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Total reduced inorganic S isotope ratios (δ34SCRS) shift toward more negative values across much of the southern North Atlantic just before the onset of the Cenomanian-Turonian Ocean Anoxic Event (OAE-2). At the same time, there is no parallel isotopic change in the significantly larger pool of kerogen (organic) S, which indicates that the distribution and S-isotope composition of sulfide in the environment likely did not drive the change in δ34SCRS. Here, we investigate possible explanations for the negative shift in δ34SCRS values and their divergence from organic S by isolating iron sulfides for morphological identification and grain-specific isotopic analysis using secondary ion mass spectrometry (SIMS). In pre- and syn-OAE-2 sedimentary rocks from Demerara Rise, we find four distinct morphologies of iron sulfides: pyrite framboids (1–20 μm diameter), irregular pyrite aggregates (1–38 μm diameter), large cemented pyrite aggregates (~60 μm diameter), and irregular and cemented aggregates of the pyrite polymorph marcasite (1–45 μm diameter). These different textural groups have distinct S-isotopic compositions that are largely consistent through the onset of OAE-2. As such, the secular change in bulk δ34SCRS values likely reflects the changing proportions of these phases stratigraphically across OAE-2. All textural groups feature resolvable intra-grain δ34S variability, suggesting that the environments in which they formed were characterized by dynamic sulfide δ34S values and/or by partial closed-system distillation. We use grain-specific δ34S distributions to rule out shoaling of the chemocline within the sediments as a mechanism for the observed decrease in δ34SCRS. Instead, we propose that changes in the reactivity of the iron species delivered to Demerara Rise over the ~200 kyr leading up to the onset of OAE-2 impacted the relative contributions of pyrite with S-isotope signatures reflecting the water column, shallow sediments, and deeper sediments to the bulk sedimentary δ34SCRS value. Specifically, the change in iron reactivity at the onset of OAE-2 favored the production of 34S-depleted large, cemented aggregates and framboids at the expense of more 34S-enriched irregular aggregates. Our results underscore that bulk δ34SCRS measurements integrate multiple reduced phases that form via distinct reaction mechanisms and potentially in different parts of the depositional environment. Grain-specific SIMS analyses dramatically enrich our ability to interpret pyrite isotopic patterns in the geologic record.

Determining whether inputs are out-of-distribution (OOD) is an essential building block for safely deploying machine learning models in the open world. However, previous methods relying on the softmax confidence score suffer from overconfident posterior distributions for OOD data. We propose a unified framework for OOD detection that uses an energy score. We show that energy scores better distinguish in- and out-of-distribution samples than the traditional approach using the softmax scores. Unlike softmax confidence scores, energy scores are theoretically aligned with the probability density of the inputs and are less susceptible to the overconfidence issue. Within this framework, energy can be flexibly used as a scoring function for any pre-trained neural classifier as well as a trainable cost function to shape the energy surface explicitly for OOD detection. On a CIFAR-10 pre-trained WideResNet, using the energy score reduces the average FPR (at TPR 95%) by 18.03% compared to the softmax confidence score. With energy-based training, our method outperforms the state-of-the-art on common benchmarks.

The sulfur (S) isotope composition of pyrite in the sedimentary record has played an important part in our understanding of the evolution of biogeochemical cycles throughout Earth history. However, the kinetics of pyritization are complex and depend strongly on the reactivity and mineralogy of available iron. As a second major sink for sulfide in anoxic sediments, organic matter (OM) provides essential context for reconstructing the distribution and isotopic composition of environmental sulfide. To first order, roughly parallel pyrite and OM δ 34 S profiles reflect changes in sulfide, while independent patterns require alternative explanations, including changes in iron availability or OM characteristics. We apply this framework to Ocean Anoxic Event 2 (OAE-2, ∼94 Mya), a period of enhanced burial of reduced C and S (in OM and pyrite) that has been associated with an expansion of reducing marine conditions. We present paired S-isotope records for pyrite and OM along with profiles of OM S:C ratio and S redox speciation from four well-characterized lithologic sections with a range of depositional environments (Pont d'Issole, Cismon, Tarfaya Basin, and Demerara Rise) to reconstruct both local redox structure and global mechanisms impacting the C, S and Fe cycles around OAE-2. OM sulfurization appears to be a major control on OM preservation at all four sites. Similar to modern anoxic environments, there is a positive correlation between OM S:C ratios and TOC concentrations for sites with more reducing conditions, implying a link between OM sulfurization and burial. At consistently anoxic sites like Tarfaya Basin and Demerara Rise, strongly sulfurized OM with a consistent S redox speciation and S-isotope composition most likely formed rapidly in sinking particles before, during, and after OAE-2. Particle-hosted OM sulfurization may therefore have been a central mechanism facilitating the massive burial of OM in anoxic environments during this and other periods of enhanced global carbon burial. At the same time, a nearly 25‰ negative shift in the δ 34 S values of pyrite – but not OM – occurs at multiple, globally distributed sites prior to the onset of OAE-2, indicating slower pyritization reactions that likely reflect changes in iron delivery due to expanding regional or global anoxia. The combination of pyrite and organic S isotopes thus provides novel constraints on the interwoven cycles of carbon, iron, and sulfur across a major carbon cycle perturbation.

We factor Beamer’s push-pull, also known as direction-optimized breadth-first-search (DOBFS) into 3 separable optimizations, and analyze them for generalizability, asymptotic speedup, and contribution to overall speedup. We demonstrate that masking is critical for high performance and can be generalized to all graph algorithms where the sparsity pattern of the output is known a priori. We show that these graph algorithm optimizations, which together constitute DOBFS, can be neatly and separably described using linear algebra and can be expressed in the GraphBLAS linear-algebra-based framework. We provide experimental evidence that with these optimizations, a DOBFS expressed in a linear-algebra-based graph framework attains competitive performance with state-of-the-art graph frameworks on the GPU and on a multi-threaded CPU, achieving 101 GTEPS on a Scale 22 RMAT graph.

We implement two novel algorithms for sparse-matrix dense-matrix multiplication (SpMM) on the GPU. Our algorithms expect the sparse input in the popular compressed-sparse-row (CSR) format and thus do not require expensive format conversion. While previous SpMM work concentrates on thread-level parallelism, we additionally focus on latency hiding with instruction-level parallelism and load-balancing. We show, both theoretically and experimentally, that the proposed SpMM is a better fit for the GPU than previous approaches. We identify a key memory access pattern that allows efficient access into both input and output matrices that is crucial to getting excellent performance on SpMM. By combining these two ingredients—(i) merge-based load-balancing and (ii) row-major coalesced memory access—we demonstrate a 4.1 × peak speedup and a 31.7% geomean speedup over state-of-the-art SpMM implementations on real-world datasets.

In this study, we provide an extensive survey on wide spectrum of scheduling methods for multitasking among graphics processing unit (GPU) computing tasks. We then design several schedulers and explain in detail the selected methods we have developed to implement our scheduling strategies. Next, we compare the performance of schedulers on various workloads running on Fermi and Kepler architectures and arrive at the following major conclusions: (1) Small kernels benefit from running kernels concurrently. (2) The combination of small kernels, high-priority kernels with longer runtimes, and lower-priority kernels with shorter runtimes benefits from a CPU scheduler that dynamically changes kernel order on the Fermi architecture. (3) Because of limitations of existing GPU architectures, currently CPU schedulers outperform their GPU counterparts. We also provide results and observations obtained from implementing and evaluating our schedulers on the NVIDIA Jetson TX1 system-on-chip architecture. We observe that although TX1 has the newer Maxwell architecture, the mechanism used for scheduler timings behaves differently on TX1 compared to Kepler leading to incorrect timings. In this paper, we describe our methods that allow us to report correct timings for CPU schedulers running on TX1. Finally, we propose new research directions involving the investigation of additional scheduling strategies.

The GraphBLAS standard (GraphBlas.org) is being developed to bring the potential of matrix-based graph algorithms to the broadest possible audience. Mathematically, the GraphBLAS defines a core set of matrix-based graph operations that can be used to implement a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the mathematics of the GraphBLAS. Graphs represent connections between vertices with edges. Matrices can represent a wide range of graphs using adjacency matrices or incidence matrices. Adjacency matrices are often easier to analyze while incidence matrices are often better for representing data. Fortunately, the two are easily connected by matrix multiplication. A key feature of matrix mathematics is that a very small number of matrix operations can be used to manipulate a very wide range of graphs. This composability of a small number of operations is the foundation of the GraphBLAS. A standard such as the GraphBLAS can only be effective if it has low performance overhead. Performance measurements of prototype GraphBLAS implementations indicate that the overhead is low.

In this work, we introduced k-d darts as a particular type of higherdimensional sampling. We described a k-d dart framework for hyperplanes of general dimension k, and then demonstrated efficiency and accuracy over three applications using k = 1, and accuracy for one application using k = 1. In particular, darts produce accurate estimates of the volume of an object regardless of the dimension, orientation, and aspect ratio of the object. Axis-aligned darts are universally preferable to unaligned ones for sampling square domains, and we expect this to extend to hyperrectangles, such as bounding boxes. Darts also produce accurate mean estimates for function integration. © 2014 ACM 0730-0301/2014/01-ART3 15.00.

In this paper, we present a GPU implementation of a two-dimensional shallowwater model. Water simulations are useful for modeling floods, river/reservoirbehavior, and dam break scenarios. Our GPU implementation shows vastperformance improvements over the original Fortran implementation. By takingadvantage of the GPU, researchers and engineers will be able to study watersystems more efficiently and in greater detail.

We present parallel algorithms and implementations of a bzip2-like lossless data compression scheme for GPU architectures. Our approach parallelizes three main stages in the bzip2 compression pipeline: Burrows-Wheeler transform (BWT), move-to-front transform (MTF), and Huffman coding. In particular, we utilize a two-level hierarchical sort for BWT, design a novel scan-based parallel MTF algorithm, and implement a parallel reduction scheme to build the Huffman tree. For each algorithm, we perform detailed performance analysis, discuss its strengths and weaknesses, and suggest future directions for improvements. Overall, our GPU implementation is dominated by BWT performance and is 2.78x slower than bzip2, with BWT and MTF-Huffman respectively 2.89x and 1.34x slower on average. © 2012 IEEE.

We provide a simple algorithm and data structures for d-dimensional unbiased maximal Poisson-disk sampling. We use an order of magnitude less memory and time than the alternatives. Our results become more favorable as the dimension increases. This allows us to produce bigger samplings. Domains may be non-convex with holes. The generated point cloud is maximal up to round-off error. The serial algorithm is provably bias-free. For an output sampling of size n in fixed dimension d, we use a linear memory budget and empirical Θ(n) runtime. No known methods scale well with dimension, due to the "curse of dimensionality." The serial algorithm is practical in dimensions up to 5, and has been demonstrated in 6d. We have efficient GPU implementations in 2d and 3d. The algorithm proceeds through a finite sequence of uniform grids. The grids guide the dart throwing and track the remaining disk-free area. The top-level grid provides an efficient way to test if a candidate dart is disk-free. Our uniform grids are like quadtrees, except we delay splits and refine all leaves at once. Since the quadtree is flat it can be represented using very little memory: we just need the indices of the active leaves and a global level. Also it is very simple to sample from leaves with uniform probability. © 2012 The Author(s).

Fluctuations in marine oxygen concentrations have been invoked as a primary driver for changes in biodiversity throughout Earth history. Expansions in reducing marine conditions are commonly invoked as key causal mechanisms for mass extinctions, while increases in marine oxygenation are becoming an increasingly common causal mechanism invoked for biodiversification events. Here we utilize a multiproxy approach to constrain local and global marine paleoredox conditions throughout the late Cambrian-Early Ordovician from two drill core successions in Baltoscandia. Local paleoredox proxies such as manganese concentrations and iron speciation reveal that both sites in the Baltic paleobasin had persistently anoxic and predominantly euxinic (anoxic and sulfidic) bottom water conditions throughout the study interval. Corresponding trace metal datasets indicate nuanced contraction and expansion of global anoxic and euxinic conditions along continental margins during the late Cambrian-Early Ordovician. Lastly, thallium isotope data from these locally reducing sections suggest a global expansion of oxygenated shelf and deeper marine environments from the late Cambrian into the Early Ordovician. This evidence for increasingly oxic marine environments coincides with increases in burrowing depth and tiering in marine animals, as well as diversification of body fossils throughout this ~8-million-year interval. The collective geochemical datasets provide some of the first direct paleoredox evidence for an increase in marine oxygen concentrations as a key mechanism for the Ordovician radiation of marine life., (© 2023 John Wiley & Sons Ltd.)

The timing and connections between global cooling, marine redox conditions, and biotic turnover are underconstrained for the Late Ordovician. The second most severe mass extinction occurred at the end of the Ordovician period, resulting in ~85% loss of marine species between two extinction pulses. As the only "Big 5" extinction that occurred during icehouse conditions, this interval is an important modern analog to constrain environmental feedbacks. We present a previously unexplored thallium isotope records from two paleobasins that record global marine redox conditions and document two distinct and rapid excursions suggesting vacillating (de)oxygenation. The strong temporal link between these perturbations and extinctions highlights the possibility that dynamic marine oxygen fluctuations, rather than persistent, stable global anoxia, played a major role in driving the extinction. This evidence for rapid oxygen changes leading to mass extinction has important implications for modern deoxygenation and biodiversity declines.

Background: Coronavirus disease (COVID-19) can cause severe illness and death. Predictors of poor outcome collected on hospital admission may inform clinical and public health decisions., Methods: We conducted a retrospective observational cohort investigation of 297 adults admitted to 8 academic and community hospitals in Georgia, United States, during March 2020. Using standardized medical record abstraction, we collected data on predictors including admission demographics, underlying medical conditions, outpatient antihypertensive medications, recorded symptoms, vital signs, radiographic findings, and laboratory values. We used random forest models to calculate adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for predictors of invasive mechanical ventilation (IMV) and death., Results: Compared with age <45 years, ages 65-74 years and ≥75 years were predictors of IMV (aORs, 3.12 [95% CI, 1.47-6.60] and 2.79 [95% CI, 1.23-6.33], respectively) and the strongest predictors for death (aORs, 12.92 [95% CI, 3.26-51.25] and 18.06 [95% CI, 4.43-73.63], respectively). Comorbidities associated with death (aORs, 2.4-3.8; P < .05) included end-stage renal disease, coronary artery disease, and neurologic disorders, but not pulmonary disease, immunocompromise, or hypertension. Prehospital use vs nonuse of angiotensin receptor blockers (aOR, 2.02 [95% CI, 1.03-3.96]) and dihydropyridine calcium channel blockers (aOR, 1.91 [95% CI, 1.03-3.55]) were associated with death., Conclusions: After adjustment for patient and clinical characteristics, older age was the strongest predictor of death, exceeding comorbidities, abnormal vital signs, and laboratory test abnormalities. That coronary artery disease, but not chronic lung disease, was associated with death among hospitalized patients warrants further investigation, as do associations between certain antihypertensive medications and death., (Published by Oxford University Press for the Infectious Diseases Society of America 2020.)

The Cretaceous-Paleogene (K-Pg) mass extinction is marked globally by elevated concentrations of iridium, emplaced by a hypervelocity impact event 66 million years ago. Here, we report new data from four independent laboratories that reveal a positive iridium anomaly within the peak-ring sequence of the Chicxulub impact structure, in drill core recovered by IODP-ICDP Expedition 364. The highest concentration of ultrafine meteoritic matter occurs in the post-impact sediments that cover the crater peak ring, just below the lowermost Danian pelagic limestone. Within years to decades after the impact event, this part of the Chicxulub impact basin returned to a relatively low-energy depositional environment, recording in unprecedented detail the recovery of life during the succeeding millennia. The iridium layer provides a key temporal horizon precisely linking Chicxulub to K-Pg boundary sections worldwide., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

Objective: To assess the effect of morphine equivalent dose-days (MED-D) on the total cost for acute low back pain (LBP) workers' compensation claims., Methods: Simple random samples of 123 opioid and 141 nonopioid acute LBP claims were obtained. Opioid claims were divided into low, medium, and high subgroups for MED-D, MED, and prescription duration. Subgroup mean total costs were compared to the nonopioid group using multivariate regression analyses., Results: MED-D and prescription duration were each, respectively, associated with significantly increased total costs at both medium and high levels. Increasing MED had a negative association with total cost, though stratification by duration abrogated this perceived trend. Interaction testing indicated MED and duration together better explained cost than MED alone., Conclusion: MED-D is a better predictor of total cost in acute LBP claims than MED alone.

SARS-CoV-2, the novel coronavirus that causes coronavirus disease 2019 (COVID-19), was first detected in the United States during January 2020 (1). Since then, >980,000 cases have been reported in the United States, including >55,000 associated deaths as of April 28, 2020 (2). Detailed data on demographic characteristics, underlying medical conditions, and clinical outcomes for persons hospitalized with COVID-19 are needed to inform prevention strategies and community-specific intervention messages. For this report, CDC, the Georgia Department of Public Health, and eight Georgia hospitals (seven in metropolitan Atlanta and one in southern Georgia) summarized medical record-abstracted data for hospitalized adult patients with laboratory-confirmed* COVID-19 who were admitted during March 2020. Among 305 hospitalized patients with COVID-19, 61.6% were aged <65 years, 50.5% were female, and 83.2% with known race/ethnicity were non-Hispanic black (black). Over a quarter of patients (26.2%) did not have conditions thought to put them at higher risk for severe disease, including being aged ≥65 years. The proportion of hospitalized patients who were black was higher than expected based on overall hospital admissions. In an adjusted time-to-event analysis, black patients were not more likely than were nonblack patients to receive invasive mechanical ventilation † (IMV) or to die during hospitalization (hazard ratio [HR] = 0.63; 95% confidence interval [CI] = 0.35-1.13). Given the overrepresentation of black patients within this hospitalized cohort, it is important for public health officials to ensure that prevention activities prioritize communities and racial/ethnic groups most affected by COVID-19. Clinicians and public officials should be aware that all adults, regardless of underlying conditions or age, are at risk for serious illness from COVID-19., Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. James M. Blum reports personal fees from Clew Medical, outside the submitted work. No other potential conflicts of interest were disclosed.

Ediacaran sediments record an unusual global carbon cycle perturbation that has been linked to widespread oceanic oxygenation, the Shuram negative C isotope excursion (NCIE). However, proxy-based estimates of global ocean redox conditions during this event have been limited largely due to proxy specificity (e.g., euxinic sediments for Mo and U isotopes). Modern global seawater documents a homogenous Tl isotope composition (ε 205 Tl = -6.0) due to significant manganese oxide burial, which is recorded in modern euxinic sediments. Here, we provide new data documenting that sediments deposited beneath reducing but a non-sulfidic water column from the Santa Barbara Basin (ε 205 Tl = -5.6 ± 0.1) also faithfully capture global seawater Tl isotope values. Thus, the proxy utilization of Tl isotopes can extend beyond strictly euxinic settings. Second, to better constrain the global redox conditions during the Shuram NCIE, we measured Tl isotopes of locally euxinic and ferruginous shales of the upper Doushantuo Formation, South China. The ε 205 Tl values of these shales exhibit a decreasing trend from ≈-3 to ≈-8, broadly coinciding with the onset of Shuram NCIE. There are ε 205 Tl values (-5.1 to -7.8) during the main Shuram NCIE interval that approach values more negative than modern global seawater. These results suggest that manganese oxide burial was near or even greater than modern burial fluxes, which is likely linked to an expansion of oxic conditions. This ocean oxygenation may have been an important trigger for the Shuram NCIE and evolution of Ediacaran-type biota. Subsequently, Tl isotopes show an increasing trend from the modern ocean value to values near the modern global inputs or even heavier (ε 205 Tl ≈ -2.5 ~ 0.4), occurring prior to recovery from the NCIE. These records may suggest that there was a decrease in the extent of oxygenated conditions in the global oceans during the late stage of the Shuram NCIE., (© 2020 John Wiley & Sons Ltd.)

Polyhedral meshes are increasingly becoming an attractive option with particular advantages over traditional meshes for certain applications. What has been missing is a robust polyhedral meshing algorithm that can handle broad classes of domains exhibiting arbitrary curved boundaries and sharp features. In addition, the power of primal-dual mesh pairs, exemplified by Voronoi-Delaunay meshes, has been recognized as an important ingredient in numerous formulations. The VoroCrust algorithm is the first provably correct algorithm for conforming Voronoi meshing for non-convex and possibly non-manifold domains with guarantees on the quality of both surface and volume elements. A robust refinement process estimates a suitable sizing field that enables the careful placement of Voronoi seeds across the surface circumventing the need for clipping and avoiding its many drawbacks. The algorithm has the flexibility of filling the interior by either structured or random samples, while all sharp features are preserved in the output mesh. We demonstrate the capabilities of the algorithm on a variety of models and compare against state-of-the-art polyhedral meshing methods based on clipped Voronoi cells establishing the clear advantage of VoroCrust output.

Objective: American College of Occupational and Environmental Medicine's (ACOEM's) evidence-based guidelines for acute low back pain (LBP) were used to assess relationships between guideline adherence and worker's compensation costs., Methods: Treatments at first appointments were abstracted. Two scoring tools were utilized to assess each patient's treatment plan. One score assessed ACOEM Guideline compliance while the second utilized mean expert scores of the perceived value of each treatment. Claim costs were log-transformed and compared with scores., Results: There is a significant trend between increased compliance and decreasing costs. Medical and total costs trended lower by an average $352.90 and $586.20 per unit of compliance score respectively. No outlier cost claims were in the best guidelines compliance groups., Conclusion: This study shows a statistically significant trend in the relationship between adherence to ACOEM guidelines for initial management of work-related LBP and decreasing claim costs.

By about 2.0 billion years ago (Ga), there is evidence for a period best known for its extended, apparent geochemical stability expressed famously in the carbonate-carbon isotope data. Despite the first appearance and early innovation among eukaryotic organisms, this period is also known for a rarity of eukaryotic fossils and an absence of organic biomarker fingerprints for those organisms, suggesting low diversity and relatively small populations compared to the Neoproterozoic era. Nevertheless, the search for diagnostic biomarkers has not been performed with guidance from paleoenvironmental redox constrains from inorganic geochemistry that should reveal the facies that were most likely hospitable to these organisms. Siltstones and shales obtained from drill core of the ca. 1.3-1.4 Ga Roper Group from the McArthur Basin of northern Australia provide one of our best windows into the mid-Proterozoic redox landscape. The group is well dated and minimally metamorphosed (of oil window maturity), and previous geochemical data suggest a relatively strong connection to the open ocean compared to other mid-Proterozoic records. Here, we present one of the first integrated investigations of Mesoproterozoic biomarker records performed in parallel with established inorganic redox proxy indicators. Results reveal a temporally variable paleoredox structure through the Velkerri Formation as gauged from iron mineral speciation and trace-metal geochemistry, vacillating between oxic and anoxic. Our combined lipid biomarker and inorganic geochemical records indicate at least episodic euxinic conditions sustained predominantly below the photic zone during the deposition of organic-rich shales found in the middle Velkerri Formation. The most striking result is an absence of eukaryotic steranes (4-desmethylsteranes) and only traces of gammacerane in some samples-despite our search across oxic, as well as anoxic, facies that should favor eukaryotic habitability and in low maturity rocks that allow the preservation of biomarker alkanes. The dearth of Mesoproterozoic eukaryotic sterane biomarkers, even within the more oxic facies, is somewhat surprising but suggests that controls such as the long-term nutrient balance and other environmental factors may have throttled the abundances and diversity of early eukaryotic life relative to bacteria within marine microbial communities. Given that molecular clocks predict that sterol synthesis evolved early in eukaryotic history, and (bacterial) fossil steroids have been found previously in 1.64 Ga rocks, then a very low environmental abundance of eukaryotes relative to bacteria is our preferred explanation for the lack of regular steranes and only traces of gammacerane in a few samples. It is also possible that early eukaryotes adapted to Mesoproterozoic marine environments did not make abundant steroid lipids or tetrahymanol in their cell membranes., (© 2019 John Wiley & Sons Ltd.)

Late Archaean sedimentary rocks contain compelling geochemical evidence for episodic accumulation of dissolved oxygen in the oceans along continental margins before the Great Oxidation Event. However, the extent of this oxygenation remains poorly constrained. Here we present thallium and molybdenum isotope compositions for anoxic organic-rich shales of the 2.5 billion-year-old Mount McRae Shale from Western Australia, which previously yielded geochemical evidence of a transient oxygenation event. During this event, we observe an anti-correlation between thalium and molybdenum isotope data, including two shifts to higher molybdenum and lower thalium isotope compositions. Our data indicate pronounced burial of manganese oxides in sediments elsewhere in the ocean at these times, which requires that water columns above portions of the ocean floor were fully oxygenated: all the way from the air-sea interface to well below the sediment-water interface. Well-oxygenated continental shelves were likely the most important sites of manganese oxide burial and mass-balance modeling results suggest that fully oxygenated water columns were at least a regional-scale feature of early-Earth's oceans 2.5 billion years ago., Competing Interests: Competing interests: The authors declare no competing interests.

For this study, we generated thallium (Tl) isotope records from two anoxic basins to track the earliest changes in global bottom water oxygen contents over the Toarcian Oceanic Anoxic Event (T-OAE; ∼183 Ma) of the Early Jurassic. The T-OAE, like other Mesozoic OAEs, has been interpreted as an expansion of marine oxygen depletion based on indirect methods such as organic-rich facies, carbon isotope excursions, and biological turnover. Our Tl isotope data, however, reveal explicit evidence for earlier global marine deoxygenation of ocean water, some 600 ka before the classically defined T-OAE. This antecedent deoxygenation occurs at the Pliensbachian/Toarcian boundary and is coeval with the onset of initial large igneous province (LIP) volcanism and the initiation of a marine mass extinction. Thallium isotopes are also perturbed during the T-OAE interval, as defined by carbon isotopes, reflecting a second deoxygenation event that coincides with the acme of elevated marine mass extinctions and the main phase of LIP volcanism. This suggests that the duration of widespread anoxic bottom waters was at least 1 million years in duration and spanned early to middle Toarcian time. Thus, the Tl data reveal a more nuanced record of marine oxygen depletion and its links to biological change during a period of climatic warming in Earth's past and highlight the role of oxygen depletion on past biological evolution., Competing Interests: The authors declare no conflict of interest.

The Cretaceous/Palaeogene mass extinction eradicated 76% of species on Earth 1,2 . It was caused by the impact of an asteroid 3,4 on the Yucatán carbonate platform in the southern Gulf of Mexico 66 million years ago 5 , forming the Chicxulub impact crater 6,7 . After the mass extinction, the recovery of the global marine ecosystem-measured as primary productivity-was geographically heterogeneous 8 ; export production in the Gulf of Mexico and North Atlantic-western Tethys was slower than in most other regions 8-11 , taking 300 thousand years (kyr) to return to levels similar to those of the Late Cretaceous period. Delayed recovery of marine productivity closer to the crater implies an impact-related environmental control, such as toxic metal poisoning 12 , on recovery times. If no such geographic pattern exists, the best explanation for the observed heterogeneity is a combination of ecological factors-trophic interactions 13 , species incumbency and competitive exclusion by opportunists 14 -and 'chance' 8,15,16 . The question of whether the post-impact recovery of marine productivity was delayed closer to the crater has a bearing on the predictability of future patterns of recovery in anthropogenically perturbed ecosystems. If there is a relationship between the distance from the impact and the recovery of marine productivity, we would expect recovery rates to be slowest in the crater itself. Here we present a record of foraminifera, calcareous nannoplankton, trace fossils and elemental abundance data from within the Chicxulub crater, dated to approximately the first 200 kyr of the Palaeocene. We show that life reappeared in the basin just years after the impact and a high-productivity ecosystem was established within 30 kyr, which indicates that proximity to the impact did not delay recovery and that there was therefore no impact-related environmental control on recovery. Ecological processes probably controlled the recovery of productivity after the Cretaceous/Palaeogene mass extinction and are therefore likely to be important for the response of the ocean ecosystem to other rapid extinction events.

We study the problem of decomposing a volume with a smooth boundary into a collection of Voronoi cells. Unlike the dual problem of conforming Delaunay meshing, a principled solution to this problem for generic smooth surfaces remained elusive. VoroCrust leverages ideas from weighted α -shapes and the power crust algorithm to produce unweighted Voronoi cells conforming to the surface, yielding the first provably-correct algorithm for this problem. Given a κ -sparse ε -sample, we work with the balls of radius δ times the local feature size centered at each sample. The corners of the union of these balls on both sides of the surface are the Voronoi sites and the interface of their cells is a watertight surface reconstruction embedded in the dual shape of the union of balls. With the surface protected, the enclosed volume can be further decomposed by generating more sites inside it. Compared to clipping-based algorithms, VoroCrust cells are full Voronoi cells, with convexity and fatness guarantees. Compared to the power crust algorithm, VoroCrust cells are not filtered, are unweighted, and offer greater flexibility in meshing the enclosed volume by either structured or randomly genenerated samples.

The rates of marine deoxygenation leading to Cretaceous Oceanic Anoxic Events are poorly recognized and constrained. If increases in primary productivity are the primary driver of these episodes, progressive oxygen loss from global waters should predate enhanced carbon burial in underlying sediments-the diagnostic Oceanic Anoxic Event relic. Thallium isotope analysis of organic-rich black shales from Demerara Rise across Oceanic Anoxic Event 2 reveals evidence of expanded sediment-water interface deoxygenation ~43 ± 11 thousand years before the globally recognized carbon cycle perturbation. This evidence for rapid oxygen loss leading to an extreme ancient climatic event has timely implications for the modern ocean, which is already experiencing large-scale deoxygenation.

Chemical weathering consumes atmospheric carbon dioxide through the breakdown of silicate minerals and is thought to stabilize Earth's long-term climate. However, the potential influence of silicate weathering on atmospheric pCO 2 levels on geologically short timescales (10 3 -10 5 years) remains poorly constrained. Here we focus on the record of a transient interval of severe climatic warming across the Toarcian Oceanic Anoxic Event or T-OAE from an open ocean sedimentary succession from western North America. Paired osmium isotope data and numerical modelling results suggest that weathering rates may have increased by 215% and potentially up to 530% compared to the pre-event baseline, which would have resulted in the sequestration of significant amounts of atmospheric CO 2 . This process would have also led to increased delivery of nutrients to the oceans and lakes stimulating bioproductivity and leading to the subsequent development of shallow-water anoxia, the hallmark of the T-OAE. This enhanced bioproductivity and anoxia would have resulted in elevated rates of organic matter burial that would have acted as an additional negative feedback on atmospheric pCO 2 levels. Therefore, the enhanced weathering modulated by initially increased pCO 2 levels would have operated as both a direct and indirect negative feedback to end the T-OAE.

The ocean-atmosphere system is typically envisioned to have gone through a unidirectional oxygenation with significant oxygen increases in the earliest (ca. 635 Ma), middle (ca. 580 Ma), or late (ca. 560 Ma) Ediacaran Period. However, temporally discontinuous geochemical data and the patchy metazoan fossil record have been inadequate to chart the details of Ediacaran ocean oxygenation, raising fundamental debates about the timing of ocean oxygenation, its purported unidirectional rise, and its causal relationship, if any, with the evolution of early animal life. To better understand the Ediacaran ocean redox evolution, we have conducted a multi-proxy paleoredox study of a relatively continuous, deep-water section in South China that was paleogeographically connected with the open ocean. Iron speciation and pyrite morphology indicate locally euxinic (anoxic and sulfidic) environments throughout the Ediacaran in this section. In the same rocks, redox sensitive element enrichments and sulfur isotope data provide evidence for multiple oceanic oxygenation events (OOEs) in a predominantly anoxic global Ediacaran-early Cambrian ocean. This dynamic redox landscape contrasts with a recent view of a redox-static Ediacaran ocean without significant change in oxygen content. The duration of the Ediacaran OOEs may be comparable to those of the oceanic anoxic events (OAEs) in otherwise well-oxygenated Phanerozoic oceans. Anoxic events caused mass extinctions followed by fast recovery in biologically diversified Phanerozoic oceans. In contrast, oxygenation events in otherwise ecologically monotonous anoxic Ediacaran-early Cambrian oceans may have stimulated biotic innovations followed by prolonged evolutionary stasis., (© 2016 John Wiley & Sons Ltd.)

We introduce an algorithmic framework for tuning the spatial density of disks in a maximal random packing, without changing the sizing function or radii of disks. Starting from any maximal random packing such as a Maximal Poisson-disk Sampling (MPS), we iteratively relocate, inject (add), or eject (remove) disks, using a set of three successively more-aggressive local operations. We may achieve a user-defined density, either more dense or more sparse, almost up to the theoretical structured limits. The tuned samples are conflict-free, retain coverage maximality, and, except in the extremes, retain the blue noise randomness properties of the input. We change the density of the packing one disk at a time, maintaining the minimum disk separation distance and the maximum domain coverage distance required of any maximal packing. These properties are local, and we can handle spatially-varying sizing functions. Using fewer points to satisfy a sizing function improves the efficiency of some applications. We apply the framework to improve the quality of meshes, removing non-obtuse angles; and to more accurately model fiber reinforced polymers for elastic and failure simulations.

Quality improvement or high reliability in medicine is an evolving science where we seek to integrate evidence-based medicine, structural resources, process management, leadership models, culture, and education. Newborn Associates is a community-based neonatology practice that staffs and manages neonatal intensive care units (NICU's) at Central Mississippi Medical Center, Mississippi Baptist Medical Center, River Oaks Hospital, St Dominic's Hospital and Woman's Hospital within the Jackson, Mississippi, metropolitan area. These hospitals participate in the Vermont-Oxford Neonatal Network (VON), which is a voluntary national network of about 1000 NICU groups that submit data allowing them to benchmark their patient outcome. This network currently holds data on 1.5 million infants. Participation may also include the Newborn Improvement Quality Collaborative (NICQ) which is an intensive quality improvement program where 40-60 of the almost 1000 VON centers participate each year or the iNICQ, which is an internet-based collaborative involving about 150 centers per year. From 2008-2009, our group concentrated efforts on quality improvement which included consolidating resources of three corporately managed hospitals to allow focused care of babies under 800-1000 grams at a single center, expanding participation in the VON NICQ to include all physicians and centers, and establishing a group QI focused committee aimed at sharing practice bundles and adopting quality improvement methodology. The goal of this article is to report the impact of these QI activities on survival of the smallest preterm infants who weigh less than 1500 grams at birth. Two epochs were compared: 2006-2009, and 2010-2013. 551 VLBW (< 1 500 grams) infants from epoch I were compared to 583 VLBW infants from epoch 2. Mortality in this group decreased from 18% to 11.1% (OR 0.62,95% CI 0.44-0.88). Mortality in the 501-750 grams birth weight category decreased from 45.7% to 18% (OR 0.39,95% CI 0.21-0.74). Improved survival was noted in all centers over the time period. These findings suggest that a physician-driven, multidisciplinary, individualized and multifactorial quality improvement effort can positively impact the care of extremely preterm infants in the community NICU setting.

The Mesozoic Era is characterized by numerous oceanic anoxic events (OAEs) that are diagnostically expressed by widespread marine organic-carbon burial and coeval carbon-isotope excursions. Here we present coupled high-resolution carbon- and sulfur-isotope data from four European OAE 2 sections spanning the Cenomanian-Turonian boundary that show roughly parallel positive excursions. Significantly, however, the interval of peak magnitude for carbon isotopes precedes that of sulfur isotopes with an estimated offset of a few hundred thousand years. Based on geochemical box modeling of organic-carbon and pyrite burial, the sulfur-isotope excursion can be generated by transiently increasing the marine burial rate of pyrite precipitated under euxinic (i.e., anoxic and sulfidic) water-column conditions. To replicate the observed isotopic offset, the model requires that enhanced levels of organic-carbon and pyrite burial continued a few hundred thousand years after peak organic-carbon burial, but that their isotope records responded differently due to dramatically different residence times for dissolved inorganic carbon and sulfate in seawater. The significant inference is that euxinia persisted post-OAE, but with its global extent dwindling over this time period. The model further suggests that only ~5% of the global seafloor area was overlain by euxinic bottom waters during OAE 2. Although this figure is ~30× greater than the small euxinic fraction present today (~0.15%), the result challenges previous suggestions that one of the best-documented OAEs was defined by globally pervasive euxinic deep waters. Our results place important controls instead on local conditions and point to the difficulty in sustaining whole-ocean euxinia.

Carbonates from approximately 2.3-2.1 billion years ago show markedly positive δ(13)C values commonly reaching and sometimes exceeding +10‰. Traditional interpretation of these positive δ(13)C values favors greatly enhanced organic carbon burial on a global scale, although other researchers have invoked widespread methanogenesis within the sediments. To resolve between these competing models and, more generally, among the mechanisms behind Earth's most dramatic carbon isotope event, we obtained coupled stable isotope data for carbonate carbon and carbonate-associated sulfate (CAS). CAS from the Lomagundi interval shows a narrow range of δ(34)S values and concentrations much like those of Phanerozoic and modern marine carbonate rocks. The δ(34)S values are a close match to those of coeval sulfate evaporites and likely reflect seawater composition. These observations are inconsistent with the idea of diagenetic carbonate formation in the methanic zone. Toward the end of the carbon isotope excursion there is an increase in the δ(34)S values of CAS. We propose that these trends in C and S isotope values track the isotopic evolution of seawater sulfate and reflect an increase in pyrite burial and a crash in the marine sulfate reservoir during ocean deoxygenation in the waning stages of the positive carbon isotope excursion.

Tumor progression usually proceeds through several sequential stages, any of which could be targets for interrupting the progression process if one understood these steps at the molecular level. We extracted nascent plasma cell tumor (PCT) cells from within inflammatory oil granulomas (OG) isolated from IP pristane-injected BALB/c.iMyc(Eμ) mice at 5 different time points during tumor progression. We used laser capture microdissection to collect incipient PCT cells and analyzed their global gene expression on Affymetrix Mouse Genome 430A microarrays. Two independent studies were performed with different sets of mice. Analysis of the expression data used ANOVA and Bayesian estimation of temporal regulation. Genetic pathway analysis was performed using MetaCore (GeneGo) and IPA (Ingenuity). The gene expression profiles of PCT samples and those of undissected OG samples from adjacent sections showed that different genes and pathways were mobilized in the tumor cells during tumor progression, compared with their stroma. Our analysis implicated several genetic pathways in PCT progression, including biphasic (up- and then down-regulation) of the Spp1/osteopontin-dependent network and up-regulation of mRNA translation/protein synthesis. The latter led to a biologic validation study that showed that the AMPK-activating diabetes drug, metformin, was a potent specific PCT inhibitor in vitro.

The advent of readily available temporal imaging or time series volumetric (4D) imaging has become an indispensable component of treatment planning and adaptive radiotherapy (ART) at many radiotherapy centers. Deformable image registration (DIR) is also used in other areas of medical imaging, including motion corrected image reconstruction. Due to long computation time, clinical applications of DIR in radiation therapy and elsewhere have been limited and consequently relegated to offline analysis. With the recent advances in hardware and software, graphics processing unit (GPU) based computing is an emerging technology for general purpose computation, including DIR, and is suitable for highly parallelized computing. However, traditional general purpose computation on the GPU is limited because the constraints of the available programming platforms. As well, compared to CPU programming, the GPU currently has reduced dedicated processor memory, which can limit the useful working data set for parallelized processing. We present an implementation of the demons algorithm using the NVIDIA 8800 GTX GPU and the new CUDA programming language. The GPU performance will be compared with single threading and multithreading CPU implementations on an Intel dual core 2.4 GHz CPU using the C programming language. CUDA provides a C-like language programming interface, and allows for direct access to the highly parallel compute units in the GPU. Comparisons for volumetric clinical lung images acquired using 4DCT were carried out. Computation time for 100 iterations in the range of 1.8-13.5 s was observed for the GPU with image size ranging from 2.0 x 10(6) to 14.2 x 10(6) pixels. The GPU registration was 55-61 times faster than the CPU for the single threading implementation, and 34-39 times faster for the multithreading implementation. For CPU based computing, the computational time generally has a linear dependence on image size for medical imaging data. Computational efficiency is characterized in terms of time per megapixels per iteration (TPMI) with units of seconds per megapixels per iteration (or spmi). For the demons algorithm, our CPU implementation yielded largely invariant values of TPMI. The mean TPMIs were 0.527 spmi and 0.335 spmi for the single threading and multithreading cases, respectively, with <2% variation over the considered image data range. For GPU computing, we achieved TPMI =0.00916 spmi with 3.7% variation, indicating optimized memory handling under CUDA. The paradigm of GPU based real-time DIR opens up a host of clinical applications for medical imaging.