-brain barrier (BBB). hCMEC/D3 cells between passage 25 and 35 are most often applied in research, remained phenotypically nontransformed, and cells maintained many characteristics of human brain endothelial cells. Also hCMEC/D3 was thought to have conserved a normal diploid karyotype over all these passages. Here we characterized the cell line using high-resolution multicolor fluorescence in situ hybridization (FISH) approaches and revealed a complex karyotype in the 30th passage. Clonal cryptic unbalanced structural rearrangements and numerical aberrations were discovered and described as follows: 45 approximately 48,XX, -X,del(5)(q11)[2],del(9)(q11)[3],+9[3],del(11)(q13 approximately 14)[2], der(14)t(14;21)(q32.33;q22.3)[28],der(15)t(9;15)(p11;p11)[13], dup(15)(p11q11)[5],der(21)t(17;21)(p12;q22)[9],-22[6][cp28]. In summary, a complex karyotype with clonal unbalanced chromosomal rearrangements is present in hCMEC/D3. Thus, we solicit to include molecular cytogenetics in the testing of all cell lines prior to application of their use in complex studies.
Isolation of Erythropoietin Receptor Agonist Peptides Using Evolved Phage Libraries (1998)

Cyclic peptides capable of activating the erythropoietin receptor (EPOR) were isolated from phage display libraries by screening with a novel EPOR-IgG fusion protein reagent. A parental clone ERB1 (EPO Receptor Binder 1) was first isolated from a phage display library displaying 38 random amino acids as an N-terminal fusion with the M13 minor capsid protein, pill. An evolved library was then produced from the parental sequence using an oligonucleotide saturation mutagenesis strategy which yielded EPOR binding sequences with 20 times the relative affinity of ERB1. Two synthetic peptides were constructed from these sequences both of which bind the EPO receptor in specific ELISA, and act as full agonists in EPO dependent cell proliferation assays. These peptides are 18 amino acids in length, disulfide-bonded, and have a minimum consensus sequence of CXXGWVGXCXXW, where X represents positions tolerant of several amino acids.
A main speaker decision for a distributed telepresence system (2013)

In this paper, we propose a method to detect a main speaker and automatically change into one's high definition (HD) video for a distributed telepresence system, so that the users feel immersive and convenient. In contrast to centralized systems, user equipment (UE) performs the main speaker decision (MSD) with a time synchronization using network time protocol (NTP). The MSD method includes a voice activity detection (VAD) and post-corrections to remove unwanted voice detections and share the same main speaker. We emphasize an audio signal of the main speaker to become more immersive. The proposed approach is applied to the telepresence system developed by ETRI and shows good performances <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">.</sup>
Extraction and Inhibition of Enzymatic Activity of Botulinum Neurotoxins/A1, /A2, and /A3 by a Panel of Monoclonal Anti-BoNT/A Antibodies (2009)

Botulinum neurotoxins (BoNTs) are extremely potent toxins that are capable of causing death or respiratory failure leading to long-term intensive care. Treatment includes serotype-specific antitoxins, which must be administered early in the course of the intoxication. Rapidly determining human exposure to BoNT is an important public health goal. In previous work, our laboratory focused on developing Endopep-MS, a mass spectrometry-based endopeptidase method for detecting and differentiating BoNT/A-G serotypes in buffer and BoNT/A, /B, /E, and /F in clinical samples. We have previously reported the effectiveness of antibody-capture to purify and concentrate BoNTs from complex matrices, such as clinical samples. Because some antibodies inhibit or neutralize the activity of BoNT, the choice of antibody with which to extract the toxin is critical. In this work, we evaluated a panel of 16 anti-BoNT/A monoclonal antibodies (mAbs) for their ability to inhibit the in vitro activity of BoNT/A1, /A2, and /A3 complex as well as the recombinant LC of A1. We also evaluated the same antibody panel for the ability to extract BoNT/A1, /A2, and /A3. Among the mAbs, there were significant differences in extraction efficiency, ability to extract BoNT/A subtypes, and inhibitory effect on BoNT catalytic activity. The mAbs binding the C-terminal portion of the BoNT/A heavy chain had optimal properties for use in the Endopep-MS assay.
Temperature-Gradient Furnace for Solidification Experiments (1985)

Gradients are controllable from zero to 500 degrees C/cm. Typical temperature profile superimposed on partial cross section of furnace. Steepness of gradient varied by adjusting flow of energy to and from different zones of furnace. Specimen placed in ampoule moved inside ceramic tube according to needs of experiment. Furnace provides axial temperature profiles for material processing experiments.
Fabrication and Assessment of Crumb-Rubber-Modified Coatings with Anticorrosive Properties (2015)

Scrap tires continue to be a major source of waste due to the lack of valuable and effective disposal routes. A viable solution to this problem is to recycle crumb rubber (CR)-a granulated material derived from scrap tires-and use it to develop other valuable products. Herein we report the fabrication and characterization of CR-modified coatings with anticorrosive properties on metal substrates. By varying the particle size and concentration of CR, we have determined the coating composition that offers the highest level of erosion protection. Images from a scanning electron microscope (SEM) reveal that CR is homogenously dispersed in the coating, especially when fine particles are used. As the concentration of CR increases, the hardness of the coating decreases as a result of the elastic properties of CR. More importantly, the erosion rate of the coating decreases due to increased ductility. Following Potentiodynamic tests, the utilization of these coatings proved to be beneficial as they showed good protection against aqueous corrosion when tested in 0.5 M NaCl solution. Our newly developed coatings offer an incentive to recycling CR and open up a safe and sustainable route to the disposal of scrap tires.
Expanding the Model-Tracing Architecture: A 3rd Generation Intelligent Tutor for Algebra Symbolization (2008)

Following Computer Aided Instruction systems, 2nd generation tutors are Model-Tracing Tutors (MTTs) (Anderson & Pelletier, 1991) which are intelligent tutoring systems that have been very successful at aiding student learning, but have not reached the level of performance of experienced human tutors (Anderson et al., 1995). To that end, this paper presents a new architecture called ATM ("Adding a Tutorial Model"), which is an extension to model-tracing, that allows these tutors to engage in a dialog that is more like those in which experienced human tutors engage. Specifically, while MTTs provide hints toward doing the next problemsolving step, this 3rd generation of tutors, the ATM architecture, adds the capability to ask questions towards thinking about the knowledge behind the next problem-solving step. We present a new tutor built in ATM, called Ms. Lindquist, which is designed to carry on a tutorial dialog about algebra symbolization. The difference between ATM and MTT is the separate tutorial model that encodes pedagogical content knowledge in the form of different tutorial strategies, which were partially developed by observing an experienced human tutor. Ms. Lindquist has tutored thousands of students at www.AlgebraTutor.org. Future work will reveal if Ms. Lindquist is a better tutor because of the addition of the tutorial model.