cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3122179
title: Critical Filter Hydrograph and Field Site Data

description: These files represent hydrographs and associated field data. Please see the readme file for more information. Each .zip file contains an illustrated readme/methods file.
DOI: 10.6084/m9.figshare.3122179.v1
title: Critical Filter Hydrograph and Field Site Data

description: These files represent hydrographs and associated field data. Please see the readme file for more information. Each .zip file contains an illustrated readme/methods file.
DOI: 10.6084/m9.figshare.3122173.v1
title: Goodreads Social Reviews for Book Impact Assessment: A Multidisciplinary Study

description: Appendixes for an articles submitted to Journal of the Association for Information Science and Technology entitled: Goodreads Social Reviews for Book Impact Assessment: A Multidisciplinary Study
DOI: 10.6084/m9.figshare.3122437.v2
title: Day 1: Introduction to microarrays

description: Slides from: Practical course in microarray data analysisKI, 2015
DOI: 10.6084/m9.figshare.3122113
title: Reproductive Capacity, Developmental Plasticity, and Evolution in C. elegans

description: Data from extended L1 arrest (starvation) experiments in C. elegans. Data includes population counts, experimental evolution results, and time-series interpolations. Data accompany "Genotype-specific developmental plasticity shapes the timing and robustness of reproductive capacity in Caenorhabditis elegans", bioRxiv, doi:10.1101/045609.<br>http://www.biorxiv.org/content/early/2016/03/24/045609
DOI: 10.6084/m9.figshare.3122110
title: DIC and Cardiopulmonary Arrest1.xlsx

description: CPA and DIC<br><br>
DOI: 10.6084/m9.figshare.3122173.v2
title: Goodreads Social Reviews for Book Impact Assessment: A Multidisciplinary Study

description: Appendixes for an articles submitted to Journal of the Association for Information Science and Technology entitled: Goodreads Social Reviews for Book Impact Assessment: A Multidisciplinary Study
DOI: 10.6084/m9.figshare.3122113.v1
title: Developmental Plasticity and Evolution Data for 15 Distinct C. elegans Genotypes

description: Data from extended L1 arrest (starvation) experiments in C. elegans. Data includes population counts, experimental evolution results, and time-series interpolations. Data accompany a forthcoming manuscript.
DOI: 10.6084/m9.figshare.3122104
title: Drake_NewPhyt_2016_WTC3_RtoGPP_forfigshare.zip

description: Photosynthesis and respiration at the leaf and canopy scales for Eucalyptus tereticornis trees grown in whole-tree chambers at the Hawkesbury Forest Experiment. <br>Eucalyptus tereticornis trees were field-grown in large (9-m-tall) whole-tree chambers and exposed to ambient or +3 degrees C warming near Richmond, NSW, Australia. Files contain data regarding the meteorology experienced by each tree (air temperature, air humidity, incident light, etc), tree growth (diameter and stem length), tree moisture status (predawn and midday leaf water potentials), and the exchange of CO2 and H2O of leaves, branch wood, and whole tree canopies. Extensive documentation for each datafile exist within the zipfile.<br><br>These data files were used for the manuscript: <br><br>Drake JE, MG Tjoelker, MJ Aspinwall, PB Reich, CVM Barton, BE Medlyn, R Duursma, (accepted by New Phytologist) Does physiological acclimation to climate warming stabilize the ratio of canopy respiration to photosynthesis?<br>
DOI: 10.6084/m9.figshare.3122113.v2
title: Developmental Plasticity and Evolution Data for 15 Distinct C. elegans Genotypes

description: Data from extended L1 arrest (starvation) experiments in C. elegans. Data includes population counts, experimental evolution results, and time-series interpolations. Data accompany "Genotype-specific developmental plasticity shapes the timing and robustness of reproductive capacity in Caenorhabditis elegans", bioRxiv, doi:10.1101/045609.<br>http://www.biorxiv.org/content/early/2016/03/24/045609
DOI: 10.6084/m9.figshare.3122101
title: Mameyes River morphology data

description: These (.txt) files represent data collected within the Mameyes River as part of the Luquillo Critical Zone Observatory. See dataset readme file for detailed information. The files contain measurements of the average river depth and discharge at the banks as well as measurements of the median bed sediment diameter. These measurements are provided with a distance that relates to a longitudinal profile taken from aerial lidar data.
DOI: 10.6084/m9.figshare.3122110.v1
title: Data set1.xlsx

description: CPA and DIC<br><br>
DOI: 10.6084/m9.figshare.3122101.v2
title: Mameyes River morphology data

description: These (.txt) files represent data collected within the Mameyes River as part of the Luquillo Critical Zone Observatory. See dataset readme file for detailed information. The files contain measurements of the average river depth and discharge at the banks as well as measurements of the median bed sediment diameter. These measurements are provided with a distance that relates to a longitudinal profile taken from aerial lidar data.
DOI: 10.6084/m9.figshare.3122101.v1
title: Mameyes River field data compilation

description: These (.txt) files represent data collected within the Mameyes River as part of the Luquillo Critical Zone Observatory. See dataset readme file for detailed information. The files contain measurements of the average river depth and discharge at the banks as well as measurements of the median bed sediment diameter. These measurements are provided with a distance that relates to a longitudinal profile taken from aerial lidar data.
DOI: 10.4225/03/57428ae7bba44
title: X-ray crystal structure of the streptococcal specific phage lysin PlyC

description: Bacteriophages deploy lysins that degrade the bacterial cell wall and facilitate virus egress from the host. When applied exogenously, these enzymes destroy susceptible microbes and, accordingly, have potential as therapeutic agents. The most potent lysin identified to date is PlyC, an enzyme assembled from two components (PlyCA and PlyCB) that is specific for streptococcal species. Here the structure of the PlyC holoenzyme reveals that a single PlyCA moiety is tethered to a ring-shaped assembly of eight PlyCB molecules. Structure-guided mutagenesis reveals that the bacterial cell wall binding is achieved through a cleft on PlyCB. Unexpectedly, our structural data reveal that PlyCA contains a glycoside hydrolase domain in addition to the previously recognized cysteine, histidine-dependent amidohydrolases/peptidases catalytic domain. The presence of eight cell wall-binding domains together with two catalytic domains may explain the extraordinary potency of the PlyC holoenyzme toward target bacteria.
DOI: 10.4225/03/57428bc60169c
title: Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4. (2NO4)

description: DehIVa is a haloacid dehalogenase (EC 3.8.1.2) from the soil and water borne bacterium Burkholderia cepacia MBA4, which belongs to the functionally variable haloacid dehalogenase (HAD) superfamily of enzymes. The haloacid dehalogenases catalyse the removal of halides from haloacids resulting in a hydroxlated product. These enzymes are of interest for their potential to degrade recalcitrant halogenated environmental pollutants and their use in the synthesis of industrial chemicals. The haloacid dehalogenases utilise a nucleophilic attack on the substrate by an aspartic acid residue to form an enzyme-substrate ester bond and concomitantly cleaving of the carbon-halide bond and release of a hydroxylated product following ester hydrolysis. We present the crystal structures of both the substrate-free DehIVa refined to 1.93 A resolution and DehIVa covalently bound to l-2-monochloropropanoate trapped as a reaction intermediate, refined to 2.7 A resolution. Electron density consistent with a previously unidentified yet anticipated water molecule in the active site poised to donate its hydroxyl group to the product and its proton to the catalytic Asp11 is evident. It has been unclear how substrate enters the active site of this and related enzymes. The results of normal mode analysis (NMA) are presented and suggest a means whereby the predicted global dynamics of the enzyme allow for entry of the substrate into the active site. In the context of these results, the possible role of Arg42 and Asn178 in a `lock down` mechanism affecting active site access is discussed. In silico substrate docking of enantiomeric substrates has been examined in order to evaluate the enzymes enantioselectivity.<br>
DOI: 10.4225/03/57428baa46529
title: Structure of the Plasmodium falciparum PfA-M17_ZnZn (3KQZ)

description: Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the X-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here we present the X-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with anti-malarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centres in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA-M17 active sites now permits a rational approach in the development of a novel class of two-target and/or combination anti-malarial therapy.<br>
DOI: 10.4225/03/57428b9355bfe
title: Structure of the Plasmodium falciparum PfA-M17_BES (3KR4)

description: Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the X-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here we present the X-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with anti-malarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centres in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA-M17 active sites now permits a rational approach in the development of a novel class of two-target and/or combination anti-malarial therapy.
DOI: 10.4225/03/57428b78679d4
title: The high resolution crystal structure of a native thermostable serpin reveals the complex mechanism underpinning the stressed to relaxed transition. (1SNG)

description: Serpins fold into a native metastable state and utilize a complex conformational change to inhibit target proteases. An undesirable result of this conformational flexibility is that most inhibitory serpins are heat sensitive, forming inactive polymers at elevated temperatures. However, the prokaryote serpin, thermopin, from Thermobifida fusca is able to function in a heated environment. We have determined the 1.8 A x-ray crystal structure of thermopin in the native, inhibitory conformation. A structural comparison with the previously determined 1.5 A structure of cleaved thermopin provides detailed insight into the complex mechanism of conformational change in serpins. Flexibility in the shutter region and electrostatic interactions at the top of the A beta-sheet (the breach) involving the C-terminal tail, a unique structural feature of thermopin, are postulated to be important for controlling inhibitory activity and triggering conformational change, respectively, in the native state. Here we have discussed the structural basis of how this serpin reconciles the thermodynamic instability necessary for function with the stability required to withstand elevated temperatures.
DOI: 10.4225/03/57428b5a592f0
title: Synthesis of new (-)-Bestatin-based inhibitor libraries reveals a novel binding mode in the S1 pocket of the essential malaria M1 metalloaminopeptidase.

description: The essential malarial PfA-M1 metalloaminopeptidase is a validated drug target that functions in the terminal stages of hemoglobin digestion. The natural product dipeptide mimetic, bestatin, is a potent inhibitor of PfA-M1 and provides an excellent scaffold for the development of novel research tools as well as more effective PfA-M1 inhibitors. Here we present a new, efficient and high yielding protocol for the synthesis of bestatin-derivatives from commercially available natural and unnatural N-Boc-D-amino acids. We developed a diverse library of bestatin derivatives with variants at the sidechain of either the Œ±-hydroxy-Œ≤-amino acid or the adjacent natural Œ±-amino acid. Surprisingly we found that large aromatic rings at the P1 position resulted in potent inhibition against PfA-M1, while small hydrophobic sidechains were favored at the P1‚Äô position. These data contrast previous studies that suggested the primary substrate specificity (S1) pocket of the PfA-M1 enzyme is unable to accommodate side-chains much larger than a P1 phenylalanine. To understand these apparently contradictory data, we determined the X-ray crystal structure of the PfA-M1 / bestatin-Tyr(OBzl) complex. The structure revealed a substantial inhibitor-induced rearrangement of the primary loop that forms the S1 pocket that permits accommodation of the bestatin-Tyr(OBzl) inhibitor. These findings are in contrast to most proteases where the S1 pocket is considered to define primary enzyme specificity through substantial rigidity. Taken together, our data provide important insights for the rational design of more potent and selective inhibitors of this enzyme, which may eventually be of therapeutic value for the treatment of malaria.
DOI: 10.4225/03/57428b277afc1
title: A common fold mediates vertebrate defense and bacterial attack (2QP2)

description: Protein crystallography raw diffraction images and unmerged reflection intensities Collection size: 36.1 GB Number of datasets: 5 Citation: Rosado et. al. (2007) A common fold mediates vertebrate defense and bacterial attack. Science. In Press. Proteins containing membrane attack complex/perforin (MACPF) domains play important roles in vertebrate immunity, embryonic development, and neural-cell migration. In vertebrates, the ninth component of complement and perforin form oligomeric pores that lyse bacteria and kill virus-infected cells, respectively. However, the mechanism of MACPF function is unknown. We determined the crystal structure of a bacterial MACPF protein, Plu-MACPF from Photorhabdus luminescens, to 2.0 angstrom resolution. The MACPF domain reveals structural similarity with poreforming cholesterol-dependent cytolysins (CDCs) from Gram-positive bacteria. This suggests that lytic MACPF proteins may use a CDC-like mechanism to form pores and disrupt cell membranes. Sequence similarity between bacterial and vertebrate MACPF domains suggests that the fold of the CDCs, a family of proteins important for bacterial pathogenesis, is probably used by vertebrates for defense against infection.
DOI: 10.4225/03/57428b07d325e
title: Defining the interaction of perforin with calcium and the phospholipid membrane

description: Following its secretion from cytotoxic lymphocytes into the immune synapse, perforin binds to target cell membranes through its Ca2 + -dependent C2 domain. Membrane-bound perforin then forms pores that allow passage of pro-apoptopic granzymes into the target cell. In the present study, structural and biochemical studiesrevealthatCa2+ bindingtriggersaconformationalchange in the C2 domain that permits four key hydrophobic residues to interact with the plasma membrane. However, in contrast with previous suggestions, these movements and membrane binding do not trigger irreversible conformational changes in the pore-forming MACPF (membrane attack complex/perforin- like) domain, indicating that subsequent monomer–monomer interactions at the membrane surface are required for perforin pore formation.
DOI: 10.4225/03/57428abde1b40
title: Crystal structure of scabies mite inactivated protease paralogue S-D1 (SMIPP-S-D1) (3H7T)

description: The scabies mite (Sarcoptes scabiei) is a parasitic mite responsible for major morbidity in disadvantaged communities and immuno-compromised patients worldwide. In addition to the physical discomfort caused by the disease, scabies infestations facilitate infection by Streptococcal species via skin lesions, resulting in a high prevalence of rheumatic fever/heart disease in affected communities. The scabies mite produces 33 proteins that are closely related to the dust mite group 3 allergen and belong to the S1-like protease family (chymotrypsin-like). However, all but one of these molecules contain mutations in the conserved active-site catalytic triad that are predicted to render them catalytically inactive. These molecules are thus termed Scabies Mite Inactivated Protease Paralogues (SMIPPs). The precise function of SMIPPs remains unclear. However, it has been suggested that these proteins may function by binding and protecting target substrates from cleavage by host immune proteases, thus preventing the host from mounting an effective immune challenge. In order to begin to understand the structural basis for SMIPP function, we solved the crystal structures of SMIPP-S-I1 and SMIPP-S-D1 at 1.85 and 2.0 A resolution respectively. Both structures adopt the characteristic serine protease fold, albeit with large structural variations over much of the molecule. In both structures, mutations in the catalytic triad together with occlusion of the S1 subsite by a conserved Tyr200 residue is predicted to block substrate ingress. Accordingly, we show that both proteases lack catalytic function. Attempts to restore function (via site directed mutagenesis of catalytic residues as well as Tyr200) were unsuccessful. Taken together, these data suggest that SMIPPs have lost the ability to bind substrates in a classical "canonical" fashion, and instead have evolved alternative functions in the lifecycle of the Scabies mite.<br>
DOI: 10.6084/m9.figshare.3121987
title: Measuring Nonlinear Granger Causality in Mean

description: We propose model-free measures for Granger causality in mean between random variables. Unlike the existing measures, ours are able to detect and quantify nonlinear causal effects. The new measures are based on nonparametric regressions and defined as logarithmic functions of restricted and unrestricted mean square forecast errors. They are easily and consistently estimated by replacing the unknown mean square forecast errors by their nonparametric kernel estimates. We derive the asymptotic normality of nonparametric estimator of causality measures, which we use to build tests for their statistical significance. We establish the validity of smoothed local bootstrap that one can use in finite sample settings to perform statistical tests. Monte Carlo simulations reveal that the proposed test has good finite sample size and power properties for a variety of data-generating processes and different sample sizes. Finally, the empirical importance of measuring nonlinear causality in mean is also illustrated. We quantify the degree of nonlinear predictability of equity risk premium using variance risk premium. Our empirical results show that the variance risk premium is a very good predictor of risk premium at horizons less than 6 months. We also find that there is a high degree of predictability at the 1-month horizon, that can be attributed to a nonlinear causal effect. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3121987.v1
title: Measuring Nonlinear Granger Causality in Mean

description: We propose model-free measures for Granger causality in mean between random variables. Unlike the existing measures, ours are able to detect and quantify nonlinear causal effects. The new measures are based on nonparametric regressions and defined as logarithmic functions of restricted and unrestricted mean square forecast errors. They are easily and consistently estimated by replacing the unknown mean square forecast errors by their nonparametric kernel estimates. We derive the asymptotic normality of nonparametric estimator of causality measures, which we use to build tests for their statistical significance. We establish the validity of smoothed local bootstrap that one can use in finite sample settings to perform statistical tests. Monte Carlo simulations reveal that the proposed test has good finite sample size and power properties for a variety of data-generating processes and different sample sizes. Finally, the empirical importance of measuring nonlinear causality in mean is also illustrated. We quantify the degree of nonlinear predictability of equity risk premium using variance risk premium. Our empirical results show that the variance risk premium is a very good predictor of risk premium at horizons less than 6 months. We also find that there is a high degree of predictability at the 1-month horizon, that can be attributed to a nonlinear causal effect. Supplementary materials for this article are available online.