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Author Nash, W.P.; Boasso, A.M.; Steenkamp, M.M.; Larson, J.L.; Lubin, R.E.; Litz, B.T. url  doi
openurl 
  Title Posttraumatic stress in deployed Marines: prospective trajectories of early adaptation Type Journal Article
  Year 2015 Publication Journal of Abnormal Psychology Abbreviated Journal J Abnorm Psychol  
  Volume (down) 124 Issue 1 Pages 155-171  
  Keywords  
  Abstract We examined the course of PTSD symptoms in a cohort of U.S. Marines (N = 867) recruited for the Marine Resiliency Study (MRS) from a single infantry battalion that deployed as a unit for 7 months to Afghanistan during the peak of conflict there. Data were collected via structured interviews and self-report questionnaires 1 month prior to deployment and again at 1, 5, and 8 months postdeployment. Second-order growth mixture modeling was used to disaggregate symptom trajectories; multinomial logistic regression and relative weights analysis were used to assess the role of combat exposure, prior life span trauma, social support, peritraumatic dissociation, and avoidant coping as predictors of trajectory membership. Three trajectories best fit the data: a low-stable symptom course (79%), a new-onset PTSD symptoms course (13%), and a preexisting PTSD symptoms course (8%). Comparison in a separate MRS cohort with lower levels of combat exposure yielded similar results, except for the absence of a new-onset trajectory. In the main cohort, the modal trajectory was a low-stable symptoms course that included a small but clinically meaningful increase in symptoms from predeployment to 1 month postdeployment. We found no trajectory of recovery from more severe symptoms in either cohort, suggesting that the relative change in symptoms from predeployment to 1 month postdeployment might provide the best indicator of first-year course. The best predictors of trajectory membership were peritraumatic dissociation and avoidant coping, suggesting that changes in cognition, perception, and behavior following trauma might be particularly useful indicators of first-year outcomes.  
  Address VA Boston Healthcare System  
  Corporate Author Thesis  
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  Language English Summary Language Original Title  
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  ISSN 0021-843X ISBN Medium  
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  Notes PMID:25419860 Approved no  
  Call Number UU @ jana.mullerova @ Serial 42197  
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Author Boulfelfel, S.E.; Ravikovitch, P.I.; Sholl, D.S. doi  openurl
  Title Modeling Diffusion of Linear Hydrocarbons in Silica Zeolite LTA Using Transition Path Sampling Type Journal Article
  Year 2015 Publication Abbreviated Journal The Journal of Physical Chemistry C  
  Volume (down) 119 Issue 27 Pages 15643-15653  
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  Abstract The diffusivities of linear hydrocarbons (CH4, C2H6, C2H4, C3H8, C3H6, and C4H10) in pure silica zeolite LTA (ITQ-29) are computed at 300 K and infinite dilution. To overcome the time scale problem arising from the slow diffusion process at room temperature, we used transition path sampling (TPS). The influence of framework flexibility on diffusion is investigated by combining TPS simulations with fully flexible molecular dynamics performed in the NpT ensemble. The ensemble of the collected reactive trajectories was used to characterize sets of transition states, and the corresponding configurations were analyzed to construct window size distributions during the molecular hopping events. The diffusion process is affected by framework flexibility, and the influence of framework flexibility on diffusion of propane and butane is much larger than for methane and ethane. The diffusivities of linear hydrocarbons (CH4, C2H6, C2H4, C3H8, C3H6, and C4H10) in pure silica zeolite LTA (ITQ-29) are computed at 300 K and infinite dilution. To overcome the time scale problem arising from the slow diffusion process at room temperature, we used transition path sampling (TPS). The influence of framework flexibility on diffusion is investigated by combining TPS simulations with fully flexible molecular dynamics performed in the NpT ensemble. The ensemble of the collected reactive trajectories was used to characterize sets of transition states, and the corresponding configurations were analyzed to construct window size distributions during the molecular hopping events. The diffusion process is affected by framework flexibility, and the influence of framework flexibility on diffusion of propane and butane is much larger than for methane and ethane.  
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  ISSN 1932-7447 ISBN Medium  
  Area Expedition Conference  
  Notes Times cited: 17 Approved no  
  Call Number AG @ matthewjvarga @ Serial 46121  
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Author Zoi, I.; Motley, M.W.; Antoniou, D.; Schramm, V.L.; Schwartz, S.D. url  openurl
  Title Enzyme homologues have distinct reaction paths through their transition states Type Journal Article
  Year 2015 Publication Abbreviated Journal J Phys Chem B  
  Volume (down) 119 Issue 9 Pages 3662-3668  
  Keywords  
  Abstract Recent studies of the bacterial enzymes EcMTAN and VcMTAN showed that they have different binding affinities for the same transition state analogue. This was surprising given the similarity of their active sites. We performed transition path sampling simulations of both enzymes to reveal the atomic details of the catalytic chemical step, which may be the key for explaining the inhibitor affinity differences. Even though all experimental data would suggest the two enzymes are almost identical, subtle dynamic differences manifest in differences of reaction coordinate, transition state structure, and eventually significant differences in inhibitor binding. Unlike EcMTAN, VcMTAN has multiple distinct transition states, which is an indication that multiple sets of coordinated protein motions can reach a transition state. Reaction coordinate information is only accessible from transition path sampling approaches, since all experimental approaches report averages. Detailed knowledge could have a significant impact on pharmaceutical design.  
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  Call Number AG @ matthewjvarga @ Serial 46250  
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Author Masterson, J.E.; Schwartz, S.D. doi  openurl
  Title Evolution Alters the Enzymatic Reaction Coordinate of Dihydrofolate Reductase Type Journal Article
  Year 2015 Publication Abbreviated Journal The Journal of Physical Chemistry B  
  Volume (down) 119 Issue 3 Pages 989-996  
  Keywords  
  Abstract How evolution has affected enzyme function is a topic of great interest in the field of biophysical chemistry. Evolutionary changes from Escherichia coli dihydrofolate reductase (ecDHFR) to human dihydrofolate reductase (hsDHFR) have resulted in increased catalytic efficiency and an altered dynamic landscape in the human enzyme. Here, we show that a subpicosecond protein motion is dynamically coupled to hydride transfer catalyzed by hsDHFR but not ecDHFR. This motion propagates through residues that correspond to mutational events along the evolutionary path from ecDHFR to hsDHFR. We observe an increase in the variability of the transition states, reactive conformations, and times of barrier crossing in the human system. In the hsDHFR active site, we detect structural changes that have enabled the coupling of fast protein dynamics to the reaction coordinate. These results indicate a shift in the DHFR family to a form of catalysis that incorporates rapid protein dynamics and a concomitant shift to a more flexible path through reactive phase space.  
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  Series Volume Series Issue Edition  
  ISSN 1520-6106 ISBN Medium  
  Area Expedition Conference  
  Notes NULL Times cited: 12 Approved no  
  Call Number AG @ matthewjvarga @ Serial 46517  
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Author Pan, X.; Schwartz, S.D. url  openurl
  Title Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations Type Journal Article
  Year 2015 Publication Abbreviated Journal J Phys Chem B  
  Volume (down) 119 Issue 17 Pages 5430-5436  
  Keywords  
  Abstract It has long been recognized that the structure of a protein creates a hierarchy of conformations interconverting on multiple time scales. The conformational heterogeneity of the Michaelis complex is of particular interest in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD(+)). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they show a strong variance in their propensity toward the on-enzyme chemical step. In this study, microsecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network of the Michaelis complex and the structures of the substates at atomistic scales. They also shed light on the complete picture of the catalytic mechanism of LDH.  
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  Series Volume Series Issue Edition  
  ISSN 1520-6106 ISBN Medium  
  Area Expedition Conference  
  Notes Approved no  
  Call Number AG @ matthewjvarga @ Serial 46553  
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Author Shao, Y.; Gan, Z.; Epifanovsky, E.; Gilbert, A.T.B.; Wormit, M.; Kussmann, J.; Lange, A.W.; Behn, A.; Deng, J.; Feng, X.; Ghosh, D.; Goldey, M.; Horn, P.R.; Jacobson, L.D.; Kaliman, I.; Khaliullin, R.Z.; Kuś, T.; Landau, A.; Liu, J.; Proynov, E.I.; Rhee, Y.M.; Richard, R.M.; Rohrdanz, M.A.; Steele, R.P.; Sundstrom, E.J.; Woodcock, H.L.; Zimmerman, P.M.; Zuev, D.; Albrecht, B.; Alguire, E.; Austin, B.; Beran, G.J.O.; Bernard, Y.A.; Berquist, E.; Brandhorst, K.; Bravaya, K.B.; Brown, S.T.; Casanova, D.; Chang, C.-M.; Chen, Y.; Chien, S.H.; Closser, K.D.; Crittenden, D.L.; Diedenhofen, M.; DiStasio, R.A.; Do, H.; Dutoi, A.D.; Edgar, R.G.; Fatehi, S.; Fusti-Molnar, L.; Ghysels, A.; Golubeva-Zadorozhnaya, A.; Gomes, J.; Hanson-Heine, M.W.D.; Harbach, P.H.P.; Hauser, A.W.; Hohenstein, E.G.; Holden, Z.C.; Jagau, T.-C.; Ji, H.; Kaduk, B.; Khistyaev, K.; Kim, J.; Kim, J.; King, R.A.; Klunzinger, P.; Kosenkov, D.; Kowalczyk, T.; Krauter, C.M.; Lao, K.U.; Laurent, A.D.; Lawler, K.V.; Levchenko, S.V.; Lin, C.Y.; Liu, F.; Livshits, E.; Lochan, R.C.; Luenser, A.; Manohar, P.; Manzer, S.F.; Mao, S.-P.; Mardirossian, N.; Marenich, A.V.; Maurer, S.A.; Mayhall, N.J.; Neuscamman, E.; Oana, C.M.; Olivares-Amaya, R.; O’Neill, D.P.; Parkhill, J.A.; Perrine, T.M.; Peverati, R.; Prociuk, A.; Rehn, D.R.; Rosta, E.; Russ, N.J.; Sharada, S.M.; Sharma, S.; Small, D.W.; Sodt, A.; Stein, T.; Stück, D.; Su, Y.-C.; Thom, A.J.W.; Tsuchimochi, T.; Vanovschi, V.; Vogt, L.; Vydrov, O.; Wang, T.; Watson, M.A.; Wenzel, J.; White, A.; Williams, C.F.; Yang, J.; Yeganeh, S.; Yost, S.R.; You, Z.-Q.; Zhang, I.Y.; Zhang, X.; Zhao, Y.; Brooks, B.R.; Chan, G.K.L.; Chipman, D.M.; Cramer, C.J.; Goddard, W.A.; Gordon, M.S.; Hehre, W.J.; Klamt, A.; Schaefer, H.F.; Schmidt, M.W.; Sherrill, C.D.; Truhlar, D.G.; Warshel, A.; Xu, X.; Aspuru-Guzik, A.; Baer, R.; Bell, A.T.; Besley, N.A.; Chai, J.-D.; Dreuw, A.; Dunietz, B.D.; Furlani, T.R.; Gwaltney, S.R.; Hsu, C.-P.; Jung, Y.; Kong, J.; Lambrecht, D.S.; Liang, W.Z.; Ochsenfeld, C.; Rassolov, V.A.; Slipchenko, L.V.; Subotnik, J.E.; Van Voorhis, T.; Herbert, J.M.; Krylov, A.I.; Gill, P.M.W.; Head-Gordon, M. doi  openurl
  Title Advances in molecular quantum chemistry contained in the Q-Chem 4 program package Type Journal Article
  Year 2015 Publication Abbreviated Journal Molecular Physics  
  Volume (down) 113 Issue 2 Pages 184-215  
  Keywords Q-CHEM computational modelling density functional theory electron correlation electronic structure theory quantum chemistry software  
  Abstract A summary of the technical advances that are incorporated in the fourth major release of the Q-CHEM quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order M\oller--Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr 2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.  
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  Series Volume Series Issue Edition  
  ISSN 0026-8976 ISBN Medium  
  Area Expedition Conference  
  Notes Times cited: 1649 Approved no  
  Call Number AG @ matthewjvarga @ Serial 46209  
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Author Slik, J.W.F.; Arroyo-Rodríguez, V.; Aiba, S.-I.; Alvarez-Loayza, P.; Alves, L.F.; Ashton, P.; Balvanera, P.; Bastian, M.L.; Bellingham, P.J.; van den Berg, E.; Bernacci, L.; da Conceição Bispo, P.; Blanc, L.; Böhning-Gaese, K.; Boeckx, P.; Bongers, F.; Boyle, B.; Bradford, M.; Brearley, F.Q.; Breuer-Ndoundou Hockemba, M.; Bunyavejchewin, S.; Calderado Leal Matos, D.; Castillo-Santiago, M.; Catharino, E.L.M.; Chai, S.-L.; Chen, Y.; Colwell, R.K.; Chazdon, R.L.; Clark, C.; Clark, D.B.; Clark, D.A.; Culmsee, H.; Damas, K.; Dattaraja, H.S.; Dauby, G.; Davidar, P.; DeWalt, S.J.; Doucet, J.-L.; Duque, A.; Durigan, G.; Eichhorn, K.A.O.; Eisenlohr, P.V.; Eler, E.; Ewango, C.; Farwig, N.; Feeley, K.J.; Ferreira, L.; Field, R.; de Oliveira Filho, A.T.; Fletcher, C.; Forshed, O.; Franco, G.; Fredriksson, G.; Gillespie, T.; Gillet, J.-F.; Amarnath, G.; Griffith, D.M.; Grogan, J.; Gunatilleke, N.; Harris, D.; Harrison, R.; Hector, A.; Homeier, J.; Imai, N.; Itoh, A.; Jansen, P.A.; Joly, C.A.; de Jong, B.H.J.; Kartawinata, K.; Kearsley, E.; Kelly, D.L.; Kenfack, D.; Kessler, M.; Kitayama, K.; Kooyman, R.; Larney, E.; Laumonier, Y.; Laurance, S.; Laurance, W.F.; Lawes, M.J.; Amaral, I.L. do; Letcher, S.G.; Lindsell, J.; Lu, X.; Mansor, A.; Marjokorpi, A.; Martin, E.H.; Meilby, H.; Melo, F.P.L.; Metcalfe, D.J.; Medjibe, V.P.; Metzger, J.P.; Millet, J.; Mohandass, D.; Montero, J.C.; de Morisson Valeriano, M.; Mugerwa, B.; Nagamasu, H.; Nilus, R.; Ochoa-Gaona, S.; Onrizal; Page, N.; Parolin, P.; Parren, M.; Parthasarathy, N.; Paudel, E.; Permana, A.; Piedade, M.T.F.; Pitman, N.C.A.; Poorter, L.; Poulsen, A.D.; Poulsen, J.; Powers, J.; Prasad, R.C.; Puyravaud, J.-P.; Razafimahaimodison, J.-C.; Reitsma, J.; dos Santos, J.R.; Roberto Spironello, W.; Romero-Saltos, H.; Rovero, F.; Rozak, A.H.; Ruokolainen, K.; Rutishauser, E.; Saiter, F.; Saner, P.; Santos, B.A.; Santos, F.; Sarker, S.K.; Satdichanh, M.; Schmitt, C.B.; Schöngart, J.; Schulze, M.; Suganuma, M.S.; Sheil, D.; da Silva Pinheiro, E.; Sist, P.; Stevart, T.; Sukumar, R.; Sun, I.-F.; Sunderland, T.; Suresh, H.S.; Suzuki, E.; Tabarelli, M.; Tang, J.; Targhetta, N.; Theilade, I.; Thomas, D.W.; Tchouto, P.; Hurtado, J.; Valencia, R.; van Valkenburg, J.L.C.H.; Van Do, T.; Vasquez, R.; Verbeeck, H.; Adekunle, V.; Vieira, S.A.; Webb, C.O.; Whitfeld, T.; Wich, S.A.; Williams, J.; Wittmann, F.; Wöll, H.; Yang, X.; Adou Yao, C.Y.; Yap, S.L.; Yoneda, T.; Zahawi, R.A.; Zakaria, R.; Zang, R.; de Assis, R.L.; Garcia Luize, B.; Venticinque, E.M. url  openurl
  Title An estimate of the number of tropical tree species Type Journal Article
  Year 2015 Publication Abbreviated Journal Proceedings of the National Academy of Sciences  
  Volume (down) 112 Issue 24 Pages 7472-7477  
  Keywords  
  Abstract The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher’s alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼40,000 and ∼53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼19,000–25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼4,500–6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.  
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  Call Number CES @ dilipnaidu.gt @ Serial 43105  
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Author Suarez, J.; Schramm, V.L. doi  openurl
  Title Isotope-specific and amino acid-specific heavy atom substitutions alter barrier crossing in human purine nucleoside phosphorylase Type Journal Article
  Year 2015 Publication Abbreviated Journal Proceedings of the National Academy of Sciences  
  Volume (down) 112 Issue 36 Pages 11247-11251  
  Keywords Born--Oppenheimer enzymes femtosecond dynamics heavy enzymes pre--steady-state chemistry transition state coupling  
  Abstract <jats:p>Computational chemistry predicts that atomic motions on the femtosecond timescale are coupled to transition-state formation (barrier-crossing) in human purine nucleoside phosphorylase (PNP). The prediction is experimentally supported by slowed catalytic site chemistry in isotopically labeled PNP (<jats:sup>13</jats:sup>C, <jats:sup>15</jats:sup>N, and <jats:sup>2</jats:sup>H). However, other explanations are possible, including altered volume or bond polarization from carbon-deuterium bonds or propagation of the femtosecond bond motions into slower (nanoseconds to milliseconds) motions of the larger protein architecture to alter catalytic site chemistry. We address these possibilities by analysis of chemistry rates in isotope-specific labeled PNPs. Catalytic site chemistry was slowed for both [<jats:sup>2</jats:sup>H]PNP and [<jats:sup>13</jats:sup>C, <jats:sup>15</jats:sup>N]PNP in proportion to their altered protein masses. Secondary effects emanating from carbon–deuterium bond properties can therefore be eliminated. Heavy-enzyme mass effects were probed for local or global contributions to catalytic site chemistry by generating [<jats:sup>15</jats:sup>N, <jats:sup>2</jats:sup>H]His<jats:sub>8</jats:sub>-PNP. Of the eight His per subunit, three participate in contacts to the bound reactants and five are remote from the catalytic sites. [<jats:sup>15</jats:sup>N, <jats:sup>2</jats:sup>H]His<jats:sub>8</jats:sub>-PNP had reduced catalytic site chemistry larger than proportional to the enzymatic mass difference. Altered barrier crossing when only His are heavy supports local catalytic site femtosecond perturbations coupled to transition-state formation. Isotope-specific and amino acid specific labels extend the use of heavy enzyme methods to distinguish global from local isotope effects.</jats:p  
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  Notes Times cited: 18 Approved no  
  Call Number AG @ matthewjvarga @ Serial 46225  
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Author Manuel, A.P.; Lambert, J.; Woodside, M.T. openurl 
  Title Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories Type Journal Article
  Year 2015 Publication Abbreviated Journal Proc. Natl. Acad. Sci. U.S.A.  
  Volume (down) 112 Issue 23 Pages 7183-7188  
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  Call Number AG @ matthewjvarga @ Serial 46816  
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Author Borges, R.M. openurl 
  Title How mutualisms between plants and insects are stabilized Type Journal Article
  Year 2015 Publication Abbreviated Journal Current Science  
  Volume (down) 108 Issue 10 Pages 1862-1868  
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  Notes Approved no  
  Call Number CES @ dilipnaidu.gt @ Serial 43028  
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