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1.
J Phys Chem B ; 124(34): 7421-7432, 2020 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-32696649

RESUMO

Theoretical description of liquids, especially liquid water, is an ongoing subject with important implications in various domains such as homogeneous catalysis; solvation of molecular, ionic, and biomolecular species; and reactivity. Various formalisms exist to describe liquids, each one displaying its own balance between accuracy and computational cost that defines its range of applications. The present article revisits the ability of the density-functional-based tight-binding (SCC-DFTB) approach to model liquids by focusing on liquid water and liquid benzene under ambient conditions. To do so, we benchmark a recent correction for the SCC-DFTB atomic charges that allows for a drastic improvement of the pair radial distribution functions of liquid water as compared to both experimental data and density-functional theory results performed in the generalized-gradient approximation. We also report the coupling of the deMonNano and i-PI codes to perform path-integral molecular dynamics. This allows us to rationalize the impact of nuclear quantum effects on the SCC-DFTB description of liquid water. This study evidences the rather good ability of SCC-DFTB to describe liquid water and liquid benzene. As the first example of application, we also present results for a benzene molecule solvated in water with the perspectives of further studies devoted to solvent/water interfaces.

2.
J Phys Chem Lett ; 11(12): 4826-4833, 2020 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-32496780

RESUMO

The molecular structure of dense homogeneous fluid water-methane mixtures has been determined for the first time using high-pressure neutron-scattering techniques at 1.7 and 2.2 GPa. A mixed state with a fully H-bonded water network is revealed. The hydration shell of the methane molecules is, however, revealed to be pressure-dependent with an increase in the water coordination between 1.7 and 2.2 GPa. In parallel, ab initio molecular dynamics simulations have been performed to provide insight into the microscopic mechanisms associated with the phenomenon of mixing. These calculations reproduce the observed phase change from phase separation to mixing with increasing pressure. The calculations also reproduce the experimentally observed structural properties. Unexpectedly, the simulations show mixing is accompanied by a subtle enhancement of the polarization of methane. Our results highlight the key role played by fine electronic effects on miscibility and the need to readjust our fundamental understanding of hydrophobicity to account for these.

3.
Soft Matter ; 2020 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-32510065

RESUMO

The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their proximity to biological interfaces and can play an important role in processes such as protein folding and aggregation. In this work, we study the dynamics of water near glutamine surfaces-a system of interest in studies of neurodegenerative diseases. Combining molecular-dynamics simulations and stochastic modelling, we study how the mean first-passage time and related statistics of water molecules escaping subnanometer-sized regions vary from the interface to the bulk. Our analysis reveals a dynamical complexity that reflects underlying chemical and geometrical properties of the glutamine surfaces. From the first-passage time statistics of water molecules, we infer their space-dependent diffusion coefficient in directions normal to the surfaces. Interestingly, our results suggest that the mobility of water varies over a longer length scale than the chemical potential associated with the water-protein interactions. The synergy of molecular dynamics and first-passage techniques opens the possibility for extracting space-dependent diffusion coefficients in more complex, inhomogeneous environments that are commonplace in living matter.

4.
J Phys Chem B ; 124(11): 2180-2190, 2020 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-32032486

RESUMO

The structural evolution of supercooled liquid water as we approach the glass transition temperature continues to be an active area of research. Here, we use molecular dynamics simulations of TIP4P/ice water to study the changes in the connected regions of empty space within the liquid, which we investigate using the Voronoi-voids network. We observe two important features: supercooling enhances the fraction of nonspherical voids and different sizes of voids tend to cluster forming a percolating network. By examining order parameters such as the local structure index (LSI), tetrahedrality and topological defects, we show that water molecules near large void clusters tend to be slightly more tetrahedral than those near small voids, with a lower population of under- and overcoordinated defects. We show further that the distribution of closed rings of water molecules around small and large void clusters maintain a balance between 6 and 7 membered rings. Our results highlight the changes of the dual voids and water network as a structural hallmark of supercooling and provide insights into the molecular origins of cooperative effects underlying density fluctuations on the subnanometer and nanometer length scale. In addition, the percolation of the voids and the hydrogen bond network around the voids may serve as useful order parameters to investigate density fluctuations in supercooled water.

5.
Nat Commun ; 11(1): 901, 2020 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-32060273

RESUMO

The origin of the apparent negative charge at hydrophobic-water interfaces has fueled debates in the physical chemistry community for decades. The most common interpretation given to explain this observation is that negatively charged hydroxide ions (OH-) bind strongly to the interfaces. Using first principles calculations of extended air-water and oil-water interfaces, we unravel a mechanism that does not require the presence of OH-. Small amounts of charge transfer along hydrogen bonds and asymmetries in the hydrogen bond network due to topological defects can lead to the accumulation of negative surface charge at both interfaces. For water near oil, some spillage of electron density into the oil phase is also observed. The computed surface charge densities at both interfaces is approximately [Formula: see text] in agreement with electrophoretic experiments. We also show, using an energy decomposition analysis, that the electronic origin of this phenomena is rooted in a collective polarization/charge transfer effect.

6.
Photodiagnosis Photodyn Ther ; 30: 101674, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31996322

RESUMO

BACKGROUND: Potential complications during fixed orthodontic procedures are white spot lesions (WSLs) and tooth decay. This study evaluated the anti-biofilm activity of an orthodontic adhesive (OA) incorporating curcumin (Cur) doped Poly lactic-co-glycolic acid nanoparticles (Cur-PLGA-NPs), which can have the highest concentration of Cur-PLGA-NPs and shear bond strength (SBS) value simultaneously, against cariogenic bacteria i.e., Streptococcus mutans. MATERIALS AND METHODS: Following synthesis and confirmation of Cur-PLGA-NPs, SBS and adhesive remnant index (ARI) of the modified orthodontic adhesives (MOA) containing Cur-PLGA-NPs (3, 5, 7, and 10 % wt.) were measured using universal testing machine and stereomicroscope, respectively. After artificial aging (continuously rinsed up to 180 days), the residual anti-biofilm ability of MOA which can have the highest concentration of Cur-PLGA-NPs and SBS value simultaneously were determined by anti-biofilm assay following photoexcited enamel slab bonded brackets by MOA containing Cur-PLGA-NPs against S. mutans biofilms using crystal violet assay. RESULTS: Adhesive with 7 % wt. Cur-PLGA-NPs revealed the highest concentration of Cur-PLGA-NPs and SBS value (16.19 ± 2.69 MPa, P < 0.05) simultaneously. No statistically significant difference in ARI scores was observed between the MOA and control (Transbond XT without the Cur-PLGA-NPs). On days 15, 30, 60, 90 and 120 there was a considerable decrease in optical density (OD) of preformed S. mutans biofilms on photoexcited enamel slab bonded brackets using MOA containing 7 % wt. Cur-PLGA-NPs, to 94.1 %, 79.6 %, 69.6 %, 69.4 %, and, 55.1 % respectively in comparison to the control group (all, P < 0.05). From days 150 onwards, microbial biofilm formation was progressively increased on enamel slab bonded brackets using MOA containing 7 % wt. Cur-PLGA-NPs compared to the control group (OA). Although chlorhexidine (2 %; as positive control) showed significant activity against pre-formed S. mutans biofilms on enamel slab bonded brackets using OA (99.1 % biofilm reduction; P = 0.001), its activity was slightly higher but not significant than photoexcited enamel slab bonded brackets using MOA containing 7 % wt. Cur-PLGA-NPs on the days 15 and 30 (both, P > 0.05). CONCLUSIONS: The 7 % wt. Cur-PLGA-NPs can serve as an orthodontic adhesive antimicrobial additive as exposure to blue laser provides an acceptable antimicrobial effect against cariogenic bacteria for a considerable time.

7.
Eat Weight Disord ; 25(2): 415-425, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30446937

RESUMO

BACKGROUND AND PURPOSE: Recent research demonstrates a significant relationship between weight status and impaired reaction time in young, adult, and elderly individuals. However, most such studies were performed on small samples, used only body mass index as the body obesity index, used simple reaction time, and oftentimes did not consider some potential confounders such as age, socioeconomic status, or physical activity in their studies. The present study explored the relationship between various reaction time tasks and various obesity indices in a sample of youth. METHODS: Two hundred and thirty-four young males (19-24 years) underwent standard anthropometry, various information processing tasks (e.g., clinical reaction time, simple audio and visual reaction time, and choice reaction time), as well as an inhibitory control task (congruent and incongruent Simon reaction time). RESULTS: Results revealed no significant relationship between any of the information processing tests and body mass index, nor for fat percentage, waist circumference, and waist-to-height ratio after adjustment for potential confounders. A weak positive association was observed only between congruent Simon reaction time (but not incongruent Simon reaction time) and waist circumference in participants (t value = 0.199; Std error = 0.0014; p = 0.047; Cohen's f2 = 0.09). CONCLUSION: Inhibitory control, but not information processing speed, was associated only with waist circumference in apparently healthy young men. LEVEL OF EVIDENCE: Level I, experimental study.

8.
J Mol Graph Model ; 96: 107510, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-31877402

RESUMO

Molecular chaperone Heat Shock Protein 90 (Hsp90) represents an interesting chemotherapeutic target for cancer treatments as it plays a role in cancer proliferation. Thus, continued effort to identify novel inhibitors of this target is an important task. Drug design using computational approach has gained significant attention in recent years. This work aims to propose docking protocols to re-purpose FDA-approved drugs targeting Hsp90. Sensitivity of results to different docking protocols such apo, holo and receptor ensembles (relaxed complex) structures, the role of water and conformational changes of Hsp90, are described. We show that the protein conformation and water have effects on drug binding. Holo relaxed complex receptors ensembles improves the binding energy of ligands to the protein. We also compare and contrast structural stability of three drugs namely: ezetimibe, pitavastatin and vilazodon in the Hsp90 protein. The results obtained serves as a possible basis towards developing Hsp90 inhibitors.

9.
Phys Chem Chem Phys ; 21(43): 23931-23942, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31661536

RESUMO

There is a growing body of experimental work showing that protein aggregates associated with amyloid fibrils feature intrinsic fluorescence. In order to understand the microscopic origin of this behavior observed in non-aromatic aggregates of peptides and proteins, we conducted a combined experimental and computational study on the optical properties of amyloid-derived oligopeptides in the near-UV region. We have focused on a few model systems having charged termini (zwitterionic) or acetylated termini. For the zwitterionic system, we were able to simulate the longer tail absorption in the near UV (250-350 nm), supporting the experimental results in terms of excitation spectra. We analyzed the optical excitations responsible for the low-energy absorption and found a large role played by charge-transfer states around the termini. These charge-transfer excitations are very sensitive to the conformation of the peptide and in realistic fibrils may involve inter and intra chain charge reorganization.


Assuntos
Proteínas Amiloidogênicas/química , Proteínas Amiloidogênicas/metabolismo , Teoria da Densidade Funcional , Microscopia de Força Atômica , Espectrofotometria , Termodinâmica
10.
J Phys Chem Lett ; 10(18): 5585-5591, 2019 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-31469575

RESUMO

Some liquids are characterized by the presence of large voids with dendritic shapes and for this reason are dubbed transiently porous. By using a battery of data analysis tools, we demonstrate that liquid water and methane are both characterized by transient porosity. We show that the thermodynamics of porosity is distinct from that associated with cavitation á la classical nucleation theory. The shapes of dendritic voids in both liquids with very different chemistries resemble those of small polymers. We further show, using free energy calculations, that the cost of solvating small hydrophobic polymers in water is consistent with the work associated with creating dendritic voids. The entropic and enthalpic contributions associated with hosting these polymers can thus be rationalized by the thermodynamics of fluctuations in bulk water.

11.
Phys Chem Chem Phys ; 21(29): 16083-16094, 2019 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-31298261

RESUMO

The behavior of water at the surfaces of solid amino acid crystals has received little attention despite its importance in nucleation processes. In this work, we take a first step to fill this gap by using molecular dynamics simulations to study the structural and dynamical properties of water near the (100), (010) and (001) surfaces of l-glutamine crystals. These highly hydrophilic surfaces serve as excellent model systems for interrogating the behavior of water. Despite having the same molecular composition, water at each surface displays characteristic structural, orientational and dynamical correlations. This behavior is tuned by how the different chemical groups of amino acids make contact with the liquid phase. All three surfaces yield a glassy layer of interfacial water which is reflected in different ways such as the presence of a rotationally arrested layer of water molecules and substantial slow down of the diffusion of water near the interface. By increasing the concentration of molecules in solution, we show that the binding of glutamine molecules to the crystal surface creates a crowded environment involving pockets of trapped water molecules altering the water dynamics in a highly non-trivial manner suggesting that the solvent dynamics may have important implications on crystal nucleation.

12.
J Chem Phys ; 150(11): 114701, 2019 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-30901998

RESUMO

Heat transfer between a silver nanoparticle and surrounding water has been studied using molecular dynamics (MD) simulations. The thermal conductance (Kapitza conductance) at the interface between a nanoparticle and surrounding water has been calculated using four different approaches: transient with/without temperature gradient (internal thermal resistance) in the nanoparticle, steady-state non-equilibrium, and finally equilibrium simulations. The results of steady-state non-equilibrium and equilibrium are in agreement but differ from the transient approach results. MD simulation results also reveal that in the quenching process of a hot silver nanoparticle, heat dissipates into the solvent over a length-scale of ∼2 nm and over a time scale of less than 5 ps. By introducing a continuum solid-like model and considering a heat conduction mechanism in water, it is observed that the results of the temperature distribution for water shells around the nanoparticle agree well with the MD results. It is also found that the local water thermal conductivity around the nanoparticle is greater by about 50% than that of bulk water. These results have important implications for understanding heat transfer mechanisms in nanofluid systems and also for cancer photothermal therapy, wherein an accurate local description of heat transfer in an aqueous environment is crucial.

13.
Adv Biomed Res ; 7: 124, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30211137

RESUMO

Background: Cutaneous leishmaniasis is one of the most important public health problems in many developing countries. Sand flies, as vectors, transmit infectious forms of the parasite to the vertebrate hosts. Poldokhtar, South West of Iran, is one of the endemic foci of diseases with a little information about it. In this paper, we have tried to gather some useful information to control and to prevent this disease in this region. Materials and Methods: The present study was conducted to determine the vector(s), the parasite, and the species composition of sand flies in the Poldokhtar County during the months from July to September 2015. Sticky paper traps were used to collect sand flies from July to September. Species identification was done based on available diagnostic keys. Nested-polymerase chain reaction was performed to diagnosis the Leishmania infection of sand flies, and restriction fragment length polymorphism was used to identify the Leishmania species. Results: A total of 2000 specimens comprising 8 species of sand flies (6 Phlebotomus and 2 Sergentomyia) were identified. Phlebotomus papatasi was the dominant species outdoor and Sergentomyia sintoni was the dominant species indoor. Among the 163 specimens of female P. papatasi, just 10 of them (6.1%) were positive to Leishmania major parasites. Conclusion: This is the first report of Leishmania infection of P. papatasi to L. major in this region. The results revealed that the high density of P. papatasi in outdoor and their infection with L. major is attributed that this species can play a major role as a principle vector in this region.

14.
Neurobiol Aging ; 72: 14-22, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30172922

RESUMO

We examined the relationship among white matter (WM) tract integrity, WM hyperintensities (WMH), lobar gray matter (GM) volumes, and cognition in the cross-sectional Framingham Offspring Study. Six hundred eighty participants (71.7 ± 7.7 years) completed cognitive testing and magnetic resonance imaging. Diffusion tensor imaging probabilistic tractography was used to reconstruct major WM tracts. We computed tract-specific mean fractional anisotropy (FA) and tract-specific WMH ratio. Linear regressions identified relations between tracts and lobar GM volumes. Partial least squares regression examined associations between integrity of combined tracts, lobar GM volumes and cognition, including scores of memory and processing speed. Five tracts were particularly vulnerable to WMH, and tract-specific WMH volumes were inversely associated with tract-specific FA (p values < 0.05). Tract-specific FA related to lobar GM volumes. Memory was associated with lobar GM, while processing speed related to both tract integrity and lobar GM volumes. We conclude that subtle microstructural WM tract degeneration relates to specific lobar GM atrophy. The integrity of associated WM tracts and GM lobes differentially impacts memory and processing speed.


Assuntos
Envelhecimento/patologia , Envelhecimento/fisiologia , Córtex Cerebral/patologia , Córtex Cerebral/fisiologia , Cognição/fisiologia , Disfunção Cognitiva/fisiopatologia , Imagem por Ressonância Magnética/métodos , Substância Branca/patologia , Idoso , Idoso de 80 Anos ou mais , Córtex Cerebral/diagnóstico por imagem , Córtex Cerebral/fisiopatologia , Envelhecimento Cognitivo/fisiologia , Imagem de Tensor de Difusão/métodos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Substância Branca/diagnóstico por imagem
15.
J Phys Chem Lett ; 9(17): 5029-5033, 2018 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-30113846

RESUMO

The effect of nanoconfinement on the self-dissociation of water constitutes an open problem whose elucidation poses a serious challenge to experiments and simulations alike. In slit pores of width ≈1 nm, recent first-principles calculations have predicted that the dissociation constant of H2O increases by almost 2 orders of magnitude [ Muñoz-Santiburcio and Marx, Phys. Rev. Lett. 2017 , 119 , 056002 ]. In the present study, quantum mechanics-molecular mechanics simulations are employed to compute the dissociation free-energy profile of water in a (6,6) carbon nanotube. According to our results, the equilibrium constant Kw drops by 3 orders of magnitude with respect to the bulk phase value, at variance with the trend predicted for confinement in two dimensions. The higher barrier to dissociation can be ascribed to the undercoordination of the hydroxide and hydronium ions in the nanotube and underscores that chemical reactivity does not exhibit a monotonic behavior with respect to pore size but may vary substantially with the characteristic length scale and dimensionality of the confining media.

16.
J Phys Chem B ; 122(32): 7895-7906, 2018 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-30019898

RESUMO

Herein, we use recently developed data science algorithms to illustrate the complexity of the water network surrounding the hydrated peptide tri-alanine extracted from molecular dynamics simulations. We estimate the dimensionality of water variables and show that it is sensitive to the underlying secondary structure of the peptide. We show that water wires threading the peptide encode important information on the secondary structure. Interestingly, the free-energy landscape as revealed by the water wires is very rough for α-configurations and rather smooth for ß-configurations. The structured nature of the free-energy landscape is washed out if one uses more standard collective variables such as the number of hydrogen bonds around the peptide. Our results provide fresh insights into the molecular ingredients behind the coupling of protein and solvent degrees of freedom relevant for many biophysical and chemical processes.


Assuntos
Oligopeptídeos/química , Água/química , Algoritmos , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Oligopeptídeos/metabolismo , Estrutura Secundária de Proteína , Termodinâmica
17.
Phys Rev E ; 97(6-1): 062113, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30011567

RESUMO

We develop a graph-based model of the hydrogen-bond network in water, with a view toward quantitatively modeling the molecular-level correlational structure of the network. The networks formed are studied by the constructing the model on two infinite-dimensional lattices. Our models are built bottom up, based on microscopic information coming from atomistic simulations, and we show that the predictions of the model are consistent with known results from ab initio simulations of liquid water. We show that simple entropic models can predict the correlations and clustering of local-coordination defects around tetrahedral waters observed in the atomistic simulations. We also find that orientational correlations between bonds are longer ranged than density correlations, determine the directional correlations within closed loops, and show that the patterns of water wires within these structures are also consistent with previous atomistic simulations. Our models show the existence of density and compressibility anomalies, as seen in the real liquid, and the phase diagram of these models is consistent with the singularity-free scenario previously proposed by Sastry and coworkers [Phys. Rev. E 53, 6144 (1996)1063-651X10.1103/PhysRevE.53.6144].

18.
J Chem Phys ; 148(22): 222826, 2018 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-29907069

RESUMO

In this work, we use ab initio molecular dynamics simulations to elucidate the electronic properties of three hydrated zwitterionic amino acids, namely proline, hydroxyproline, and alanine, the former two forming an important constituent of collagen. In all three systems, we find a substantial amount of charge transfer between the amino acids and surrounding solvent, which, rather surprisingly, also involves the reorganization of electron density near the hydrophobic non-polar groups. Water around proline appears to be slightly more polarized, as reflected by the enhanced water dipole moment in its hydration shell. This observation is also complemented by an examination of the IR spectra of the three systems where there is a subtle red and blue shift in the O-H stretch and bend regions, respectively, for proline. We show that polarizability of these amino acids as revealed by a dipole moment analysis involves a significant enhancement from the solvent and that this also involves non-polar groups. Our results suggest that quantum mechanical effects are likely to be important in understanding the coupling between biomolecules and water in general and in hydrophobic interactions.


Assuntos
Alanina/química , Hidroxiprolina/química , Simulação de Dinâmica Molecular , Prolina/química , Teoria Quântica , Água/química
19.
Life (Basel) ; 8(1)2018 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-29301382

RESUMO

The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a "covalent-bond stage" to a "hydrogen-bond stage" in prebiotic chemistry.

20.
Biol Sport ; 35(4): 355-362, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30765921

RESUMO

The present study aimed to explore the association between physical fitness (PF) and cognitive performance in a sample of 19-24 year old males. Two hundred and eleven young males (20.2±1.5 years) participated in the study. Cognitive functioning tasks including information processing speed and inhibitory control were measured in addition to PF and motor fitness components such as aerobic fitness, static strength, explosive strength, agility and speed. Regression analysis showed that after adjustment for potential confounders (e.g. age, socioeconomic status, adiposity and physical activity), aerobic fitness (represented by shorter time in the one-mile run) was positively associated with composite inhibitory control scores (standardized ß=0.17; p=0.04) and negatively associated with ∆ Simon (standardized ß= -0.21; p=0.04). Explosive strength was negatively associated with composite information processing scores (standardized ß= -0.24; P=0.01), and composite inhibitory control scores (standardized ß= -0.22; p=0.02). Speed of movement, agility and static strength were not associated with any of the cognitive tests. In conclusion, aerobic fitness and explosive strength but not speed, agility or static strength might be indicators of underlying cognitive functioning tasks in 19-24 year old males.

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