Spin-polarization-induced structural selectivity in Pd3X_3X and Pt3X_3X (X=3dX=3d) compounds

Spin-polarization is known to lead to important {\it magnetic} and {\it optical} effects in open-shell atoms and elemental solids, but has rarely been implicated in controlling {\it structural} selectivity in compounds and alloys. Here we show that spin-polarized electronic structure calculations are crucial for predicting the correct $T=0$ crystal structures for Pd$_3X$ and Pt$_3X$ compounds. Spin-polarization leads to (i) stabilization of the $L1_2$ structure over the $DO_{22}$ structure in Pt$_3$Cr, Pd$_3$Cr, and Pd$_3$Mn, (ii) to the stabilization of the $DO_{22}$ structure over the $L1_2$ structure in Pd$_3$Co and to (iii) ordering (rather than phase-separation) in Pt$_3$Co and Pd$_3$Cr. The results are analyzed in terms of first-principles local spin density calculations.Comment: 4 pages, REVTEX, 3 eps figures, to appear in PR

Point-charge electrostatics in disordered alloys

A simple analytic model of point-ion electrostatics has been previously proposed in which the magnitude of the net charge q_i on each atom in an ordered or random alloy depends linearly on the number N_i^(1) of unlike neighbors in its first coordination shell. Point charges extracted from recent large supercell (256-432 atom) local density approximation (LDA) calculations of Cu-Zn random alloys now enable an assessment of the physical validity and accuracy of the simple model. We find that this model accurately describes (i) the trends in q_i vs. N_i^(1), particularly for fcc alloys, (ii) the magnitudes of total electrostatic energies in random alloys, (iii) the relationships between constant-occupation-averaged charges and Coulomb shifts (i.e., the average over all sites occupied by either $A$ or $B$ atoms) in the random alloy, and (iv) the linear relation between the site charge q_i and the constant- charge-averaged Coulomb shift (i.e., the average over all sites with the same charge) for fcc alloys. However, for bcc alloys the fluctuations predicted by the model in the q_i vs. V_i relation exceed those found in the LDA supercell calculations. We find that (a) the fluctuations present in the model have a vanishing contribution to the electrostatic energy. (b) Generalizing the model to include a dependence of the charge on the atoms in the first three (two) shells in bcc (fcc) - rather than the first shell only - removes the fluctuations, in complete agreement with the LDA data. We also demonstrate an efficient way to extract charge transfer parameters of the generalized model from LDA calculations on small unit cells.Comment: 15 pages, ReVTeX galley format, 7 eps figures embedded using psfig, to be published in Phys. Rev.

A waveguide atom beamsplitter for laser-cooled neutral atoms

A laser-cooled neutral-atom beam from a low-velocity intense source is split into two beams while guided by a magnetic-field potential. We generate our multimode-beamsplitter potential with two current-carrying wires on a glass substrate combined with an external transverse bias field. The atoms bend around several curves over a $10$-cm distance. A maximum integrated flux of $1.5\cdot10^{5} \mathrm{atoms/s}$ is achieved with a current density of $5\cdot10^{4} \mathrm{Ampere/cm^{2}}$ in the 100-$\mathrm{\mu m}$ diameter wires. The initial beam can be split into two beams with a 50/50 splitting ratio

Muon-spin rotation studies of SmFeAsO_0.85 and NdFeAsO_0.85 superconductors

Measurements of the in-plane magnetic field penetration depth \lambda_{ab} in Fe-based superconductors with the nominal composition SmFeAsO_0.85 (T_c\simeq52K) and NdFeAsO_0.85 (T_c\simeq51K) were carried out by means of muon-spin-rotation. The absolute values of \lambda_{ab} at T=0 were found to be 189(5)nm and 195(5)nm for Sm and Nd substituted samples, respectively. The analysis of the magnetic penetration depth data within the Uemura classification scheme, which considers the correlation between the superconducting transition temperature T_c and the effective Fermi temperature T_F, reveal that both families of Fe-based superconductors (with and without fluorine) falls to the same class of unconventional superconductors.Comment: 5 pages, 4 figure

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output1, 2, 3, 4, 5, with important functional consequences4, 5. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs1, 2 or proteins5, 6 simultaneously, because genomic profiling methods3 could not be applied to single cells until very recently7, 8, 9, 10. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.National Institutes of Health (U.S.) (NIH Postdoctoral Fellowship (1F32HD075541-01))Charles H. Hood Foundation (Postdoctoral Fellowship)National Institutes of Health (U.S.) (NIH grant U54 AI057159)National Institutes of Health (U.S.) (NIH New Innovator Award (DP2 OD002230))National Institutes of Health (U.S.) (NIH CEGS Award (1P50HG006193-01))National Institutes of Health (U.S.) (NIH Pioneer Awards (5DP1OD003893-03))National Institutes of Health (U.S.) (NIH Pioneer Awards (DP1OD003958-01))Broad Institute of MIT and HarvardBroad Institute of MIT and Harvard (Klarman Cell Observatory

Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association

Since its outbreak in December 2019, COVID-19 has caused 100,5844,555 cases and 2,167,313 deaths as of Jan 27, 2021. Comparing our previous study of SARS-CoV-2 single nucleotide variants (SNVs) before June 2020, we found out that the SNV clustering had changed considerably since June 2020. Apart from that the group SNVs represented by two non-synonymous mutations A23403G (S: D614G) and C14408T (ORF1ab: P4715L) became dominant and carried by over 95% genomes, a few emerging groups of SNVs were recognized with sharply increased monthly occurrence ratios up to 70% in November 2020. Further investigation revealed that several SNVs were strongly associated with the mortality, but they presented distinct distribution in specific countries, e.g., Brazil, USA, Saudi Arabia, India, and Italy. SNVs including G25088T, T25A, G29861T and G29864A were adopted in a regularized logistic regression model to predict the mortality status in Brazil with the AUC of 0.84. Protein structure analysis showed that the emerging subgroups of non-synonymous SNVs and those mortality-related ones in Brazil were located on protein surface area. The clashes in protein structure introduced by these mutations might in turn affect virus pathogenesis through conformation changes, leading to the difference in transmission and virulence. Particularly, we found that SNVs tended to occur in intrinsic disordered regions (IDRs) of Spike (S) and ORF1ab, suggesting a critical role of SNVs in protein IDRs to determine protein folding and immune evasion

Cation- and vacancy-ordering in Li_xCoO_2

Using a combination of first-principles total energies, a cluster expansion technique, and Monte Carlo simulations, we have studied the Li/Co ordering in LiCoO_2 and Li-vacancy/Co ordering in CoO_2. We find: (i) A ground state search of the space of substitutional cation configurations yields the (layered) CuPt structure as the lowest-energy state in the octahedral system LiCoO_2 (and CoO_2), in agreement with the experimentally observed phase. (ii) Finite temperature calculations predict that the solid-state order- disorder transitions for LiCoO_2 and CoO_2 occur at temperatures (~5100 K and ~4400 K, respectively) much higher than melting, thus making these transitions experimentally inaccessible. (iii) The energy of the reaction E(LiCoO_2) - E(CoO_2) - E(Li) gives the average battery voltage V of a Li_xCoO_2/Li cell. Searching the space of configurations for large average voltages, we find that CuPt (a monolayer superlattice) has a high voltage (V=3.78 V), but that this could be increased by cation randomization (V=3.99 V), partial disordering (V=3.86 V), or by forming a 2-layer Li_2Co_2O_4 superlattice along (V=4.90 V).Comment: 12 Pages, RevTeX galley format, 5 figures embedded using epsf Phys. Rev. B (in press, 1998

Extracellular Hsp72 concentration relates to a minimum endogenous criteria during acute exercise-heat exposure

Extracellular heat-shock protein 72 (eHsp72) concentration increases during exercise-heat stress when conditions elicit physiological strain. Differences in severity of environmental and exercise stimuli have elicited varied response to stress. The present study aimed to quantify the extent of increased eHsp72 with increased exogenous heat stress, and determine related endogenous markers of strain in an exercise-heat model. Ten males cycled for 90 min at 50% O2peak in three conditions (TEMP, 20°C/63% RH; HOT, 30.2°C/51%RH; VHOT, 40.0°C/37%RH). Plasma was analysed for eHsp72 pre, immediately post and 24-h post each trial utilising a commercially available ELISA. Increased eHsp72 concentration was observed post VHOT trial (+172.4%) (P<0.05), but not TEMP (-1.9%) or HOT (+25.7%) conditions. eHsp72 returned to baseline values within 24hrs in all conditions. Changes were observed in rectal temperature (Trec), rate of Trec increase, area under the curve for Trec of 38.5°C and 39.0°C, duration Trec ≥ 38.5°C and ≥ 39.0°C, and change in muscle temperature, between VHOT, and TEMP and HOT, but not between TEMP and HOT. Each condition also elicited significantly increasing physiological strain, described by sweat rate, heart rate, physiological strain index, rating of perceived exertion and thermal sensation. Stepwise multiple regression reported rate of Trec increase and change in Trec to be predictors of increased eHsp72 concentration. Data suggests eHsp72 concentration increases once systemic temperature and sympathetic activity exceeds a minimum endogenous criteria elicited during VHOT conditions and is likely to be modulated by large, rapid changes in core temperature

Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family

Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined "fuzziness", often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD) is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-π interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- π contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-π hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-π model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-π contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs. © 2013 Song et al

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-