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Chemical bonding in phase-change chalcogenides. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:325706. [PMID: 38697198 DOI: 10.1088/1361-648x/ad46d6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/02/2024] [Indexed: 05/04/2024]
Abstract
Almost all phase-change memory materials (PCM) contain chalcogen atoms, and their chemical bonds have been denoted both as 'electron-deficient' [sometimes referred to as 'metavalent'] and 'electron-rich' ['hypervalent', multicentre]. The latter involve lone-pair electrons. We have performed calculations that can discriminate unambiguously between these two classes of bond and have shown that PCM have electron-rich, 3c-4e ('hypervalent') bonds. Plots of charge transferred between (ET) and shared with (ES) neighbouring atoms cannot on their own distinguish between 'metavalent' and 'hypervalent' bonds, both of which involve single-electron bonds. PCM do not exhibit 'metavalent' bonding and are not electron-deficient; the bonding is electron-rich of the 'hypervalent' or multicentre type.
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Quantitative TMT-based proteomics revealing host, dietary and microbial proteins in bovine faeces including barley serpin Z4, a prominent component in the head of beer. J Proteomics 2023; 285:104941. [PMID: 37285906 DOI: 10.1016/j.jprot.2023.104941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023]
Abstract
There has been little information about the proteome of bovine faeces or about the contribution to the faecal proteome of proteins from the host, the feed or the intestinal microbiome. Here, the bovine faecal proteome and the origin of its component proteins was assessed, while also determining the effect of treating barley, the major carbohydrate in the feed, with either ammonia (ATB) or sodium propionate (PTB) preservative. Healthy continental crossbreed steers were allocated to two groups and fed on either of the barley-based diets. Five faecal samples from each group were collected on Day 81 of the trial and analysed by quantitative proteomics using nLC-ESI-MS/MS after tandem mass tag labelling. In total, 281 bovine proteins, 199 barley proteins, 176 bacterial proteins and 190 archaeal proteins were identified in the faeces. Mucosal pentraxin, albumin and digestive enzymes were among bovine proteins identified. Serpin Z4 a protease inhibitor was the most abundant barley protein identified which is also found in barley-based beer, while numerous microbial proteins were identified, many originating bacteria from Clostridium, while Methanobrevibacter was the dominant archaeal genus. Thirty-nine proteins were differentially abundant between groups, the majority being more abundant in the PTB group compared to the ATB group. SIGNIFICANCE: Proteomic examination of faeces is becoming a valuable means to assess the health of the gastro-intestinal tract in several species, but knowledge on the proteins present in bovine faeces is limited. This investigation aimed to characterise the proteome of bovine faecal extracts in order to evaluate the potential for investigations of the proteome as a means to assess the health, disease and welfare of cattle in the future. The investigation was able to identify proteins in bovine faeces that had been (i) produced by the individual cattle, (ii) present in the barley-based feed eaten by the cattle or (iii) produced by bacteria and other microbes in the rumen or intestines. Bovine proteins identified included mucosal pentraxin, serum albumin and a variety of digestive enzymes. Barley proteins found in the faeces included serpin Z4, a protease inhibitor that is also found in beer having survived the brewing process. Bacterial and archaeal proteins in the faecal extracts were related to several pathways related to the metabolism of carbohydrates. The recognition of the range of proteins that can be identified in bovine faeces raises the possibility that non-invasive sample collection of this material could provide a novel diagnostic approach to cattle health and welfare.
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The chemical bond in solids-revisited. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:343001. [PMID: 35636399 DOI: 10.1088/1361-648x/ac7494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
This article complements an earlier topical review of the chemical bond (Jones 2018J. Phys.: Condens. Matter30153001), starting in the mid-19th century and seen from the perspective of a condensed matter physicist. The discussion of applications focused on the structure and properties of phase change materials. We review here additional aspects of chemistry, particularly some that have raised interest recently in this context. Concepts such as 'electron-rich', 'electron-deficient (excess orbital)', 'hypervalent', 'three-centre', and 'metavalent' bonds, and 'multicentre hyperbonding' are now found in the condensed matter literature. They are surveyed here, as well as the bond in metals and the 'Peierls' distortion. What are these concepts, are they related, and are they sometimes new labels for established, but unfamiliar ideas? 'Half bonds' and 'fractional valencies' play a central role in this discussion. It is remarkable that they were introduced 100 years ago, but ignored or forgotten, and have needed to be rediscovered more than once.
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Melt-quenched and as-deposited structures of amorphous selenium: a density functional/ molecular dynamics comparison. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:445401. [PMID: 34348254 DOI: 10.1088/1361-648x/ac1aa3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Molecular dynamics simulations using a density functional description of energies and forces have been carried out for a model of an as-deposited (AD) surface of amorphous selenium. The deposition model assumed the annealing (at 400 K) of layers of randomly located single atoms, followed by compression to the density used in earlier melt-quenched (MQ) simulations of amorphous Se, and by further annealing. The AD and MQ structures are predominantly twofold coordinated and similar, for example in the pair distribution functions, with notable differences: the AD structures have more defects (atoms with one and three neighbours), and the ring distributions differ. These differences are also reflected in the electronic structures of the AD and MQ samples, where the increased presence of defects in the former influences the Bader charges and the edge states of the band gap. The dominance of rings found in a previous simulation of AD structures is not found.
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Direct Observation of Incoherent Cherenkov Diffraction Radiation in the Visible Range. PHYSICAL REVIEW LETTERS 2018; 121:054802. [PMID: 30118307 DOI: 10.1103/physrevlett.121.054802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Indexed: 06/08/2023]
Abstract
We report on the observation of incoherent Cherenkov radiation emitted by a 5.3 GeV positron beam circulating in the Cornell electron-positron storage ring as the beam passes in the close vicinity of the surface of a fused silica radiator (i.e., at a distance larger than 0.8 mm). The shape of the radiator was designed in order to send the Cherenkov photons towards the detector, consisting of a compact optical system equipped with an intensified camera. The optical system allows both the measurements of 2D images and angular distribution including polarization study. The corresponding light intensity has been measured as a function of the distance between the beam and the surface of the radiator and has shown a good agreement with theoretical predictions. For highly relativistic particles, a large amount of incoherent radiation is produced in a wide spectral range. A light yield of 0.8×10^{-3} photon per particle per turn has been measured at a wavelength of 600±10 nm in a 2 cm long radiator and for an impact parameter of 1 mm. This will find applications in accelerators as noninvasive beam diagnostics for both leptons and hadrons.
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Bonding in phase change materials: concepts and misconceptions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:153001. [PMID: 29480162 DOI: 10.1088/1361-648x/aab22e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bonding concepts originating in chemistry are surveyed from a condensed matter perspective, beginning around 1850 with 'valence' and the word 'bond' itself. The analysis of chemical data in the 19th century resulted in astonishing progress in understanding the connectivity and stereochemistry of molecules, almost without input from physicists until the development of quantum mechanics in 1925 and afterwards. The valence bond method popularized by Pauling and the molecular orbital methods of Hund, Mulliken, Bloch, and Hückel play major roles in the subsequent development, as does the central part played by the kinetic energy in covalent bonding (Ruedenberg and others). 'Metallic' (free electron) and related approaches, including pseudopotential and density functional theories, have been remarkably successful in understanding structures and bonding in molecules and solids. We discuss these concepts in the context of phase change materials, which involve the rapid and reversible transition between amorphous and crystalline states, and note the confusion that some have caused, in particular 'resonance' and 'resonant bonding'.
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Density functional study of structure and dynamics in liquid antimony and Sb n clusters. J Chem Phys 2017; 146:194502. [PMID: 28527440 DOI: 10.1063/1.4983219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Density functional/molecular dynamics simulations have been performed on liquid antimony (588 atoms and six temperatures between 600 K and 1300 K) and on neutral Sb clusters with up to 14 atoms. We study structural patterns (coordination numbers, bond angles, and ring patterns, structure factors, pair distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra, dynamical structure factors, viscosity) and compare with available experimental results and with the results of our previous simulations on Bi. Three short covalent bonds characteristic of pnictogens are common in the clusters, and higher temperatures lead in the liquid to broader bond angle distributions, larger total cavity volumes, and weaker correlations between neighboring bond lengths. There are clear similarities between the properties of Sb and Bi aggregates.
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Structure of amorphous Ag/Ge/S alloys: experimentally constrained density functional study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:485304. [PMID: 26569035 DOI: 10.1088/0953-8984/27/48/485304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Density functional/molecular dynamics simulations have been performed to determine structural and other properties of amorphous Ag/Ge/S and Ge/S alloys. In the former, the calculations have been combined with experimental data (x-ray and neutron diffraction, extended x-ray absorption fine structure). Ag/Ge/As alloys have high ionic conductivity and are among the most promising candidates for future memristor technology. We find excellent agreement between the experimental results and large-scale (500 atoms) simulations in Ag/Ge/S, and we compare and contrast the structures of Ge/S and Ag/Ge/S. The calculated electronic structures, vibrational densities of states, ionic mobilities, and cavity distributions of the amorphous materials are discussed and compared with data on crystalline phases where available. The high mobility of Ag in solid state electrolyte applications is related to the presence of cavities and can occur via jumps to a neighbouring vacant site.
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Structure and dynamics in liquid bismuth and Bin clusters: A density functional study. J Chem Phys 2014; 141:194503. [DOI: 10.1063/1.4901525] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Connexin26 (GJB2) deficiency reduces active cochlear amplification leading to late-onset hearing loss. Neuroscience 2014; 284:719-729. [PMID: 25451287 DOI: 10.1016/j.neuroscience.2014.10.061] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/21/2014] [Accepted: 10/26/2014] [Indexed: 12/21/2022]
Abstract
Connexin26 (Cx26, GJB2) mutations account for >50% of nonsyndromic hearing loss. The deafness is not always congenital. A large group of these patients (∼30%) demonstrate a late-onset hearing loss, starting in childhood. They have normal hearing early in life and are therefore good candidates for applying protective and therapeutic interventions. However, the underlying deafness mechanism is unclear. In this study, we used a time-controlled, inducible gene knockout technique to knockout Cx26 expression in the cochlea after birth. We found that deletion of Cx26 after postnatal day 5 (P5) in mice could lead to late-onset hearing loss. Similar to clinical observations, the mice demonstrated progressive, mild to moderate hearing loss. The hearing loss initiated at high frequencies and then extended to the middle- and low-frequency range. The cochlea showed normal development and had no apparent hair cell loss. However, distortion product otoacoustic emission (DPOAE) was reduced. The reduction was also progressive and large at high-frequencies. Consistent with DPOAE reduction, we found that outer hair cell electromotility-associated nonlinear capacitance was shifted to the right and the slope of voltage dependence was reduced. The endocochlear potential was reduced in Cx26 conditional knockout (cKO) mice but the reduction was not associated with progressive hearing loss. These data suggest that Cx26 deficiency may impair active cochlear amplification leading to late-onset hearing loss. Our study also helps develop newer protective and therapeutic interventions to this common nonsyndromic hearing loss.
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The effect of protease, amylase, and nonstarch polysaccharide-degrading enzyme supplementation on nutrient utilization and growth performance of broiler chickens fed corn-soybean meal-based diets. Poult Sci 2014; 93:1745-53. [PMID: 24864284 DOI: 10.3382/ps.2013-03739] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A study was conducted to determine if amylase and protease addition would improve nutrient digestion during the first 2 wk of growth. The experimental treatments included a control corn-soybean meal-based diet and diets supplemented with either amylase or amylase plus protease. No effect of enzyme supplementation was observed on BW gain and feed conversion ratio. This was corroborated by similar ileal starch and protein digestibility values, which averaged 96.8, 96.8, and 96.9% and 83.9, 80.1, and 79.6%, respectively, for the control and for the amylase or amylase plus protease supplemented diets. Total tract digestibility of starch averaged 97.8, 97.7 and 97.7% for the 3 diets and was followed by a similar diet with AMEn values of 3,129, 3,129, and 3,106 kcal/kg. In another study, a 2(3) factorial arrangement of 8 dietary treatments was used to evaluate the effect of corn particle size (conventional or coarse vs. fine) and the addition of a nonstarch polysaccharide enzyme, amylase, or both on growth performance and nutrient utilization of broiler chickens from 1 to 21 d of age. Chickens fed a diet containing a conventionally ground corn (geometric mean diameter of 736 µm) showed higher (P < 0.001) BW gain (808 vs. 750 g/bird) and lower feed conversion ratio (1.27 vs. 1.32) than those consuming a fine corn-containing diet (geometric mean diameter of 482 µm). This was further substantiated by a lower AMEn content (2,852 vs. 2,972 kcal/kg). Addition of amylase had no effect on growth performance of chickens fed a conventional corn-containing diet, but improved BW gain, feed conversion ratio, and diet AMEn in those fed the finely ground corn, possibly due to increased starch digestion in the upper gut. Addition of nonstarch polysaccharide enzymes was effective for both diets, with the most pronounced effects observed in feed conversion ratio for the conventional corn-containing diet (1.27 vs. 1.23) and BW gain (750 vs. 789 g/bird) for the fine corn-containing diet. This was followed by the same magnitude of difference in diet AMEn content, which increased from 2,972 to 3,042 and 2,852 to 3,009 kcal/kg following enzyme addition.
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Fatty acids and TxA(2) generation, in the absence of platelet-COX-1 activity. Nutr Metab Cardiovasc Dis 2014; 24:428-433. [PMID: 24370448 PMCID: PMC4409424 DOI: 10.1016/j.numecd.2013.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 07/09/2013] [Accepted: 08/26/2013] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND AIMS Omega-3 fatty acids suppress Thromboxane A(2) (TxA(2)) generation via mechanisms independent to that of aspirin therapy. We sought to evaluate whether baseline omega-3 fatty acid levels influence arachidonic acid proven platelet-cyclooxygenase-1 (COX-1) independent TxA(2) generation (TxA(2) generation despite adequate aspirin use). METHODS AND RESULTS Subjects with acute myocardial infarction, stable CVD or at high risk for CVD, on adequate aspirin therapy were included in this study. Adequate aspirin action was defined as complete inhibition of platelet-COX-1 activity as assessed by <10% change in light transmission aggregometry to ≥1 mmol/L arachidonic acid. TxA(2) production was measured via liquid chromatography-tandem mass spectrometry for the stable TxA(2) metabolite 11-dehydro-thromboxane B2 (UTxB2) in urine. The relationship between baseline fatty acids, demographics and UTxB(2) were evaluated. Baseline omega-3 fatty acid levels were not associated with UTxB(2) concentration. However, smoking was associated with UTxB(2) in this study. CONCLUSION Baseline omega-3 fatty acid levels do not influence TxA(2) generation in patients with or at high risk for CVD receiving adequate aspirin therapy. The association of smoking and TxA(2) generation, in the absence of platelet COX-1 activity, among aspirin treated patients warrants further study.
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Combined dysfunctions of immune cells predict nosocomial infection in critically ill patients. Br J Anaesth 2013; 111:778-87. [PMID: 23756248 DOI: 10.1093/bja/aet205] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Nosocomial infection occurs commonly in intensive care units (ICUs). Although critical illness is associated with immune activation, the prevalence of nosocomial infections suggests concomitant immune suppression. This study examined the temporal occurrence of immune dysfunction across three immune cell types, and their relationship with the development of nosocomial infection. METHODS A prospective observational cohort study was undertaken in a teaching hospital general ICU. Critically ill patients were recruited and underwent serial examination of immune status, namely percentage regulatory T-cells (Tregs), monocyte deactivation (by expression) and neutrophil dysfunction (by CD88 expression). The occurrence of nosocomial infection was determined using pre-defined, objective criteria. RESULTS Ninety-six patients were recruited, of whom 95 had data available for analysis. Relative to healthy controls, percentage Tregs were elevated 6-10 days after admission, while monocyte HLA-DR and neutrophil CD88 showed broader depression across time points measured. Thirty-three patients (35%) developed nosocomial infection, and patients developing nosocomial infection showed significantly greater immune dysfunction by the measures used. Tregs and neutrophil dysfunction remained significantly predictive of infection in a Cox hazards model correcting for time effects and clinical confounders {hazard ratio (HR) 2.4 [95% confidence interval (CI) 1.1-5.4] and 6.9 (95% CI 1.6-30), respectively, P=0.001}. Cumulative immune dysfunction resulted in a progressive risk of infection, rising from no cases in patients with no dysfunction to 75% of patients with dysfunction of all three cell types (P=0.0004). CONCLUSIONS Dysfunctions of T-cells, monocytes, and neutrophils predict acquisition of nosocomial infection, and combine additively to stratify risk of nosocomial infection in the critically ill.
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Density functional simulations of structure and polymorphism in Ga/Sb films. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:115801. [PMID: 23423720 DOI: 10.1088/0953-8984/25/11/115801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Thin films of gallium/antimony alloys are promising candidates for phase change memories requiring rapid crystallization at high crystallization temperatures. Prominent examples are the stoichiometric form GaSb and alloys near the eutectic composition GaSb(7), but little is known about their amorphous structures or the differences between the 'as-deposited' (AD) and 'melt-quenched' (MQ) forms. We have generated these structures using 528-atom density functional/molecular dynamics simulations, and we have studied in detail and compared structural parameters (pair distribution functions, structure factors, coordination numbers, bond and ring size distributions) and electronic properties (densities of states, bond orders) for all structures. There is good agreement with x-ray diffraction data from deposited films of GaSb, and there is evidence for Sb segregation in GaSb(7).
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Schwerpunkt '84: Physikalische Forschung mit dem Computer: Das Dichtefunktional -dieMethode zur Berechnung von Bindungseigenschaften? ACTA ACUST UNITED AC 2013. [DOI: 10.1002/phbl.19840400607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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P111 Bronchoalveolar Lavage does not affect the Acute Inflammatory Response Following Bronchoscopy and Mediastinoscopy. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Amorphous Ge₁₅Te₈₅: density functional, high-energy x-ray and neutron diffraction study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:015802. [PMID: 22155923 DOI: 10.1088/0953-8984/24/1/015802] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The structure and electronic properties of amorphous Ge(15)Te(85) have been studied by combining density functional (DF) simulations with high-energy x-ray and neutron diffraction measurements. Three models with 560 atoms have been constructed using reverse Monte Carlo methods constrained to (1) agree with the experimental structure factors S(Q), and have (2) energies close to the DF minimum and (3) a semiconducting band structure. The best structure is based on the melt-quenched DF structure and has a small number of Ge-Ge bonds. It shows interlocking networks of Te and GeTe with a significant fraction (22-24%) of voids (cavities). Ge occurs with both tetrahedral and 3 + 3 defective octahedral configurations, and the coordination of Te is slightly higher than indicated by the '8 - N rule' (N is the number of valence electrons). The GeTe network includes clusters of ABAB squares (A = Ge, B = Te), and the bonding is characterized by the chemical bond orders.
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Growth performance and nutrient utilization of broiler chickens fed diets supplemented with phytase alone or in combination with citric acid and multicarbohydrase. Poult Sci 2010; 89:2221-9. [PMID: 20852113 DOI: 10.3382/ps.2010-00832] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An experiment was conducted to determine the effect of supplementing a corn-soybean meal-based diet with phytase alone or in combination with citric acid (CA) or multicarbohydrase, a preparation containing nonstarch polysaccharide-degrading enzymes, or both, on growth performance, nutrient utilization, and bone mineralization. A total of 360 one-day-old broiler chicks were assigned to 6 dietary treatments, consisting of 12 pens of 5 birds each, and were fed experimental diets from 1 to 21 d of age. The diets included a positive control (0.46% nonphytate P; 1.1% Ca) and a negative control (NC; 0.26% nonphytate P; 0.89% Ca) without or with phytase (600 U/kg) alone, phytase plus CA (5 g/kg), phytase plus multicarbohydrase (Superzyme OM; 0.6 g/kg), or phytase (Ronozyme P-CT) plus CA and multicarbohydrase. Birds fed the positive control diet had higher (P<0.05) BW gain (764 vs. 594 g/21 d) and tibia ash content (50.0 vs. 38.3%) than those fed the NC diet. Phytase improved (P<0.05) BW gain (632 g/21 d), which increased further (P<0.05) to 673 g/21 d for the phytase plus multicarbohydrase diet. In contrast to phytase alone, phytase plus multicarbohydrase supplementation improved (P<0.05) feed conversion ratio of the NC diet from 1.37 to 1.32. Tibia ash content for the NC diet increased (P<0.05) from 38.3 to 42.4% due to phytase addition. Phytase improved (P<0.05) ileal digestibility of P from 29.5 to 43%, and the addition of CA or multicarbohydrase, or both, to a phytase-supplemented diet further increased (P<0.05) P digestibility to 51.5, 53.4, and 54.3%, respectively. Phytase addition improved (P<0.05) diet AMEn content from 2,959 to 3,068 kcal/kg, which tended (P<0.06) to increase further with CA (3,150 kcal/kg) or multicarbohydrase (3,142 kcal/kg) addition. No beneficial interactions were detected between CA and multicarbohydrase for all response criteria measured. Results show that addition of multicarbohydrase to the phytase-supplemented broiler diets improved nutrient utilization and growth performance.
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Docosahexaenoic acid therapy in peroxisomal diseases: results of a double-blind, randomized trial. Neurology 2010; 75:826-30. [PMID: 20805528 DOI: 10.1212/wnl.0b013e3181f07061] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Peroxisome assembly disorders are genetic disorders characterized by biochemical abnormalities, including low docosahexaenoic acid (DHA). The objective was to assess whether treatment with DHA supplementation would improve biochemical abnormalities, visual function, and growth in affected individuals. METHODS This was a randomized, double-blind, placebo-controlled trial conducted at a single center. Treatment groups received supplements of DHA (100 mg/kg per day). The primary outcome measures were the change from baseline in the visual function and physical growth during the 1 year follow-up period. RESULTS Fifty individuals were enrolled and randomized. Two were subsequently excluded from study analysis when it was determined that they had a single enzyme disorder of peroxisomal beta oxidation. Thirty-four returned for follow-up. Nine patients died during the trial of their disorder, and 5 others were lost to follow-up. DHA supplementation was well tolerated. There was no difference in the outcomes between the treated and untreated groups in biochemical function, electroretinogram, or growth. Improvements were seen in both groups in certain individuals. CONCLUSIONS DHA supplementation did not improve the visual function or growth of treated individuals with peroxisome assembly disorders. CLASSIFICATION OF EVIDENCE This interventional study provides Class II evidence that DHA supplementation did not improve the visual function or growth of treated individuals with peroxisome assembly disorders during an average of 1 year of follow-up in patients aged 1 to 144 months.
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Comment on "Formation of large voids in the amorphous phase-change memory Ge2Sb2Te5 alloy". PHYSICAL REVIEW LETTERS 2010; 104:019603-019604. [PMID: 20366403 DOI: 10.1103/physrevlett.104.019603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Indexed: 05/29/2023]
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Density functional study of amorphous, liquid and crystalline Ge(2)Sb(2)Te(5): homopolar bonds and/or AB alternation? JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2008; 20:465103. [PMID: 21693837 DOI: 10.1088/0953-8984/20/46/465103] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The amorphous, liquid and crystalline phases of the phase change material Ge(2)Sb(2)Te(5) (GST) have been studied by means of density functional/molecular dynamics simulations. The large sample (460 atoms and 52 vacancies in the unit cell) and long simulations (hundreds of picoseconds) provide much new information. Here we extend our original analysis (2007 Phys. Rev. B 76 235201) in important ways: partial coordination numbers and radial distribution functions, bond angle distributions, new local order parameters, vibration frequencies, and the charges on atoms and vacancies. The valence band densities of states in amorphous and crystalline GST are compared with ones from x-ray photoemission spectroscopy. The results for the liquid phase are new and those for the crystalline phase much expanded. GST shows pronounced AB alternation (A: Ge, Sb; B: Te), especially in its amorphous phase, and ABAB squares play a central role in the amorphous to crystalline transition. We comment on earlier speculations concerning the nature of the amorphous to crystalline transition.
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Binary alloys of Ge and Te: order, voids, and the eutectic composition. PHYSICAL REVIEW LETTERS 2008; 100:205502. [PMID: 18518553 DOI: 10.1103/physrevlett.100.205502] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 04/15/2008] [Indexed: 05/26/2023]
Abstract
The liquid and amorphous structures of Ge0.15Te0.85 and GeTe alloys are characterized using combined density functional/molecular dynamics simulations. Te is threefold coordinated, in contrast with predictions of the "8-N rule," and Ge atoms (fourfold coordinated) show octahedral and tetrahedral bonding angles. Cubic local environment occurs in both materials, and GeTe shows a pronounced alternation of atomic types. Tetrahedral Ge coordination is more common in the eutectic Ge0.15Te0.85, which comprises corner- and edge-sharing GeTe4 units surrounded by Te. There is no Te segregation, and the material resembles neither GeTe nor Te. The ubiquitous cavities (voids) have been overlooked in Ge0.15Te0.85, where they comprise over 25% of the volume.
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Density functional calculations of ATP systems. 1. Crystalline ATP hydrates and related molecules. J Phys Chem B 2007; 110:8110-20. [PMID: 16610914 DOI: 10.1021/jp054920l] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenosine 5'-triphosphate (ATP) is an essential energy carrier in mammalian and other cells, and its hydrolysis to the diphosphate (ADP) in the presence of metal cations (e.g., Mg(2+) or Ca(2+)) is one of the most prevalent biochemical reactions. We describe here density functional (DF) calculations on closely related systems and compare the results with other calculations and available experimental data: Na(H2O)n +, Mg(H2O)n 2+, and Ca(H2O)n 2+ clusters (n = 1, 4-7), the crystalline pyrophosphates Mg(2)P(2)O(7).6H2O and alpha-CaNa(2)P(2)O(7).4H2O, and crystalline Na(2)ATP.3H2O. The last of these comprises asymmetric units of ATP dimers (monomers A and B) in a double-protonated state H(2)(ATP)(2-). The calculated structures agree well with available measurements and provide additional information, including the location of the H atoms. Analysis of the dipole moments of individual ATP monomers and their dimers shows that the crystal comprises blocks of opposing dipoles. Replacing one Na+ ion with Mg2+ or Ca2+ results in a significant elongation of the terminal bridging P-O bond. The calculations provide benchmarks for the use of DF methods in ATP systems and are used in the companion paper to study the hydrolysis of ATP at the active site of the protein actin.
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Density functional calculations of ATP systems. 2. ATP hydrolysis at the active site of actin. J Phys Chem B 2007; 110:8121-9. [PMID: 16610915 DOI: 10.1021/jp054921d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrolysis of adenosine 5'-triphosphate (ATP) at the active site of actin has been studied using density functional calculations. The active site is modeled by the triphosphate tail of ATP, an Mg cation, surrounding water molecules, and the nearby protein residues. Four reaction paths have been followed by constraining coordinates that allow phosphate stretching, nucleophilic attack of the catalytic water, and OH(-) formation via water deprotonation. The lowest-energy barrier (21.0 kcal/mol) is obtained for a dissociative reaction where the terminal phosphate breaks on approaching the catalytic water, followed by proton release via a proton wire mechanism. A higher barrier (39.6 kcal/mol) results for an associative reaction path where OH(-) is formed first, with a pentacoordinated phosphorus atom (P-O distances 2.1 A). Stretching the terminal bridging P-O bond results in bond rupture at 2.8 A with an energy barrier of 28.8 kcal/mol. The residues Gln137 and His161 are not important in the reactions, but insight into their roles in vivo has been obtained. The favored coordination of the end products H(2)PO(4)(-) and ADP(3-) includes a hydrogen bond and an O-Mg-O bridge between the phosphates as well as a hydrogen bond between H(2)PO(4)(-) and the Ser14 side chain. The total energy is 2.1 kcal/mol lower than in the initial reactants. Classical simulations of ATP- and ADP.P(i)-actin show few hydrolysis-induced differences in the protein structure, indicating that phosphate migration is necessary for a change in conformation.
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Erratum: “Density functional and Monte Carlo studies of sulfur. I. Structure and bonding in Sn rings and chains (n=2–18)” [J. Chem. Phys. 118, 9257 (2003)]. J Chem Phys 2004. [DOI: 10.1063/1.1794693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Smallest carbon nanotube is 3 a in diameter. PHYSICAL REVIEW LETTERS 2004; 92:125502. [PMID: 15089683 DOI: 10.1103/physrevlett.92.125502] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2003] [Indexed: 05/24/2023]
Abstract
Previous energetic considerations have led to the belief that carbon nanotubes (CNTs) of 4 A in diameter are the smallest stable CNTs. Using high-resolution transmission electron microscopy, we find that a stable 3 A CNT can be grown inside a multiwalled carbon nanotube. Density functional calculations indicate that the 3 A CNT is the armchair CNT(2,2) with a radial breathing mode at 787 cm(-1). Each end can be capped by half of a C12 cage (hexagonal prism) containing tetragons.
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Stability and structure of LinH molecules (n=3–6): Experimental and density functional study. J Chem Phys 2004; 120:5128-32. [PMID: 15267382 DOI: 10.1063/1.1648305] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The molecules Li(3)H and Li(4)H have been identified in mass-spectrometric measurements over solutions of hydrogen in liquid Li, and the gaseous equilibria of the reactions: Li(3)H+Li=Li(2)H+Li(2), Li(3)H+Li(2)=Li(2)H+Li(3), Li(3)H+Li=LiH+Li(3), Li(3)H+LiH=2Li(2)H, and Li(4)H+Li(2)=Li(3)H+Li(3) have been measured. Density functional calculations of Li(n)H molecules (n=3-6) provide structures, vibrational frequencies, ionization energies, and free energy functions of these molecules, and these are used to estimate the enthalpies of these reactions and the atomization energies of Li(3)H (119.4 kcal/mol) and Li(4)H (151.8 kcal/mol).
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A reactive force field simulation of liquid–liquid phase transitions in phosphorus. J Chem Phys 2004; 121:8147-57. [PMID: 15485279 DOI: 10.1063/1.1801271] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A force field model of phosphorus has been developed based on density functional (DF) computations and experimental results, covering low energy forms of local tetrahedral symmetry and more compact (simple cubic) structures that arise with increasing pressure. Rules tailored to DF data for the addition, deletion, and exchange of covalent bonds allow the system to adapt the bonding configuration to the thermodynamic state. Monte Carlo simulations in the N-P-T ensemble show that the molecular (P(4)) liquid phase, stable at low pressure P and relatively low temperature T, transforms to a polymeric (gel) state on increasing either P or T. These phase changes are observed in recent experiments at similar thermodynamic conditions, as shown by the close agreement of computed and measured structure factors in the molecular and polymer phases. The polymeric phase obtained by increasing pressure has a dominant simple cubic character, while the polymer obtained by raising T at moderate pressure is tetrahedral. Comparison with DF results suggests that the latter is a semiconductor, while the cubic form is metallic. The simulations show that the T-induced polymerization is due to the entropy of the configuration of covalent bonds, as in the polymerization transition in sulfur. The transition observed with increasing P is the continuation at high T of the black P to arsenic (A17) structure observed in the solid state, and also corresponds to a semiconductor to metal transition.
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Density functional and Monte Carlo studies of sulfur. II. Equilibrium polymerization of the liquid phase. J Chem Phys 2003. [DOI: 10.1063/1.1611475] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Density functional and Monte Carlo studies of sulfur. I. Structure and bonding in Sn rings and chains (n=2–18). J Chem Phys 2003. [DOI: 10.1063/1.1568081] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Equilibrium polymerization of cyclic carbonate oligomers. III. Chain branching and the gel transition. J Chem Phys 2002. [DOI: 10.1063/1.1505023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Equilibrium polymerization of cyclic carbonate oligomers. II. Role of multiple active sites. J Chem Phys 2002. [DOI: 10.1063/1.1466834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Reactions of Polycarbonate with Cyclohexene Oxide and Phosphites: A Density Functional Study. Macromolecules 2002. [DOI: 10.1021/ma011757t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Measurements of drill-induced temperature change in the facial nerve during mastoid surgery: a cadaveric model using diamond burs. Ann Otol Rhinol Laryngol 2001; 110:867-70. [PMID: 11558764 DOI: 10.1177/000348940111000911] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The purpose of this study was to investigate the changes in temperature in the facial nerve that occur during mastoid drilling by the facial recess approach and to confirm the beneficial effects of constant irrigation while drilling. Mastoid drilling was performed on human cadaveric temporal bones by means of 4-mm diamond burs with and without irrigation. There were 6 subjects in each group. Changes in facial nerve temperature were recorded on a continuous-output monitor. Significant changes were found in temperature for both the irrigation and non-irrigation groups (p < .0001). Constant irrigation minimized the rise in temperature. Facial recess drilling poses a potential threat to cranial nerve VII via thermal injury. The temperature elevation in the non-irrigation group was significantly greater than that in the irrigation group and was greater than the tolerable limits of peripheral nervous tissue. This finding supports the need for constant irrigation during the approach to the facial recess in mastoid surgery.
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