gebhart/patrepeval huggingface dataset:
The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access (2008)

We analyzed global gene expression in Arabidopsis in response to various hormones and in related experiments as part of the AtGenExpress project. The experimental agents included seven basic phytohormones (auxin, cytokinin, gibberellin, brassinosteroid, abscisic acid, jasmonate and ethylene) and their inhibitors. In addition, gene expression was investigated in hormone-related mutants and during seed germination and sulfate starvation. Hormone-inducible genes were identified from the hormone response data. The effects of each hormone and the relevance of the gene lists were verified by comparing expression profiles for the hormone treatments and related experiments using Pearson's correlation coefficient. This approach was also used to analyze the relationships among expression profiles for hormone responses and those included in the AtGenExpress stress-response data set. The expected correlations were observed, indicating that this approach is useful to monitor the hormonal status in the stress-related samples. Global interactions among hormones-inducible genes were analyzed in a pairwise fashion, and several known and novel hormone interactions were detected. Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that our data set is useful for identification of clusters of co-expressed genes, and to predict the functions of unknown genes, even if a gene's function is not directly related to the experiments included in AtGenExpress. Our data are available online from AtGenExpressJapan; the results of genome-wide HCA are available from PRIMe. The data set presented here will be a versatile resource for future hormone studies, and constitutes a reference for genome-wide gene expression in Arabidopsis.
Peptaibol metabolites of <i>Tolypocladium</i> <i>geodes</i> (1996)

Three antibiotic peptides, LP237-F8 (1), F5 (2), and F7 (3), were isolated from the liquid culture of the fungus Tolypocladium geodes. Chemical shift assignments of the 1 H and 13 C NMR resonances and sequencing of these metabolites were achieved by extensive high-field 2D NMR spectroscopy. The N-terminal of peptides 1 and 2 is protected with an octanoyl (Oc) fatty acid unit, whereas that of peptide 3 is protected with a decanoyl (Dec) unit. The C-terminal of all three peptides is protected with the amino alcohol leucinol (Lol). All three metabolites contain the common amino acids Ala, Phe or Tyr, Pro, and Gln, as well as the unusual amino acid α-aminoisobutyric acid (Aib). In addition, peptides 1 and 2 contain the amino acid α-amino-α-ethyl-n-pentanoic acid (α-ethylnorvaline, EtNor), which has not been previously reported as a constituent of a natural product. Metabolites 1, 2, and 3 are new members of the class of natural products known as peptaibols. Key words: Tolypocladium geodes, peptaibols, leucinol, α-amino-α-ethyl-n-pentanoic acid.
Characterization of a recombinant type II 3-deoxy-<scp>D</scp>-<i>arabino</i>-heptulosonate-7-phosphate synthase from <i>Helicobacter pylori</i> (2005)

DAH7P (3-Deoxy-D-arabino-heptulosonate 7-phosphate) synthase catalyses the condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) as the first committed step in the biosynthesis of aromatic compounds in plants and micro-organisms. Previous work has identified two families of DAH7P synthases based on sequence similarity and molecular mass, with the majority of the mechanistic and structural studies being carried out on the type I paralogues from Escherichia coli. Whereas a number of organisms possess genes encoding both type I and type II DAH7P synthases, the pathogen Helicobacter pylori has only a single, type II, enzyme. Recombinant DAH7P synthase from H. pylori was partially solubilized by co-expression with chaperonins GroEL/GroES in E. coli, and purified to homogeneity. The enzyme reaction follows an ordered sequential mechanism with the following kinetic parameters: K(m) (PEP), 3 microM; K(m) (E4P), 6 microM; and kcat, 3.3 s(-1). The enzyme reaction involves interaction of the si face of PEP with the re face of E4P. H. pylori DAH7P synthase is not inhibited by phenylalanine, tyrosine, tryptophan or chorismate. EDTA inactivates the enzyme, and activity is restored by a range of bivalent metal ions, including (in order of decreasing effectiveness) Co2+, Mn2+, Ca2+, Mg2+, Cu2+ and Zn2+. Analysis of type II DAH7P synthase sequences reveals several highly conserved motifs, and comparison with the type I enzymes suggests that catalysis by these two enzyme types occurs on a similar active-site scaffold and that the two DAH7P synthase families may indeed be distantly related.
Mechanism and specificity of formation of long chain alcohols by developing rat brain. (1981)

The enzymatic reduction of acyl-CoA to long chain alcohol by NADPH ion a particulate fraction from developing rat brain has been studied in detail. Addition of serum album in to the assay stimulated activity, due to protection of the substrate acyl-CoA from hydrolysis by an endogenous hydrolase. The optimum amount of albumin depended upon the amount of acyl-CoA added and was found to be 0.5 to 2.0 mol of albumin/mol of acyl-CoA. A series of saturated and unsaturated acyl-CoAs from C12 to C22 was tested, and it was found that the enzyme was specific for only the palmitoyl (16:0)-, stearoyl (18:0)-, and oleoyl (18:1)-CoAs, thus accounting for the observed ether lipid composition in brain. The enzyme specifically utilized only B side hydrogen of [4-3H]NADPH (2 mol/mol of alcohol formed). By various criteria, it was shown that free palmitaldehyde was not an intermediate of the reaction, implying that a single enzyme catalyzes the two consecutive reductions. However, small amounts of palmitaldehyde were produced by this system and were shown to be derived from the same enzyme; probably resulting from partial degradation of an unstable enzyme-bound intermediate. Activity was fully inhibited by sulfhydryl reagents, and from the results of substrate protection experiments, it was concluded that an essential thiol was located at the active site of the enzyme.
An evaluation of code and data optimizations in the context of disk power reduction (2005)

Disk power management is becoming increasingly important in high-end server and cluster type of environments that execute data-intensive applications. While hardware-only approaches (e.g., low-power modes supported by current disks) are successful to a certain extent, one also needs to consider the software side to achieve further energy savings. This paper first demonstrates that conventional data locality oriented code transformations are not sufficient for minimizing disk power consumption. The reason is that these optimizations do not take into account how disk-resident array data are laid out on the disk system, and consequently, fail to increase idle periods of disks, which is the primary metric using which disk power can be reduced. Instead, we propose a disk layout aware application optimization strategy that uses both code restructuring and data layout optimization. Our experimental evaluation with several benchmark codes reveal that the proposed strategy is very successful in reducing disk energy consumption without performing much worse than a pure data locality oriented scheme, as far as execution cycles are concerned. The experiments also show that the benefits coming from our approach increase with the increased number of disks; i.e., it scales very well
A new protein (J1-31 antigen, 30 kD) is expressed by astrocytes, Müller glia and ependyma (1987)

Monoclonal antibody (MAb) J1-31 raised using human brain homogenate as immunogen in mice can be used as a cell type marker for certain types of CNS macroglia, namely astrocytes, Müller cells and tanycytes as well as ciliated ependymal cells. Except for the ciliated ependymal cells, these types of macroglia express glial fibrillary acidic protein (GFAP). J1-31 antigen is an intracellular protein which has a MW of 30 kD under reducing conditions for gel electrophoresis (Singh et al., 1986). This protein is distinct from GFAP (MW 50 kD) and vimentin (MW 55 kD), the two core proteins of 10 nm IFs known to be expressed in the above types of macroglia. This conclusion is based on several criteria including temporal differences in the onset of expression of GFAP and J1-31 antigen during development of the rat cerebellum. Also, there is no detectable (by immunofluorescence microscopy) expression of J1-31 antigen in the prenatal CNS or outside the CNS where vimentin has been reported to be abundant. The most direct evidence that J1-31 antigen and GFAP are distinct proteins comes from studies on the mature ciliated ependymal cells which do not express GFAP and yet show intense immunostaining for J1-31 antigen.
Electronic band structures of carbon nanotubes with nanoscale periodic pores (2002)

Electronic energy states of carbon nanotubes with nanoscale periodic pores significantly differ from those of conventional carbon nanotubes. Moreover, some carbon nanotubes with nanoscale periodic pores possess several flat bands, which may cause the appearance of singular magnetic phenomena in one-dimensional carbon nanotubes.
Enabling access to geo-referenced information (2008)

We present Atlas.txt, a novel data-to-text natural language generation system which enables access to geo-referenced information like online census data. We first discuss initial findings from an accessibility study on geo-referenced data and outline needs requirements for visually-impaired users of such data. We then present work towards realising our data-to-text system and indicate how it aims to address this issue.
Wavelet Domain Residual Network (WavResNet) for Low-Dose X-ray CT Reconstruction (2017)

Model based iterative reconstruction (MBIR) algorithms for low-dose X-ray CT are computationally complex because of the repeated use of the forward and backward projection. Inspired by this success of deep learning in computer vision applications, we recently proposed a deep convolutional neural network (CNN) for low-dose X-ray CT and won the second place in 2016 AAPM Low-Dose CT Grand Challenge. However, some of the texture are not fully recovered, which was unfamiliar to some radiologists. To cope with this problem, here we propose a direct residual learning approach on directional wavelet domain to solve this problem and to improve the performance against previous work. In particular, the new network estimates the noise of each input wavelet transform, and then the de-noised wavelet coefficients are obtained by subtracting the noise from the input wavelet transform bands. The experimental results confirm that the proposed network has significantly improved performance, preserving the detail texture of the original images.
The nuclear magnetic resonance of 129Xe trapped in clathrates and some other solids (1988)

129 Xe NMR spectra were obtained for xenon trapped in the cages of clathrate hydrates and a clathrasil sample. The data, together with shift data for solid xenon, have yielded a linear correlation between the radius of the free space available to the xenon atom and the chemical shift. This observation cannot be rationalized by using simple binary collision theory. In order to account for the observation of anisotropic chemical shifts for xenon trapped in non-spherical environments a simple multiple-site model was developed. Several applications of 129Xe NMR spectroscopy are also presented. These include the identification of new clathrate hydrates, the use of 129Xe NMR to follow changes in site symmetry in a clathrasil and a cyclodextrin inclusion compound, and the observation of trapping sites in crystalline and amorphous solids.
Prophylactic immunization against experimental leishmaniasis. V. Mechanism of the anti-protective blocking effect induced by subcutaneous immunization against <i>Leishmania major</i> infection. (1985)

The responsiveness of BALB/c mice to protective i.v. immunization with 150,000-rad irradiated or heat-killed Leishmania major promastigotes can be totally suppressed by prior subcutaneous (s.c.) injection of the same "vaccine." Induction of this effect is leishmania specific for although prevention of protection against L. major infection can be obtained with either homologous or Leishmania donovani promastigotes, it does not follow s.c. administration of an immunogenic Trypanosoma cruzi epimastigote preparation. Multiple s.c. injections of irradiated L. major promastigotes do not inhibit the subsequent antibody response of any major isotype to i.v. immunization, but rather induce some priming. The same s.c. injections induced delayed-type hypersensitivity (DTH) reactivity that could be transferred locally or systemically, although it was weaker than in mice with cured infections. Parallel cell-mediated immunity (CMI) responses were also reflected in vitro in specific lymphocyte transformation assays. Despite this evidence of a DTH/helper type of T cell response, transfer of 5 X 10(7) viable T cell-enriched spleen cells from 4 X s.c. immunized donors to normal recipients completely abrogated the protective response to i.v. immunization. Conversely, T cell-depleted (anti-Thy-1.2 + C treated) cells were without effect. The inhibitory T cells were defined by monoclonal antibody pretreatment as possessing an Lyt-1+2-,L3T4+ phenotype. T cells from s.c. immunized donors were also shown, by mixed transfer experiments, to counteract completely the protective effect of T cells from i.v. immunized donors in 550-rad irradiated recipients. They were as potent as suppressor T cells from donors with progressive disease both in this capacity and in abrogating the prophylactic effect of sublethal irradiation itself. The similarities and differences between suppressor and immune effector T cells induced by s.c. or i.v. immunization and those arising in response to leishmanial infection itself are discussed.
Neuropeptides as modulators of macrophage functions. Regulation of cytokine production and antigen presentation by VIP and PACAP. (2001)

Vasoactive intestinal peptide (VIP) and the structurally related neuropeptide pituitary adenylate cyclase activating polypeptide (PACAP), present in the microenvironment of lymphoid organs, modulate the function of inflammatory cells through specific receptors. VIP and PACAP inhibit the production of pro-inflammatory agents and stimulate the production of anti-inflammatory cytokines in activated macrophages. The effect is mediated through specific receptors and involves shedding of the CD14 lipopolysaccharide (LPS) receptor and the transcriptional regulation of cytokine genes through effects on de novo expression or nuclear translocation of NFkappaB, cAMP-element binding protein (CREB), c-Jun, and interferon regulatory factor 1 (IRF-1). The in vivo administration of VIP/PACAP results in a similar pattern of cytokine modulation which, presumably, mediates the protective effect of VIP/PACAP in a high-endotoxic murine model for septic shock. VIP/PACAP reduce the expression of the costimulatory B7.1/B7.2 molecules and the subsequent stimulatory activity for T helper (Th) cells in stimulated macrophages. In contrast, in unstimulated macrophages, VIP/PACAP induce specific B7.2 expression and promote Th2 cell differentiation. We propose that VIP/PACAP act as endogenous factors that regulate immune homeostasis and that the physiological consequences of VIP/PACAP presence in the immune microenvironment depend on the timing of the neuropeptide release and the activation stage of the neighboring immune cells.
Downregulation of calcitonin receptor mRNA expression by calcitonin during human osteoclast-like cell differentiation. (1995)

Calcitonin inhibits both osteoclast formation and bone resorption, and is a primary treatment for patients with hypercalcemia and increased bone turnover. However, the clinical utility of calcitonin is limited because patients become refractory to calcitonin after several days (the calcitonin "escape phenomenon"). The molecular basis for calcitonin "escape" is unclear. To determine the regulatory mechanisms controlling calcitonin receptor (CTR) expression in osteoclasts and their precursors, we treated immature mononuclear precursors for human osteoclast-like multinucleated cells (MNC) formed in vitro with 1,25-(OH)2D3, to induce their differentiation to committed mononuclear precursors, and mature multinucleated osteoclasts, and used reverse transcriptase (RT)-PCR to assess expression of CTR mRNA in both committed mononuclear precursors and MNC. The PCR fragment produced was cloned and sequenced to confirm that it was derived from CTR mRNA. CTR mRNA expression was detected in mononuclear MNC precursors after 7 d of 1,25-(OH)2D3 treatment. It was also present in osteoclast-like MNC and highly purified giant cells from osteoclastomas, but not in monocytes or macrophage polykaryons formed in vitro. Calcitonin markedly decreased CTR but not actin mRNA expression in giant cells and MNC after 12 h, and removal of calcitonin restored CTR mRNA expression. Similarly, calcitonin decreased calcitonin-induced adenylate cyclase activity. These data suggest: (a) downregulation of CTR gene expression by calcitonin may in part explain the calcitonin "escape phenomenon"; and (b) expression of CTR mRNA occurs in mononuclear osteoclast precursors within 7 d after exposure to 1,25-(OH)2D3.
The effect of joint stiffness on simulation of the complete gait cycle (2002)

A computer simulation of paraplegic, walker assisted gait through multiple gait cycles is described. Computational problems associated with changing constraints during transitions between phases of gait are avoided by modeling foot-to-floor contact as an external force. Net joint torques, computed from kinematic data by inverse dynamics and transformed into sine functions, are used to drive limb motion. Model instability is overcome by emulating the effects of 'stiffness' at the joints by using proportional-derivative (PD) controllers. Maximum joint torques needed to achieve stable gait were found to be within normal physiological range. Joint kinematics and foot contact forces generally followed a normal gait pattern producing a forward displacement of approximately 0.8 m/s at a walking frequency of 0.5 Hz. The most significant deviation from a normal walking pattern was excessive hip abduction during stance phase causing a waddling (medial-lateral sway) motion. A quantitative measurement of the dynamic stability of the simulation is calculated based on Floquet theory.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
"A veritable bucket of facts" origins of the data base management system (2006)

The data base concept derives from early military on-line systems, and was not originally associated with the specific technologies of modern data base management systems. While the idea of an integrated data base, or "bucket of facts," spread into corporate data processing and management circles during the early 1960s, it was seldom realized in practice. File-processing packages were among the very first distributed as supported products, but only in the late 1960s were they first called "data base management systems," in large part through the actions of the Data Base Task Group of the Committee on Data Systems Languages (CODASYL). As the DBMS concept spread, the data base itself was effectively redefined as the informational content of a packaged DBMS. Throughout the process, managerial descriptions of the data base as a flexible and integrated repository for all corporate data stood in sharp contrast with the useful but limited nature of actual systems.
A Correlation Analysis of Concentrations and a Simulation of Flow Rate for a Mine Water (1987)

Estimating methods of the flow rate and concentrations of the components of a mine water from measured results for the past yearhave been investigated in order to develop a new treating process of the mine water applied a technique of foam fractionation.The summary of the result was as follows:(1) Concentrationof the mine water components did not change at random, but varied almost all together.(2) A correlation line have been obtained by the analysis of eigenvectors about the correlation coefficient matrix of the mine water.(3) The variation of the flowrate depended mainly on the amount of rain except a snowy season.(4) A relation between the amount of rain and the flow rateof the mine water has been analyzed, using the physical model consisted of two vessels.
Lipid Involvement in Viral Infections: Present and Future Perspectives for the Design of Antiviral Strategies (2013)

Lipid Involvement in Viral Infections: Present and Future Perspectives for the Design of Antiviral Strategies
Standard Reference Data for the Thermophysical Properties of Biofuels (2010)

Abstract The thermophysical properties of biofuels are required for the efficient design of their chemical processing, distribution, and utilization. We provide a review of biofuel properties research at the National Institute of Standards and Technology (NIST). We are expanding two Standard Reference Databases to include biofuels. The ThermoData Engine will collect and evaluate all published property data on biofuel components. The NIST Reference Fluid Thermodynamic and Transport Properties database is a calculational database providing properties of biofuel components and blends based on thermodynamic and transport models. The property models in the databases implement an equation of state approach based on well defined reference fluids. Complex mixtures, including blends of biofuels with conventional fuels, are modeled as “surrogate blends,” i.e., a blend of perhaps a dozen components that captures the essential characteristics of a complex fuel. Surrogate blends are formulated from a “suite” of well-characterized pure compounds. Property measurements for the pure compounds in the surrogate suite include but are not limited to density, speed of sound, and viscosity. We have also carried out measurements on actual biofuel samples. A recent extension of the distillation curve that we have developed at NIST is proving very valuable in characterizing fuels. This “advanced distillation curve method” provides much more quantitative information than the traditional method, including chemical characterization of the different “cuts” as the distillation proceeds. We present examples of our measurements and models completed to date and outline future plans.
Battery pack circuit design for safety and protection (2002)

Do our fast-paced lifestyles drive new technology, or is new technology partly to blame for continuing to increase the pace of our lifestyles? We want to be connected and productive - or entertained - even during our traditional times of leisure and recreation. Our tools for connectivity and productivity - and our toys for entertainment - support us by continuing to become smaller, lighter and more mobile, even as functionality increases. This drive toward increasing portability, mobility and functionality has had many interesting results. One result is that high-energy battery packs are becoming pervasive in our professional and personal lives. But the high power-delivery and energy-storage capabilities of packs for these power-hungry devices generally remain invisible to end-users. In reality, most packs have the potential not only for damaging themselves, but also for imposing damage on their surroundings, even if used exclusively in accordance with manufacturers` instructions. And newer battery technologies that offer longer runtimes or less weight can pose higher risks. This paper compares and contrasts the characteristics of various safety practices and devices used in designing and assembling high-energy battery packs.