gebhart/patrepeval huggingface dataset:
Genetic analysis of the 5-azacytidine sensitivity of Escherichia coli K-12 (1987)

DNA containing 5-azacytidine (5-azaC) has been shown to form stable detergent-resistant complexes with cytosine methylases. We reasoned that if 5-azaC treatment causes protein-DNA cross-links in vivo, then mutations in DNA repair and recombination genes may increase the sensitivity of a cell to 5-azaC. We found that although recA (defective) and lexA (induction-negative) mutants of Escherichia coli were very sensitive to the drug, mutations in uvrA and ung genes had little effect on cell lethality. The sensitivity of recA strains to 5-azaC was dose dependent and was enhanced by the overproduction of a DNA cytosine methylase in the cell. Unexpectedly, a strain of E. coli carrying a recA mutation and a deletion of the DNA cytosine methylase gene (dcm) was found to be significantly sensitive to 5-azaC. Study of mutations in the pyrimidine salvage pathway of E. coli suggests that direct phosphorylation of 5-azaC, rather than phosphorylation of its degradation products, is largely responsible for the lethal effects of the drug. The addition of uracil to the growth medium has little effect on cell lethality of recA mutants, but it partially reversed the inhibition of cell growth caused by 5-azaC. This reversal of the bacteriostatic effects of the drug could not be achieved by adding cytosine or orotic acid to the growth medium and required the presence of functional UMP-pyrophosphorylase (gene upp) in the cell.
Utility of the Photoplethysmogram in Circulatory Monitoring (2008)

The photoplethysmogram is a noninvasive circulatory signal related to the pulsatile volume of blood in tissue and is displayed by many pulse oximeters and bedside monitors, along with the computed arterial oxygen saturation. The photoplethysmogram is similar in appearance to an arterial blood pressure waveform. Because the former is noninvasive and nearly ubiquitous in hospitals whereas the latter requires invasive measurement, the extraction of circulatory information from the photoplethysmogram has been a popular subject of contemporary research. The photoplethysmogram is a function of the underlying circulation, but the relation is complicated by optical, biomechanical, and physiologic covariates that affect the appearance of the photoplethysmogram. Overall, the photoplethysmogram provides a wealth of circulatory information, but its complex etiology may be a limitation in some novel applications.
Hydronium (cycloheptylammonio)methylene-1,1-bisphosphonate (hydronium incadronate) (2003)

The structure of the title compound, H(3)O(+).C(8)H(18)NO(6)P(2)(-), adopts a zwitterionic form containing an alkylammonium group, a hydronium ion, and two negatively charged phosphonate groups. The cycloheptyl side chain adopts a twist-chair conformation. The crystal packing is dominated by an extensive hydrogen-bonding network.
A Novel Agonist Anti-Human OX40L Monoclonal Antibody That Stimulates T Cell Proliferation and Enhances Cytokine Secretion (2009)

OX40L (CD252), a membrane-bound member of the tumor necrosis factor superfamily, is known to be a critical co-stimulatory molecule during immune response. Here, we describe an agonistic mouse anti-human OX40L monoclonal antibody (clone 1E7) recognizing a novel epitope of OX40L antigen. Using this antibody, we found that OX40L was transiently upregulated on CD4(+) T cells during the early stage of activation. Cross-linking of OX40L with monoclonal antibody 1E7 markedly promoted T cell proliferation and activation and enhanced cytokine production, demonstrating that OX40L transmitted a signal to T cells. Thus, OX40L may play an important role in the early phase of T cell activation and proliferation.
Determination of Unbound Bilirubin in the Serum of Newborns (1974)

Abstract An enzymatic assay is described for non-albuminbound bilirubin in the serum of newborn infants. Unbound bilirubin is oxidized to colorless compounds by ethyl hydroperoxide in the presence of horseradish peroxidase (EC 1.11.1.7), while albumin-bound bilirubin is protected from oxidation. Because the equilibrium between albumin and bilirubin occurs rapidly, the oxidation step is rate limiting, and the initial oxidation velocity of total bilirubin is proportional to the unbound bilirubin concentration. By titrating serum with bilirubin in vitro, the association constant and binding capacity of high-affinity sites for albumin binding can be determined. Normal human serum albumin tightly binds 1 mole of bilirubin per mole of albumin (binding constant, 2-4 x 108 liter/mol). Although weaker secondary binding occurs, the unbound bilirubin fraction increases rapidly after the high-affinity binding sites are saturated. Compromised newborns may have a decreased apparent binding capacity and (or) binding affinity. The method can be used to assess the risk of a jaundiced infant for bilirubin encephalopathy.
Removal of lead ions from aqueous solutions by adsorption onto chemically modified silk cotton hulls by different oxidizing agents (2012)

ABSTRACT In the present study, the removal of lead ions from aqueous solutions was studied using activated carbons prepared from silk cotton hulls by three different acid activation methods; they are named as concentrated (conc.) H 2 SO 4 (AC), mixture of conc. H 2 SO 4 + H 2 O 2 (AC1), and mixture of conc.H 2 SO 4 + NH 4 S 2 O 8 (AC2). The surface properties of the adsorbent materials were determined by the Fourier Transform infrared spectroscopy, thermogravimetric analysis, Brunauer–Emmette–Teller, scanning electron microscope, and energy dispersive X‐ray analyses. From the thermogravimetric analysis result, the formation of carboxylic acid and lactones are present in the order AC2 &gt; AC1 &gt; AC. Brunauer–Emmette–Teller result shows that the activated carbons are macroporous in nature. Batch adsorption experiments were performed as a function of pH, adsorbent dose, contact time, initial metal ion concentration, and temperature. The experimental equilibrium adsorption data fits well for the Langmuir, Freundlich, and Tempkin equations. The maximum adsorption capacities were 40.00 mg g −1 for AC and 83.33 mg g −1 for AC1 and AC2, respectively. Adsorption kinetic data were modeled using the pseudo‐first‐order and pseudo‐second‐order, and intraparticle diffusion equations and its rate constants were evaluated. The adsorption process followed the pseudo‐second‐order reaction kinetics, suggesting that it is presumably chemisorption. The calculations of the thermodynamic parameters revealed that the adsorption process was endothermic, but it is feasible and spontaneous under natural conditions. The reversibility of the process has been studied in a qualitative manner, and it shows that the spent activated carbons can be effectively regenerated for further use easily. © 2012 Curtin University of Technology and John Wiley &amp; Sons, Ltd.
Towards Unified Human Parsing and Pose Estimation (2014)

We study the problem of human body configuration analysis, more specifically, human parsing and human pose estimation. These two tasks, ie identifying the semantic regions and body joints respectively over the human body image, are intrinsically highly correlated. However, previous works generally solve these two problems separately or iteratively. In this work, we propose a unified framework for simultaneous human parsing and pose estimation based on semantic parts. By utilizing Parselets and Mixture of Joint-Group Templates as the representations for these semantic parts, we seamlessly formulate the human parsing and pose estimation problem jointly within a unified framework via a tailored and-or graph. A novel Grid Layout Feature is then designed to effectively capture the spatial co-occurrence/occlusion information between/within the Parselets and MJGTs. Thus the mutually complementary nature of these two tasks can be harnessed to boost the performance of each other. The resultant unified model can be solved using the structure learning framework in a principled way. Comprehensive evaluations on two benchmark datasets for both tasks demonstrate the effectiveness of the proposed framework when compared with the state-of-the-art methods.
High concentrations of a novel peptide, neuropeptide Y, in the innervation of mouse and rat heart. (1984)

A newly discovered bioactive peptide, neuropeptide Y (NPY), has been found in the innervation of the mouse and rat heart by immunocytochemistry, NPY-immuno-reactive nerves were very dense around the nodal tissues. They also surrounded the coronary arteries and arterioles and were found in close association with the cardiac muscle. The distribution of NPY-containing nerves paralleled that of noradrenergic fibers, demonstrated by the use of antibodies to the catecholamine-converting enzymes tyrosine hydroxylase and dopamine beta-hydroxylase. Furthermore, NPY was seen to be present in a proportion of intrinsic neurons mostly found in the atria and in close proximity to the nodal tissue. The concentrations of extractable NPY-immunoreactive material (about 150 pmol/g in whole mouse heart) by far surpasses those of the other peptides so far reported in the cardiac tissue. High performance liquid chromatography demonstrated the NPY immunoreactivity to elute in a single sharp peak, in an identical position to brain NPY.
Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z (2011)

Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of known genome sequence for which a plasmid has been reported.
Molecular cloning and characterization of a full‐length cDNA clone for human plasminogen (1987)

A human liver cDNA library enriched for full-length clones was screened for plasminogen cDNA using a synthetic 24-nucleotide probe derived from a reported partial cDNA sequence. 12 positive clones were identified and one of these was characterized in detail. The 2.7 kb insert contains the complete coding region. At 5 positions, it gives residues different from those reported in a previous amino acid sequence analysis of the protein. The present results show an extra Ile at position 65, Gln instead of Glu at positions 53 and 342, Asn at position 88 instead of Asp, and Asp at position 453 rather than Asn. In the 3'-non-coding region an extension of 29 bases is found which does not contain any structure compatible with a known polyadenylation signal. Instead, the consensus signal AATAAA is placed at a distance of 46 bases upstream of the poly(A)-tail.
Association of various T cell-surface molecules with the cytoskeleton. Effect of cross-linking and activation (1991)

The association of various surface molecules with the cytoskeleton in resting peripheral blood T cells was examined by assaying the capacity of detergent to solubilize them. Cytoskeletal association was assessed by staining T cells with a fluorescein-conjugated mAb, resuspending the cells in buffer with or without the nonionic detergent, NP-40, and determining the capacity of the detergent to remove the mAb from the cell surface by using flow microfluorimetry. MAb to CD3, the TCR, and CD45 were completely removed from the cell surface by detergent. In contrast, 7 to 50% of mAb to CD2, CD4, CD8, CD11a/CD18, CD44, and class I MHC molecules were resistant to detergent solubilization, demonstrating that a fraction of these molecules was constitutively associated with the cytoskeleton. The effect of cross-linking these molecules with a mAb and a secondary goat anti-mouse Ig was also examined. Cross-linking CD3 or the TCR induced cytoskeletal association of these molecules. In addition, cross-linking increased the fraction of CD2, CD4, CD8, CD11a/CD18, CD44, and class I MHC molecules that was associated with the cytoskeleton. In contrast, cross-linking CD45 did not induce an association with the cytoskeleton. The effect of T cell activation on the cytoskeletal association of these molecules was also examined. Stimulation of T cells with ionomycin and PMA greatly increased the expression of CD2 and CD44 without increasing the number of molecules associated with the cytoskeleton. Stimulation with PMA alone had no effect on the expression of CD2 or CD44, but was found to decrease the percentage of these molecules associated with the cytoskeleton. Stimulation with ionomycin and PMA increased both the expression of class I MHC molecules and the number of molecules associated with the cytoskeleton proportionally. Finally, stimulation with ionomycin and PMA decreased CD3 expression, but increased the number of CD3 molecules associated with the cytoskeleton. The data establish a pattern of cytoskeletal association of T cell-surface molecules that is a characteristic of each individual molecule and can be altered by cross-linking. Moreover, the results indicate that the association of various T cell surface molecules with the cytoskeleton is a dynamic process that varies with the state of activation and or differentiation of the cells.
A first-principles potential energy surface for Eley–Rideal reaction dynamics of H atoms on Cu(111) (1999)

We have performed first-principles total-energy calculations of low-dimensional sections of the electronically adiabatic potential energy surface (PES) that are relevant for the Eley–Rideal (ER) reaction of H atoms on a rigid Cu(111) surface. These calculations were performed within density-functional theory using a plane-wave and pseudopotential method and the generalized gradient approximation for the exchange-correlation energy. The calculated energy points for various configurations of one and two atoms on the Cu(111) surface were used to construct a model PES that can be used in ER reaction dynamics calculations.
Serum-Free Medium Supplemented with High-Concentration FGF2 for Cell Expansion Culture of Human Ear Chondrocytes Promotes Redifferentiation Capacity (2002)

For tissue engineering of autologous cartilage, cell expansion is needed to obtain the cell numbers required. Standard expansion media contain bovine serum. This has several disadvantages, that is, the risk of transmitting diseases and serum-batch variations. The aim of this study was to find a serum-free medium with at least the same potential to expand cell numbers as serum-containing media. Ear chondrocytes of three young children were expanded in either serum-containing medium (SCM; DMEM with 10% fetal calf serum) or serum-free medium (SFM; DMEM with ITS+) supplemented with 5 or 100 ng/mL fibroblast growth factor-2 (FGF2). To promote cell adherence onto the culture flask, the serum-free conditions were cultured with 10% serum for 1 day after each trypsinization. After the fourth passage, the chondrocytes were encapsuled in alginate beads and redifferentiated in a SFM (DMEM with ITS+, hydrocortisone, and L-ascorbic acid) supplemented with 10 ng/mL IGF-I and 10 ng/mL TGFbeta-2. Results showed that expansion in SFM with 100 ng/mL FGF2 was comparable to expansion in SCM. Redifferentiation with SFM with IGF-I and TGFbeta-2 showed high collagen type II expression and high GAG/DNA production regardless of which expansion medium had been used. However, chondrocytes expanded in SFM with 100 ng/mL FGF2 resulted in less positive cells for collagen type I and 11-fibrau (a fibroblast membrane marker). The present study shows that it is possible to use serum-free medium for tissue engineering of cartilage. Expansion of immature ear chondrocytes in SFM supplemented with high-concentration FGF2 resulted in high cell numbers, which in addition had better redifferentiation capacity than cells expanded in medium with 10% serum.
Macroconidium Formation in Submerged Cultures by a Non-Sporulating Strain of Gibberella zeae (1965)

SUMMARYThe typical New Jersey corn stalk-rotting strain of G. zeae does not sporulate in laboratory surface culture. This organism produced, in a normal manner, abundant, typical macrospores only in shake culture on a medium consisting of simple-salts, yeast extract, and carboxymethylcellulose. Under these conditions aeration by shaking and carboxymethylcellulose was necessary for spore production. The nutritional condition of the inoculum influenced the extent of sporulation. Exclusion of KH2PO4 from the sporulation medium significantly reduced sporulation. Sporulation of G. zeae was poor in shake cultures of PD, V-8, Czapeks and Parks media.
Hydration and structure—the two sides of the insulin aggregation process (2004)

Aggregation of bovine insulin under monomer, and dimer-promoting conditions has been probed by FT-IR spectroscopy and DSC/PPC calorimetry. This approach enabled linking of characteristic aggregation-hallmarking conformational events (such as partial unfolding, and subsequent refolding into aggregated β-strands) to different stages of protein hydration. Aggregation of insulin in 20% acetic acid occurs at a markedly lower temperature than in pure water and is further enhanced in the presence of charge-shielding ions (0.1 M NaCl). While acetic acid makes the protein molecule more permissive to the solvent penetration (seen as the enhanced H/D-exchange), NaCl does not have this effect. The calorimetric data reveals that, while the aggregation itself is exothermic, in the absence of the co-solvent it is preceded by an endothermic transition. In either case, the negative heat capacity changes suggest a substantial reduction in the number of water–protein contacts upon aggregation. This has been supported by pressure perturbation calorimetry, which showed a simultaneous release of water molecules bound to the protein. The aggregation of insulin appears to be driven mostly by hydrophobic interactions and, as such, involves a rearrangement of hydrophobic side-chain amino acid residues that leads to the overall reduction in number of unfavorable protein–water contacts. The study points to the intricate nature of the acetic acid effect on insulin aggregation, which is likely to involve changing the structure of the solvating water, and direct binding to the protein.
An experimental extracted model for latchup analysis in CMOS process (2009)

The latchup phenomenon is analyzed theoretically. A practical analytical model derived from Ebers-Moll formulations is proposed to analyze, simulate, and predict latchup, with favorable legitimacy and flexibility. The model parameters are extracted on 0.25 um CMOS process from experiments. The extracted model can predict latchup successfully in circuit level when applied in SPICE.
Agreement between expert-system and human raters' scores on complex constructed-response quantitative items. (1991)

This study evaluated agreement betwen expert-system and human scores on 12 constructed-response algebra word problems taken by Graduate Record Examination General Test examinees. Ideas are discussed for using expert systems in large-scale assessment programs and in interactive diagnostic assessment.
On the Evaluation of Dialogue Systems with Next Utterance Classification (2016)

An open challenge in constructing dialogue systems is developing methods for automatically learning dialogue strategies from large amounts of unlabelled data. Recent work has proposed Next-Utterance-Classification (NUC) as a surrogate task for building dialogue systems from text data. In this paper we investigate the performance of humans on this task to validate the relevance of NUC as a method of evaluation. Our results show three main findings: (1) humans are able to correctly classify responses at a rate much better than chance, thus confirming that the task is feasible, (2) human performance levels vary across task domains (we consider 3 datasets) and expertise levels (novice vs experts), thus showing that a range of performance is possible on this type of task, (3) automated dialogue systems built using state-of-the-art machine learning methods have similar performance to the human novices, but worse than the experts, thus confirming the utility of this class of tasks for driving further research in automated dialogue systems.
Thioredoxin 2 Is Involved in the Oxidative Stress Response inEscherichia coli (2000)

Two genes encoding thioredoxin are found on the Escherichia coli genome. Both of them are capable of reducing protein disulfide bonds in vivo and in vitro. The catalytic site contains a Cys-X(1)-X(2)-Cys motif in a so-called thioredoxin fold. Thioredoxin 2 has two additional pairs of cysteines in a non-conserved N-terminal domain. This domain does not appear to be important for the function of thioredoxin 2 in donating electrons to ribonucleotide reductase, 3'-phosphoadenylsulfate-reductase, or the periplasmic disulfide isomerase DsbC. Our results suggests that the two thioredoxins are equivalent for most of the in vivo functions that were tested. On the other hand, transcriptional regulation is different. The expression of trxC is regulated by the transcriptional activator OxyR in response to oxidative stress. Oxidized OxyR binds directly to the trxC promoter and induces its expression in response to elevated hydrogen peroxide levels or the disruption of one or several of the cytoplasmic redox pathways. Mutants lacking thioredoxins 1 and 2 are more resistant to high levels of hydrogen peroxide, whereas they are more sensitive to diamide, a disulfide bond-inducing agent.
Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis (2000)

The AC-rich motif, Pal-box, is an important cis-acting element for gene expression involved in phenylpropanoid biosynthesis. A cDNA clone (Ntlim1) encoding a Pal-box binding protein was isolated by Southwestern screening. The deduced amino acid sequence is highly similar to the members of the LIM protein family that contain a zinc finger motif. Moreover, Ntlim1 had a specific DNA binding ability and transiently activated the transcription of a beta-glucuronidase reporter gene driven by the Pal-box sequence in tobacco protoplasts. The transgenic tobacco plants with antisense Ntlim1 showed low levels of transcripts from some key phenylpropanoid pathway genes such as phenylalanine ammonia-lyase, hydroxycinnamate CoA ligase and cinnamyl alcohol dehydrogenase. Furthermore, a 27% reduction of lignin content was observed in the transgenic tobacco with antisense Ntlim1.
Synthetic microbial chemistry, XVII. Synthesis of the complement inhibitor (−)‐K‐76 and of related compounds (1988)

Abstract The complement inhibitor (−)‐K‐76 ( 1 ) was synthesized starting from ( S )‐3‐hydroxy‐2,2‐dimethylcyclohexanone ( 3 ) employing dihydroxy sesquiterpene ester 2 as the key intermediate. The diastereomer 26 of 2 yielded the β‐diol isomer 49 of (−)‐K‐76, and 26 ′ gave another diastereomer 47 ′ of O ‐methyl K‐76.