Discovery of novel plasma biomarkers for future incident venous thromboembolism by untargeted synchronous precursor selection mass spectrometry proteomics.

Essentials Discovery of predictive biomarkers of venous thromboembolism (VTE) may aid risk stratification. A case-control study where plasma was sampled before the occurrence of VTE was established. We generated untargeted plasma proteomic profiles of 200 individuals by use of mass spectrometry. Assessment of the biomarker potential of 501 proteins yielded 46 biomarker candidates. ABSTRACT: Background Prophylactic anticoagulant treatment may substantially reduce the incidence of venous thromboembolism (VTE) but entails considerable risk of severe bleeding. Identification of individuals at high risk of VTE through the use of predictive biomarkers is desirable in order to achieve a favorable benefit-to-harm ratio. Objective We aimed to identify predictive protein biomarker candidates of VTE. Methods We performed a case-control study of 200 individuals that participated in the Tromsø Study, a population-based cohort, where blood samples were collected before the VTE events occurred. Untargeted tandem mass tag-synchronous precursor selection-mass spectrometry (TMT-SPS-MS3)-based proteomic profiling was used to study the plasma proteomes of each individual. Results Of the 501 proteins detected in a sufficient number of samples to allow multivariate analysis, 46 proteins were associated with VTE case-control status with P-values below the 0.05 significance threshold. The strongest predictive biomarker candidates, assessed by statistical significance, were transthyretin, vitamin K-dependent protein Z and protein/nucleic acid deglycase DJ-1. Conclusions Our untargeted approach of plasma proteome profiling revealed novel predictive biomarker candidates of VTE and confirmed previously reported candidates, thereby providing conceptual support for the validity of the study. A larger nested case-control study will be conducted to validate our findings.

Ab initio study of several static and dynamic properties of bulk liquid Ni near melting.

Several static and dynamic properties of bulk liquid Ni at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the static structure factor, which underlines a marked local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, and the calculated dynamic structure factors, S(q,ω), show a good agreement with the inelastic x-ray scattering measurements. The obtained dispersion relation closely follows that obtained from the inelastic x-ray scattering measurements; moreover we analyze the possible reasons behind its discrepancy with respect to the dispersion relation derived from the inelastic neutron scattering data. The dynamical processes behind the S(q,ω) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. We have found that the transverse current spectral functions exhibit some features which, so far, had previously been shown by high pressure liquid metals only. Furthermore, the calculated S(q,ω) show, within some q-range, the appearance of transverse-like excitation modes, similar to those recently found in other liquid metals. Finally, results are also reported for several transport coefficients.

An ab initio study of the structure and dynamics of bulk liquid Cd and its liquid-vapor interface.

Several static and dynamic properties of bulk liquid Cd at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals collective density excitations with an associated dispersion relation which points to a small positive dispersion. Results are also reported for several transport coefficients. Additional simulations have also been performed at a slightly higher temperature in order to study the structure of the free liquid surface. The ionic density profile shows an oscillatory behavior with two different wavelengths, as the spacing between the outer and first inner layer is different from that between the other inner layers. The calculated reflectivity shows a marked maximum whose origin is related to the surface layering, along with a shoulder located at a much smaller wavevector transfer.

Static, dynamic and electronic properties of expanded fluid mercury in the metal-nonmetal transition range. An ab initio study.

Fluid Hg undergoes a metal-nonmetal (M-NM) transition when expanded toward a density of around 9 g cm(-3). We have performed ab initio molecular dynamics simulations for several thermodynamic states around the M-NM transition range and the associated static, dynamic and electronic properties have been analyzed. The calculated static structure shows a good agreement with the available experimental data. It is found that the volume expansion decreases the number of nearest neighbors from 10 (near the triple point) to around 8 at the M-NM transition region. Moreover, these neighbors are arranged into two subshells and the decrease in the number of neighbors occurs in the inner subshell. The calculated dynamic structure factors agree fairly well with their experimental counterparts obtained by inelastic x-ray scattering experiments, which display inelastic side peaks. The derived dispersion relation exhibits some positive dispersion for all the states, although its value around the M-NM transition region is not as marked as suggested by the experiment. We have also calculated the electronic density of states, which shows the appearance of a gap at a density of around 8.3 g cm(-3).

Characterization of a yeast culture extract compound stimulating the growth of an anaerobic cellulolytic consortium.

In this work the compound obtained from yeast culture extract (YCE) that stimulated the activity of an anaerobic cellulolytic consortium (ACC) was characterized. YCE were obtained at different pH (4, 7 and 10) and ultra-filtered 300 and 30 kDa membranes (UYE). The 30 kDa UYE was heated to 60 °C, 90 °C and 120 °C and gel filtered (GYF). Mid infrared spectroscopy, protein and carbohydrate analysis of GYF were conducted. Results showed that YCE, UYE and GYF significantly stimulated (p < 0.05) the biomass production, acetate concentration and carboxymethyl cellulase activity of the ACC, in relation to the control. The GYF had an estimated molecular mass of 4 kDa. Mid-infrared and biochemical analysis of GYF suggested that the active compound is a peptide.

ATP-binding cassette transporter ABCB5 gene is expressed with variability in malignant melanoma.

BACKGROUND: Melanoma is a malignant neoplasm with high metastatic disease risk and elevated mortality. Incidence of melanoma varies according to geographic region and genetic BACKGROUND: Epidemiological studies indicate that acral melanoma (AM) is among the most common melanomas in the Mexican population. While extensive studies have identified genes associated with melanoma, little is known about the genes involved in the pathogenesis of AM. OBJECTIVE: To compare the gene expression patterns between primary melanoma and normal skin. METHODS: We used 10 samples of fresh acral melanomas and normal skin for the study of differential gene expression and 22 samples of melanoma for in situ hybridization. RESULTS: We first identified a gene that was present in a sample of AM and absent in normal skin. DNA sequencing of this differentially expressed gene revealed that it corresponded to ABCB5, a gene recently implicated in the regulation of progenitor cell fusion. Furthermore, we detected ABCB5 expression in other melanoma specimens by RT-PCR. We showed that nine out of ten melanomas were positive for ABCB5 while only one melanoma and normal skin samples were negative. All ABCB5 expressing melanomas had variable gene expression according to in situ hybridization studies, suggesting that the ABCB5 gene may be differentially regulated by individual melanomas. CONCLUSIONS: The ABCB5 gene may be related to the properties of chemoresistance and aggressiveness of melanoma. The high expression found in samples of acral melanoma may provide more insight on the pathogenesis of this common type of melanoma in the Mexican population, frequently associated with poor prognosis.

Influence of an aerobic fungus grown on solid culture on ruminal degradability and on a mixture culture of anaerobic cellulolytic bacteria.

In this work, the effect of a solid fungal culture of Aspergillus niger (An) grown on coffee pulp on the in situ ruminal degradability (RD) of corn stover was evaluated. In addition, the effect of its extracts on the in vitro dry matter disappearance (IVDMD) and on a mixed culture of anaerobic cellulolytic bacteria (MCACB) was also investigated. The solid ferment was a crude culture of An, grown on coffee pulp. Regarding in situ RD, a significant difference (p < 0.05) was found between treatment with 200 g/day of the solid culture and control (no solid culture added) on dry matter, crude protein and neutral detergent fibre on RD. All the water extracts (pH 4, 7 and 10) enhanced IVDMD and stimulated the cellulolytic activity on a MCACB. Ultrafiltration results showed that active compounds with a molecular weight lower than 30 kDa were responsible for the effect on MCACB. Such results suggest that the effects of the solid An culture in RD are related to the presence of water soluble compounds having a molecular weight lower than 30 kDa.

Ab initio molecular dynamics study of the static, dynamic, and electronic properties of liquid mercury at room temperature.

We report a study on several static, dynamic, and electronic properties of liquid Hg at room temperature. We have performed ab initio molecular dynamics simulations using Kohn-Sham density functional theory combined with a nonlocal ultrasoft pseudopotential. The calculated static structure shows good agreement with the available experimental data. We present results for the single-particle dynamics, and recent experimental data are analyzed. The calculated dynamic structure factors S(q,omega) fairly agree with their experimental counterparts as measured by inelastic x-ray (and neutron) scattering experiments. The dispersion relation exhibits a positive dispersion, which however is not so marked as suggested by the experiment; moreover, its slope at the long-wavelength limit provides a good estimate of the experimental sound velocity. We have also analyzed the dynamical processes behind the S(q,omega) in terms of a model including a relaxation mechanism with both fast and slow characteristic time scales.

Transverse acoustic excitations in liquid Ga.

The transverse acoustic excitation modes were detected by inelastic x-ray scattering in liquid Ga in the Q range above 9 nm(-1) although liquid Ga is mostly described by a hard-sphere liquid. An ab initio molecular dynamics simulation clearly supports this finding. From the detailed analysis for the S(Q,omega) spectra with a good statistic quality, the lifetime of 0.5 ps and the propagating length of 0.4-0.5 nm can be estimated for the transverse acoustic phonon modes, which may correspond to the lifetime and size of cages formed instantaneously in liquid Ga.

Structural and dynamical properties of liquid Mg. An orbital-free molecular dynamics study.

Several static and dynamic properties of liquid magnesium near melting have been evaluated by the orbital-free ab initio molecular dynamics method. The calculated static structure shows good agreement with recent experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of an important icosahedral short-range order in the liquid. As for the dynamic structure, we obtain collective density excitations with an associated dispersion relation which closely follows recent experimental results. Accurate estimates have also been obtained for several transport coefficients.

Structural, dynamic, and electronic properties of liquid tin: An ab initio molecular dynamics study.

We report on a study of several structural, dynamic, and electronic properties of liquid Sn at a thermodynamic state close to the triple point (573 K) and another one at a higher temperature (1273 K). This study has been performed by ab initio molecular dynamics simulations using 205 atoms and around 20 ps of simulation time. The calculated static structures show a good agreement with the available experimental data. The dynamic structure factors fairly agree with their experimental counterparts obtained by inelastic x-ray scattering experiments, which display inelastic side peaks. The calculated dispersion relations exhibit a positive dispersion, although not so marked as suggested by the experiment; moreover, its slope at the long-wavelength limit compares favorably with the experimental sound velocity. Electron densities near selected triplets of atoms are similar to those appearing in the solid phases, but these features have an extremely short lifetime, so they should not be considered as solid remnants in the melt.

Polymeric [dihydrobis(pyrazol-1-yl)borato]potassium(I) and three dihydrobis(pyrazol-1-yl)borate-magnesium(I) compounds obtained by disproportionation of the Grignard reagent.

Reaction of the Grignard reagent with polydentate nitrogen-donor ligands yields new species with rare magnesium coordination and possible catalytic activity. In the first of the title compounds, poly[[mu4-dihydrobis(pyrazol-1-yl)borato-kappa2N,N']potassium(I)], [K(C6H8BN4)]n, (I), polymeric chains form a two-dimensional network in the [100] plane. Each potassium ion is coordinated by four N atoms of pyrazolyl ligands, while weak (mu-BH)...K+ interactions additionally stabilize the structure. The K and B atoms both lie on a mirror plane. In three new structures obtained by disproportionation of the Grignard reagent, each Mg atom is bound to a kappa2N,N'-type ligand, forming the basal plane, and tetrahydrofuran molecules occupy the axial positions. Di-mu-chlorido-bis[dihydridobis(pyrazol-1-yl)borato]tris(tetrahydrofuran)dimagnesium(II), [Mg2(C6H8BN4)2Cl2(C4H8O)3], (II), adopts a dimeric structure with mu-Cl-Mg interactions. One of the Mg atoms has an octahedral coordination, while the other has a distorted square-pyramidal environment. However, in the bis-chelate compounds bis[dihydridobis(pyrazol-1-yl)borato-kappa2N,N'](tetrahydrofuran-kappaO)magnesium(II), [Mg(C6H8BN4)2(C4H8O)], (III), and bis[dihydridobis(pyrazol-1-yl)borato-kappa2N,N']bis(tetrahydrofuran-kappaO)magnesium(II), [Mg(C6H8BN4)2(C4H8O)2], (IV), the Mg atoms have square-pyramidal and octahedral environments, respectively. The Mg atom in (IV) lies on an inversion centre.

Structure of the liquid-vapor interfaces of Ga, In and the eutectic Ga-In alloy-an ab initio study.

We report the results of ab initio molecular dynamics simulations for the liquid-vapor interface of the liquid metals Ga, In and the eutectic binary alloy Ga-In (16.5% In) for which experimental data are available. The study was performed by using samples of 3000 particles in a slab geometry with periodic boundary conditions. In those systems, the total ionic density distributions along the normal to the interface display some layering and in the case of the Ga-In alloy there appears a highly enriched layer of the lower surface tension component located outermost at the interface. The results are compared with the available experimental data.

Interplay between the ionic and electronic density profiles in liquid metal surfaces.

First-principles molecular-dynamics simulations have been performed for the liquid-vapor interfaces of liquid Li, Mg, Al, and Si. We analyze the oscillatory ionic and valence electronic density profiles obtained, their wavelengths, and the mechanisms behind their relative phase shift.

Liquid-vapor interface in liquid binary alloys: an ab initio molecular dynamics study.

We report the results of an ab initio molecular dynamics simulation of the liquid-vapor interface of two binary liquid alloys, Na(0.3)K(0.7) and Li(0.4)Na(0.6), whose bulk behavior exhibits rather differing ordering tendencies. The study has been performed using samples of 2000 and 3000 particles, respectively, in a slab geometry with periodic boundary conditions. In both cases, the total ionic density distributions along the normal to the interface display some layering with a virtually pure monolayer of the lower surface tension component located outermost at the interface. However, the two systems behave very differently below the interface which can be accounted for by their different ordering tendencies in the bulk.

Viscoelastic model for the dynamic structure factors of binary systems.

This paper presents the viscoelastic model for the Ashcroft-Langreth dynamic structure factors of liquid binary mixtures. We also provide expressions for the Bhatia-Thornton dynamic structure factors and, within these expressions, show how the model reproduces both the dynamic and the self-dynamic structure factors corresponding to a one-component system in the appropriate limits (pseudobinary system or zero concentration of one component). In particular we analyze the behavior of the concentration-concentration dynamic structure factor and longitudinal current, and their corresponding counterparts in the one-component limit, namely, the self-dynamic structure factor and self-longitudinal current. The results for several lithium alloys with different ordering tendencies are compared with computer simulation data, leading to a good qualitative agreement, and showing the natural appearance in the model of the fast sound phenomenon.

Microscopic dynamics in the liquid Li-Na alloy: an ab initio molecular dynamics study.

We present results for several structural and dynamical properties of the liquid Li(1-x)Na(x) alloy. The study has been carried out by means of the orbital-free ab initio molecular dynamics method, combined with local ionic pseudopotentials constructed within the same framework. We obtain good agreement with the available experimental data, reproducing accurately, the strong homocoordinating tendencies exhibited by this alloy. The calculated partial dynamic structure factors exhibit clear side peaks whose frequencies, for q

Surface structure of liquid Li and Na: an ab initio molecular dynamics study.

Molecular dynamics simulations of the liquid-vapor interfaces of liquid metals have been performed using first principles methods. Results are presented for liquid lithium and sodium near their respective triple points, for samples of 2000 particles in a slab geometry. The atomic density profiles show a pronounced stratification extending several atomic diameters into the bulk, which is similar to that already experimentally observed in liquid K, Ga, In, and Hg.

Collective ionic dynamics in the liquid Na-Cs alloy: an ab initio molecular dynamics study.

We present results for several structural and dynamical properties of the liquid Na-Cs alloy. The study has been carried out by means of the orbital-free ab initio molecular dynamics method, combined with local ionic pseudopotentials constructed within the same framework. The results show good agreement with the available experimental data, reproducing the homocoordinating tendency exhibited by this alloy.