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Results for “Systematics”
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Systematic electronic structure in the cuprate parent state from quantum many-body simulations
The quantitative description of correlated electron materials remains a modern computational challenge. We demonstrate a numerical strategy to simulate correlated materials at the fully ab initio level beyond the solution of effective low-energy models and apply it to gain a detailed microscopic understanding across a family of cuprate superconducting materials in their parent undoped states. We uncover microscopic trends in the electron correlations and reveal the link between the material composition and magnetic energy scales through a many-body picture of excitation processes involving the buffer layers. Our work illustrates a path toward a quantitative and reliable understanding of more complex states of correlated materials at the ab initio many-body level.
Systematic Analysis of Metabolic Bottlenecks in the Methylerythritol 4-Phosphate (MEP) Pathway of Zymomonas mobilis
Engineered microorganisms have the potential to convert renewable substrates into biofuels and valuable bioproducts, which offers an environmentally sustainable alternative to fossil-fuel-derived products. Isoprenoids are a diverse class of biologically derived compounds that have commercial applications as various commodity chemicals, including biofuels and biofuel precursor molecules.
Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation
Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, can reveal the co-occurrence of microbes, providing a glimpse into the network of associations in these communities. However, the inference of networks from 16S data involves numerous steps, each requiring specific tools and parameter choices. Moreover, the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and identify the steps that contribute substantially to the variance. We further determine the tools and parameters that generate robust co-occurrence networks and develop consensus network algorithms based on benchmarks with mock and synthetic data sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows these default tools and parameters and can help explore the outcome of these combinations of choices on the inferred networks. We envisage that this pipeline could be used for integrating multiple data sets and generating comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes.
Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase
ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.
Systematic Study of the Cathode Compositional Dependency of Cross-Talk Behavior in Li-Ion Battery
While LiNi x Mn y Co 1-x-y O 2 (NMC) is one of the most widely used cathode materials for lithium-ion batteries (LIBs), the composition of NMC is evolving to Ni-rich NMC to achieve higher lithium capacity that fulfills the constant demand for LIBs with ever-higher energy densities. The change in the composition of NMC affects electrochemical features and electrode cross-talk, which explains the performance change during cycling. Here in this study, we introduce various NMC materials (LiNi 0.5 Mn 0.3 Co 0.2 O 2 , LiNi 0.6 Mn 0.2 Co 0.2 O 2 and LiNi 0.8 Mn 0.1 Co 0.1 O 2 ) to reveal how the NMC composition affects electrode cross-talk. The study reveals that NMC composition strongly affects transition metal dissolution; dissolution of manganese linearly decreases as its stoichiometric ratio in NMC decreases, while dissolution of nickel is only prominent in LiNi 0.8 Mn 0.1 Co 0.1 O 2 . Aged electrolyte samples are characterized with high-performance liquid chromatography, and two electrolyte decomposition species, C 8 H 16 O 5 and C 9 H 18 O 5 , are identified across all samples.
The Efficacy and Safety of Mesalamine and Probiotics in Mild‐to‐Moderate Ulcerative Colitis: A Systematic Review and Meta‐Analysis
Objective . To evaluate the efficacy and safety of mesalamine in conjunction with probiotics for ulcerative colitis. Methods . Random controlled trials (RCTs) were searched in PubMed, EMBASE, Cochrane Library, China National Knowledge Infrastructure, Wanfang, and VIP (VIP Database for Chinese Technical Periodicals) from inception to October 2019. Methodological quality was assessed by the Cochrane Collaboration tool. The quality of evidence was rated by the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE). Data analysis was carried out in Review Manager 5.3. Results . A total of fifteen studies met the criteria for inclusion. Thirteen studies reported the clinical efficacy, three studies provided data on the clinical symptom scores, two trials reported disease activity index, four studies evaluated endoscopic score, and twelve studies reported adverse events. For ulcerative colitis (UC), mesalamine and probiotics had better clinical efficacy than mesalamine alone (≤8 weeks: RR = 1.12, 95% CI: 1.07–1.18, P < 0.0001; >8 weeks: RR = 1.25, 95% CI: 1.11–1.41, P = 0.0003). On the clinical symptom scores, disease activity index, and endoscopic score, UC patients receiving mesalamine and probiotics had significant difference than patients receiving mesalazine alone (MD = −2.02, 95% CI: −3.28 to −0.76, P = 0.002; MD = −1.20, 95% CI: −1.76 to −0.65, P < 0.001; and MD = −0.42, 95% CI: −0.61 to −0.23, P < 0.0001, respectively). There was no statistically significant difference in adverse events between the two groups (RR = 0.88, 95% CI: 0.54 to 1.43, P = 0.60). Conclusion . Our meta‐analysis results supported that mesalamine and probiotics were effective and safe in treating ulcerative colitis.
A Systematic Review and Meta-Analysis of Tai Chi Training in Cardiorespiratory Fitness of Elderly People
Objectives. The purpose of this study was to investigate the influence of Tai Chi on cardiorespiratory fitness (CRF) in elderly people using meta-analysis. Methods. This study used seven electronic databases and data retrieved from randomized controlled trials (RCTs) investigating the role of Tai Chi on CRF in the elderly. All these 24 RCTs were screened and selected from 7 literature databases. The Stata 11.2 software (StataCorp, USA) was used for the meta-analysis, subgroup analysis, and bias test, while the Cochrane Collaboration’s tool was used for the assessment of the risk of bias (RoB). 4 researchers independently participated in sample selection, data extraction, and RoB assessment. Results. Following the inclusion criteria, 24 eligible studies were included in our analysis. The meta-analysis indicated that Tai Chi practice significantly increased the maximum rate of oxygen consumption (VO2 max) (weighted mean difference (WMD) = 3.76, 95% CI: 1.25 to 6.26, P < 0.1 ), leading to an overall reduction in the heart rate (HR) (WMD = −1.84, 95% CI: −2.04 to −1.63, P ≤ 0.001 ) and an increase in the O2 pulse (WMD = 0.94, 95% CI: 0.60 to 1.28, P ≤ 0.001 ) in individuals who practiced Tai Chi regularly compared with those who did not. The subgroup analysis suggested that overall in those who practiced Tai Chi, males (WMD = 1.48, 95% CI: 0.85 to 2.12, P ≤ 0.001 ) had higher O2 pulse than females (WMD = 0.73, 95% CI: 0.33 to 1.12, P ≤ 0.001 ). The subgroup analysis also showed an increase in the vital capacity (VC) (WMD = 316.05, 95% CI: 239.74 to 392.35, P ≤ 0.001 ) in individuals practicing Tai Chi. When the samples were further stratified by Tai Chi practicing time, the subgroup analysis suggested that individuals practicing Tai Chi over a period of 24 weeks showed no significant difference in VC (WMD = 82.95, 95% CI: -98.34 to 264.23, P = 0.370 ), while those practicing Tai Chi over a period of 48 weeks showed a significant increase (WMD = 416.62, 95% CI: 280.68 to 552.56, P ≤ 0.001 ). Furthermore, the subgroup analysis demonstrated that the increase in VC is significantly correlated with the Tai Chi practicing time (WMD = 344.97, 95% CI: 227.88 to 442.06, P ≤ 0.001 ). Conclusion. Regular Tai Chi practice could improve the CRF in the elderly, as indicated by significant improvement in indicators including VO2max, O2pulse, VC, and HR. However, gender and practice time might influence the overall beneficial outcomes.
A systematic review of oncoplastic volume replacement breast surgery: oncological safety and cosmeti
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Systematic correction of the density functional theory spectra via a quantum Monte Carlo approach
Numerical outputs and driver scripts supporting auxiliary-boson corrected diffusion Monte Carlo (ABCDMC) benchmarks on second-row neutral atoms, cations, and dications, plus a C2 molecule active-space study. Includes NIST reference energies, ABCDMC timestep extrapolation summaries, orbital generation inputs, singles-only CASCI driver scripts, an O-atom basis-set convergence study, and the PyQMC boson code snapshot used for the calculations.
Speeding genomic island discovery through systematic design of reference database composition
Background Genomic islands (GIs) are mobile genetic elements that integrate site-specifically into bacterial chromosomes, bearing genes that affect phenotypes such as pathogenicity and metabolism. GIs typically occur sporadically among related bacterial strains, enabling comparative genomic approaches to GI identification. For a candidate GI in a query genome, the number of reference genomes with a precise deletion of the GI serves as a support value for the GI. Our comparative software for GI identification was slowed by our original use of large reference genome databases (DBs). Here we explore smaller species-focused DBs. Results With increasing DB size, recovery of our reliable prophage GI calls reached a plateau, while recovery of less reliable GI calls (FPs) increased rapidly as DB sizes exceeded ~500 genomes; i.e., overlarge DBs can increase FP rates. Paradoxically, relative to prophages, FPs were both more frequently supported only by genomes outside the species and more frequently supported only by genomes inside the species; this may be due to their generally lower support values. Setting a DB size limit for our SMA ll R anked T ailored (SMART) DB design speeded runtime ~65-fold. Strictly intra-species DBs would tend to lower yields of prophages for small species (with few genomes available); simulations with large species showed that this could be partially overcome by reaching outside the species to closely related taxa, without an FP burden. Employing such taxonomic outreach in DB design generated redundancy in the DB set; as few as 2984 DBs were needed to cover all 47894 prokaryotic species. Conclusions Runtime decreased dramatically with SMART DB design, with only minor losses of prophages. We also describe potential utility in other comparative genomics projects.
Metadata for a systematic description of signal data
This chapter aims to provide a comprehensive overview of metadata types that may be useful during system design, optimization, and automation. Metadata are grouped into three main categories: (a) metadata describing signal generation, (b) metadata describing signal quality, and (c) contextual information in the form of annotations. Each of these categories is introduced and explained in three separate sections. Importantly, this chapter mainly answers what is considered metadata. To a lesser degree, recommendations are made regarding the selection of metadata for long-term storage. Chapter 4 will explain where and how to store metadata. Chapters 5 and 6 explain how to collect certain metadata through dedicated sensor validation tests (Chapter 5) or algorithmic analysis (Chapter 6).
Assessing Systematic Errors in Simulation Studies of Mu2e
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Exploiting Commonly-Reported Age-Hardening Data and Discovering Systematics Across Metallic Alloys and Alloy Systems to Identify Corrosion’s Most Influential Factors
This work explored ways to data mine legacy literature and predict solid-solid precipitation in support of simpler assessment of corrosion propensity in metallic alloys. Of interest was locating the peak age watershed (maximum hardness or strength), beyond which lies the regime termed “overaging.” A diligent search of literature and reference books, discussions with SMEs, and application of various algorithms showed that none of the premises going in held up to scrutiny.
IC W20_phadiagurox Highlight: Systematics of the ambient melting points of stoichiometric uranium oxides [Slides]
Abstract not provided.
Systematic Study of Potential False Azimuthal Asymmetries in SpinQuest
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Systematic Enterprise Risk Management by Integrating the RISMC Toolkit and Cost-Benefit Analysis (Final Report)
The goal of this research is to theorize and quantify the relationships between safety and the financial performance of nuclear power plants (NPPs). The Socio-Technical Risk Analysis (SoTeRiA) theoretical framework, which connects the social aspects (e.g., safety culture) and structural features (e.g., safety practices) of an organization with organizational safety and financial risks, is used to theorize the direct and indirect relationships between safety and the financial performance of NPPs. An Integrated Enterprise Risk Management (I-ERM) methodological framework is developed to operationalize SoTeRiA to quantify NPP safety and financial performance in a unified platform where their underlying physical degradation mechanisms, coupled with maintenance performance (considering human and organizational factors), are explicitly incorporated to depict the interconnections and dependencies between safety and financial performance. In this study, NPP safety refers to both occupational safety and system safety (estimated from Probabilistic Risk Assessment, PRA), and financial performance refers to the monetary values associated with NPP operation and maintenance (O&M) strategies. This report covers a case study demonstrating the feasibility of the I-ERM methodological framework. More detailed development of one of the I-ERM modules, i.e., Probabilistic Physics-of-Failure (PPoF) analysis, and its connection with other I-ERM modules is demonstrated in a second case study. The outcome of this research will help NPP decision-makers create cost-saving maintenance strategies while maintaining safety by providing cost- and risk-informed recommendations regarding maintenance work processes and operational strategies.