Chemical bonding in phase-change chalcogenides.

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.

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.

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.

The chemical bond in solids-revisited.

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.

Melt-quenched and as-deposited structures of amorphous selenium: a density functional/ molecular dynamics comparison.

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.

Direct Observation of Incoherent Cherenkov Diffraction Radiation in the Visible Range.

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.

Bonding in phase change materials: concepts and misconceptions.

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'.

Density functional study of structure and dynamics in liquid antimony and Sbn clusters.

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.

Collective excitations and viscosity in liquid Bi.

The analysis of extensive density functional/molecular dynamics simulations (over 500 atoms, up to 100 ps) of liquid bismuth at four temperatures between 573 K and 1023 K has provided details of the dynamical structure factors, the dispersion of longitudinal and transverse collective modes, and related properties (power spectrum, viscosity, and sound velocity). Agreement with available inelastic x-ray and neutron scattering data and with previous simulations is generally very good. The results show that density functional/molecular dynamics simulations can give dynamical information of good quality without the use of fitting functions, even at long wavelengths.

Structure of amorphous Ag/Ge/S alloys: experimentally constrained density functional study.

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.

Connexin26 (GJB2) deficiency reduces active cochlear amplification leading to late-onset hearing loss.

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.

Structure and dynamics in liquid bismuth and Bi(n) clusters: a density functional study.

Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available. While the three short covalent bonds typical to pnictogens are characteristic in both liquid and clusters, the number of large voids and the total cavity volume is much larger in the liquid at 1023 K, with larger local concentration variations. The inclusion of spin-orbit coupling results in a lowering of the cohesive energies in Bin clusters of 0.3-0.5 eV/atom.

Cardiotonic steroids induce anti-angiogenic and anti-proliferative profiles in first trimester extravillous cytotrophoblast cells.

OBJECTIVE: Preeclampsia (preE), is characterized by abnormal placental invasion and function. Marinobufagenin (MBG), a cardiotonic steroid (CTS), inhibits cytotrophoblast (CTB) cell functions that are critical for normal placental development. This study tests the hypothesis that CTSs induce anti-angiogenic and anti-proliferative effects in CTB cells. METHODS: Human extravillous CTB cells of the line Sw-71, derived from first trimester chorionic villus tissue, were incubated with 0, 0.1, 1, 10, and 100 nM of each of three CTSs (MBG, cinobufatalin (CINO) and ouabain (OUB)) for 48 h. Thereafter, levels of pro-angiogenic (vascular endothelial growth factor (VEGF165), placental growth factor (PlGF)) and anti-angiogenic (soluble fms-like tyrosine kinase-1 (sFlt-1), soluble endoglin (sEng)) factors were measured in culture media using ELISA kits. Expression of three receptors (VEGF receptor 1 (VEGFR1), angiogenic angiotensin type 1 receptor (AT1) and anti-angiogenic angiotensin type 2 receptor (AT2)) were assayed using immunoblotting (western blots) in cell lysates. RESULTS: sFlt-1 and sEng secretion were increased while VEGF165 and PIGF were decreased in the culture media of CTB cells treated with 1 nM or more of each CTSs (p < 0.01 for each). The AT2 receptor expression was up-regulated (p < 0.05) in CTB cells treated with 1 nM or more of MBG and CINO and with 100 nM OUB, while AT1 and VEGFR1 expressions decreased (p < 0.05) with 1 nM or more of MBG and 10 nM or more of CINO and OUB. CONCLUSIONS: CTSs influence extravillous CTB cells to induce an anti-angiogenic and anti-proliferative profile.

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.

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.

Fatty acids and TxA(2) generation, in the absence of platelet-COX-1 activity.

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.

Combined dysfunctions of immune cells predict nosocomial infection in critically ill patients.

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.

Density functional simulations of structure and polymorphism in Ga/Sb films.

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).

Amorphous Ge15Te85: density functional, high-energy x-ray and neutron diffraction study.

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.

Growth performance and nutrient utilization of broiler chickens fed diets supplemented with phytase alone or in combination with citric acid and multicarbohydrase.

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.

Docosahexaenoic acid therapy in peroxisomal diseases: results of a double-blind, randomized trial.

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.