A method to computationally screen for tunable properties of crystalline alloys

Conventionally, high-throughput computational materials searches start from an input set of bulk compounds extracted from material databases, and this set is screened for candidate materials for specific applications. In contrast, many functional materials, and especially semiconductors, are heavily engineered alloys or solid solutions of multiple compounds rather than a single bulk compound. To improve our ability to design functional materials, in this work we propose a framework and open-source code to automatically construct possible "alloy pairs" and "alloy systems" and detect "alloy members" from a set of existing, experimental or calculated ordered compounds, without requiring any additional metadata beyond their crystal structure. We provide analysis tools to estimate stability across each alloy. As a demonstration, we apply this framework to all inorganic materials in the Materials Project database to create a new database of over 600,000 unique alloy pair entries that can then be used in materials discovery studies to search for materials with tunable properties. This new database has been incorporated into the Materials Project website and linked with corresponding material identifiers for any user to query and explore. Using an example of screening for p-type transparent conducting materials, we demonstrate how using this methodology reveals candidate material systems that might otherwise have been excluded by a traditional screening. This work lays a foundation from which materials databases can go beyond stoichiometric compounds, and approach a more realistic description of compositionally tunable materials

Air Pollution and Odor in Communities Near Industrial Swine Operations

BackgroundOdors can affect health and quality of life. Industrialized animal agriculture creates odorant compounds that are components of a mixture of agents that could trigger symptoms reported by neighbors of livestock operations.ObjectiveWe quantified swine odor episodes reported by neighbors and the relationships of these episodes with environmental measurements.MethodsBetween September 2003 and September 2005, 101 nonsmoking volunteers living within 1.5 mi of industrial swine operations in 16 neighborhoods in eastern North Carolina completed twice-daily odor diaries for approximately 2 weeks. Meteorological conditions, hydrogen sulfide, and particulate matter ≤ 10 μm in aerodynamic diameter (PM10) were monitored in each neighborhood. We used mixed models to partition odor variance within and between people and between neighborhoods, and to quantify relationships between environmental factors and odor.ResultsParticipants reported 1,655 episodes of swine odor. In nine neighborhoods, odor was reported on more than half of study-days. Odor ratings were related to temperature, PM10, and semivolatile PM10 in standard but not mixed models. In mixed models, odor increased 0.15 ± 0.05 units (mean ± SE) for a 1-ppb increase in H2S, and 0.45 ± 0.14 units for a 10-μg/m3 increase in PM10 at wind speeds > 6.75 miles per hour. The odds of reporting a change in daily activities due to odor increased 62% for each unit increase in average odor during the prior 12 hr (t-value = 7.17).ConclusionsThis study indicates that malodor from swine operations is commonly present in these communities and that the odors reported by neighbors are related to objective environmental measurements and interruption of activities of daily life

Designing transparent conductors using forbidden optical transitions

Many semiconductors present weak or forbidden transitions at their fundamental band gaps, inducing a widened region of transparency. This occurs in high-performing n-type transparent conductors (TCs) such as Sn-doped In2O3 (ITO), however thus far the presence of forbidden transitions has been neglected in searches for new p-type TCs. To address this, we first compute high-throughput absorption spectra across ~18,000 semiconductors, showing that over half exhibit forbidden or weak optical transitions at their band edges. Next, we demonstrate that compounds with highly localized band edge states are more likely to present forbidden transitions. Lastly, we search this set for p-type and n-type TCs with forbidden or weak transitions. Defect calculations yield unexplored TC candidates such as ambipolar BeSiP2, Zr2SN2 and KSe, p-type BAs, Au2S, and AuCl, and n-type Ba2InGaO5, GaSbO4, and KSbO3, among others. We share our data set via the MPContribs platform, and we recommend that future screenings for optical properties use metrics representative of absorption features rather than band gap alone

Podocytes Produce and Secrete Functional Complement C3 and Complement Factor H

Podocytes are an important part of the glomerular filtration barrier and the key player in the development of proteinuria, which is an early feature of complement mediated renal diseases. Complement factors are mainly liver-born and present in circulation. Nevertheless, there is a growing body of evidence for additional sites of complement protein synthesis, including various cell types in the kidney. We hypothesized that podocytes are able to produce complement components and contribute to the local balance of complement activation and regulation. To investigate the relevant balance between inhibiting and activating sides, our studies focused on complement factor H (CFH), an important complement regulator, and on C3, the early key component for complement activation. We characterized human cultured podocytes for the expression and secretion of activating and regulating complement factors, and analyzed the secretion pathway and functional activity. We studied glomerular CFH and C3 expression in puromycin aminonucleoside (PAN) -treated rats, a model for proteinuria, and the physiological mRNA-expression of both factors in murine kidneys. We found, that C3 and CFH were expressed in cultured podocytes and expression levels differed from those in cultivated glomerular endothelial cells. The process of secretion in podocytes was stimulated with interferon gamma and located in the Golgi apparatus. Cultured podocytes could initiate the complement cascade by the splitting of C3, which can be shown by the generation of C3a, a functional C3 split product. C3 contributed to external complement activation. Podocyte-secreted CFH, in conjunction with factor I, was able to split C3b. Podocytes derived from a patient with a CFH mutation displayed impaired cell surface complement regulation. CFH and C3 were synthesized in podocytes of healthy C57Bl/6-mice and were upregulated in podocytes of PAN treated rats. These data show that podocytes produce functionally active complement components, and could therefore influence the local glomerular complement activation and regulation. This modulating effect should therefore be considered in all diseases where glomerular complement activation occurs. Furthermore, our data indicate a potential novel role of podocytes in the innate immune system

Modelling distributions of Aedes aegypti and Aedes albopictus using climate, host density and interspecies competition.

Florida faces the challenge of repeated introduction and autochthonous transmission of arboviruses transmitted by Aedes aegypti and Aedes albopictus. Empirically-based predictive models of the spatial distribution of these species would aid surveillance and vector control efforts. To predict the occurrence and abundance of these species, we fit a mixed-effects zero-inflated negative binomial regression to a mosquito surveillance dataset with records from more than 200,000 trap days, representative of 53% of the land area and ranging from 2004 to 2018 in Florida. We found an asymmetrical competitive interaction between adult populations of Aedes aegypti and Aedes albopictus for the sampled sites. Wind speed was negatively associated with the occurrence and abundance of both vectors. Our model predictions show high accuracy (72.9% to 94.5%) in validation tests leaving out a random 10% subset of sites and data since 2017, suggesting a potential for predicting the distribution of the two Aedes vectors

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Nanomechanical detection of antibiotic-mucopeptide binding in a model for superbug drug resistance

The alarming growth of the antibiotic-resistant superbugs methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) is driving the development of new technologies to investigate antibiotics and their modes of action. We report the label-free detection of vancomycin binding to bacterial cell wall precursor analogues (mucopeptides) on cantilever arrays, with 10 nM sensitivity and at clinically relevant concentrations in blood serum. Differential measurements quantified binding constants for vancomycin-sensitive and vancomycin-resistant mucopeptide analogues. Moreover, by systematically modifying the mucopeptide density we gain new insights into the origin of surface stress. We propose that stress is a product of a local chemical binding factor and a geometrical factor describing the mechanical connectivity of regions affected by local binding in terms of a percolation process. Our findings place BioMEMS devices in a new class of percolative systems. The percolation concept will underpin the design of devices and coatings to significantly lower the drug detection limit and may also impact on our understanding of antibiotic drug action in bacteria.Comment: Comments: This paper consists of the main article (6 pages, 5 figures) plus Supplemental Material (6 pages, 3 figures). More details are available at http://www.london-nano.co

sFDvent: A global trait database for deep‐sea hydrothermal‐vent fauna

Motivation: Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite grow‐ ing interest in a trait‐based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single re‐ pository for species traits for deep‐sea chemosynthesis‐based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFD‐ vent (sDiv‐funded trait database for the Functional Diversity of vents). We formed a funded working group to select traits appropriate to: (a) capture the performance of vent species and their influence on ecosystem processes, and (b) compare trait‐based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal‐vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we characterise the sFDvent da‐ tabase, describe our approach, and evaluate its scope. Finally, we compare the sFD‐ vent database to similar databases from shallow‐marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross‐ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique DOI. Main types of variable contained: Six hundred and forty‐six vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided. Spatial location and grain: Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid‐ocean ridges and 6 back‐arc spreading centres. Time period and grain: sFDvent includes information on deep‐sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every 5 years. Major taxa and level of measurement: Deep‐sea hydrothermal‐vent fauna with spe‐ cies‐level identification present or in progress. Software format: .csv and MS Excel (.xlsx).This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

CTL Responses of High Functional Avidity and Broad Variant Cross-Reactivity Are Associated with HIV Control

Cytotoxic T lymphocyte (CTL) responses targeting specific HIV proteins, in particular Gag, have been associated with relative control of viral replication in vivo. However, Gag-specific CTL can also be detected in individuals who do not control the virus and it remains thus unclear how Gag-specific CTL may mediate the beneficial effects in some individuals but not in others. Here, we used a 10mer peptide set spanning HIV Gag-p24 to determine immunogen-specific T-cell responses and to assess functional properties including functional avidity and cross-reactivity in 25 HIV-1 controllers and 25 non-controllers without protective HLA class I alleles. Our data challenge the common belief that Gag-specific T cell responses dominate the virus-specific immunity exclusively in HIV-1 controllers as both groups mounted responses of comparable breadths and magnitudes against the p24 sequence. However, responses in controllers reacted to lower antigen concentrations and recognized more epitope variants than responses in non-controllers. These cross-sectional data, largely independent of particular HLA genetics and generated using direct ex-vivo samples thus identify T cell responses of high functional avidity and with broad variant reactivity as potential functional immune correlates of relative HIV control