cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3159730
title: Identifying Structural Models of Committee Decisions With Heterogeneous Tastes and Ideological Bias

description: In practice, members of a committee often make different recommendations despite a common goal and shared sources of information. We study the nonparametric identification and estimation of a structural model, where such discrepancies are rationalized by the members’ unobserved types, which consist of ideological bias while weighing different sources of information, and tastes for multiple objectives announced in the policy target. We consider models with and without strategic incentives for members to make recommendations that conform to the final committee decision. We show that pure-strategy Bayesian Nash equilibria exist in both cases, and that the variation in common information recorded in the data helps us to recover the distribution of private types from the members’ choices. Building on the identification result, we estimate a structural model of interest rate decisions by the Monetary Policy Committee (MPC) at the Bank of England. We find some evidence that the external committee members are less affected by strategic incentives for conformity in their recommendations than the internal members. We also find that the difference in ideological bias between external and internal members is statistically insignificant. Supplementary materials for this article are available online.
DOI: 10.18462/iir.rankine.2020.1144
title: Dynamic analysis of energy recovery utilizing thermal storage from batch-wise metal casting.
DOI: 10.6084/m9.figshare.3159727.v1
title: Programming with models: writing statistical algorithms for general model structures with NIMBLE

description: We describe NIMBLE, a system for programming statistical algorithms for general model structures within R. NIMBLE is designed to meet three challenges: flexible model specification, a language for programming algorithms that can use different models, and a balance between high-level programmability and execution efficiency. For model specification, NIMBLE extends the BUGS language and creates model objects, which can manipulate variables, calculate log probability values, generate simulations, and query the relationships among variables. For algorithm programming, NIMBLE provides functions that operate with model objects using two stages of evaluation. The first stage allows specialization of a function to a particular model and/or nodes, such as creating a Metropolis-Hastings sampler for a particular block of nodes. The second stage allows repeated execution of computations using the results of the first stage. To achieve efficient second-stage computation, NIMBLE compiles models and functions via C++, using the Eigen library for linear algebra, and provides the user with an interface to compiled objects. The NIMBLE language represents a compilable domain-specific language (DSL) embedded within R. This paper provides an overview of the design and rationale for NIMBLE along with illustrative examples including importance sampling, Markov chain Monte Carlo (MCMC) and Monte Carlo expectation maximization (MCEM).
DOI: 10.6084/m9.figshare.3159730.v2
title: Identifying Structural Models of Committee Decisions With Heterogeneous Tastes and Ideological Bias

description: In practice, members of a committee often make different recommendations despite a common goal and shared sources of information. We study the nonparametric identification and estimation of a structural model, where such discrepancies are rationalized by the members’ unobserved types, which consist of ideological bias while weighing different sources of information, and tastes for multiple objectives announced in the policy target. We consider models with and without strategic incentives for members to make recommendations that conform to the final committee decision. We show that pure-strategy Bayesian Nash equilibria exist in both cases, and that the variation in common information recorded in the data helps us to recover the distribution of private types from the members’ choices. Building on the identification result, we estimate a structural model of interest rate decisions by the Monetary Policy Committee (MPC) at the Bank of England. We find some evidence that the external committee members are less affected by strategic incentives for conformity in their recommendations than the internal members. We also find that the difference in ideological bias between external and internal members is statistically insignificant. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3159730.v1
title: Identifying Structural Models of Committee Decisions with Heterogeneous Tastes and Ideological Bias

description: In practice, members of a committee often make different recommendations despite a common goal and shared sources of information. We study the nonparametric identification and estimation of a structural model where such discrepancies are rationalized by the members’ unobserved types, which consist of ideological bias while weighing different sources of information, and tastes for multiple objectives announced in the policy target. We consider models with and without strategic incentives for members to make recommendations that conform to the final committee decision. We show that pure-strategy Bayesian Nash equilibria exist in both cases, and that the variation in common information recorded in the data helps us to recover the distribution of private types from the members’ choices. Building on the identification result, we estimate a structural model of interest rate decisions by the Monetary Policy Committee (MPC) at the Bank of England. We find some evidence that the external committee members are less affected by strategic incentives for conformity in their recommendations than the internal members. We also find that the difference in ideological bias between external and internal members is statistically insignificant.
DOI: 10.6084/m9.figshare.3159700
title: Penalized Versus Constrained Generalized Eigenvalue Problems

description: We investigate the difference between using an ℓ<sub>1</sub> penalty versus an ℓ<sub>1</sub> constraint in generalized eigenvalue problems arising in multivariate analysis. Our main finding is that the ℓ<sub>1</sub> penalty may fail to provide very sparse solutions; a severe disadvantage for variable selection that can be remedied by using an ℓ<sub>1</sub> constraint. Our claims are supported both by empirical evidence and theoretical analysis. Finally, we illustrate the advantages of the ℓ<sub>1</sub> constraint in the context of discriminant analysis and principal component analysis. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3159700.v2
title: Penalized Versus Constrained Generalized Eigenvalue Problems

description: We investigate the difference between using an ℓ<sub>1</sub> penalty versus an ℓ<sub>1</sub> constraint in generalized eigenvalue problems arising in multivariate analysis. Our main finding is that the ℓ<sub>1</sub> penalty may fail to provide very sparse solutions; a severe disadvantage for variable selection that can be remedied by using an ℓ<sub>1</sub> constraint. Our claims are supported both by empirical evidence and theoretical analysis. Finally, we illustrate the advantages of the ℓ<sub>1</sub> constraint in the context of discriminant analysis and principal component analysis. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3159700.v1
title: Penalized versus constrained generalized eigenvalue problems

description: We investigate the difference between using an ℓ<sub>1</sub> penalty versus an ℓ<sub>1</sub> constraint in generalized eigenvalue problems arising in multivariate analysis. Our main finding is that the ℓ<sub>1</sub> penalty may fail to provide very sparse solutions; a severe disadvantage for variable selection that can be remedied by using an ℓ<sub>1</sub> constraint. Our claims are supported both by empirical evidence and theoretical analysis. Finally, we illustrate the advantages of the ℓ<sub>1</sub> constraint in the context of discriminant analysis and principal component analysis.
DOI: 10.6084/m9.figshare.3159679
title: Impact of the Arg 16 allele of the B2AR gene on the effect of withdrawal of LABA in patients with moderate to severe asthma

description: <i>Introduction</i>: Long-acting beta agonists (LABAs) are effective for controlling asthma, however questions about their safety have led to concerns over use. Genetic polymorphisms at the 16 amino acid position of the beta-2 adrenergic receptor gene (B2AR) may be associated with increased risk. <i>Methods</i>: A randomized, double blind study was conducted in patients with moderate to severe asthma being treated with combined inhaled corticosteroids/LABA (ICS/LABA), comparing the effect of LABA continuation versus withdrawal on asthma outcomes among patients stratified by B2AR genotype (Arg/Arg vs. Gly/Gly at the 16th amino acid position). <i>Results</i>: 67 participants (31 Arg/Arg, 36 Gly/Gly) were randomized to receive fluticasone alone (F) or continue combined fluticasone/salmeterol (F/S) after a run-in period on F/S. Among Gly/Gly subjects, those in the F/S treatment group showed improvement in AM PEFR (+ 8.4 L/s) whereas those receiving F alone experienced a reduction in AM PEFR over the study period (−14.4 L/s), (<i>p</i> = 0.06). There was no significant difference in morning peak expiratory flow rate (AM PEFR) in Arg/Arg participants randomized to receive F/S (−15.7L) vs F alone (−5.6 L/s) (<i>p</i> = 0.61). There was no significant difference in exacerbations in the Arg/Arg subjects treated with F/S compared with those treated with F (<i>p</i> = 0.65). <i>Conclusions</i>: Withdrawal of LABA therapy in asthmatics with the Arg/Arg genotype at the 16th amino acid position of B2AR did not lead to significant improvement in AM PEFR. LABA withdrawal in the Gly/Gly genotype however led to a borderline significant decline in AM PEFR.
DOI: 10.6084/m9.figshare.3159679.v2
title: Impact of the Arg 16 allele of the B2AR gene on the effect of withdrawal of LABA in patients with moderate to severe asthma

description: <i>Introduction</i>: Long-acting beta agonists (LABAs) are effective for controlling asthma, however questions about their safety have led to concerns over use. Genetic polymorphisms at the 16 amino acid position of the beta-2 adrenergic receptor gene (B2AR) may be associated with increased risk. <i>Methods</i>: A randomized, double blind study was conducted in patients with moderate to severe asthma being treated with combined inhaled corticosteroids/LABA (ICS/LABA), comparing the effect of LABA continuation versus withdrawal on asthma outcomes among patients stratified by B2AR genotype (Arg/Arg vs. Gly/Gly at the 16th amino acid position). <i>Results</i>: 67 participants (31 Arg/Arg, 36 Gly/Gly) were randomized to receive fluticasone alone (F) or continue combined fluticasone/salmeterol (F/S) after a run-in period on F/S. Among Gly/Gly subjects, those in the F/S treatment group showed improvement in AM PEFR (+ 8.4 L/s) whereas those receiving F alone experienced a reduction in AM PEFR over the study period (−14.4 L/s), (<i>p</i> = 0.06). There was no significant difference in morning peak expiratory flow rate (AM PEFR) in Arg/Arg participants randomized to receive F/S (−15.7L) vs F alone (−5.6 L/s) (<i>p</i> = 0.61). There was no significant difference in exacerbations in the Arg/Arg subjects treated with F/S compared with those treated with F (<i>p</i> = 0.65). <i>Conclusions</i>: Withdrawal of LABA therapy in asthmatics with the Arg/Arg genotype at the 16th amino acid position of B2AR did not lead to significant improvement in AM PEFR. LABA withdrawal in the Gly/Gly genotype however led to a borderline significant decline in AM PEFR.
DOI: 10.6084/m9.figshare.3159679.v1
title: Impact of the Arg 16 Allele of the B2AR Gene on the Effect of Withdrawal of LABA in Patients with Moderate to Severe Asthma

description: Introduction: Long acting beta agonists (LABAs) are effective for controlling asthma, however questions about their safety have led to concerns over use. Genetic polymorphisms at the 16 amino acid position of the beta-2 adrenergic receptor gene (B2AR) may be associated with increased risk. Methods: A randomized, double blind study was conducted in patients with moderate to severe asthma being treated with combined inhaled corticosteroids/LABA (ICS/LABA), comparing the effect of LABA continuation versus withdrawal on asthma outcomes among patients stratified by B2AR genotype (Arg/Arg vs. Gly/Gly at the 16<sup>th</sup> amino acid position). Results: 67 participants (31 Arg/Arg, 36 Gly/Gly) were randomized to receive fluticasone alone (F) or continue combined fluticasone/salmeterol (F/S) after a run-in period on F/S. Among Gly/Gly subjects, those in the F/S treatment group showed improvement in AM PEFR (+ 8.4 L/s) whereas those receiving F alone experienced a reduction in AM PEFR over the study period (−14.4 L/s), (p = 0.06). There was no significant difference in morning peak expiratory flow rate (AM PEFR) in Arg/Arg participants randomized to receive F/S (−15.7L) vs F alone (−5.6 L/s) (p = 0.61). There was no significant difference in exacerbations in the Arg/Arg subjects treated with F/S compared with those treated with F (p = 0.65). Conclusions: Withdrawal of LABA therapy in asthmatics with the Arg/Arg genotype at the 16<sup>th</sup> amino acid position of B2AR did not lead to significant improvement in AM PEFR. LABA withdrawal in the Gly/Gly genotype however led to a borderline significant decline in AM PEFR.
DOI: 10.6084/m9.figshare.3159634
title: Plastic ingestion by estuarine mullet <i>Mugil cephalus</i> (Mugilidae) in an urban harbour, KwaZulu-Natal, South Africa

description: Coastal urban environments have high plastic pollution levels, and hence interactions between plastic debris and marine life are frequent. We report on plastic ingestion by mullet <i>Mugil cephalus</i> in Durban Harbour, KwaZulu-Natal, South Africa. Of 70 mullet (13.0–19.5 cm total length), 73% had plastic particles in their guts, with a mean of 3.8 particles per fish (SD 4.7). Plastic ingestion showed no relation to digestive tract content or fish length. White and clear plastic fibres were ingested most commonly. This urban population of <i>M. cephalus</i> had a higher incidence of plastic ingestion than has been reported in studies on fish from other coastal areas or the oceanic environment.
DOI: 10.6084/m9.figshare.3159589
title: Systematics and evolutionary significance of the small Abrocomidae from the early Miocene of southern South America

description: Octodontoidea is the most species-rich clade among hystricomorph rodents, and has a fossil record going back to at least the late Oligocene. Affinities of fossils previous to the late Miocene differentiation of the extant families Abrocomidae, Echimyidae and Octodontidae are controversial, essentially because these fossils may share few apomorphies with modern species. In fact, pre-late Miocene representatives of Abrocomidae had not been recognised until very recently. Here we revise the early Miocene genus <i>Acarechimys</i>, originally assigned to Echimyidae, and alternatively to stem Octodontoidea or to Octodontidae. A systematic and parsimony-based phylogenetic analysis of the species traditionally included in <i>Acarechimys</i> showed that this genus is part of stem Abrocomidae. These results are primarily supported by morphology of the mandible and lower molars. <i>Acarechimys</i> is here restricted to three species, <i>A. minutus</i>, <i>A. pulchellus</i> and <i>Acarechimys pascuali</i> sp. nov., while another species, <i>A. constans</i>, is here transferred to a new abrocomid genus. The remaining species were nested within Octodontidae. According to these results, Abrocomidae might have been as diverse as its sister clade Octodontidae-Echimyidae during the late Oligocene–early Miocene. Extinction of this diversity would have resulted in marked loss of evolutionary history, with extant abrocomids being currently restricted to late-diverged euhypsodont representatives.
DOI: 10.6084/m9.figshare.3159583
title: EHB Genomes Not Genbank Cleared

description: Links to public repositories for genomes which haven't been cleared by Genbank yet<br>For Curtobacterium 9128, JGI files can be found here: https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2602042068<br>For Pantoea 9133, JGI files can be found here: https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2602042078<br>For Rhizobium 9140, JGI files can be found here:https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2602042090<br>
DOI: 10.6084/m9.figshare.3159634.v2
title: Plastic ingestion by estuarine mullet <i>Mugil cephalus</i> (Mugilidae) in an urban harbour, KwaZulu-Natal, South Africa

description: Coastal urban environments have high plastic pollution levels, and hence interactions between plastic debris and marine life are frequent. We report on plastic ingestion by mullet <i>Mugil cephalus</i> in Durban Harbour, KwaZulu-Natal, South Africa. Of 70 mullet (13.0–19.5 cm total length), 73% had plastic particles in their guts, with a mean of 3.8 particles per fish (SD 4.7). Plastic ingestion showed no relation to digestive tract content or fish length. White and clear plastic fibres were ingested most commonly. This urban population of <i>M. cephalus</i> had a higher incidence of plastic ingestion than has been reported in studies on fish from other coastal areas or the oceanic environment.
DOI: 10.6084/m9.figshare.3159583.v1
title: EHB Genomes Not Genbank Cleared

description: Links to public repositories for genomes which haven't been cleared by Genbank yet<br>For Curtobacterium 9128, JGI files can be found here: https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2602042068<br>For Pantoea 9133, JGI files can be found here: https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2602042078<br>For Rhizobium 9140, JGI files can be found here:https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2602042090<br>
DOI: 10.6084/m9.figshare.3159589.v2
title: Systematics and evolutionary significance of the small Abrocomidae from the early Miocene of southern South America

description: Octodontoidea is the most species-rich clade among hystricomorph rodents, and has a fossil record going back to at least the late Oligocene. Affinities of fossils previous to the late Miocene differentiation of the extant families Abrocomidae, Echimyidae and Octodontidae are controversial, essentially because these fossils may share few apomorphies with modern species. In fact, pre-late Miocene representatives of Abrocomidae had not been recognised until very recently. Here we revise the early Miocene genus <i>Acarechimys</i>, originally assigned to Echimyidae, and alternatively to stem Octodontoidea or to Octodontidae. A systematic and parsimony-based phylogenetic analysis of the species traditionally included in <i>Acarechimys</i> showed that this genus is part of stem Abrocomidae. These results are primarily supported by morphology of the mandible and lower molars. <i>Acarechimys</i> is here restricted to three species, <i>A. minutus</i>, <i>A. pulchellus</i> and <i>Acarechimys pascuali</i> sp. nov., while another species, <i>A. constans</i>, is here transferred to a new abrocomid genus. The remaining species were nested within Octodontidae. According to these results, Abrocomidae might have been as diverse as its sister clade Octodontidae-Echimyidae during the late Oligocene–early Miocene. Extinction of this diversity would have resulted in marked loss of evolutionary history, with extant abrocomids being currently restricted to late-diverged euhypsodont representatives.
DOI: 10.6084/m9.figshare.3159496
title: Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism

description: Dopamine D2 receptor (D2R) plays a pivotal role in nervous systems. Its dysfunction leads to the schizophrenia, Parkinson’s diseases and drug addiction. Since the crystal structure of the D2R was not solved yet, discovering of potent and highly selective anti-psychotic drugs carry challenges for different neurodegenerative diseases. In the current study, we modeled the three-dimensional (3D) structure of the D2R based on a recently crystallized structure of the dopamine D3 receptor. These two receptors share a high amino acid sequence homology (&gt;70%). The interaction of the modeled receptor with well-known atypical and typical anti-psychotic drugs and the inhibition mechanisms of drugs at the catalytic domain were studied via atomistic molecular dynamics simulations. Our results revealed that, class-I and class-II forms of atypical and typical D2R antagonists follow different pathways in the inhibition of the D2Rs.
DOI: 10.6084/m9.figshare.3159523
title: Functional characterization of hypothetical proteins of <i>Mycobacterium tuberculosis</i> with possible esterase/lipase signature: a cumulative <i>in silico</i> and <i>in vitro</i> approach

description: The functional aspect of several mycobacterium proteins annotated as hypothetical are yet to be discovered. In the present investigation, <i>in silico</i> approaches were used to predict the biological function of some of the unknown <i>Mtb</i> proteins, which were further validated by wet lab experiments. After screening thousands of <i>Mtb</i> proteins, functionally unknown hypothetical proteins Rv0421c, Rv0519c, Rv0774c, Rv1191, Rv1592c, and Rv3591c were chosen on the basis of their importance in <i>Mtb</i> life cycle. All these proteins posses the α/β-hydrolase topological fold, characteristic of lipases/esterases, with serine, aspartate, and histidine as the putative members of the catalytic triad. The catalytic serine is located in pentapeptide motif “GXSXG” and oxyanion residue is in dipeptide motif HG. To further support our observation, molecular docking was performed with conventional synthetic lipolytic substrates (pNP-esterss) and specific lipase/esterase inhibitors (tetrahydrolipstatin and phenylmethanesulfonyl fluoride (PMSF)). Significant docking score and strong interaction of substrates/inhibitors with these proteins revealed that these could be possible lipases/esterases. To validate the <i>in silico</i> studies, these genes were cloned from <i>Mtb</i> genome and the proteins were over-expressed in pQE-30/<i>Escherichia coli</i> M15 system. The expressed proteins were purified to homogeneity and enzymatic activity was determined using pNP esters as substrate. The enzyme activity of recombinant proteins was inhibited by tetrahydrolipstatin and PMSF pre-treatment. Outcome of the present investigation provided a basic platform to analyze and characterize unknown hypothetical proteins.