Publications by authors named "Daniel Crawford"

143 Publications

Modeling Complex Solvent Effects on the Optical Rotation of Chiral Molecules: A Combined Molecular Dynamics and Density Functional Theory Study.

J Phys Chem A 2021 Apr 8. Epub 2021 Apr 8.

Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.

The challenge of assigning the absolute stereochemical configuration to a chiral compound can be overcome accurate ab initio predictions of optical rotation, a sensitive molecular property that is further complicated by solvent effects. The solvent's "chiral imprint"-the transfer of the chirality from the solute to the surrounding achiral solvent-is explored here using conformational averaging and time-dependent density-functional theory. These complex solvent effects are taken into account simple averaging over a molecular dynamics trajectory together with the explicit quantum mechanical consideration of the solvent molecules within the solute's cybotactic region and implicit modeling of the bulk solvent. We consider several axes along which the system's optical rotation varies, including the sampling of the dynamical trajectory, the quality of the one-electron basis set, and the use of continuum solvent models to account for bulk effects.
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http://dx.doi.org/10.1021/acs.jpca.1c00803DOI Listing
April 2021

Structure Elucidation and Confirmation of Phloroglucinols from the Roots of by Comparison of Experimental and Calculated ECD Spectra and Specific Rotations.

J Nat Prod 2021 Apr 6. Epub 2021 Apr 6.

Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.

Eight phloroglucinols from were recently reported to have good to moderate antiplasmodial and anticancer activities, consistent with other phloroglucinol derivatives isolated from natural sources. Chiroptical properties were previously calculated and compared to experimental data for compound as a means to deduce its absolute configuration. Tentative assignments for the remaining compounds were also reported based on these data. In order to arrive at stereochemical assignments for phloroglucinols and -, ECD spectra and specific rotations were computed for all stereoisomers of each compound. Molecular orbital analyses were also carried out for the most energetically favorable conformers of each compound. Absolute configurations are reported for all eight phloroglucinols for the first time.
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http://dx.doi.org/10.1021/acs.jnatprod.0c01208DOI Listing
April 2021

Bland Embolization of Benign Liver Tumors: Review of the Literature and a Single Center Experience.

J Clin Med 2021 Feb 9;10(4). Epub 2021 Feb 9.

Division of Vascular and Interventional Radiology, Mayo Clinic Arizona, Phoenix, AZ 85054, USA.

Transarterial embolization has shown promise as a safe, effective, and less invasive treatment modality for benign liver lesions (hemangioma, focal nodular hyperplasia (FNH), and hepatic adenoma (HA)) with fewer complications compared to surgical intervention. There is no consensus regarding the most appropriate embolization material(s) for the treatment of benign liver tumors. The purpose of this study was to review the current literature regarding the transarterial embolization of benign liver tumors and to share our single center experience. This was a non-blinded, retrospective, single-institution review of the bland embolization of benign liver tumors. Clinical data and imaging before and after embolization were used to evaluate lesion response to transarterial embolization. Twelve patients were included in the study. Five patients with six hemangiomas were treated. Pain was a presenting complaint in all five of these patients. The median change in tumor volume was -12.4% and ranged from -30.1% to +42.3%. One patient with two FNH lesions was treated, and both lesion volumes decreased by more than 50%. Six patients with 10 adenomas were treated. Pain was a presenting complaint in three patients, and five patients had a lesion >5 cm. The median change in tumor volume was -67.0% and ranged from -92.9% to +65.8%. Bland transarterial embolization of liver hemangiomas, FNH, and HA can be an effective and minimally invasive treatment modality to control the size and/or symptoms of these lesions. There is a variable response depending on tumor type and the embolization materials used.
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http://dx.doi.org/10.3390/jcm10040658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7915444PMC
February 2021

Targeting G542X CFTR nonsense alleles with ELX-02 restores CFTR function in human-derived intestinal organoids.

J Cyst Fibros 2021 Feb 5. Epub 2021 Feb 5.

Eloxx Pharmaceuticals, Inc., 950 Winter Street, Waltham, MA 02451 USA. Electronic address:

Background: Promoting full-length protein production is a requisite step to address some of the remaining unmet medical need for those with Cystic Fibrosis (CF) nonsense alleles. ELX-02 promotes read-through of mRNA transcripts bearing nonsense mutations, including the most common CF nonsense allele G542X, in several different preclinical models including human bronchial epithelial cells. Here we evaluate ELX-02 mediated read-through using the CFTR-dependent Forskolin-induced swelling (FIS) assay across a selection of G542X genotype patient derived organoids (PDOs).

Methods: CFTR functional restoration was evaluated in ELX-02 treated G542X homozygous and heterozygous PDOs in the CFTR-dependent FIS assay. CFTR mRNA abundance and integrity were evaluated by qPCR and Nanostring analysis while PDO protein was detected by capillary based size-exclusion chromatography.

Results: PDOs homozygous for G542X or heterozygous with a second minimally functional allele had significantly increased CFTR activity with ELX-02 in a dose-dependent fashion across a variety of forskolin induction concentrations. The functional increases are similar to those obtained with tezacaftor/ivacaftor in F508del homozygous PDOs. Increased CFTR C- and B-band protein was observed in accordance with increased function. In addition, ELX-02 treatment of a G542X/G542X PDO results in a 5-fold increase in CFTR mRNA compared with vehicle treated, resulting in normalization of CFTR mRNA as measured via Nanostring.

Conclusions: These data with ELX-02 in PDOs are consistent with previous G542X model evaluations. These results also support the on-going clinical evaluation of ELX-02 as a read-through agent for CF caused by the G542X allele.
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http://dx.doi.org/10.1016/j.jcf.2021.01.009DOI Listing
February 2021

How rapidly do self-compatible populations evolve selfing? Mating system estimation within recently evolved self-compatible populations of Azorean (Asteraceae).

Ecol Evol 2020 Dec 20;10(24):13990-13999. Epub 2020 Nov 20.

Department of Ecology & Evolutionary Biology University of Kansas Lawrence KS USA.

Genome-wide genotyping and Bayesian inference method (BORICE) were employed to estimate outcrossing rates and paternity in two small plant populations of (Asteraceae) on Graciosa island in the Azores. These two known extant populations of on Graciosa have recently evolved self-compatibility. Despite the expectation that selfing would occur at an appreciable rate (self-incompatible populations of the same species show low but nonzero selfing), high outcrossing was found in progeny arrays from maternal plants in both populations. This is inconsistent with an immediate transition to high selfing following the breakdown of a genetic incompatibility system. This finding is surprising given the small population sizes and the recent colonization of an island from self-incompatible colonists of from another island in the Azores, and a potential paucity of pollinators, all factors selecting for selfing through reproductive assurance. The self-compatible lineage(s) likely have high inbreeding depression (ID) that effectively halts the evolution of increased selfing, but this remains to be determined. Like their progeny, all maternal plants in both populations are fully outbred, which is consistent with but not proof of high ID. High multiple paternity was found in both populations, which may be due in part to the abundant pollinators observed during the flowering season.
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http://dx.doi.org/10.1002/ece3.6992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771160PMC
December 2020

PNO++: Perturbed Pair Natural Orbitals for Coupled Cluster Linear Response Theory.

J Chem Theory Comput 2021 Jan 22;17(1):290-301. Epub 2020 Dec 22.

Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.

Reduced-scaling methods are needed to make accurate and systematically improvable coupled cluster linear response methods for the calculation of molecular properties tractable for large molecules. In this paper, we examine the perturbed pair natural orbital-based PNO++ approach that creates an orbital space optimized for response properties derived from a lower-cost field-perturbed density matrix. We analyze truncation errors in correlation energies, dynamic polarizabilities, and specific rotations from a coupled cluster singles and doubles (CCSD) reference. We find that incorporating a fixed number of orbitals from the pair natural orbital (PNO) space into the PNO++ method-a new method presented here, the "combined PNO++" approach-recovers accuracy in the CCSD correlation energy while preserving the well-behaved convergence behavior of the PNO++ method for linear response properties.
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http://dx.doi.org/10.1021/acs.jctc.0c01086DOI Listing
January 2021

Plastid Phylogenomics of (Cichorieae; Asteraceae): Insights Into Structural Organization and Molecular Evolution of an Endemic Lineage From the Juan Fernández Islands.

Front Plant Sci 2020 5;11:594272. Epub 2020 Nov 5.

Department of Biological Sciences, Sungkyunkwan University, Suwon-si, South Korea.

D. Don comprises 11 species endemic to the Juan Fernández islands in Chile. They demonstrate spectacular and unusual growth forms of rosette trees with extremely variable morphology and occupy wide ecological ranges on the islands. These unique plants are now highly threatened with extinction with very small population sizes, typically consisting of 10 or fewer individuals in wild. Despite morphological and ecological divergence among species of , their monophyly has been supported in previous studies, but with little resolution among subgeneric groups. We assembled seven complete plastome sequences from seven species of , including representatives from three subgenera, and carried out comparative phylogenomic analyses. The plastomes are highly conserved in gene content and order, with size ranging from 152,199 to 152,619 bp and containing 130 genes (87 coding genes, 6 rRNA genes, and 37 tRNA genes). Plastid phylogenomic analyses based on both the complete plastome sequences and 81 concatenated coding genes only show nested within ensu lato, and also that inter-subgeneric relationships are fully resolved. Subg. is resolved as sister to the remaining species of the genus and a sister relationship between the two subgenera and . Ten mutation hotspots from LSC and SSC regions and variable SSRs are identified as potential chloroplast markers for future phylogenetic and phylogeographic studies of and related groups.
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http://dx.doi.org/10.3389/fpls.2020.594272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7674203PMC
November 2020

Theory and implementation of a novel stochastic approach to coupled cluster.

J Chem Phys 2020 Oct;153(14):144117

Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.

We present a detailed discussion of our novel diagrammatic coupled cluster Monte Carlo (diagCCMC) [Scott et al. J. Phys. Chem. Lett. 10, 925 (2019)]. The diagCCMC algorithm performs an imaginary-time propagation of the similarity-transformed coupled cluster Schrödinger equation. Imaginary-time updates are computed by the stochastic sampling of the coupled cluster vector function: each term is evaluated as a randomly realized diagram in the connected expansion of the similarity-transformed Hamiltonian. We highlight similarities and differences between deterministic and stochastic linked coupled cluster theory when the latter is re-expressed as a sampling of the diagrammatic expansion and discuss details of our implementation that allow for a walker-less realization of the stochastic sampling. Finally, we demonstrate that in the presence of locality, our algorithm can obtain a fixed errorbar per electron while only requiring an asymptotic computational effort that scales quartically with system size, independent of the truncation level in coupled cluster theory. The algorithm only requires an asymptotic memory cost scaling linearly, as demonstrated previously. These scaling reductions require no ad hoc modifications to the approach.
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http://dx.doi.org/10.1063/5.0026513DOI Listing
October 2020

Intravitreal administration of small molecule read-through agents demonstrate functional activity in a nonsense mutation mouse model.

Exp Eye Res 2020 12 2;201:108274. Epub 2020 Oct 2.

Eloxx Pharmaceuticals, Inc., 950 Winter Street, Waltham, MA, 02451, USA. Electronic address:

The prevalence of nonsense mutations as a class within genetic diseases such as inherited retinal disorders (IRDs) presents an opportunity to develop a singular, common therapeutic agent for patients whose treatment options are otherwise limited. We propose a novel approach to addressing IRDs utilizing Eukaryotic Ribosome Selective Glycosides, ELX-01 and ELX-06, delivered to the eye by intravitreal (IVT) injection. We assessed read-through activity in vitro using a plasmid-based dual luciferase assay and in vivo in a mouse model of oculocutaneous albinism type 2. These models interrogate a naturally occurring R262X nonsense mutation in the OCA2 gene. ELX-01 and ELX-06 both produced a concentration-dependent increase in read-through of the OCA2 R262X mutation in the dual luciferase assay, with an effect at the top concentration which is superior to both gentamicin and G418. When testing both compounds in vivo, a single IVT injection produced a dose-dependent increase in melanin, consistent with compound read-through activity and functional restoration of the Oca2 protein. These results establish that ELX-01 and ELX-06 produce read-through of a premature stop codon in the OCA2 gene both in vitro and in vivo. The in vivo results suggest that these compounds can be dosed IVT to achieve read-through at the back of the eye. These data also suggest that ELX-01 or ELX-06 could serve as a common therapeutic agent across nonsense mutation-mediated IRDs and help to establish a target exposure range for development of a sustained release IVT formulation.
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http://dx.doi.org/10.1016/j.exer.2020.108274DOI Listing
December 2020

Genome-wide genotyping estimates mating system parameters and paternity in the island species Tolpis succulenta.

Am J Bot 2020 08;107(8):1189-1197

Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7534, USA.

Premise: The mating system has profound consequences, not only for ecology and evolution, but also for the conservation of threatened or endangered species. Unfortunately, small populations are difficult to study owing to limits on sample size and genetic marker diversity. Here, we estimated mating system parameters in three small populations of an island plant using genomic genotyping. Although self-incompatible (SI) species are known to often set some self-seed, little is known about how "leaky SI" affects selfing rates in nature or the role that multiple paternity plays in small populations.

Methods: We generalized the BORICE mating system program to determine the siring pattern within maternal families. We applied this algorithm to maternal families from three populations of Tolpis succulenta from Madeira Island and genotyped the progeny using RADseq. We applied BORICE to estimate each individual offspring as outcrossed or selfed, the paternity of each outcrossed offspring, and the level of inbreeding of each maternal plant.

Results: Despite a functional self-incompatibility system, these data establish T. succulenta as a pseudo-self-compatible (PSC) species. Two of 75 offspring were strongly indicated as products of self-fertilization. Despite selfing, all adult maternal plants were fully outbred. There was high differentiation among and low variation within populations, consistent with a history of genetic isolation of these small populations. There were generally multiple sires per maternal family. Twenty-two percent of sib contrasts (between outcrossed offspring within maternal families) shared the same sire.

Conclusions: Genome-wide genotyping, combined with appropriate analytical methods, enables estimation of mating system and multiple paternity in small populations. These data address questions about the evolution of reproductive traits and the conservation of threatened populations.
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http://dx.doi.org/10.1002/ajb2.1515DOI Listing
August 2020

Direct, Percutaneous, Cervical Thoracic Duct Access under Ultrasound Guidance.

J Vasc Interv Radiol 2020 09 25;31(9):1499-1501. Epub 2020 Jul 25.

Division of Interventional Radiology, Washington University in St. Louis School of Medicine, 510 South Kingshighway Boulevard St. Louis, MO 63110.

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http://dx.doi.org/10.1016/j.jvir.2020.04.001DOI Listing
September 2020

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

J Chem Phys 2020 May;152(18):184108

Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.
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http://dx.doi.org/10.1063/5.0006002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7228781PMC
May 2020

Machine-Learning Coupled Cluster Properties through a Density Tensor Representation.

J Phys Chem A 2020 Jun 2;124(23):4861-4871. Epub 2020 Jun 2.

Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.

The introduction of machine-learning (ML) algorithms to quantum mechanics enables rapid evaluation of otherwise intractable expressions at the cost of prior training on appropriate benchmarks. Many computational bottlenecks in the evaluation of accurate electronic structure theory could potentially benefit from the application of such models, from reducing the complexity of the underlying wave function parameter space to circumventing the complications of solving the electronic Schrödinger equation entirely. Applications of ML to electronic structure have thus far been focused on learning molecular properties (mainly the energy) from geometric representations. While this line of study has been quite successful, highly accurate models typically require a "big data" approach with thousands of training data points. Herein, we propose a general, systematically improvable scheme for wave function-based ML of arbitrary molecular properties, inspired by the underlying equations that govern the canonical approach to computing the properties. To this end, we combine the established ML machinery of the with a new reduced density matrix representation. The resulting model provides quantitative accuracy in both the electronic energy and dipoles of small molecules using only a few dozen training points per system.
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http://dx.doi.org/10.1021/acs.jpca.0c02804DOI Listing
June 2020

ELX-02 Generates Protein via Premature Stop Codon Read-Through without Inducing Native Stop Codon Read-Through Proteins.

J Pharmacol Exp Ther 2020 08 6;374(2):264-272. Epub 2020 May 6.

Eloxx Pharmaceuticals, Inc., Waltham, Massachusetts.

ELX-02 is a clinical stage, small-molecule eukaryotic ribosomal selective glycoside acting to induce read-through of premature stop codons (PSCs) that results in translation of full-length protein. However, improved read-through at PSCs has raised the question of whether native stop codon (NSC) fidelity would be impacted. Here, we compare read-through by ELX-02 in PSC and NSC contexts. DMS-114 cells containing a PSC in the gene were treated with ELX-02 and tested for increased nuclear p53 protein expression while also monitoring two other proteins for NSC read-through. Additionally, blood samples were taken from healthy subjects pre- and post-treatment with ELX-02 (0.3-7.5 mg/kg). These samples were processed to collect white blood cells and then analyzed by western blot to identify native and potentially elongated proteins from NSC read-through. In a separate experiment, lymphocytes cultivated with vehicle or ELX-02 (20 and 100 μg/ml) were subjected to proteomic analysis. We found that ELX-02 produced significant read-through of the PSC found in mRNA in DMS-114 cells, resulting in increased p53 protein expression and consistent with decreased nonsense-mediated mRNA degradation. NSC read-through protein products were not observed in either DMS-114 cells or in clinical samples from subjects dosed with ELX-02. The number of read-through proteins identified by using proteomic analysis was lower than estimated, and none of the NSC read-through products identified with >2 peptides showed dose-dependent responses to ELX-02. Our results demonstrate significant PSC read-through by ELX-02 with maintained NSC fidelity, thus supporting the therapeutic utility of ELX-02 in diseases resulting from nonsense alleles. SIGNIFICANCE STATEMENT: ELX-02 produces significant read-through of premature stop codons leading to full-length functional protein, demonstrated here by using the mutation in the gene of DMS-114 cells. In addition, three complementary techniques suggest that ELX-02 does not promote read-through of native stop codons at concentrations that lead to premature stop codon read-through. Thus, ELX-02 may be a potential therapeutic option for nonsense mutation-mediated genetic diseases.
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http://dx.doi.org/10.1124/jpet.120.265595DOI Listing
August 2020

Dose reduction using digital fluoroscopy versus digital subtraction angiography in endovascular aneurysm repair: A prospective randomized trial.

J Vasc Surg 2020 12 8;72(6):1938-1945. Epub 2020 Apr 8.

Department of Radiology, Mayo Clinic, Scottsdale, Ariz.

Objective: Endovascular aneurysm repair (EVAR) can result in high radiation dose to patients and operators. This prospective randomized study aimed to assess whether patient radiation dose sustained during EVAR could be decreased by predominantly using digital fluoroscopy (DF) vs the standard technique using digital subtraction angiography (DSA).

Methods: Between February 2011 and June 2017, patients with EVAR of infrarenal abdominal aortic aneurysms were prospectively enrolled and randomly assigned to a standard treatment DSA cohort or a DF cohort in which two or fewer DSA acquisitions were allowed for confirmatory imaging. Primary end points included dose-area product (DAP) and cumulative air kerma. Secondary end points included technical success and conversion to DSA standard treatment (if DF was inadequate for visualization).

Results: For all 43 patients enrolled (26 in the DF cohort, 17 in the DSA cohort), technical success was 100%. Of the 26 DF patients, 5 (19%) required conversion to the DSA cohort. In an intention-to-treat analysis, mean DAP was significantly lower in the DF cohort than in the DSA cohort (132 vs 174 Gy·cm; P = .04). When patients were separated by number of DSA acquisitions (two or fewer vs three or more), mean DAP decreased 41% (109 vs 185 Gy·cm; P = .005) and cumulative air kerma decreased 40% (578 vs 964 mGy; P = .004).

Conclusions: In most patients (81%), DF or limited DSA was adequate for visualization during EVAR. In both intention-to-treat DF and limited-DSA cohorts, mean DAP was significantly decreased. If image quality allows, a DF-only or limited-DSA approach to EVAR decreases radiation dose.
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http://dx.doi.org/10.1016/j.jvs.2020.02.050DOI Listing
December 2020

Investigating neutron activated contrast agent imaging for tumor localization in proton therapy: a feasibility study for proton neutron gamma-x detection (PNGXD).

Phys Med Biol 2020 01 24;65(3):035005. Epub 2020 Jan 24.

Department of Physics, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, Ontario M5B 2K3, Canada. Author to whom any correspondence should be addressed.

Proton neutron gamma-x detection (PNGXD) is a novel imaging concept being investigated for tumor localization during proton therapy that uses secondary neutron interactions with a gadolinium contrast agent (GDCA) to produce characteristic photons within the 40-200 keV energy region. The purpose of this study is to experimentally investigate the feasibility of implementing this procedure by performing experimental measurements on a passive double scattering proton treatment unit. Five experimental measurements were performed with varying concentrations and irradiation conditions. Photon spectra were measured with a 25 mm, 1 mm thick uncollimated X-123 CdTe spectrometer. For a 10.4 Gy administration on a 100 ml volume phantom with 10 mg g Gd solution placed in a water phantom, 1129  ±  184 K-shell Gd counts were detected. For an administered dose of 21 Gy and the same Gd solution measured in air, resulted in 3296  ±  256 counts. A total of 1094  ±  171, 421  ±  150 and 23  ±  141 K-shell Gd counts were measured for Gd concentrations of 10 mg g, 1 mg g and 0 mg g for 7 Gy dose in air. The signal to noise ratio for these five measurements were: 7, 15, 6, 3, and 0.2, respectively. The spectrum contained 43 keV K and 49 keV K peaks, however a small amount of 79.5 and 181.9 keV prompt gamma rays were detected from gadolinium neutron capture. This discrepancy is due to a drop in the intrinsic detection efficiency of the CdTe spectrometer over this energy range. The measurements were compared with Monte-Carlo simulation to determine the contributions of Gd neutron capture from internal and external neutrons on a passive scattering proton therapy unit and to investigate the discrepancy in detected characteristic x-rays versus prompt gamma rays.
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http://dx.doi.org/10.1088/1361-6560/ab63b5DOI Listing
January 2020

Community/public health nurses' responsibility to ensure adequate nutrition for hungry families.

Public Health Nurs 2019 09;36(5):587-588

Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ, USA.

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http://dx.doi.org/10.1111/phn.12663DOI Listing
September 2019

Ex vivo quantification of lanthanum and gadolinium in post-mortem human tibiae with estimated barium and iodine concentrations using K x-ray fluorescence.

Physiol Meas 2019 09 3;40(8):085006. Epub 2019 Sep 3.

Department of Physics, Ryerson University, 350 Victoria St., Toronto, Ontario M5B 2K3, Canada. Authors contributed equally to this work.

Objectives: Lanthanum (La) and gadolinium (Gd) are known to deposit in bone of exposed populations, namely those who are orally administered lanthanum carbonate (LaC, La(CO)) or are injected with Gd-based contrast agents, respectively. In this work, bone La and Gd concentrations from the environment and diet were measured using x-ray fluorescence in ten post-mortem human tibiae. As a secondary objective, bone barium (Ba) and iodine concentrations were estimated.

Approach: Two calibration lines were produced for La and Gd and the minimum detection limits (MDLs) of the system were determined using a 180° irradiation-detection geometry.

Main Results: The MDLs of the system were 0.4 µg La g bone mineral and 0.5 µg Gd g bone mineral. The mean concentrations were  -0.02  ±  0.1 µg La g bone mineral and 0.1  ±  0.2 µg Gd g bone mineral in tibiae. The average Ba and iodine concentrations estimated from the experimental La calibration line and Monte-Carlo derived sensitivity factors were determined to be 3.4  ±  0.8 µg Ba g bone mineral and  -0.5  ±  0.3 µg iodine g bone mineral. Since it was discovered that four donors previously received an iodine-based contrast agent, the mean concentrations in these donors was 27.8  ± 28.4 µg iodine g bone mineral.

Significance: The XRF system has determined baseline concentrations of these four heavy metals in trace quantities from natural exposure pathways (with the exception of iodine in four donors). This indicates that the system can measure low levels in ex vivo tibiae samples and can potentially be further developed for in vivo studies involving live subjects who are directly exposed to these metals.
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http://dx.doi.org/10.1088/1361-6579/ab3c0eDOI Listing
September 2019

Basis Set Superposition Errors in the Many-Body Expansion of Molecular Properties.

J Phys Chem A 2019 May 13;123(20):4500-4511. Epub 2019 May 13.

Department of Chemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States.

The underlying reasons for the poor convergence of the venerated many-body expansion (MBE) for higher-order response properties are investigated, with a particular focus on the impact of basis set superposition errors. Interaction energies, dipole moments, dynamic polarizabilities, and specific rotations are computed for three chiral solutes in explicit water cages of varying sizes using the MBE including corrections based on the site-site function counterpoise (or "full-cluster" basis) approach. In addition, we consider other possible causes for the observed oscillatory behavior of the MBE, including numerical precision, basis set size, choice of density functional, and snapshot geometry. Our results indicate that counterpoise corrections are necessary for damping oscillations and achieving reasonable convergence of the MBE for higher order properties. However, oscillations in the expansion cannot be completely eliminated for chiroptical properties such as specific rotations due to their inherently nonadditive nature, thus limiting the efficacy of the MBE for studying solvated chiral compounds.
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http://dx.doi.org/10.1021/acs.jpca.9b03864DOI Listing
May 2019

Chronology of reproductive investment determines predation risk aversion in a felid-ungulate system.

Ecol Evol 2019 Mar 26;9(6):3264-3275. Epub 2019 Feb 26.

Warnell School of Forestry and Natural Resources University of Georgia Athens Georgia.

Fear of predators can behaviorally mediate prey population dynamics, particularly when predation risk influences reproductive investment. However, the costs of reproductive investment may mitigate predation risk aversion relative to periods when the link between reproductive output and prey behavior is weaker.We posit that intensity of reproductive investment in ungulates may predict their response to predation risk such that the sexes increase risk exposure during biological seasons that are pivotal to reproductive success, such as the fawn-rearing and breeding seasons for females and males, respectively.We examined the activity patterns of sympatric white-tailed deer (), a sexually segregated polygynous ungulate, and Florida panthers () in the context of the "risky times - risky places hypothesis" and the reproductive strategy hypothesis. We compared detection rates and diel activity overlap of both species using motion-triggered camera traps positioned on ( = 120) and off ( = 60) anthropogenic trails across five reproductive seasons.Florida panthers were nocturnal and primarily observed on-trail providing an experimental framework with risky times and risky places. Contrary to studies in other taxa inversely correlating prey reproductive investment to predation risk, the sexes of deer were more risk prone during sex-specific seasons associated with intense reproductive investment.Our results suggest spatiotemporally variable predation risk influences sex-specific behavioral decision-making in deer such that reproductive success is maximized.
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http://dx.doi.org/10.1002/ece3.4947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434540PMC
March 2019

Correction to: Factors driving adaptive radiation in plants of oceanic islands: a case study from the Juan Fernández Archipelago.

J Plant Res 2019 Mar;132(2):295

Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria.

The article Factors driving adaptive radiation in plants of oceanic islands: a case study from the Juan Fernández Archipelago, written by Koji Takayama, Daniel J. Crawford, Patricio López‑Sepúlveda, Josef Greimler, Tod F. Stuessy was originally published electronically on the publisher's internet portal (currently SpringerLink) on 13 March 2018 without open access.
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http://dx.doi.org/10.1007/s10265-019-01092-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404661PMC
March 2019

Diagrammatic Coupled Cluster Monte Carlo.

J Phys Chem Lett 2019 Mar 14;10(5):925-935. Epub 2019 Feb 14.

Department of Chemistry , University of Cambridge , Cambridge CB2 1TN , United Kingdom.

We propose a modified coupled cluster Monte Carlo algorithm that stochastically samples connected terms within the truncated Baker-Campbell-Hausdorff expansion of the similarity-transformed Hamiltonian by construction of coupled cluster diagrams on the fly. Our new approach-diagCCMC-allows propagation to be performed using only the connected components of the similarity-transformed Hamiltonian, greatly reducing the memory cost associated with the stochastic solution of the coupled cluster equations. We show that for perfectly local, noninteracting systems diagCCMC is able to represent the coupled cluster wavefunction with a memory cost that scales linearly with system size. The favorable memory cost is observed with the only assumption of fixed stochastic granularity and is valid for arbitrary levels of coupled cluster theory. Significant reduction in memory cost is also shown to smoothly appear with dissociation of a finite chain of helium atoms. This approach is also shown not to break down in the presence of strong correlation through the example of a stretched nitrogen molecule. Our novel methodology moves the theoretical basis of coupled cluster Monte Carlo closer to deterministic approaches.
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http://dx.doi.org/10.1021/acs.jpclett.9b00067DOI Listing
March 2019

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

J Chem Phys 2018 Nov;149(18):180901

Department of Chemistry, Department of Bioengineering, Department of Chemical and Biomolecular Engineering, Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, USA.

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding of the molecular phenomena that underlie and control chemical processes, which is manifested in a large number of community software projects and codes. The CMS community is now poised to take the next transformative steps of better training in modern software design and engineering methods and tools, increasing interoperability through more systematic adoption of agreed upon standards and accepted best-practices, overcoming unnecessary redundancy in software effort along with greater reproducibility, and increasing the deployment of new software onto hardware platforms from in-house clusters to mid-range computing systems through to modern supercomputers. This in turn will have future impact on the software that will be created to address grand challenge science that we illustrate here: the formulation of diverse catalysts, descriptions of long-range charge and excitation transfer, and development of structural ensembles for intrinsically disordered proteins.
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http://dx.doi.org/10.1063/1.5052551DOI Listing
November 2018