98 results on '"Shepherd JJ"'
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2. CO adsorption on Pt(111) studied by periodic coupled cluster theory.
- Author
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Carbone JP, Irmler A, Gallo A, Schäfer T, Van Benschoten WZ, Shepherd JJ, and Grüneis A
- Abstract
We present an application of periodic coupled-cluster theory to the calculation of CO adsorption energies on the Pt(111) surface for different adsorption sites. The calculations employ a range of recently developed theoretical and computational methods. In particular, we use a recently introduced coupled-cluster ansatz, denoted as CCSD(cT), to compute correlation energies of the metallic Pt surface with and without adsorbed CO molecules. The convergence of Hartree-Fock adsorption energy contributions with respect to randomly shifted k -meshes is discussed. Recently introduced basis set incompleteness error corrections make it possible to achieve well-converged correlation energy contributions to the adsorption energies. We show that CCSD(cT) theory predicts the correct order of adsorption energies for the considered adsorption sites. Furthermore, we find that binding of the CO molecule to the top and fcc site is dominated by Hartree-Fock and correlation energy contributions, respectively.
- Published
- 2024
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3. Modulation of Fe-Fe distance and spin in diiron complexes using tetradentate ligands with different flanking donors.
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Spielvogel KD, Campbell EJ, Chowdhury SR, Benner F, Demir S, Hatzis GP, Petras HR, Sembukuttiarachchige D, Shepherd JJ, Thomas CM, Vlaisavljevich B, and Daly SR
- Abstract
Here we report the synthesis and characterization of diiron complexes containing triaryl N
4 and N2 S2 ligands derived from o -phenylenediamine. The complexes display significant differences in Fe-Fe distances and magnetic properties that depend on the identity of the flanking NMe2 and SMe donor groups.- Published
- 2024
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4. Sampling the reciprocal Coulomb potential in finite anisotropic cells.
- Author
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Schäfer T, Van Benschoten WZ, Shepherd JJ, and Grüneis A
- Abstract
We present a robust strategy to numerically sample the Coulomb potential in reciprocal space for periodic Born-von Karman cells of general shape. Our approach tackles two common issues of plane-wave based implementations of Coulomb integrals under periodic boundary conditions: the treatment of the singularity at the Brillouin-zone center and discretization errors, which can cause severe convergence problems in anisotropic cells, necessary for the calculation of low-dimensional systems. We apply our strategy to the Hartree-Fock and coupled cluster (CC) theories and discuss the consequences of different sampling strategies on different theories. We show that sampling the Coulomb potential via the widely used probe-charge Ewald method is unsuitable for CC calculations in anisotropic cells. To demonstrate the applicability of our developed approach, we study two representative, low-dimensional use cases: the infinite carbon chain, for which we report the first periodic CCSD(T) potential energy surface, and a surface slab of lithium hydride, for which we demonstrate the impact of different sampling strategies for calculating surface energies. We find that our Coulomb sampling strategy serves as a vital solution, addressing the critical need for improved accuracy in plane-wave based CC calculations for low-dimensional systems., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)
- Published
- 2024
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5. Electronic Free Energy Surface of the Nitrogen Dimer Using First-Principles Finite Temperature Electronic Structure Methods.
- Author
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Van Benschoten WZ, Petras HR, and Shepherd JJ
- Abstract
We use full configuration interaction and density matrix quantum Monte Carlo methods to calculate the electronic free energy surface of the nitrogen dimer within the free-energy Born-Oppenheimer approximation. As the temperature is raised from T = 0, we find a temperature regime in which the internal energy causes bond strengthening. At these temperatures, adding in the entropy contributions is required to cause the bond to gradually weaken with increasing temperature. We predict a thermally driven dissociation for the nitrogen dimer between 22,000 to 63,200 K depending on symmetries and basis set. Inclusion of more spatial and spin symmetries reduces the temperature required. The origin of these observations is explored using the structure of the density matrix at various temperatures and bond lengths.
- Published
- 2023
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6. Electronic specific heat capacities and entropies from density matrix quantum Monte Carlo using Gaussian process regression to find gradients of noisy data.
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Van Benschoten WZ, Weiler L, Smith GJ, Man S, DeMello T, and Shepherd JJ
- Abstract
We present a machine learning approach to calculating electronic specific heat capacities for a variety of benchmark molecular systems. Our models are based on data from density matrix quantum Monte Carlo, which is a stochastic method that can calculate the electronic energy at finite temperature. As these energies typically have noise, numerical derivatives of the energy can be challenging to find reliably. In order to circumvent this problem, we use Gaussian process regression to model the energy and use analytical derivatives to produce the specific heat capacity. From there, we also calculate the entropy by numerical integration. We compare our results to cubic splines and finite differences in a variety of molecules in which Hamiltonians can be diagonalized exactly with full configuration interaction. We finally apply this method to look at larger molecules where exact diagonalization is not possible and make comparisons with more approximate ways to calculate the specific heat capacity and entropy., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)
- Published
- 2023
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7. How the Exchange Energy Can Affect the Power Laws Used to Extrapolate the Coupled Cluster Correlation Energy to the Thermodynamic Limit.
- Author
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Mihm TN, Weiler L, and Shepherd JJ
- Abstract
Finite size error is commonly removed from coupled cluster theory calculations by N
-1 extrapolations over correlation energy calculations of different system sizes ( N ), where the N-1 scaling comes from the total energy rather than the correlation energy. However, previous studies in the quantum Monte Carlo community suggest an exchange-energy-like power law of N-2/3 should also be present in the correlation energy when using the conventional Coulomb interaction. The rationale for this is that the total energy goes as N-1 and the exchange energy goes as N-2/3 ; thus, the correlation energy should be a combination of these two power laws. Further, in coupled cluster theory, these power laws are related to the low G scaling of the transition structure factor, S ( G ), which is a property of the coupled cluster wave function calculated from the amplitudes. We show here that data from coupled cluster doubles calculations on the uniform electron gas fit a function with a low G behavior of S ( G ) ∼ G . The prefactor for this linear term is derived from the exchange energy to be consistent with an N-2/3 power law at large N . Incorporating the exchange structure factor into the transition structure factor results in a combined structure factor of S ( G ) ∼ G2 , consistent with an N-1 scaling of the exchange-correlation energy. We then look for the presence of an N-2/3 power law in the energy. To do so, we first develop a plane-wave cutoff scheme with less noise than the traditional basis set used for the uniform electron gas. Then, we collect data from a wide range of electron numbers and densities to systematically test five methods using N-1 scaling, N-2/3 scaling, or combinations of both scaling behaviors. We find that power laws that incorporate both N-1 and N-2/3 scaling perform better than either alone, especially when the prefactor for N-2/3 scaling can be found from exchange energy calculations.- Published
- 2023
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8. Machine learning for a finite size correction in periodic coupled cluster theory calculations.
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Weiler L, Mihm TN, and Shepherd JJ
- Abstract
We introduce a straightforward Gaussian process regression (GPR) model for the transition structure factor of metal periodic coupled cluster singles and doubles (CCSD) calculations. This is inspired by the method introduced by Liao and Grüneis for interpolating over the transition structure factor to obtain a finite size correction for CCSD [K. Liao and A. Grüneis, J. Chem. Phys. 145, 141102 (2016)] and by our own prior work using the transition structure factor to efficiently converge CCSD for metals to the thermodynamic limit [Mihm et al., Nat. Comput. Sci. 1, 801 (2021)]. In our CCSD-FS-GPR method to correct for finite size errors, we fit the structure factor to a 1D function in the momentum transfer, G. We then integrate over this function by projecting it onto a k-point mesh to obtain comparisons with extrapolated results. Results are shown for lithium, sodium, and the uniform electron gas.
- Published
- 2022
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9. Piecewise interaction picture density matrix quantum Monte Carlo.
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Van Benschoten WZ and Shepherd JJ
- Abstract
The density matrix quantum Monte Carlo (DMQMC) set of methods stochastically samples the exact N-body density matrix for interacting electrons at finite temperature. We introduce a simple modification to the interaction picture DMQMC (IP-DMQMC) method that overcomes the limitation of only sampling one inverse temperature point at a time, instead allowing for the sampling of a temperature range within a single calculation, thereby reducing the computational cost. At the target inverse temperature, instead of ending the simulation, we incorporate a change of picture away from the interaction picture. The resulting equations of motion have piecewise functions and use the interaction picture in the first phase of a simulation, followed by the application of the Bloch equation once the target inverse temperature is reached. We find that the performance of this method is similar to or better than the DMQMC and IP-DMQMC algorithms in a variety of molecular test systems.
- Published
- 2022
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10. A shortcut to the thermodynamic limit for quantum many-body calculations of metals.
- Author
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Mihm TN, Schäfer T, Ramadugu SK, Weiler L, Grüneis A, and Shepherd JJ
- Abstract
Computationally efficient and accurate quantum mechanical approximations to solve the many-electron Schrödinger equation are crucial for computational materials science. Methods such as coupled cluster theory show potential for widespread adoption if computational cost bottlenecks can be removed. For example, extremely dense k-point grids are required to model long-range electronic correlation effects, particularly for metals. Although these grids can be made more effective by averaging calculations over an offset (or twist angle), the resultant cost in time for coupled cluster theory is prohibitive. We show here that a single special twist angle can be found using the transition structure factor, which provides the same benefit as twist averaging with one or two orders of magnitude reduction in computational time. We demonstrate that this not only works for metal systems but also is applicable to a broader range of materials, including insulators and semiconductors., (© 2021. The Author(s).)
- Published
- 2021
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11. The Sign Problem in Density Matrix Quantum Monte Carlo.
- Author
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Petras HR, Van Benschoten WZ, Ramadugu SK, and Shepherd JJ
- Abstract
Density matrix quantum Monte Carlo (DMQMC) is a recently developed method for stochastically sampling the N -particle thermal density matrix to obtain exact-on-average energies for model and ab initio systems. We report a systematic numerical study of the sign problem in DMQMC based on simulations of atomic and molecular systems. In DMQMC, the density matrix is written in an outer product basis of Slater determinants. In principle, this means that DMQMC needs to sample a space that scales in the system size, N , as O[(exp(N))
2 ]. In practice, removing the sign problem requires a total walker population that exceeds a system-dependent critical walker population ( Nc ), imposing limitations on both storage and compute time. We establish that Nc for DMQMC is the square of Nc for FCIQMC. By contrast, the minimum Nc in the interaction picture modification of DMQMC (IP-DMQMC) is only linearly related to the Nc for FCIQMC. We find that this difference originates from the difference in propagation of IP-DMQMC versus canonical DMQMC: the former is asymmetric, whereas the latter is symmetric. When an asymmetric mode of propagation is used in DMQMC, there is a much greater stochastic error and is thus prohibitively expensive for DMQMC without the interaction picture adaptation. Finally, we find that the equivalence between IP-DMQMC and FCIQMC seems to extend to the initiator approximation, which is often required to study larger systems with large basis sets. This suggests that IP-DMQMC offers a way to ameliorate the cost of moving between a Slater determinant space and an outer product basis.- Published
- 2021
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12. Iron-Catalyzed Halogen Exchange of Trifluoromethyl Arenes*.
- Author
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Dorian A, Landgreen EJ, Petras HR, Shepherd JJ, and Williams FJ
- Subjects
- Catalysis, Electrons, Indicators and Reagents, Halogens, Iron
- Abstract
The facile production of ArCF
2 X and ArCX3 from ArCF3 using catalytic iron(III)halides is reported, which constitutes the first iron-catalyzed halogen exchange for non-aromatic C-F bonds. Theoretical calculations suggest direct activation of C-F bonds by iron coordination. ArCX3 and ArCF2 X products of the reaction are synthetically valuable due to their diversification potential. In particular, chloro- and bromodifluoromethyl arenes (ArCF2 Cl, ArCF2 Br respectively) provide access to a myriad of difluoromethyl arene derivatives (ArCF2 R). To optimize for mono-halogen exchange, a statistical method called Design of Experiments was used. Optimized parameters were successfully applied to electron rich and electron deficient aromatic substrates, and to the late stage diversification of flufenoxuron, a commercial insecticide. These methods are highly practical, being run at convenient temperatures and using inexpensive common reagents., (© 2021 Wiley-VCH GmbH.)- Published
- 2021
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13. Power Laws Used to Extrapolate the Coupled Cluster Correlation Energy to the Thermodynamic Limit.
- Author
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Mihm TN, Yang B, and Shepherd JJ
- Abstract
Recent calculations using coupled cluster on solids have raised the discussion of using a N
-1/3 power law to fit the correlation energy when extrapolating to the thermodynamic limit, an approach which differs from the more commonly used N-1 power law, which is, for example, often used by quantum Monte Carlo methods. In this paper, we present one way to reconcile these viewpoints. Coupled cluster doubles calculations were performed on uniform electron gases reaching system sizes of 922 electrons for an extremely wide range of densities (0.1 < rs < 100.0) to study how the correlation energy approaches the thermodynamic limit. The data were corrected for the basis set incompleteness error and use a selected twist angle approach to mitigate the finite size error from shell filling effects. Analyzing these data, we initially find that a power law of N-1/3 appears to fit the data better than a N-1 power law in the large system size limit. However, we provide an analysis of the transition structure factor showing that N-1 still applies to large system sizes and that the apparent N-1/3 power law occurs only at low N .- Published
- 2021
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14. Accelerating convergence to the thermodynamic limit with twist angle selection applied to methods beyond many-body perturbation theory.
- Author
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Mihm TN, Van Benschoten WZ, and Shepherd JJ
- Abstract
We recently developed a scheme to use low-cost calculations to find a single twist angle where the coupled cluster doubles energy of a single calculation matches the twist-averaged coupled cluster doubles energy in a finite unit cell. We used initiator full configuration interaction quantum Monte Carlo as an example of an exact method beyond coupled cluster doubles theory to show that this selected twist angle approach had comparable accuracy in methods beyond coupled cluster. Furthermore, at least for small system sizes, we show that the same twist angle can also be found by comparing the energy directly (at the level of second-order Moller-Plesset theory), suggesting a route toward twist angle selection, which requires minimal modification to existing codes that can perform twist averaging.
- Published
- 2021
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15. NECI: N-Electron Configuration Interaction with an emphasis on state-of-the-art stochastic methods.
- Author
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Guther K, Anderson RJ, Blunt NS, Bogdanov NA, Cleland D, Dattani N, Dobrautz W, Ghanem K, Jeszenszki P, Liebermann N, Manni GL, Lozovoi AY, Luo H, Ma D, Merz F, Overy C, Rampp M, Samanta PK, Schwarz LR, Shepherd JJ, Smart SD, Vitale E, Weser O, Booth GH, and Alavi A
- Abstract
We present NECI, a state-of-the-art implementation of the Full Configuration Interaction Quantum Monte Carlo (FCIQMC) algorithm, a method based on a stochastic application of the Hamiltonian matrix on a sparse sampling of the wave function. The program utilizes a very powerful parallelization and scales efficiently to more than 24 000 central processing unit cores. In this paper, we describe the core functionalities of NECI and its recent developments. This includes the capabilities to calculate ground and excited state energies, properties via the one- and two-body reduced density matrices, as well as spectral and Green's functions for ab initio and model systems. A number of enhancements of the bare FCIQMC algorithm are available within NECI, allowing us to use a partially deterministic formulation of the algorithm, working in a spin-adapted basis or supporting transcorrelated Hamiltonians. NECI supports the FCIDUMP file format for integrals, supplying a convenient interface to numerous quantum chemistry programs, and it is licensed under GPL-3.0.
- Published
- 2020
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16. Using Density Matrix Quantum Monte Carlo for Calculating Exact-on-Average Energies for ab Initio Hamiltonians in a Finite Basis Set.
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Petras HR, Ramadugu SK, Malone FD, and Shepherd JJ
- Abstract
We here apply the recently developed initiator density matrix quantum Monte Carlo (i-DMQMC) to a variety of atoms and molecules in vacuum. i-DMQMC samples the exact density matrix of a Hamiltonian at finite temperature and combines the accuracy of full configuration interaction quantum Monte Carlo (FCIQMC)-full configuration interaction (FCI) or exact energies in a finite basis set-with finite temperature. In order to explore the applicability of i-DMQMC for molecular systems, we choose to study a recently developed test set by Rubenstein and co-workers: Be, H
2 O, and H10 at near-equilibrium and stretched geometries. We find that, for Be and H2 O, i-DMQMC delivers energies with submillihartree accuracy when compared with finite temperature FCI. For H2 O and both geometries of H10 , we examine the difference between FT-AFQMC and i-DMQMC, which, in turn, estimates the difference in canonical versus grand canonical energies. We close with two discussions: one of simulation settings (initiator error, the interaction picture, and different basis sets), and another of energy difference calculations in the form of specific heat capacity and ionization potential calculations.- Published
- 2020
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17. Fully Quantum Embedding with Density Functional Theory for Full Configuration Interaction Quantum Monte Carlo.
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Petras HR, Graham DS, Ramadugu SK, Goodpaster JD, and Shepherd JJ
- Abstract
We here develop a fully quantum embedded version of initiator full configuration interaction quantum Monte Carlo ( i -FCIQMC) and apply it to study an ionic bond (lithium hydride, LiH) and a covalent bond (hydrogen flouride, HF) physisorbed to a benzene molecule. The embedding is performed using a recently developed Huzinaga projection operator approach, which affords good synergy with i -FCIQMC by minimizing the number of orbitals in the calculation. When considering the dissociation energy of these bonds into closed-shell ionic fragments, we find that i -FCIQMC embedded in density functional theory ( i -FCIQMC-in-DFT) delivers comparable accuracy with coupled cluster singles and doubles with perturbative triples embedded in density functional theory (CCSD(T)-in-DFT). In treating the bond dissociation energy curve of HF, i -FCIQMC-in-DFT has improved accuracy over CCSD(T)-in-DFT due to the presence of strong correlation. We discuss the implications of the new i -FCIQMC-in-DFT method as applied to bond breaking in catalysis.
- Published
- 2019
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18. The Influence of Redox-Innocent Donor Groups in Tetradentate Ligands Derived from o -Phenylenediamine: Electronic Structure Investigations with Nickel.
- Author
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Spielvogel KD, Coughlin EJ, Petras H, Luna JA, Benson A, Donahue CM, Kibasa A, Lee K, Salacinski R, Bart SC, Shaw SK, Shepherd JJ, and Daly SR
- Abstract
The continued development of redox-active ligands requires an understanding as to how ligand modifications and related factors affect the locus of redox activity and spin density in metal complexes. Here we describe the synthesis, characterization, and electronic structure of nickel complexes containing triaryl NNNN ( 1 ) and SNNS ( 2 ) ligands derived from o -phenylenediamine. The tetradentate ligands in 1 and 2 were investigated and compared to those in metal complexes with compositionally similar ligands to determine how ligand-centered redox properties change when redox-active flanking groups are replaced with redox-innocent NMe
2 or SMe. A derivative of 2 in which the phenylene backbone was replaced with ethylene ( 3 ) was also prepared to interrogate the importance of o -phenylenediamine for ligand-centered redox activity. Cyclic voltammograms collected for 1 and 2 revealed two fully reversible ligand-centered redox events. Remarkably, several quasi-reversible ligand-centered redox waves were also observed for 3 despite the absence of the o -phenylenediamine subunit. Oxidizing 1 and 2 with silver salts containing different counteranions (BF4 - , OTf- , NTf2 - ) allowed the electrochemically generated complexes to be analyzed as a function of different oxidation states using single-crystal X-ray diffraction (XRD), EPR spectroscopy, and S K-edge X-ray absorption spectroscopy. The experimental data are corroborated by DFT calculations, and together, they reveal how the location of unpaired spin density and electronic structure in singly and doubly oxidized salts of 1 and 2 varies depending on the coordinating ability of the counteranions and exogenous ligands such as pyridine.- Published
- 2019
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19. An optimized twist angle to find the twist-averaged correlation energy applied to the uniform electron gas.
- Author
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Mihm TN, McIsaac AR, and Shepherd JJ
- Abstract
We explore an alternative to twist averaging in order to obtain more cost-effective and accurate extrapolations to the thermodynamic limit (TDL) for coupled cluster doubles (CCD) calculations. We seek a single twist angle to perform calculations at, instead of integrating over many random points or a grid. We introduce the concept of connectivity, a quantity derived from the nonzero four-index integrals in an MP2 calculation. This allows us to find a special twist angle that provides appropriate connectivity in the energy equation, which yields results comparable to full twist averaging. This special twist angle effectively makes the finite electron number CCD calculation represent the TDL more accurately, reducing the cost of twist-averaged CCD over N
s twist angles from Ns CCD calculations to Ns MP2 calculations plus one CCD calculation.- Published
- 2019
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20. The HANDE-QMC Project: Open-Source Stochastic Quantum Chemistry from the Ground State Up.
- Author
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Spencer JS, Blunt NS, Choi S, Etrych J, Filip MA, Foulkes WMC, Franklin RST, Handley WJ, Malone FD, Neufeld VA, Di Remigio R, Rogers TW, Scott CJC, Shepherd JJ, Vigor WA, Weston J, Xu R, and Thom AJW
- Abstract
Building on the success of Quantum Monte Carlo techniques such as diffusion Monte Carlo, alternative stochastic approaches to solve electronic structure problems have emerged over the past decade. The full configuration interaction quantum Monte Carlo (FCIQMC) method allows one to systematically approach the exact solution of such problems, for cases where very high accuracy is desired. The introduction of FCIQMC has subsequently led to the development of coupled cluster Monte Carlo (CCMC) and density matrix quantum Monte Carlo (DMQMC), allowing stochastic sampling of the coupled cluster wave function and the exact thermal density matrix, respectively. In this Article, we describe the HANDE-QMC code, an open-source implementation of FCIQMC, CCMC and DMQMC, including initiator and semistochastic adaptations. We describe our code and demonstrate its use on three example systems; a molecule (nitric oxide), a model solid (the uniform electron gas), and a real solid (diamond). An illustrative tutorial is also included.
- Published
- 2019
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21. Plasmonic support-mediated activation of 1 nm platinum clusters for catalysis.
- Author
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Wieghold S, Nienhaus L, Knoller FL, Schweinberger FF, Shepherd JJ, Lyding JW, Heiz U, Gruebele M, and Esch F
- Abstract
Nanometer-sized metal clusters are prime candidates for photoactivated catalysis, based on their unique tunable optical and electronic properties, combined with a large surface-to-volume ratio. Due to the very small optical cross sections of such nanoclusters, support-mediated plasmonic activation could potentially make activation more efficient. Our support is a semi-transparent gold film, optimized to work in a back-illumination geometry. It has a surface plasmon resonance excitable in the 510-540 nm wavelength range. Pt
n clusters (size distribution peaked at n = 46 atoms) have been deposited onto this support and investigated for photoactivated catalytic performance in the oxidative decomposition of methylene blue. The Pt cluster catalytic activity under illumination exceeds that of the gold support by more than an order of magnitude per active surface area. To further investigate the underlying mechanism of plasmon-induced catalysis, the clusters have been imaged with optically-assisted scanning tunneling microscopy under illumination. The photoactivation of the Pt clusters via plasmonic excitation of the support and subsequential electronic excitation of the clusters can be imaged with nanometer resolution. The light-induced tunneling current on the clusters is enhanced relative to the gold film support.- Published
- 2017
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22. Speed Limit for Triplet-Exciton Transfer in Solid-State PbS Nanocrystal-Sensitized Photon Upconversion.
- Author
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Nienhaus L, Wu M, Geva N, Shepherd JJ, Wilson MWB, Bulović V, Van Voorhis T, Baldo MA, and Bawendi MG
- Abstract
Hybrid interfaces combining inorganic and organic materials underpin the operation of many optoelectronic and photocatalytic systems and allow for innovative approaches to photon up- and down-conversion. However, the mechanism of exchange-mediated energy transfer of spin-triplet excitons across these interfaces remains obscure, particularly when both the macroscopic donor and acceptor are composed of many separately interacting nanoscopic moieties. Here, we study the transfer of excitons from colloidal lead sulfide (PbS) nanocrystals to the spin-triplet state of rubrene molecules. By reducing the length of the carboxylic acid ligands on the nanocrystal surface from 18 to 4 carbon atoms, thinning the effective ligand shell from 13 to 6 Å, we are able to increase the characteristic transfer rate by an order of magnitude. However, we observe that the energy transfer rate asymptotes for shorter separation distances (≤10 Å) which we attribute to the reduced Dexter coupling brought on by the increased effective dielectric constant of these solid-state devices when the aliphatic ligands are short. This implies that the shortest ligands, which hinder long-term colloidal stability, offer little advantage for energy transfer. Indeed, we find that hexanoic acid ligands are already sufficient for near-unity transfer efficiency. Using nanocrystals with these optimal-length ligands in an improved solid-state device structure, we obtain an upconversion efficiency of (7 ± 1)% with excitation at λ = 808 nm.
- Published
- 2017
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23. A structural and mechanistic study of π-clamp-mediated cysteine perfluoroarylation.
- Author
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Dai P, Williams JK, Zhang C, Welborn M, Shepherd JJ, Zhu T, Van Voorhis T, Hong M, and Pentelute BL
- Subjects
- Amino Acid Motifs, Calorimetry, Magnetic Resonance Spectroscopy, Models, Molecular, Mutation, Protein Conformation, Thermodynamics, Cysteine chemistry, Proteins chemistry, Proteins genetics
- Abstract
Natural enzymes use local environments to tune the reactivity of amino acid side chains. In searching for small peptides with similar properties, we discovered a four-residue π-clamp motif (Phe-Cys-Pro-Phe) for regio- and chemoselective arylation of cysteine in ribosomally produced proteins. Here we report mutational, computational, and structural findings directed toward elucidating the molecular factors that drive π-clamp-mediated arylation. We show the significance of a trans conformation prolyl amide bond for the π-clamp reactivity. The π-clamp cysteine arylation reaction enthalpy of activation (ΔH
‡ ) is significantly lower than a non-π-clamp cysteine. Solid-state NMR chemical shifts indicate the prolyl amide bond in the π-clamp motif adopts a 1:1 ratio of the cis and trans conformation, while in the reaction product Pro3 was exclusively in trans. In two structural models of the perfluoroarylated product, distinct interactions at 4.7 Å between Phe1 side chain and perfluoroaryl electrophile moiety are observed. Further, solution19 F NMR and isothermal titration calorimetry measurements suggest interactions between hydrophobic side chains in a π-clamp mutant and the perfluoroaryl probe. These studies led us to design a π-clamp mutant with an 85-fold rate enhancement. These findings will guide us toward the discovery of small reactive peptides to facilitate abiotic chemistry in water.- Published
- 2017
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24. Salt Effect Accelerates Site-Selective Cysteine Bioconjugation.
- Author
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Dai P, Zhang C, Welborn M, Shepherd JJ, Zhu T, Van Voorhis T, and Pentelute BL
- Abstract
Highly efficient and selective chemical reactions are desired. For small molecule chemistry, the reaction rate can be varied by changing the concentration, temperature, and solvent used. In contrast for large biomolecules, the reaction rate is difficult to modify by adjusting these variables because stringent biocompatible reaction conditions are required. Here we show that adding salts can change the rate constant over 4 orders of magnitude for an arylation bioconjugation reaction between a cysteine residue within a four-residue sequence (π-clamp) and a perfluoroaryl electrophile. Biocompatible ammonium sulfate significantly enhances the reaction rate without influencing the site-specificity of π-clamp mediated arylation, enabling the fast synthesis of two site-specific antibody-drug conjugates that selectively kill HER2-positive breast cancer cells. Computational and structure-reactivity studies indicate that salts may tune the reaction rate through modulating the interactions between the π-clamp hydrophobic side chains and the electrophile. On the basis of this understanding, the salt effect is extended to other bioconjugation chemistry, and a new regioselective alkylation reaction at π-clamp cysteine is developed.
- Published
- 2016
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25. Accurate Exchange-Correlation Energies for the Warm Dense Electron Gas.
- Author
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Malone FD, Blunt NS, Brown EW, Lee DK, Spencer JS, Foulkes WM, and Shepherd JJ
- Abstract
The density matrix quantum Monte Carlo (DMQMC) method is used to sample exact-on-average N-body density matrices for uniform electron gas systems of up to 10^{124} matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the k-space configuration path-integral formalism disagree by up to ∼10% at certain reduced temperatures T/T_{F}≤0.5 and densities r_{s}≤1. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that the DMQMC method can calculate free energies directly and present exact free energies for T/T_{F}≥1 and r_{s}≤2.
- Published
- 2016
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26. Communication: Convergence of many-body wave-function expansions using a plane-wave basis in the thermodynamic limit.
- Author
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Shepherd JJ
- Abstract
Basis set incompleteness error and finite size error can manifest concurrently in systems for which the two effects are phenomenologically well-separated in length scale. When this is true, we need not necessarily remove the two sources of error simultaneously. Instead, the errors can be found and remedied in different parts of the basis set. This would be of great benefit to a method such as coupled cluster theory since the combined cost of nocc (6)nvirt (4) could be separated into nocc (6) and nvirt (4) costs with smaller prefactors. In this Communication, we present analysis on a data set due to Baardsen and co-workers, containing 2D uniform electron gas coupled cluster doubles energies for rs = 0.5, 1.0, and 2.0 a.u. at a wide range of basis set sizes and particle numbers. In obtaining complete basis set limit thermodynamic limit results, we find that within a small and removable error the above assertion is correct for this simple system. We then use this method to obtain similar results for the 3D electron gas at rs = 1.0, 2.0, and 5.0 a.u. and make comparison to the Ceperley-Alder quantum Monte Carlo results. This approach allows for the combination of methods which separately address finite size effects and basis set incompleteness error.
- Published
- 2016
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27. Using full configuration interaction quantum Monte Carlo in a seniority zero space to investigate the correlation energy equivalence of pair coupled cluster doubles and doubly occupied configuration interaction.
- Author
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Shepherd JJ, Henderson TM, and Scuseria GE
- Abstract
Over the past few years, pair coupled cluster doubles (pCCD) has shown promise for the description of strong correlation. This promise is related to its apparent ability to match results from doubly occupied configuration interaction (DOCI), even though the latter method has exponential computational cost. Here, by modifying the full configuration interaction quantum Monte Carlo algorithm to sample only the seniority zero sector of Hilbert space, we show that the DOCI and pCCD energies are in agreement for a variety of 2D Hubbard models, including for systems well out of reach for conventional configuration interaction algorithms. Our calculations are aided by the sign problem being much reduced in the seniority zero space compared with the full space. We present evidence for this and then discuss the sign problem in terms of the wave function of the system which appears to have a simplified sign structure.
- Published
- 2016
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28. Interaction picture density matrix quantum Monte Carlo.
- Author
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Malone FD, Blunt NS, Shepherd JJ, Lee DK, Spencer JS, and Foulkes WM
- Abstract
The recently developed density matrix quantum Monte Carlo (DMQMC) algorithm stochastically samples the N-body thermal density matrix and hence provides access to exact properties of many-particle quantum systems at arbitrary temperatures. We demonstrate that moving to the interaction picture provides substantial benefits when applying DMQMC to interacting fermions. In this first study, we focus on a system of much recent interest: the uniform electron gas in the warm dense regime. The basis set incompleteness error at finite temperature is investigated and extrapolated via a simple Monte Carlo sampling procedure. Finally, we provide benchmark calculations for a four-electron system, comparing our results to previous work where possible.
- Published
- 2015
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29. Unbiased reduced density matrices and electronic properties from full configuration interaction quantum Monte Carlo.
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Overy C, Booth GH, Blunt NS, Shepherd JJ, Cleland D, and Alavi A
- Abstract
Properties that are necessarily formulated within pure (symmetric) expectation values are difficult to calculate for projector quantum Monte Carlo approaches, but are critical in order to compute many of the important observable properties of electronic systems. Here, we investigate an approach for the sampling of unbiased reduced density matrices within the full configuration interaction quantum Monte Carlo dynamic, which requires only small computational overheads. This is achieved via an independent replica population of walkers in the dynamic, sampled alongside the original population. The resulting reduced density matrices are free from systematic error (beyond those present via constraints on the dynamic itself) and can be used to compute a variety of expectation values and properties, with rapid convergence to an exact limit. A quasi-variational energy estimate derived from these density matrices is proposed as an accurate alternative to the projected estimator for multiconfigurational wavefunctions, while its variational property could potentially lend itself to accurate extrapolation approaches in larger systems.
- Published
- 2014
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30. Range-separated Brueckner coupled cluster doubles theory.
- Author
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Shepherd JJ, Henderson TM, and Scuseria GE
- Abstract
We introduce a range-separation approximation to coupled cluster doubles (CCD) theory that successfully overcomes limitations of regular CCD when applied to the uniform electron gas. We combine the short-range ladder channel with the long-range ring channel in the presence of a Bruckner renormalized one-body interaction and obtain ground-state energies with an accuracy of 0.001 a.u./electron across a wide range of density regimes. Our scheme is particularly useful in the low-density and strongly correlated regimes, where regular CCD has serious drawbacks. Moreover, we cure the infamous overcorrelation of approaches based on ring diagrams (i.e., the particle-hole random phase approximation). Our energies are further shown to have appropriate basis set and thermodynamic limit convergence, and overall this scheme promises energetic properties for realistic periodic and extended systems which existing methods do not possess.
- Published
- 2014
- Full Text
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31. Coupled cluster channels in the homogeneous electron gas.
- Author
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Shepherd JJ, Henderson TM, and Scuseria GE
- Abstract
We discuss diagrammatic modifications to the coupled cluster doubles (CCD) equations, wherein different groups of terms out of rings, ladders, crossed-rings, and mosaics can be removed to form approximations to the coupled cluster method, of interest due to their similarity with various types of random phase approximations. The finite uniform electron gas (UEG) is benchmarked for 14- and 54-electron systems at the complete basis set limit over a wide density range and performance of different flavours of CCD is determined. These results confirm that rings generally overcorrelate and ladders generally undercorrelate; mosaics-only CCD yields a result surprisingly close to CCD. We use a recently developed numerical analysis [J. J. Shepherd and A. Grüneis, Phys. Rev. Lett. 110, 226401 (2013)] to study the behaviours of these methods in the thermodynamic limit. We determine that the mosaics, on forming the Brueckner one-body Hamiltonian, open a gap in the effective one-particle eigenvalues at the Fermi energy. Numerical evidence is presented which shows that methods based on this renormalisation have convergent energies in the thermodynamic limit including mosaic-only CCD, which is just a renormalised MP2. All other methods including only a single channel, namely, ladder-only CCD, ring-only CCD, and crossed-ring-only CCD, appear to yield divergent energies; incorporation of mosaic terms prevents this from happening.
- Published
- 2014
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32. Exploring genomes with a game engine.
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Shepherd JJ, Zhou L, Arndt W, Zhang Y, Zheng WJ, and Tang J
- Subjects
- Humans, Genome, Video Games
- Abstract
More and more evidence indicates that the 3D conformation of eukaryotic genomes is a critical part of genome function. However, due to the lack of accurate and reliable 3D genome structural data, this information is largely ignored and most of these studies have to use information systems that view the DNA in a linear structure. Visualizing genomes in real time 3D can give researchers more insight, but this is fraught with hardware limitations since each element contains vast amounts of information that cannot be processed on the fly. Using a game engine and sophisticated video game visualization techniques enables us to construct a multi-platform real-time 3D genome viewer. The game engine-based viewer achieves much better rendering speed and can handle much larger amounts of data compared to our previous implementation using OpenGL. Combining this viewer with 3D genome models from experimental data could provide unprecedented opportunities to gain insight into the conformation-function relationships of a genome.
- Published
- 2014
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33. Explicitly correlated plane waves: accelerating convergence in periodic wavefunction expansions.
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Grüneis A, Shepherd JJ, Alavi A, Tew DP, and Booth GH
- Abstract
We present an investigation into the use of an explicitly correlated plane wave basis for periodic wavefunction expansions at the level of second-order Møller-Plesset (MP2) perturbation theory. The convergence of the electronic correlation energy with respect to the one-electron basis set is investigated and compared to conventional MP2 theory in a finite homogeneous electron gas model. In addition to the widely used Slater-type geminal correlation factor, we also derive and investigate a novel correlation factor that we term Yukawa-Coulomb. The Yukawa-Coulomb correlation factor is motivated by analytic results for two electrons in a box and allows for a further improved convergence of the correlation energies with respect to the employed basis set. We find the combination of the infinitely delocalized plane waves and local short-ranged geminals provides a complementary, and rapidly convergent basis for the description of periodic wavefunctions. We hope that this approach will expand the scope of discrete wavefunction expansions in periodic systems.
- Published
- 2013
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34. Many-body quantum chemistry for the electron gas: convergent perturbative theories.
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Shepherd JJ and Grüneis A
- Abstract
We investigate the accuracy of a number of wave function based methods at the heart of quantum chemistry for metallic systems. Using the Hartree-Fock wave function as a reference, perturbative (Møller-Plesset) and coupled cluster theories are used to study the uniform electron gas model. Our findings suggest that nonperturbative coupled cluster theories are acceptable for modeling electronic interactions in metals while perturbative coupled cluster theories are not. Using screened interactions, we propose a simple modification to the widely used coupled cluster singles and doubles plus perturbative triples method that lifts the divergent behavior and is shown to give very accurate correlation energies for the homogeneous electron gas.
- Published
- 2013
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35. Investigation of the full configuration interaction quantum Monte Carlo method using homogeneous electron gas models.
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Shepherd JJ, Booth GH, and Alavi A
- Abstract
Using the homogeneous electron gas (HEG) as a model, we investigate the sources of error in the "initiator" adaptation to full configuration interaction quantum Monte Carlo (i-FCIQMC), with a view to accelerating convergence. In particular, we find that the fixed-shift phase, where the walker number is allowed to grow slowly, can be used to effectively assess stochastic and initiator error. Using this approach we provide simple explanations for the internal parameters of an i-FCIQMC simulation. We exploit the consistent basis sets and adjustable correlation strength of the HEG to analyze properties of the algorithm, and present finite basis benchmark energies for N = 14 over a range of densities 0.5 ≤ r(s) ≤ 5.0 a.u. A single-point extrapolation scheme is introduced to produce complete basis energies for 14, 38, and 54 electrons. It is empirically found that, in the weakly correlated regime, the computational cost scales linearly with the plane wave basis set size, which is justifiable on physical grounds. We expect the fixed-shift strategy to reduce the computational cost of many i-FCIQMC calculations of weakly correlated systems. In addition, we provide benchmarks for the electron gas, to be used by other quantum chemical methods in exploring periodic solid state systems.
- Published
- 2012
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36. Effects of serotonergic agents on survival and hemolymph composition of the larval mosquito Aedes aegypti (Diptera: Culicidae, L.) in vivo: does serotonin regulate hemolymph acid-base homeostasis?
- Author
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Clark TM, Lawecki JL, Shepherd JJ, Hirschler AN, and Samandu TR
- Subjects
- Alanine analogs & derivatives, Alanine pharmacology, Animals, Body Water metabolism, Hydrogen-Ion Concentration, Lethal Dose 50, Methiothepin pharmacology, Osmotic Pressure, Quipazine analogs & derivatives, Quipazine pharmacology, Salinity, Serotonin Antagonists pharmacology, Selective Serotonin Reuptake Inhibitors pharmacology, Sodium metabolism, Acid-Base Equilibrium drug effects, Aedes physiology, Hemolymph chemistry, Larva drug effects, Larva metabolism, Serotonin Agents pharmacology
- Abstract
The role of serotonin in the regulation of larval Aedes aegypti hemolymph composition was investigated in vivo using two reuptake inhibitors (SSRIs), alaproclate HCl and 6-nitroquipazine maleate, and the receptor antagonist methiothepin mesylate. Larvae were placed in media differing in pH and salinity in the presence and absence of serotonergic agents. The toxicity of each agent was strongly influenced by ambient pH. For each agent, toxicity was negligible in acidic media, intermediate in neutral media and greatest in alkaline media. By contrast, toxicity of all agents was independent of salinity. No effects on mass-specific body water or hemolymph volume were observed whereas hemolymph osmotic pressure, Na(+) concentrations and pH differed significantly among treatments. 6-nitroquipazine caused a decrease in Na(+) from 115+/-1.7 to 103+/-0.9 mmol l(-1), and alaproclate caused alkalosis of the hemolymph from pH 7.55+/-0.026 to pH 7.72+/-0.044. Methiothepin decreased hemolymph osmotic pressure from 329+/-9.9 to 304+/-8.8 and showed the greatest overall toxicity. Control larvae excreted net base in pH 4 media (1.4 micromol g(-1) h(-1)) and net acid in pH 7 (1.2 micromol g(-1) h(-1)) and pH 11 (5.1 micromol g(-1) h(-1)) media. In pH 4 media, alaproclate and methiothepin caused a shift to net H(+) excretion (1.1 and 1.5 micromol g(-1) h(1), respectively) whereas these agents did not influence acid excretion rates in pH 7 or pH 11 media. The hypothesis that serotonin is involved in hemolymph acid-base balance is discussed.
- Published
- 2009
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37. Scaling of xylem vessels and veins within the leaves of oak species.
- Author
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Coomes DA, Heathcote S, Godfrey ER, Shepherd JJ, and Sack L
- Subjects
- Models, Biological, Species Specificity, Plant Leaves cytology, Quercus anatomy & histology, Xylem cytology
- Abstract
General models of plant vascular architecture, based on scaling of pipe diameters to remove the length dependence of hydraulic resistance within the xylem, have attracted strong interest. However, these models have neglected to consider the leaf, an important hydraulic component; they assume all leaves to have similar hydraulic properties, including similar pipe diameters in the petiole. We examine the scaling of the leaf xylem in 10 temperate oak species, an important hydraulic component. The mean hydraulic diameter of petiole xylem vessels varied by 30% among the 10 oak species. Conduit diameters narrowed from the petiole to the midrib to the secondary veins, consistent with resistance minimization, but the power function scaling exponent differed from that predicted for stems. Leaf size was an organizing trait within and across species. These findings indicate that leaf vasculature needs to be included in whole-plant scaling models, for these to accurately reflect and predict whole-plant transport and its implications for performance and ecology.
- Published
- 2008
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38. Malignant thymic carcinoid is not prevented by transcervical thymectomy in multiple endocrine neoplasia type 1.
- Author
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Burgess JR, Giles N, and Shepherd JJ
- Subjects
- Adolescent, Carcinoid Tumor surgery, Humans, Male, Octreotide, Parathyroidectomy, Thymus Neoplasms surgery, Treatment Failure, Carcinoid Tumor prevention & control, Multiple Endocrine Neoplasia Type 1 surgery, Thymectomy, Thymus Neoplasms prevention & control
- Abstract
Multiple endocrine neoplasia type 1 (MEN 1) is an autosomal dominant tumour syndrome. It is characterized by primary hyperparathyroidism, pituitary neoplasia and foregut lineage neuroendocrine neoplasia. Malignant thymic carcinoid tumours are an uncommon but important manifestation of MEN 1. Transcervical thymectomy is often advocated as prophylaxis against thymic carcinoids, although there is a paucity of evidence to support the efficacy of this procedure. This is the first report of a malignant thymic carcinoid occurring in an MEN 1 patient following prior parathyroidectomy and transcervical thymectomy. It is concluded that transcervical thymectomy does not reliably provide prophylaxis against thymic carcinoid.
- Published
- 2001
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39. Phenotype and phenocopy: the relationship between genotype and clinical phenotype in a single large family with multiple endocrine neoplasia type 1 (MEN 1).
- Author
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Burgess JR, Nord B, David R, Greenaway TM, Parameswaran V, Larsson C, Shepherd JJ, and Teh BT
- Subjects
- Adult, Case-Control Studies, Chi-Square Distribution, Female, Genetic Markers, Genotype, Haplotypes, Heterozygote, Humans, Male, Multiple Endocrine Neoplasia Type 1 diagnosis, Pedigree, Phenotype, Polymorphism, Single-Stranded Conformational, Sequence Analysis, DNA, Multiple Endocrine Neoplasia Type 1 genetics
- Abstract
Background: The majority of reports describing the natural history and prognosis of multiple endocrine neoplasia type 1 (MEN 1) utilize phenotypic rather than molecular genetic criteria to establish a diagnosis of MEN 1., Objectives and Patients: We sought to determine the spectrum of endocrine abnormality amongst 152 members (64 gene carriers and 88 noncarriers) of a large MEN 1 family in whom a determination of MEN 1 status had previously been made by phenotype screening. The predictive utility of both clinical and molecular screening techniques are described., Results: A novel IVS2-3 (C-G) MEN1 mutation was identified in affected members of this family. Seven (10%) of 71 individuals satisfying clinical diagnostic criteria for MEN 1 were found to be genetically negative (excluded by mutation analysis and haplotyping) for MEN 1. These cases of MEN 1 phenocopy comprised four cases of primary hyperparathyroidism, two 'nonsecretory' pituitary adenoma and one case of coincident prolactinoma and hyperparathyroidism. Three of the patients with hyperparathyroidism had previously required parathyroidectomy and each had achieved normocalcaemia following parathyroid resection. Predictive genetic testing prospectively identified three children with the MEN 1 genotype. Serum calcium was normal at the time of their initial molecular genetic diagnosis. In each case hyperparathyroidism subsequently developed during adolescence., Conclusion: Multiple endocrine neoplasia type 1 phenocopy is an important differential diagnosis in patients exhibiting an multiple endocrine neoplasia type 1 phenotype. This is a relevant consideration, particularly when the diagnosis of multiple endocrine neoplasia type 1 is made using sensitive, but nonspecific, criteria such as mild hyperparathyroidism, pituitary micoadenoma, and hyperprolactinaemia. Confirmatory genetic testing should be undertaken to confirm clinical diagnoses of multiple endocrine neoplasia type 1.
- Published
- 2000
- Full Text
- View/download PDF
40. Preoperative sestamibi scanning and surgical findings at bilateral, unilateral, or minimal reoperation for recurrent hyperparathyroidism after subtotal parathyroidectomy in patients with multiple endocrine neoplasia type 1.
- Author
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Shepherd JJ, Burgess JR, Greenaway TM, and Ware R
- Subjects
- Adult, Humans, Hyperparathyroidism genetics, Hyperparathyroidism surgery, Middle Aged, Multiple Endocrine Neoplasia Type 1 genetics, Prospective Studies, Recurrence, Reoperation, Sensitivity and Specificity, Tasmania, Time Factors, Tomography, Emission-Computed, Single-Photon methods, Hyperparathyroidism diagnostic imaging, Multiple Endocrine Neoplasia Type 1 diagnostic imaging, Parathyroid Glands diagnostic imaging, Parathyroidectomy, Preoperative Care, Radiopharmaceuticals, Technetium Tc 99m Sestamibi
- Abstract
Hypotheses: Preoperative parathyroid radioisotope scanning is of little or no value in patients with multiple endocrine neoplasia type 1 when 4 or more hypertrophied glands are present. Scanning using technetium Tc 99m sestamibi and single photon emission computed tomography will achieve a high level of sensitivity and specificity after 3 or more glands have previously been removed, justifying limited surgical reexploration., Design: In a prospective study, the preoperative documented report of the predicted site of residual parathyroid was compared with the surgical findings in 13 patients having 19 scans and 17 reoperations., Setting: All patients belonged to one family, previously described as Tasman family 1, and were confirmed by genetic testing as having multiple endocrine neoplasia type 1. In 10 of 13 patients, reexploration was being undertaken more than 10 years after the first operation., Main Outcome Measures: Scanning was regarded as successful when the documented preoperative report correctly predicted the side and quadrant in which a gland was found at surgery. Surgery was regarded as successful when calcium levels decreased to or below normal levels and were maintained., Results: All 13 scans before first reexploration were successful in identifying the location of a residual parathyroid. From a statistical viewpoint, this equates to 100% sensitivity and 92% specificity. However, despite accurate localization of 1 residual gland in every patient, 7 supernumerary glands in 4 patients and 1 parathyroid remnant in a fifth patient were not localized so that sensitivity in locating all glands in every patient was only 61%. Scans performed for persistent hypercalcemia 48 to 72 hours after reexploration in 2 patients were unsuccessful in demonstrating any residual parathyroid. Scans performed 3 months after surgery in the same 2 patients and a third patient were successful, with sensitivity and specificity of 100%. Apart from patient 11, who awaits reexploration, normocalcemia was eventually achieved in every patient, with 11 of 12 having an initial period of hypocalcemia., Conclusions: Three months after reexploration and trimming or resection with transplant of half a gland left at first operation, sestamibi scanning achieved sensitivity and specificity of 100% in locating supernumerary parathyroids in patients with multiple endocrine neoplasia type 1 and persistent hypercalcemia. Before first reexploration, however, scans rarely provided new information, predominantly showing only the hypertrophied half-gland remnant.
- Published
- 2000
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41. Octreotide improves biochemical, radiologic, and symptomatic indices of gastroenteropancreatic neoplasia in patients with multiple endocrine neoplasia type 1 (MEN-1). Implications for an integrated model of MEN-1 tumorigenesis.
- Author
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Burgess JR, Greenaway TM, Parameswaran V, and Shepherd JJ
- Subjects
- Aged, Female, Gastrins blood, Humans, Middle Aged, Antineoplastic Agents, Hormonal therapeutic use, Gastrointestinal Neoplasms drug therapy, Models, Biological, Multiple Endocrine Neoplasia Type 1 drug therapy, Octreotide therapeutic use, Pancreatic Neoplasms drug therapy
- Abstract
Background: Multiple endocrine neoplasia type 1 (MEN-1) is an autosomal dominant tumor syndrome associated with parathyroid, gastroenteropancreatic (GEP), and pituitary neoplasia. Gastrinoma and GEP malignancy are common life-threatening endocrine complications of MEN-1. An effective management strategy for these disorders remains to be determined. The authors attempted to determine the role of the somatostatin analogue, octreotide, in ameliorating features of hypergastrinemic GEP neoplasia associated with MEN-1., Methods: Five MEN-1 patients with hypergastrinemia and either symptoms of GEP neoplasia or hepatic metastases received a trial of octreotide, 100 microg subcutaneously, three times daily for 3 months., Results: Treatment with octreotide was associated with a rapid symptomatic and biochemical response. In all patients serum gastrin fell to < 25% of the pretreatment value. The serum glycoprotein-alphasubunit (a marker of enterochromaffin-like [ECL] cell hyperplasia, gastric carcinoidosis, and disseminated enteropancreatic malignancy) was elevated at baseline in three patients. In each case the serum glycoprotein-alphasubunit normalized after treatment with octreotide. Hepatic metastases were present in two patients at baseline. The size of the metastases diminished by up to 15% during the period of octreotide treatment. Four patients reported symptoms prior to treatment: lethargy, easy fatigability, and generalized musculoskeletal discomfort. A marked symptomatic improvement occurred in each case. No patient experienced side effects related to octreotide therapy and all elected to remain on treatment after completion of the trial., Conclusions: Octreotide is a safe and effective adjunct to surgical strategies for the management of GEP neoplasia in hypergastrinemic MEN-1 patients., (Copyright 1999 American Cancer Society.)
- Published
- 1999
42. Osteoporosis in multiple endocrine neoplasia type 1: severity, clinical significance, relationship to primary hyperparathyroidism, and response to parathyroidectomy.
- Author
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Burgess JR, David R, Greenaway TM, Parameswaran V, and Shepherd JJ
- Subjects
- Adult, Aged, Female, Humans, Middle Aged, Severity of Illness Index, Hyperparathyroidism etiology, Hyperparathyroidism surgery, Multiple Endocrine Neoplasia Type 1 complications, Osteoporosis etiology, Osteoporosis prevention & control, Parathyroidectomy
- Abstract
Background: Sporadic primary hyperparathyroidism (PHPT) occurs most frequently in postmenopausal women. Multiple endocrine neoplasia type 1 (MEN 1) is an autosomal-dominant disease in which mild to moderate PHPT develops in most gene carriers by 20 years of age. Primary hyperparathyroidism associated with MEN 1 is typically recurrent, despite initially successful subtotal parathyroidectomy. Osteoporosis is considered a complication of sporadic PHPT and an indication for parathyroidectomy. In the setting of MEN 1, however, the relationship of bone mass to PHPT, fracture risk, and parathyroidectomy is unknown., Hypothesis: Parathyroidectomy improves bone mineral density for patients with primary hyperparathyroidism in the setting of MEN 1., Design: Case series., Setting: Tertiary referral center., Patients: Twenty-nine women with MEN 1 belonging to a single family with a history of MEN 1., Interventions: Parathyroidectomy., Main Outcome Measures: Bone mineral density (BMD) and history of skeletal fracture., Results: Osteopenia and osteoporosis were diagnosed in 41% and 45% of patients, respectively. Forty-four percent of patients with uncontrolled PHPT had severe osteopenia (T score, <-2.0) by 35 years of age. Reduction in BMD was greatest at the femoral neck. Reduced BMD was associated with an increased likelihood of skeletal fracture (P = .05). Patients with uncontrolled PHPT had lower femoral neck and lumbar spine BMDs than those in whom PHPT was controlled by parathyroidectomy (P = .005 and .02, respectively). Successful parathyroidectomy improved femoral neck and lumbar spine BMDs by a mean +/- SEM of 5.2% +/- 2.5% and 3.2% +/- 2.9%, respectively., Conclusions: Osteoporosis is a frequent and early complication of PHPT in MEN 1. Despite difficulty in achieving a cure of PHPT in MEN 1, parathyroidectomy has an important role in the optimization of BMD for patients with MEN 1.
- Published
- 1999
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43. Enteropancreatic malignancy associated with multiple endocrine neoplasia type 1: risk factors and pathogenesis.
- Author
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Burgess JR, Greenaway TM, Parameswaran V, Challis DR, David R, and Shepherd JJ
- Subjects
- Adenoma etiology, Adult, Female, Gastrins blood, Humans, Hyperparathyroidism etiology, Hyperparathyroidism therapy, Male, Middle Aged, Neoplasm Metastasis, Retrospective Studies, Risk Factors, Gastrinoma etiology, Multiple Endocrine Neoplasia Type 1 complications, Pancreatic Neoplasms etiology
- Abstract
Background: Enteropancreatic malignancy is an important cause of morbidity and mortality associated with multiple endocrine neoplasia type 1 (MEN 1). However, the risk factors and mechanisms of the tumorigenesis of this malignancy are poorly understood., Methods: The authors conducted a retrospective study of factors associated with the development of malignant enteropancreatic tumor in 69 patients with MEN 1 belonging to a single family., Results: Metastatic enteropancreatic tumor and gastrinoma were identified in 20% and 36% of patients, respectively. Compared with MEN 1 patients who did not have an immediate family history of enteropancreatic malignancy, MEN 1 patients with a first-degree relative affected by enteropancreatic malignancy had an increased risk of developing disseminated tumor (odds ratio, 3.7; P < 0.05). In addition, hypergastrinemia and advanced age were both associated with a significant increase in the risk of enteropancreatic malignancy. Elevated serum glycoprotein alpha subunit levels were associated with enterochromaffin-like cell hyperplasia, gastric carcinoid formation, and disseminated enteropancreatic tumor in hypergastrinemic patients (P < 0.05)., Conclusions: Disease modifier factors act in concert with the MEN 1 gene to modulate the development of enteropancreatic neoplasia. It is possible to identify MEN 1 patients at high risk for developing aggressive enteropancreatic tumors. Heritable disease modifier factor(s) affecting enteropancreatic malignancy appear to reside at loci distinct from that of the MEN 1 gene.
- Published
- 1998
- Full Text
- View/download PDF
44. Expression of the MEN-1 gene in a large kindred with multiple endocrine neoplasia type 1.
- Author
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Burgess JR, Greenaway TM, and Shepherd JJ
- Subjects
- Adrenal Cortex, Adrenal Gland Neoplasms diagnosis, Adrenal Gland Neoplasms genetics, Adult, Age Factors, Carcinoid Tumor diagnosis, Carcinoid Tumor genetics, Digestive System Neoplasms diagnosis, Digestive System Neoplasms genetics, Humans, Hyperparathyroidism diagnosis, Hyperparathyroidism genetics, Pituitary Neoplasms diagnosis, Pituitary Neoplasms genetics, Prognosis, Gene Expression Regulation, Neoplastic, Multiple Endocrine Neoplasia Type 1 diagnosis, Multiple Endocrine Neoplasia Type 1 genetics
- Abstract
In 1983 a large family with MEN-1 (designated Tasman 1) was identified in Tasmania. Kindred screening and case follow-up over the subsequent 15 years has yielded data on over 160 MEN-1-affected patients. Hyperparathyroidism is present in over 60% of gene carriers by age 20 years and 95% by age 30 years. Hyperplasia is the characteristic pathological finding. Kaplan-Meier analysis indicates hyperparathyroidism recurs in the majority of patients despite near-total parathyroidectomy. Gastrinoma, 'nonfunctioning' pancreatic adenoma and insulinoma occur in up to 60, 50 and 10% of patients, respectively. Metastatic gastroenteropancreatic (GEP) tumours develop in up to 35% of family members, being frequent in some branches of Tasman 1, whilst rare in others. Pituitary disease developed in 19% of patients. Prolactinoma and 'nonfunctioning' adenoma account for 76 and 24%, respectively, of pituitary abnormalities. Prolactinomas exhibit clustering within branches of the Tasman 1 kindred. Adrenal adenomas occur in 36% of patients. The majority of adrenal lesions are benign and nonsecretory and develop in association with pancreatic neoplasia. Carcinoid tumours are uncommon but important malignancies. Malignant thymic carcinoid occurs in male patients, whereas bronchial carcinoid occurs predominantly in women. Prior to recognition of MEN-1 in Tasman 1, complications of hyperparathyroidism and malignancy accounted for the majority of patient mortality. Since commencement of prospective screening, malignant GEP tumours and cardiovascular disease have become the most prevalent causes of death amongst MEN-1-affected patients.
- Published
- 1998
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- View/download PDF
45. The outcome of subtotal parathyroidectomy for the treatment of hyperparathyroidism in multiple endocrine neoplasia type 1.
- Author
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Burgess JR, David R, Parameswaran V, Greenaway TM, and Shepherd JJ
- Subjects
- Adult, Calcium blood, Female, Humans, Hyperparathyroidism blood, Hyperparathyroidism etiology, Male, Multiple Endocrine Neoplasia Type 1 blood, Parathyroid Neoplasms blood, Retrospective Studies, Treatment Outcome, Hyperparathyroidism surgery, Multiple Endocrine Neoplasia Type 1 complications, Parathyroid Neoplasms complications, Parathyroidectomy methods
- Abstract
Background: The efficacy of subtotal parathyroidectomy for the treatment of hyperparathyroidism in multiple endocrine neoplasia type 1 (MEN 1) is unclear. The long-term outcome and optimal timing of operation remain controversial., Objective: To determine the long-term outcome of parathyroidectomy for primary hyperparathyroidism in the presence of MEN 1., Design: Case series and retrospective analysis., Setting: Tertiary referral center., Patients: Patients with MEN 1 from 2 families., Interventions: Subtotal parathyroidectomy, ie, resection of 3 1/2 parathyroid glands from each patient., Main Outcome Measures: Recurrence of hyperparathyroidism., Results: Thirty-seven patients underwent subtotal parathyroidectomy. Overall, persistent postoperative hypoparathyroidism developed in 24%, normocalcemia was maintained in 46%, and hyperparathyroidism recurred in 30%. However, after adjustment for the duration of follow-up (by using the Kaplan-Meier method), the cumulative recurrence rates for hyperparathyroidism were 15% at 2 years, 23% at 4 years, 55% at 8 years, and 67% after 8 years. Early recurrence of hyperparathyroidism (within 5 years of operation) was less likely to develop in patients in whom ionized calcium levels of 1.00 mmol/L (4.00 mg/dL) or less were achieved during the perioperative period than in patients in whom this degree of hypocalcemia failed to develop (P=.01)., Conclusions: While relatively long periods of disease remission are possible after subtotal parathyroidectomy, our results indicate that recurrent hyperparathyroidism eventually develops in most patients with MEN 1.
- Published
- 1998
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46. Spectrum of pituitary disease in multiple endocrine neoplasia type 1 (MEN 1): clinical, biochemical, and radiological features of pituitary disease in a large MEN 1 kindred.
- Author
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Burgess JR, Shepherd JJ, Parameswaran V, Hoffman L, and Greenaway TM
- Subjects
- Adenoma diagnostic imaging, Adenoma genetics, Adenoma physiopathology, Adult, Female, Humans, Male, Middle Aged, Multiple Endocrine Neoplasia Type 1 diagnostic imaging, Pituitary Gland physiopathology, Pituitary Neoplasms diagnostic imaging, Prolactin metabolism, Prolactinoma diagnostic imaging, Prolactinoma genetics, Prolactinoma physiopathology, Prospective Studies, Radiography, Retrospective Studies, Tasmania, Multiple Endocrine Neoplasia Type 1 genetics, Multiple Endocrine Neoplasia Type 1 physiopathology, Pituitary Neoplasms genetics, Pituitary Neoplasms physiopathology
- Abstract
Prolactinomas and somatotropinomas are reported to be the pituitary lesions most frequently associated with multiple endocrine neoplasia type 1 (MEN 1). However, few reports have documented the full spectrum of pituitary disease in this condition. We report herein the clinical, biochemical (PRL, alpha-subunit, insulin-like growth factor-I, cortisol, and thyroid function), and radiological (magnetic resonance imaging and computerized tomography scan) characteristics of pituitary disease occurring in a single MEN 1 pedigree containing 165 MEN 1-affected members. Pituitary lesions were detected in 30 (18%) of 165 patients overall. In the subgroup of MEN 1 patients (n = 131) living after recognition of MEN 1 in the kindred, pituitary lesions were detected in 25 (19%). In 76% of patients with pituitary lesions, the diagnosis was made by prospective screening; the remainder sought medical attention for symptomatic pituitary disease. Prolactinomas accounted for 76%, and nonfunctioning adenomas accounted for the remaining 24%. alpha-Subunit elevation was observed in 29% of 41 patients tested, and an aggressive alpha-subunit secreting macroadenoma developed in 1 subject with a previously documented prolactinoma. Progression of pituitary disease occurred in 47% of patients with prolactinoma. There were no cases of Cushing's disease, thyrotropinoma, or somatotropinoma. We conclude that 1) in addition to prolactinomas, nonfunctioning pituitary tumors are common in MEN 1; 2) alpha-subunit hypersecretion is frequent in MEN 1; 3) comprehensive screening may identify many clinically significant but asymptomatic pituitary lesions; and 4) prolactinomas occurring in MEN 1 may behave more aggressively than sporadic prolactinomas.
- Published
- 1996
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47. Adrenal lesions in a large kindred with multiple endocrine neoplasia type 1.
- Author
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Burgess JR, Harle RA, Tucker P, Parameswaran V, Davies P, Greenaway TM, and Shepherd JJ
- Subjects
- Adrenal Gland Neoplasms diagnosis, Adrenal Gland Neoplasms pathology, Adult, Female, Humans, Male, Middle Aged, Multiple Endocrine Neoplasia Type 1 pathology, Pancreatic Neoplasms diagnosis, Pancreatic Neoplasms genetics, Sensitivity and Specificity, Tomography, X-Ray Computed, Adrenal Gland Neoplasms genetics, Multiple Endocrine Neoplasia Type 1 genetics
- Abstract
Objective: To review the prevalence and natural history of adrenal lesions occurring in patients from a single kindred with multiple endocrine neoplasia type 1 (MEN-1)., Design: Case series., Setting: Tertiary referral center., Patients: Medical records of 33 patients from the Tasman 1 MEN-1 kindred who had undergone abdominal computed tomographic (CT) scanning were reviewed. In 30 patients, the results of abdominal ultrasonographic examinations were available for correlation with CT scan. Computed tomographic and ultrasound scans of 18 patients were reviewed by a radiologist blinded to the patients' clinical details. Three patients underwent adrenalectomy, and the histopathologic material was reviewed., Main Outcome Measures: Computed tomographic and ultrasound scans., Results: Adrenal lesions were detected in 12 patients (36%) by CT scan examination. Ultrasound imaged 58% of these lesions. Pancreatic lesions were present in all cases of adrenal disease. Follow-up was available for 8 patients with adrenal disease. Over 5.5 years, 6 patients (75%) had stable disease, 1 patient had an adrenal lesion that enlarged by 5 mm, and 1 patient had a lesion that enlarged by 50 mm. Adrenal histopathologic material was available in 3 patients. Macronodular cortical hyperplasia was present in 2 patients and a cortical adenoma present in 1 patient. Another kindred had bilateral macronodular cortical hyperplasia at autopsy., Conclusions: Adrenal lesions are common in MEN-1 and occur in association with pancreatic disease. Abdominal CT scan is more sensitive than ultrasonographic examination in detecting adrenal disease. Primary hypersecretory syndromes of the adrenal glands appear to be rare, and the majority of lesions follow an indolent clinical course.
- Published
- 1996
- Full Text
- View/download PDF
48. Effective control of bone pain by octreotide in a patient with metastatic gastrinoma.
- Author
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Burgess JR, Shepherd JJ, Murton FJ, Parameswaran V, and Greenaway TM
- Subjects
- Adult, Combined Modality Therapy, Female, Follow-Up Studies, Humans, Liver Neoplasms secondary, Middle Aged, Multiple Endocrine Neoplasia Type 1 pathology, Multiple Endocrine Neoplasia Type 1 therapy, Palliative Care, Antineoplastic Agents, Hormonal therapeutic use, Bone Neoplasms secondary, Gastrinoma secondary, Hormones therapeutic use, Octreotide therapeutic use, Pain drug therapy, Pancreatic Neoplasms pathology
- Published
- 1996
- Full Text
- View/download PDF
49. Prolactinomas in a large kindred with multiple endocrine neoplasia type 1: clinical features and inheritance pattern.
- Author
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Burgess JR, Shepherd JJ, Parameswaran V, Hoffman L, and Greenaway TM
- Subjects
- Adult, Chromosomes, Human, Pair 11, Female, Humans, Hyperparathyroidism complications, Male, Pancreatic Diseases complications, Pedigree, Multiple Endocrine Neoplasia Type 1 genetics, Pituitary Neoplasms genetics, Prolactinoma genetics
- Abstract
Multiple endocrine neoplasia type 1 (MEN 1) is associated with neoplasia and hyperfunction of the parathyroid and pituitary glands, pancreatic islet cells, and neuroendocrine cells of the gut. The inheritance pattern is autosomal dominant, and the underlying genetic defect is situated at chromosome 11q13. The MEN 1 gene behaves as a defective copy of a normally constitutive tumor suppressor gene. Development of the MEN 1 phenotype, however, is a multistep and multifactorial process. The Tasman 1 genealogy is the largest MEN 1 pedigree detected to date. Thus far, 90 related members with MEN 1 have been screened for evidence of prolactinoma. Prolactinomas were found in 18 patients (20%). Prolactinomas were not evenly distributed in the genealogy; in 2 branches of the overall genealogy prolactinomas were present in 50% or more of MEN 1-affected members. The familial distribution of prolactinomas in these branches was consistent with an autosomal dominant mode of inheritance. In the remainder of the pedigree, prolactinomas were uncommon and did not display this inheritance pattern. This pedigree represents one of the largest published MEN 1 genealogies in which the risk of developing prolactinoma follows an autosomal dominant pattern of transmission. It is the first to demonstrate an inheritance pattern for prolactinomas acting in addition to, yet distinct from, the inheritance of the underlying MEN 1 gene defect. These findings are consistent with the existence of an undefined second genetic defect involved in the pathogenesis of prolactinoma in MEN 1.
- Published
- 1996
- Full Text
- View/download PDF
50. P53 tumour suppressor gene expression in hyperparathyroidism.
- Author
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Subramaniam P, Wilkinson S, and Shepherd JJ
- Subjects
- Calcium blood, Humans, Hyperparathyroidism pathology, Hyperparathyroidism surgery, Hyperplasia, Immunohistochemistry, Multiple Endocrine Neoplasia Type 1 genetics, Parathyroid Glands pathology, Parathyroid Hormone blood, Parathyroid Neoplasms genetics, Parathyroidectomy, Genes, p53, Hyperparathyroidism genetics
- Abstract
Background: Mutations of the p53 tumour suppressor gene lead to the loss of control of normal cellular proliferation and differentiation and have been shown to be associated with the development of malignancy., Method: Archival paraffin resection specimens from 86 cases of hyperparathyroidism treated surgically using the rabbit polyclonal CMI antibody were investigated to detect p53 immunoreactivity in these sections., Results: Eighteen of the 86 sections examined (21%) showed nuclear immunoreactivity. No correlation was detected between tumour histology and p53 immunoreactivity (P = 0.45), nor was there any correlation between tumour clonality and immunoreactivity (P = 0.54). Multiple endocrine neoplasia type 1 (MEN 1) status did not correlate with p53 immunoreactivity. A significant correlation between p53 immunoreactivity and preparathyroidectomy calcium levels of > 1.5 mmol/L was detected (P < 0.005) although no correlation was noted between p53 immunoreactivity and higher levels of preparathyroidectomy intact parathyroid hormone (PTH) levels., Conclusion: A relationship is postulated between abnormal serum calcium regulation and p53 mutation in hypercalcaemic states associated with hyperparathyroidism.
- Published
- 1996
- Full Text
- View/download PDF
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