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At least 73 records · Page 4

Reproducibility in materials informatics: lessons from ‘A general-purpose machine learning framework for predicting properties of inorganic materials’

The integration of machine learning techniques in materials discovery has become prominent in materials science research and has been accompanied by an increasing trend towards open data and open-source tools to propel the field. Despite the increasing usefulness and capabilities of these tools, developers neglecting to follow reproducible practices presents a significant barrier for other researchers looking to use or build upon their work. In this study, we investigate the challenges encountered while attempting to reproduce a section of the results presented in “A general-purpose machine learning framework for predicting properties of inorganic materials.” Our analysis identifies four major categories of challenges: (1) reporting software dependencies, (2) recording and sharing version logs, (3) sequential code organization, and (4) clarifying code references within the manuscript. The result is a proposed set of tangible action items for those aiming to make material informatics tools accessible to, and useful for the community.

36 MATERIALS SCIENCE↗

Processing of Human Reduction Mammoplasty and Mastectomy Tissues for Cell Culture

Experimental examination of normal human mammary epithelial cell (HMEC) behavior, and how normal cells acquire abnormal properties, can be facilitated by in vitro culture systems that more accurately model in vivo biology. The use of human derived material for studying cellular differentiation, aging, senescence, and immortalization is particularly advantageous given the many significant molecular differences in these properties between human and commonly utilized rodent cells1-2. Mammary cells present a convenient model system because large quantities of normal and abnormal tissues are available due to the frequency of reduction mammoplasty and mastectomy surgeries. The mammary gland consists of a complex admixture of many distinct cell types, e.g., epithelial, adipose, mesenchymal, endothelial. The epithelial cells are responsible for the differentiated mammary function of lactation, and are also the origin of the vast majority of human breast cancers. We have developed methods to process mammary gland surgical discard tissues into pure epithelial components as well as mesenchymal cells3 . The processed material can be stored frozen indefinitely, or initiated into primary culture. Surgical discard material is transported to the laboratory and manually dissected to enrich for epithelial containing tissue. Subsequent digestion of the dissected tissue using collagenase and hyaluronidase strips stromal material from the epithelia at the basement membrane. The resulting small pieces of the epithelial tree (organoids) can be separated from the digested stroma by sequential filtration on membranes of fixed pore size. Depending upon pore size, fractions can be obtained consisting of larger ductal/alveolar pieces, smaller alveolar clusters, or stromal cells. We have observed superior growth when cultures are initiated as organoids rather than as dissociated single cells. Placement of organoids in culture using lowstress inducing media supports long-term growth of normal HMEC with markers of multiple lineage types (myoepithelial, luminal, progenitor)4-5 . Sufficient numbers of cells can be obtained from one individual's tissue to allow extensive experimental examination using standardized cell batches, as well as interrogation using high throughput modalities. Cultured HMEC have been employed in a wide variety of studies examining the normal processes governing growth, differentiation, aging, and senescence, and how these normal processes are altered during immortal and malignant transformation4-15,16 . The effects of growth in the presence of extracellular matrix material, other cell types, and/or 3D culture can be compared with growth on plastic5,15. Cultured HMEC, starting with normal cells, provide an experimentally tractable system to examine factors that may propel or prevent human aging and carcinogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Quantum corrections to temperature dependent electrical conductivity of ZnO thin films degenerately doped with Si

ZnO thin films degenerately doped with Si (Si{sub x}Zn{sub 1−x}O) in the concentrations range of ∼0.5% to 5.8% were grown by sequential pulsed laser deposition on sapphire substrates at 400 °C. The temperature dependent resistivity measurements in the range from 300 to 4.2 K revealed negative temperature coefficient of resistivity (TCR) for the 0.5%, 3.8%, and 5.8% doped Si{sub x}Zn{sub 1−x}O films in the entire temperature range. On the contrary, the Si{sub x}Zn{sub 1−x}O films with Si concentrations of 1.0%, 1.7%, and 2.0% showed a transition from negative to positive TCR with increasing temperature. These observations were explained using weak localization based quantum corrections to conductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Baseplate Temperature–Dependent Vertical Composition Gradient in Pseudo–Bilayer Films for Printing Non–Fullerene Organic Solar Cells

Numerous previous reports on the sequential deposition (SD) technique have demonstrated that this approach can achieve a p–i–n active layer architecture with an ideal vertical composition gradient, which is one of the critical factors that can influence the physical processes that determine the photovoltaic performance of organic solar cells. Herein, a commonly used photovoltaic system comprised of PM6 as a donor and Y6 as an acceptor is investigated with respect to sequential blade–processing deposition to comprehensively explore the morphology characteristics as a function of baseplate temperature. A systematic study of the temperature–dependent blend morphology elucidates the SD–processed configuration merits and device physics behind temperature–controlled degree of vertical composition gradient, and constructs the temperature–microstructure–property relationship for the corresponding photovoltaic parameters. The result shows, as the temperature increases, the morphology of the active layer has undergone a distinct evolution from the pseudo–bulk heterojunction to a pseudo–planar heterojunction and then to a pseudo–planar bilayer, leading to a non–monotonic correlation between baseplate temperature and device performance. Further, this investigation not only reveals the importance of precisely controlling baseplate temperature for gaining vertical morphology control, but also provides a path toward rational optimization of device performance in the lab–to–fab transition.

14 SOLAR ENERGY↗

Effects of secondary void-initiating particles on the steady-state crack growth resistance of high-strength steel

In this investigation, we focus on the dependence of stable crack growth resistance, as measured by the short-rod fracture toughness test, on secondary void-initiating particles such as AlN and Ti-based grain-refining precipitates in a variety of high-strength steels with tempered martensitic microstructures. The model developed by Ritchie and Thompson is modified to illustrate the significant amounts of toughening that can result from the refinement of secondary particles. Analysis of the data suggests that material strength is a predominant factor in increasing the short-rod fracture toughness relative to linear-elastic measures of initiation fracture toughness, but the extent of toughening is limited by the size and number density of secondary particles in the microstructure. The variation in estimates of secondary microvoid initiation and growth strains with precipitate size reinforce the notion that primary fracture at non-metallic inclusions and secondary fracture at smaller particles occur as sequential processes with a degree of concurrence that is dependent on the state of precipitation in both particle dispersions. Toughening in this connection is maximized by increases in microvoid growth strain that result from decreases in the size and areal number density of secondary void-initiating particles. Finally, the occurrence of transient instabilities during crack extension in short-rod specimens is explained with a phenomenological model that relates crack growth stability to natural variations in the dispersion of secondary void-initiating particles in the microstructure.

42 ENGINEERING↗

Combined Effects of Three High-Energy Charged Particle Beams Important for Space Flight on Brain, Behavioral and Cognitive Endpoints in B6D2F1 Female and Male Mice

The radiation environment in deep space includes the galactic cosmic radiation with different proportions of all naturally occurring ions from protons to uranium. Most experimental animal studies for assessing the biological effects of charged particles have involved acute dose delivery for single ions and/or fractionated exposure protocols. Here, we assessed the behavioral and cognitive performance of female and male C 57 BL/6J × DBA2/J F1 (B6D2F1) mice 2 months following rapidly delivered, sequential irradiation with protons (1 GeV, 60%), 16 O (250 MeV/n, 20%), and 28 Si (263 MeV/n, 20%) at 0, 25, 50, or 200 cGy at 4-6 months of age. Cortical BDNF, CD68, and MAP-2 levels were analyzed 3 months after irradiation or sham irradiation. During the dark period, male mice irradiated with 50 cGy showed higher activity levels in the home cage than sham-irradiated mice. Mice irradiated with 50 cGy also showed increased depressive behavior in the forced swim test. When cognitive performance was assessed, sham-irradiated mice of both sexes and mice irradiated with 25 cGy showed normal responses to object recognition and novel object exploration. However, object recognition was impaired in female and male mice irradiated with 50 or 200 cGy. For cortical levels of the neurotrophic factor BDNF and the marker of microglial activation CD68, there were sex × radiation interactions. In females, but not males, there were increased CD68 levels following irradiation. In males, but not females, there were reduced BDNF levels following irradiation. A significant positive correlation between BDNF and CD68 levels was observed, suggesting a role for activated microglia in the alterations in BDNF levels. Finally, sequential beam irradiation impacted the diversity and composition of the gut microbiome. These included dose-dependent impacts and alterations to the relative abundance of several gut genera, such as Butyricicoccus and Lachnospiraceae . Thus, exposure to rapidly delivered sequential proton, 16 O ion, and 28 Si ion irradiation significantly affects behavioral and cognitive performance, cortical levels of CD68 and BDNF in a sex-dependent fashion, and the gut microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

Metabolic activation of hepatotoxic drug (benzbromarone) induced mitochondrial membrane permeability transition

The risk of drug-induced liver injury (DILI) is of great concern to the pharmaceutical industry. It is well-known that metabolic activation of drugs to form toxic metabolites (TMs) is strongly associated with DILI onset. Drug-induced mitochondrial dysfunction is also strongly associated with increased risk of DILI. However, it is difficult to determine the target of TMs associated with exacerbation of DILI because of difficulties in identifying and purifying TMs. In this study, we propose a sequential in vitro assay system to assess TM formation and their ability to induce mitochondrial permeability transition (MPT) in a one-pot process. In this assay system, freshly-isolated rat liver mitochondria were incubated with reaction solutions of 44 test drugs preincubated with liver microsomes in the presence or absence of NADPH; then, NADPH-dependent MPT pore opening was assessed as mitochondrial swelling. In this assay system, several hepatotoxic drugs, including benzbromarone (BBR), significantly induced MPT in a NADPH-dependent manner. We investigated the rationality of using BBR as a model drug, since it showed the most prominent MPT in our assay system. Both the production of a candidate toxic metabolite of BBR (1′,6-(OH){sub 2} BBR) and NADPH-dependent MPT were inhibited by several cytochrome P450 (CYP) inhibitors (clotrimazole and SKF-525A, 100 μM). In summary, this assay system can be used to evaluate comprehensive metabolite-dependent MPT without identification or purification of metabolites. - Highlights: • We constructed a sequential assay system for toxic metabolite induced MPT in one pot. • 14 drugs (e.g. benzbromarone (BBR)) induced toxic metabolite dependent MPT. • Both the production of toxic metabolite and MPT could be inhibited by CYP inhibitors. • This system could evaluate the comprehensive MPT without purification of metabolites.

60 APPLIED LIFE SCIENCES↗

Confinement of excited states in two-dimensional, in-plane, quantum heterostructures

Two-dimensional (2D) semiconductors are promising candidates for optoelectronic application and quantum information processes due to their inherent out-of-plane 2D confinement. In addition, they offer the possibility of achieving low-dimensional in-plane exciton confinement, similar to zero-dimensional quantum dots, with intriguing optical and electronic properties via strain or composition engineering. However, realizing such laterally confined 2D monolayers and systematically controlling size-dependent optical properties remain significant challenges. Here, we report the observation of lateral confinement of excitons in epitaxially grown in-plane MoSe 2 quantum dots (~15-60 nm wide) inside a continuous matrix of WSe 2 monolayer film via a sequential epitaxial growth process. Various optical spectroscopy techniques reveal the size-dependent exciton confinement in the MoSe 2 monolayer quantum dots with exciton blue shift (12-40 meV) at a low temperature as compared to continuous monolayer MoSe 2 . Finally, single-photon emission (g 2 (0) ~ 0.4) was also observed from the smallest dots at 1.6 K. Our study opens the door to compositionally engineered, tunable, in-plane quantum light sources in 2D semiconductors.

42 ENGINEERING↗

Probing the neutron-proton asymmetry dependence of the nuclear source temperature with light charged particles

The dependence of the nuclear temperature on the source neutron-proton (N/Z) asymmetry was experimentally investigated with the light charged particles (LCPs) generated from thirteen reaction systems with different N/Z asymmetries, 64 Zn on 112 Sn and 70 Zn, 64 Ni on 112,124 Sn, 58,64 Ni, 197 Au, 232 Th at 40 MeV/u. A rather weak N/Z asymmetry dependence of the source temperature was qualitatively inferred from the extracted N/Z asymmetry dependence of the apparent temperature and that of the relative temperature change by the sequential decay effects with the help of the theoretical simulations. Comparing the present result with those from our previous work and other available experimental results, a weak N/Z asymmetry dependence of nuclear temperature is commonly observed in different independent experiments and with different thermometers, except for the result reported by McIntosh et al. [Phys. Lett. B 719, 337 (2013)]. Here, the origin of the difference between the conclusion of the former group and that of McIntosh et al. was addressed, using statistical multifragmentation model (SMM) simulations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A new augmentation based algorithm for extracting maximal chordal subgraphs

If every cycle of a graph is chordal length greater than three then it contains an edge between non-adjacent vertices. Chordal graphs are of interest both theoretically, since they admit polynomial time solutions to a range of NP-hard graph problems, and practically, since they arise in many applications including sparse linear algebra, computer vision, and computational biology. A maximal chordal subgraph is a chordal subgraph that is not a proper subgraph of any other chordal subgraph. Existing algorithms for computing maximal chordal subgraphs depend on dynamically ordering the vertices, which is an inherently sequential process and therefore limits the algorithms’ parallelizability. In our paper we explore techniques to develop a scalable parallel algorithm for extracting a maximal chordal subgraph. We demonstrate that an earlier attempt at developing a parallel algorithm may induce a non-optimal vertex ordering and is therefore not guaranteed to terminate with a maximal chordal subgraph. We then give a new algorithm that first computes and then repeatedly augments a spanning chordal subgraph. After proving that the algorithm terminates with a maximal chordal subgraph, we then demonstrate that this algorithm is more amenable to parallelization and that the parallel version also terminates with a maximal chordal subgraph. That said, the complexity of the new algorithm is higher than that of the previous parallel algorithm, although the earlier algorithm computes a chordal subgraph which is not guaranteed to be maximal. Finally, we experimented with our augmentation-based algorithm on both synthetic and real-world graphs. We provide scalability results and also explore the effect of different choices for the initial spanning chordal subgraph on both the running time and on the number of edges in the maximal chordal subgraph.

97 MATHEMATICS AND COMPUTING↗

Hydrogen migration in inner-shell ionized halogenated cyclic hydrocarbons

Abstract We have studied the fragmentation of the brominated cyclic hydrocarbons bromocyclo-propane, bromocyclo-butane, and bromocyclo-pentane upon Br(3 d ) and C(1 s ) inner-shell ionization using coincidence ion momentum imaging. We observe a substantial yield of CH 3 + fragments, whose formation requires intramolecular hydrogen (or proton) migration, that increases with molecular size, which contrasts with prior observations of hydrogen migration in linear hydrocarbon molecules. Furthermore, by inspecting the fragment ion momentum correlations of three-body fragmentation channels, we conclude that CH x + fragments (with x = 0, …, 3) with an increasing number of hydrogens are more likely to be produced via sequential fragmentation pathways. Overall trends in the molecular-size-dependence of the experimentally observed kinetic energy releases and fragment kinetic energies are explained with the help of classical Coulomb explosion simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-mobility capacitively-induced two-dimensional electrons in a lateral superlattice potential

In the presence of a lateral periodic potential modulation, two-dimensional electrons may exhibit interesting phenomena, such as a graphene-like energy-momentum dispersion, Bloch oscillations, or the Hofstadter butterfly band structure. To create a sufficiently strong potential modulation using conventional semiconductor heterostructures, aggressive device processing is often required, unfortunately resulting in strong disorder that masks the sought-after effects. Here, we report a novel fabrication process flow for imposing a strong lateral potential modulation onto a capacitively induced two-dimensional electron system, while preserving the host material quality. Using this process flow, the electron density in a patterned Si/SiGe heterostructure can be tuned over a wide range, from 4.4 × 10 10 cm –2 to 1.8 × 10 11 cm –2 , with a peak mobility of 6.4 × 10 5 cm 2 /V·s. The wide density tunability and high electron mobility allow us to observe sequential emergence of commensurability oscillations as the density, the mobility, and in turn the mean free path, increase. Magnetic-field-periodic quantum oscillations associated with various closed orbits also emerge sequentially with increasing density. We show that, from the density dependence of the quantum oscillations, one can directly extract the steepness of the imposed superlattice potential. Lastly, this result is then compared to a conventional lateral superlattice model potential.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Uranium interaction with soil minerals in the presence of co-contaminants: Case Study- subsurface sediments at or below the water table

Uranium (U) contaminated subsurface systems are common on a global scale mainly because of its essential role in the production of plutonium for nuclear weapons and other nuclear energy and research activities. Studying the behavior and fate of U in these systems is challenging because of heterogeneities of different types (i.e., physical, chemical and mineralogical) and a complex network of often time-dependent hydrological, biological and chemical reactions and processes that occur sequentially or simultaneously, affecting and/or controlling U mobility. A U contaminated site, i.e., the Integrated Field Research Challenge site in Rifle, CO, USA (a former U mill site) is the focus of this discussion. The overall objectives of this chapter are to 1) provide an overview of the contamination levels (U and other co-contaminants) at this field site; 2) review and discuss different aspects of mineral-U contaminant interactions in reduced and oxidized environments, and in the presence of co-contaminants; 3) present results from a systematic macroscopic, microscopic, and spectroscopic study as an example of the current research efforts and the state-of-knowledge in this important research area; and 4) offer insightful conclusive remarks and future research needs about reactions and processes that control U and other contaminants’ fate and behavior under hydraulically saturated conditions. The implications and applications presented in this chapter are valid for U contaminated sites across the world.

As, V, Se contamination↗

Photochemical Aging Alters Secondary Organic Aerosol Partitioning Behavior

Organic aerosol is the largest fraction of the atmospheric non-refractory aerosol mass and has a significant impact on climate, visibility, and human health. A significant portion of organic aerosol is secondary organic aerosol (SOA), which forms when volatile organic compounds (VOCs) are oxidized and the reaction products partition to the particle phase. SOA formation and aging have been described using semi-volatile partitioning theory, and a typical assumption invoked is that gas-particle partitioning rapidly reaches equilibrium. However, several studies have called into question whether traditional equilibrium assumptions are valid, either due to particle-phase diffusion limitations, particle-phase reactions, or liquid/liquid phase separation and immiscibility of organic phases. Here, we investigate the ability of partitioning theory to describe laboratory SOA formation experiments using SOA mass and yield as the evaluation metric. We conduct two types of experiments; co-condensation experiments in which isoprene and a-pinene are simultaneously oxidized to form SOA, and sequential condensation experiments in which fresh isoprene SOA is exposed to aged, pre-existing isoprene- or a-pinene-derived SOA particles. In the co-condensation experiments, partitioning theory successfully predicted the time-dependent SOA concentrations without invoking diffusion limitations or organic phase separation. However, in the sequential condensation experiments, yield analysis showed that fresh isoprene SOA did not partition into either the aged a-pinene or aged isoprene SOA particles over the 4 hour experimental timescale, even at relative humidity as high as 85%. This study shows that common assumptions regarding SOA gas-particle partitioning are accurate for fresh SOA, but that these assumptions break down after SOA has been photochemically aged for modest amounts of time (~1 day). These results have important consequences for modeling SOA formation and may help to resolve some seemingly divergent conclusions regarding diffusion limitations that exist in the literature.

Secondary Organic Aerosol (SOA), gas/particle part↗

Anomaly Detection in Sequential Health Care Data using Higher-Order Network Representation

The ever-increasing use of information technology (IT) in health care presents new challenges to patient care. Information errors arising from the use of Health IT and their implications on care delivery and patient outcomes have been widely reported. Information errors can lead to changes in clinical decisions, care processes, and care outcomes, among others. An altered care process, for example, could interrupt the sequence of care, which could lead to changes in care decisions and/or changes in care outcomes. We define interruptions in the care process as anomalies in the care sequence. In this paper, we present a new approach based on the higher-order network (HON) representation to detect anomalies in sequential health care data using electronic health records. The results show that there are higher-order dependencies in health care data; and that the use of HON representation is more effective than the first-order network representation for detecting anomalies in sequential health care data.

Niu, Haoran↗

Coulomb explosion imaging of CH 3 I and CH 2 ClI photodissociation dynamics

The photodissociation dynamics of CH 3 I and CH 2 ClI at 272 nm were investigated by time-resolved Coulomb explosion imaging, with an intense non-resonant 815 nm probe pulse. Fragment ion momenta over a wide m/z range were recorded simultaneously by coupling a velocity map imaging spectrometer with a pixel imaging mass spectrometry camera. For both molecules, delay-dependent pump-probe features were assigned to ultraviolet-induced carbon-iodine bond cleavage followed by Coulomb explosion. Multi-mass imaging also allowed the sequential cleavage of both carbon-halogen bonds in CH 2 ClI to be investigated. Furthermore, delay-dependent relative fragment momenta of a pair of ions were directly determined using recoil-frame covariance analysis. These results are complementary to conventional velocity map imaging experiments and demonstrate the application of time-resolved Coulomb explosion imaging to photoinduced real-time molecular motion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Glucose assimilation rate determines the partition of flux at pyruvate between lactic acid and ethanol in Saccharomyces cerevisiae

Engineered Saccharomyces cerevisiae expressing a lactic acid dehydrogenase can metab- olize pyruvate into lactic acid. However, three pyruvate decarboxylase (PDC) isozymes drive most carbon flux toward ethanol rather than lactic acid. Deletion of endoge- nous PDCs will eliminate ethanol production, but the resulting strain suffers from C 2 auxotrophy and struggles to complete a fermentation. Engineered yeast assimilating xylose or cellobiose produce lactic acid rather than ethanol as a major product with- out the deletion of any PDC genes. We report here that sugar flux, but not sensing, contributes to the partition of flux at the pyruvate branch point in S. cerevisiae express- ing the Rhizopus oryzae lactic acid dehydrogenase (LdhA). While the membrane glucose sensors Snf3 and Rgt2 did not play any direct role in the option of predominant product, the sugar assimilation rate was strongly correlated to the partition of flux at pyruvate: fast sugar assimilation favors ethanol production while slow sugar assimilation favors lactic acid. Applying this knowledge, we created an engineered yeast capable of simultaneously converting glucose and xylose into lactic acid, increasing lactic acid production to approximately 17 g L –1 from the 12 g L –1 observed during sequential consumption of sugars. This work elucidates the carbon source-dependent effects on product selection in engineered yeast.

59 BASIC BIOLOGICAL SCIENCES↗

A holistic platform for accelerating sorbent-based carbon capture

Abstract Reducing carbon dioxide (CO 2 ) emissions urgently requires the large-scale deployment of carbon-capture technologies. These technologies must separate CO 2 from various sources and deliver it to different sinks 1,2 . The quest for optimal solutions for specific source–sink pairs is a complex, multi-objective challenge involving multiple stakeholders and depends on social, economic and regional contexts. Currently, research follows a sequential approach: chemists focus on materials design 3 and engineers on optimizing processes 4,5 , which are then operated at a scale that impacts the economy and the environment. Assessing these impacts, such as the greenhouse gas emissions over the plant’s lifetime, is typically one of the final steps 6 . Here we introduce the PrISMa (Process-Informed design of tailor-made Sorbent Materials) platform, which integrates materials, process design, techno-economics and life-cycle assessment. We compare more than 60 case studies capturing CO 2 from various sources in 5 global regions using different technologies. The platform simultaneously informs various stakeholders about the cost-effectiveness of technologies, process configurations and locations, reveals the molecular characteristics of the top-performing sorbents, and provides insights on environmental impacts, co-benefits and trade-offs. By uniting stakeholders at an early research stage, PrISMa accelerates carbon-capture technology development during this critical period as we aim for a net-zero world.

Science & Technology - Other Topics↗