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Antti J Karttunen, Denis Usvyat, Martin Schütz, Lorenzo Maschio
van der Waals interactions are known to play a key role in the formation of weakly bound solids, such as molecular or layered crystals. Here we show that the correct quantum-chemical description of van der Waals dispersion is also essential for a correct description of the relative stability between purely covalently-bound solids like silicon allotropes. To this end, we apply periodic local MP2 and DFT with Grimme's empirical -D3 correction to 11 experimentally determined or yet hypothetical crystalline silicon structures, including the most recently discovered silicon allotropes...
March 3, 2017: Physical Chemistry Chemical Physics: PCCP
Martin Schütz, Lorenzo Maschio, Antti J Karttunen, Denis Usvyat
Black phosphorus (black-P) consists of phosphorene sheets, stacked by van der Waals dispersion. In a recent study based on periodic local second-order Møller-Plesset perturbation theory (LMP2) with higher-order corrections evaluated on finite clusters, we obtained a value of -151 meV/atom for the exfoliation energy. This is almost twice as large as another recent theoretical result (around -80 meV/atom) obtained with quantum Monte Carlo (QMC). Here, we revisit this system on the basis of the recently implemented, periodically embedded ring coupled cluster (rCCD) model instead of LMP2...
March 6, 2017: Journal of Physical Chemistry Letters
Marijke J E Dekker, Daniele Marcelli, Bernard J Canaud, Paola Carioni, Yuedong Wang, Aileen Grassmann, Constantijn J A M Konings, Peter Kotanko, Karel M Leunissen, Nathan W Levin, Frank M van der Sande, Xiaoling Ye, Vaibhav Maheshwari, Len A Usvyat, Jeroen P Kooman
In hemodialysis patients extracellular fluid overload is a predictor of all-cause and cardiovascular mortality, and a relation with inflammation has been reported in previous studies. The magnitude and nature of this interaction and the effects of moderate fluid overload and extracellular fluid depletion on survival are still unclear. We present the results of an international cohort study in 8883 hemodialysis patients from the European MONDO initiative database where, during a three-month baseline period, fluid status was assessed using bioimpedance and inflammation by C-reactive protein...
May 2017: Kidney International
Cesar Flores Gama, Laura M Rosales, Georges Ouellet, Yanna Dou, Stephan Thijssen, Len Usvyat, Hanjie Zhang, Viktoriya Kuntsevich, Nathan W Levin, Peter Kotanko
BACKGROUND: Human plasma gelsolin (pGSN) is an actin-binding protein that is secreted into the extracellular fluid, with the skeletal muscle and myocardial tissues being its major source. Depletion of pGSN has been shown to be related to a variety of inflammatory and clinical conditions. METHODS: pGSN levels were prospectively determined in prevalent maintenance hemodialysis (HD) patients from 3 U.S. dialysis centers. Demographics (age, time since dialysis initiation, race, gender, body height and weight, comorbidities), inflammatory markers (C reactive protein, CRP; interleukin 6, IL-6), free triiodothyronine (fT3), and routine laboratory parameters were obtained...
2017: Blood Purification
Angelo Karaboyas, Jarcy Zee, Steven M Brunelli, Len A Usvyat, Daniel E Weiner, Franklin W Maddux, Allen R Nissenson, Michel Jadoul, Francesco Locatelli, Wolfgang C Winkelmayer, Friedrich K Port, Bruce M Robinson, Francesca Tentori
BACKGROUND: Sudden death is a leading cause of death in patients on maintenance hemodialysis therapy. During hemodialysis sessions, the gradient between serum and dialysate levels results in rapid electrolyte shifts, which may contribute to arrhythmias and sudden death. Controversies exist about the optimal electrolyte concentration in the dialysate; specifically, it is unclear whether patient outcomes differ among those treated with a dialysate potassium concentration of 3 mEq/L compared to 2 mEq/L...
February 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
Yuqi Chen, Wensheng Guo, Peter Kotanko, Len Usvyat, Yuedong Wang
Modeling hospitalization is complicated because the follow-up time can be censored due to death. In this paper, we propose a shared frailty joint model for survival time and hospitalization. A random effect semi-parametric proportional hazard model is assumed for the survival time and conditional on the follow-up time, hospital admissions or total length of stay is modeled by a generalized linear model with a nonparametric offset function of the follow-up time. We assume that the hospitalization and the survival time are correlated through a latent subject-specific random frailty...
November 1, 2016: International Journal of Biostatistics
Narayan Jayaram, Daniel Usvyat, Andrew C R Martin
BACKGROUND: Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the mediation of transcriptional regulation. Information on experimentally validated functional TFBSs is limited and consequently there is a need for accurate prediction of TFBSs for gene annotation and in applications such as evaluating the effects of single nucleotide variations in causing disease. TFBSs are generally recognized by scanning a position weight matrix (PWM) against DNA using one of a number of available computer programs...
November 2, 2016: BMC Bioinformatics
Oliver Masur, Martin Schütz, Lorenzo Maschio, Denis Usvyat
We present a periodic/finite-cluster interface for fragment-based direct local ring-coupled-cluster doubles (d-LrCCD) calculations embedded in the periodic mean field. The fragment is defined by a set of Wannier functions (WFs), obtained from a periodic Hartree-Fock calculation. The pair-specific virtual space is spanned by projected atomic orbitals (PAOs) truncated to pair domains. The computational procedure is initiated by a periodic local Møller-Plesset (LMP2) calculation. A subset of the WF pairs is then subsequently subjected to a finite-cluster d-LrCCD treatment using the local coupled cluster program of Molpro; this subset is specified by an interorbital cutoff distance...
October 11, 2016: Journal of Chemical Theory and Computation
M J E Dekker, D Marcelli, B Canaud, C J A M Konings, K M Leunissen, N W Levin, P Carioni, V Maheshwari, J G Raimann, F M van der Sande, L A Usvyat, P Kotanko, J P Kooman
BACKGROUND/OBJECTIVES: Hyponatremia is a risk factor for mortality in hemodialysis (HD) patients. It is not well known to which extent the comorbidities, malnutrition, fluid status imbalance and inflammation are related to hyponatremia and affect outcomes. SUBJECTS/METHODS: We studied 8883 patients from the European subset of the international MONitoring Dialysis Outcomes initiative. Nutritional and fluid statuses were assessed by bioimpedance spectroscopy. Fluid depletion was defined as overhydration⩽-1...
July 2016: European Journal of Clinical Nutrition
Maria Ferris, Keisha Gibson, Brett Plattner, Debbie S Gipson, Peter Kotanko, Daniele Marcelli, Cristina Marelli, Michael Etter, Paola Carioni, Gero von Gersdorff, Xiaoqi Xu, Jeroen P Kooman, Qingqing Xiao, Frank M van der Sande, Albert Power, Roberto Picoits-Filho, Lucimary Sylvestre, Katherine Westreich, Len Usvyat
BACKGROUND: The aim of this study was to describe the experience of pediatric and young adult hemodialysis (HD) patients from a global cohort. METHODS: The Pediatric Investigation and Close Collaborative Consortium for Ongoing Life Outcomes for MONitoring Dialysis Outcomes (PICCOLO MONDO) study provided de-identified electronic information of 3244 patients, ages 0-30 years from 2000 to 2012 in four regions: Asia, Europe, North America and South America. The study sample was categorized into pediatric (≤18 years old) and young adult (19-30 years old) groups based on the age at dialysis initiation...
April 2016: Clinical Kidney Journal
Andreja Marn Pernat, Vanja Peršič, Len Usvyat, Lynn Saunders, John Rogus, Franklin W Maddux, Eduardo Lacson, Peter Kotanko
OBJECTIVE: Patients with diabetes are at increased risk of foot ulcers, which may result in limb amputations. While regular foot care prevents ulcerations and amputation in those patients with diabetes not on dialysis, evidence is limited in diabetic hemodialysis patients. We investigated the association between the implementation of a routine foot check program in diabetic incident hemodialysis patients, and major lower limb amputations. METHODS: In 1/2008, monthly intradialytic foot checks were implemented as part of standard clinic care in all Fresenius Medical Care North America hemodialysis facilities...
2016: BMJ Open Diabetes Research & Care
Gero Wälz, Denis Usvyat, Tatiana Korona, Martin Schütz
We present a hierarchy of local coupled cluster (CC) linear response (LR) methods to calculate ionization potentials (IPs), i.e., excited states with one electron annihilated relative to a ground state reference. The time-dependent perturbation operator V(t), as well as the operators related to the first-order (with respect to V(t)) amplitudes and multipliers, thus are not number conserving and have half-integer particle rank m. Apart from calculating IPs of neutral molecules, the method offers also the possibility to study ground and excited states of neutral radicals as ionized states of closed-shell anions...
February 28, 2016: Journal of Chemical Physics
Dugan W Maddux, Len A Usvyat, Daniel DeFalco, Peter Kotanko, Jeroen P Kooman, Frank M van der Sande, Franklin W Maddux
BACKGROUND: Pre-dialysis chronic kidney disease (CKD) care impacts dialysis start and incident dialysis outcomes. We describe the use of late stage CKD population data coupled with CKD case management to improve dialysis start. METHODS: The Renal Care Coordinator (RCC) program is a nephrology practice and Fresenius Medical Care North America (FMCNA) partnership involving a case manager resource and data analytics. We studied patients starting dialysis between August 1, 2009 and February 28, 2013 in 9 nephrology practices partnering in the RCC program...
March 2016: Clinical Nephrology
Giuseppe Sansone, Lorenzo Maschio, Denis Usvyat, Martin Schütz, Antti Karttunen
The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal...
January 7, 2016: Journal of Physical Chemistry Letters
Carsten Müller, Denis Usvyat
A method for accurate calculations of the cohesive energy of molecular crystals is presented. The cohesive energy is evaluated as a sum of several components. The major contribution is captured by periodic Hartree-Fock (HF) coupled with the local Møller-Plesset perturbation theory of second order (LMP2) with a triple-ζ basis set. Post-MP2 corrections and corrections for the basis set incompleteness are calculated from inexpensive incremental calculations with finite clusters. This is an essential improvement with respect to the periodic LMP2 method and allows for results of benchmark quality for crystalline systems...
December 10, 2013: Journal of Chemical Theory and Computation
Denis Usvyat
A multilevel hierarchical ab initio protocol for calculating adsorption on non-conducting surfaces is presented. It employs fully periodic treatment, which reaches local Møller-Plesset perturbation theory of second order (MP2) with correction for the basis set incompleteness via the local F12 technique. Post-MP2 corrections are calculated using finite clusters. That includes the coupled cluster treatment in the local and canonical frameworks (up to perturbative quadruples) and correlated core (with MP2). Using this protocol, the potential surface of hydrogen molecules adsorbed on graphane was computed...
September 14, 2015: Journal of Chemical Physics
Giuseppe Sansone, Bartolomeo Civalleri, Denis Usvyat, Julien Toulouse, Kamal Sharkas, Lorenzo Maschio
Quantum chemistry methods exploiting density-functional approximations for short-range electron-electron interactions and second-order Møller-Plesset (MP2) perturbation theory for long-range electron-electron interactions have been implemented for periodic systems using Gaussian-type basis functions and the local correlation framework. The performance of these range-separated double hybrids has been benchmarked on a significant set of systems including rare-gas, molecular, ionic, and covalent crystals. The use of spin-component-scaled MP2 for the long-range part has been tested as well...
September 14, 2015: Journal of Chemical Physics
Denis Usvyat, Lorenzo Maschio, Martin Schütz
We introduce orbital specific virtuals (OSVs) to represent the truncated pair-specific virtual space in periodic local Møller-Plesset perturbation theory of second order (LMP2). The OSVs are constructed by diagonalization of the LMP2 amplitude matrices which correspond to diagonal Wannier-function (WF) pairs. Only a subset of these OSVs is adopted for the subsequent OSV-LMP2 calculation, namely, those with largest contribution to the diagonal pair correlation energy and with the accumulated value of these contributions reaching a certain accuracy...
September 14, 2015: Journal of Chemical Physics
Adrian M Guinsburg, Len A Usvyat, Michael Etter, Xiaoqi Xu, Stephan Thijssen, Daniele Marcelli, Bernard Canaud, Cristina Marelli, Claudia Barth, Yuedong Wang, Paola Carioni, Frank M van der Sande, Peter Kotanko, Jeroen P Kooman
BACKGROUND: Seasonal mortality differences have been reported in US hemodialysis (HD) patients. Here we examine the effect of seasons on mortality, clinical and laboratory parameters on a global scale. METHODS: Databases from the international Monitoring Dialysis Outcomes (MONDO) consortium were queried to identify patients who received in-center HD for at least 1 year. Clinics were stratified by hemisphere and climate zone (tropical or temperate). We recorded mortality and computed averages of pre-dialysis systolic blood pressure (pre-SBP), interdialytic weight gain (IDWG), serum albumin, and log C-reactive protein (CRP)...
2015: BMC Nephrology
J G Raimann, B Canaud, M Etter, J P Kooman, N W Levin, D Marcelli, C Marelli, A Power, N Duncan, F M van der Sande, P Carioni, S Thijssen, X Xu, L A Usvyat, Y Wang, P Kotanko
A recent study from the United Kingdom indicates an association between pre hemodialysis (HD) serum sodium (SNa(+)) and systolic and diastolic blood pressure (SBP and DBP) in chronic HD patients. We extend this analysis to an international cohort of incident HD patients. The Monitoring Dialysis Outcomes initiative encompasses patients from 41 countries. Over 2 years monthly pre-HD SNa(+) levels were used as predictors of pre-HD SBP and DBP in a linear mixed model (LMM) adjusted for age, gender, interdialytic weight gain, diabetes, serum albumin and calcium...
July 2016: Journal of Human Hypertension
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