More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes

Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond who is present to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes

Assessing Correlated Truncation Errors in Modern Nucleon-Nucleon Potentials

We test the BUQEYE model of correlated effective field theory (EFT) truncation errors on Reinert, Krebs, and Epelbaum's semi-local momentum-space implementation of the chiral EFT ($\chi$EFT) expansion of the nucleon-nucleon (NN) potential. This Bayesian model hypothesizes that dimensionless coefficient functions extracted from the order-by-order corrections to NN observables can be treated as draws from a Gaussian process (GP). We combine a variety of graphical and statistical diagnostics to assess when predicted observables have a $\chi$EFT convergence pattern consistent with the hypothesized GP statistical model. Our conclusions are: First, the BUQEYE model is generally applicable to the potential investigated here, which enables statistically principled estimates of the impact of higher EFT orders on observables. Second, parameters defining the extracted coefficients such as the expansion parameter $Q$ must be well chosen for the coefficients to exhibit a regular convergence pattern -- a property we exploit to obtain posterior distributions for such quantities. Third, the assumption of GP stationarity across lab energy and scattering angle is not generally met; this necessitates adjustments in future work. We provide a workflow and interpretive guide for our analysis framework, and show what can be inferred about probability distributions for $Q$, the EFT breakdown scale $\Lambda_b$, the scale associated with soft physics in the $\chi$EFT potential $m_{\rm eff}$, and the GP hyperparameters. All our results can be reproduced using a publicly available Jupyter notebook, which can be straightforwardly modified to analyze other $\chi$EFT NN potentials.Comment: 29 pages, 33 figure

Robust and Deterministic Preparation of Bosonic Logical States in a Trapped Ion

Encoding logical qubits in bosonic modes provides a potentially hardware-efficient implementation of fault-tolerant quantum information processing. Recent advancements in trapped ions and superconducting microwave cavities have led to experimental realizations of high-quality bosonic states and demonstrations of error-corrected logical qubits encoded in bosonic modes. However, current protocols for preparing bosonic code words lack robustness to common noise sources and can be experimentally challenging to implement, limiting the quality and breadth of codes that have been realized to date. Here, we combine concepts of error suppression via robust control with quantum error correction encoding and experimentally demonstrate high-fidelity, deterministic preparation of highly non-classical target bosonic states in the mechanical motion of a trapped ion. Our approach implements numerically optimized dynamical modulation of laser-driven spin-motion interactions to generate the target state in a single step. The optimized control pulses are tailored towards experimental constraints and are designed to be robust against the dominant source of error. Using these protocols, we demonstrate logical fidelities for the Gottesman-Kitaev-Preskill (GKP) state as high as $\bar{\mathcal{F}}=0.940(8)$, achieve the first realization of a distance-3 binomial logical state with an average fidelity of $\mathcal{F}=0.807(7)$, and demonstrate a 12.91(5) dB squeezed vacuum state.Comment: 12 pages, 8 figure

THE STRUCTURE OF 3,5-DI-O-BENZOYL-1,2-DIDEOXY-1-PHENYL-BETA-D-RIBOFURANOSE, C25H22O5

Mr=402.4, orthorhombic, P212~2 l, a= 4-946 (1), b= 15.887 (2), c=26.555 (2)A, V= 2086.7 (5) A 3, Z = 4, D x = 1.28 gcm -a, Cu Ka, 2 = 1.5418/k, B = 6.868 cm -1, F(000) = 848, T= 293 K, final R =0.054 for 648 observed reflections. The molecule is propeller shaped. The benzoyl groups act as protecting groups and the phenyl group is a base substitute. The crystal structure does not involve any intermolecular stacking interactions between the phenyl groups. The molecules pack in typical herring-bone-like arrays. The sugar has a fl-D configuration with C(2')-endo-C(3')-exo pucker (2T3), pseudorotation angle P = 172 (2) °, degree of pucker r m = 39 (2) °

in breast cancer

PSMD9 expression predicts radiotherapy respons

Superconductivity at 36 K in beta-Fe1.01Se with the compression of the interlayer separation under pressure

In this letter, we report that the superconductivity transition temperature in beta-Fe1.01Se increases from 8.5 to 36.7 K under applied pressure of 8.9 GPa. It then decreases at higher pressure. A dramatic change in volume is observed at the same time Tc rises, due to a collapse of the separation between the Fe2Se2 layers. A clear transition to a linear resistivity normal state is seen on cooling at all pressures. No static magnetic ordering is observed for the whole p-T phase diagram. We also report that at higher pressure (starting around 7 GPa and completed at 38 GPa), Fe1.01Se transforms to a hexagonal NiAs-type structure and displays non-magnetic, insulating behavior. The inclusion of electron correlation in band structure caculations is necessary to describe this behavior, signifying that such correlations are important in this chemical system. Our results strongly support unconventional superconductivity in beta-Fe1.01Se.Comment: 17 pages, 4 figure

A Case Matched Gender Comparison Transcriptomic Screen Identifies eIF4E and eIF5 as Potential Prognostic and Tractable Biomarkers in Male Breast Cancer

Purpose: Breast cancer (BC) affects both genders, but is understudied in men. Although still rare, male BC is being diagnosed more frequently. Treatments are wholly informed by clinical studies conducted in women, based on assumptions that underlying biology is similar. Experimental design: A transcriptomic investigation of male and female BC was performed, confirming transcriptomic data in silico. Biomarkers were immunohistochemically assessed in 697 MBCs (n=477, training; n=220, validation set) and quantified in pre- and post-treatment samples from a male BC patient receiving Everolimus and PI3K/mTOR inhibitor. Results: Gender-specific gene expression patterns were identified. eIF transcripts were up-regulated in MBC. eIF4E and eIF5 were negatively prognostic for overall survival alone (Log rank; p=0.013; HR=1.77, 1.12-2.8 and p=0.035; HR=1.68, 1.03-2.74, respectively), or when co-expressed (p=0.01; HR=2.66, 1.26-5.63), confirmed in the validation set. This remained upon multivariate Cox regression analysis (eIF4E p=0.016; HR 2.38 (1.18-4.8), eIF5 p=0.022; HR 2.55 (1.14-5.7); co-expression p=0.001; HR=7.04 (2.22-22.26)). Marked reduction in eIF4E and eIF5 expression was seen post BEZ235/Everolimus, with extended survival. Conclusions: Translational initiation pathway inhibition could be of clinical utility in male BC patients overexpressing eIF4E and eIF5. With mTOR inhibitors which target this pathway now in the clinic, these biomarkers may represent new targets for therapeutic intervention, although further independent validation is required