Automating embedded analysis capabilities and managing software complexity in multiphysics simulation part II: application to partial differential equations

A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application

Role of Peroxisome Proliferator-Activated Receptor Gamma and Its Ligands in the Treatment of Hematological Malignancies

Peroxisome proliferator-activated receptor gamma (PPARγ) is a multifunctional transcription factor with important regulatory roles in inflammation, cellular growth, differentiation, and apoptosis. PPARγ is expressed in a variety of immune cells as well as in numerous leukemias and lymphomas. Here, we review recent studies that provide new insights into the mechanisms by which PPARγ ligands influence hematological malignant cell growth, differentiation, and survival. Understanding the diverse properties of PPARγ ligands is crucial for the development of new therapeutic approaches for hematological malignancies

Impact of the GeoMIP G1 sunshade geoengineering experiment on the Atlantic meridional overturning circulation

We analyze the multi-earth system model responses of ocean temperatures and the Atlantic Meridional Overturning Circulation (AMOC) under an idealized solar radiation management scenario (G1) from the Geoengineering Model Intercomparison Project. All models simulate warming of the northern North Atlantic relative to no geoengineering, despite geoengineering substantially offsetting the increases in mean global ocean temperatures. Increases in the temperature of the North Atlantic Ocean at the surface (~0.25 K) and at a depth of 500 m (~0.10 K) are mainly due to a 10 Wm−2 reduction of total heat flux from ocean to atmosphere. Although the AMOC is slightly reduced under the solar dimming scenario, G1, relative to piControl, it is about 37% stronger than under abrupt4 × CO2 . The reduction of the AMOC under G1 is mainly a response to the heat flux change at the northern North Atlantic rather than to changes in the water flux and the wind stress. The AMOC transfers heat from tropics to high latitudes, helping to warm the high latitudes, and its strength is maintained under solar dimming rather than weakened by greenhouse gas forcing acting alone. Hence the relative reduction in high latitude ocean temperatures provided by solar radiation geoengineering, would tend to be counteracted by the correspondingly active AMOC circulation which furthermore transports warm surface waters towards the Greenland ice sheet, warming Arctic sea ice and permafrost

Marine nitrogen fixers mediate a low latitude pathway for atmospheric CO2 drawdown

Roughly a third (~30 ppm) of the carbon dioxide (CO2) that entered the ocean during ice ages is attributed to biological mechanisms. A leading hypothesis for the biological drawdown of CO2 is iron (Fe) fertilisation of the high latitudes, but modelling efforts attribute at most 10 ppm to this mechanism, leaving ~20 ppm unexplained. We show that an Fe-induced stimulation of dinitrogen (N2) fixation can induce a low latitude drawdown of 7–16 ppm CO2. This mechanism involves a closer coupling between N2 fixers and denitrifiers that alleviates widespread nitrate limitation. Consequently, phosphate utilisation and carbon export increase near upwelling zones, causing deoxygenation and deeper carbon injection. Furthermore, this low latitude mechanism reproduces the regional patterns of organic δ15N deposited in glacial sediments. The positive response of marine N2 fixation to dusty ice age conditions, first proposed twenty years ago, therefore compliments high latitude changes to amplify CO2 drawdown

Timing of primary tooth emergence among U.S. racial and ethnic groups

ObjectivesTo compare timing of tooth emergence among groups of American Indian (AI), Black and White children in the United States at 12 months of age.MethodsData were from two sources – a longitudinal study of a Northern Plains tribal community and a study with sites in Indiana, Iowa and North Carolina. For the Northern Plains study, all children (n = 223) were American Indian, while for the multisite study, children (n = 320) were from diverse racial groups. Analyses were limited to data from examinations conducted within 30 days of the child’s first birthday.ResultsAI children had significantly more teeth present (Mean: 7.8, Median: 8.0) than did Whites (4.4, 4.0, P < 0.001) or Blacks (4.5, 4.0, P < 0.001). No significant differences were detected between Black and White children (P = 0.58). There was no significant sex difference overall or within any of the racial groups.ConclusionsTooth emergence occurs at a younger age for AI children than it does for contemporary White or Black children in the United States.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135387/1/jphd12154.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135387/2/jphd12154_am.pd

Quantitative mechanical assessment of the whole prostate gland ex vivo using dynamic instrumented palpation

An instrumented palpation sensor, designed for measuring the dynamic modulus of tissue in vivo, has been developed and trialled on ex vivo whole prostate glands. The sensor consists of a flexible membrane sensor/actuator with an embedded strain gauge and is actuated using a dynamically varying airflow at frequencies of 1 and 5 Hz. The device was calibrated using an indentation stiffness measurement rig and gelatine samples with a range of static modulus similar to that reported in the literature for prostate tissue. The glands were removed from patients with diagnosed prostate cancer scheduled for radical prostatectomy, and the stiffness was measured within 30 min of surgical removal. Each prostate was later examined histologically in a column immediately below each indentation point and graded into one of the four groups; normal, benign prostatic hyperplasia, cancerous and mixed cancer and benign prostatic hyperplasia. In total, 11 prostates were assessed using multiple point probing, and the complex modulus at 1 and 5 Hz was calculated on a point-by-point basis. The device yielded values of quasi-static modulus of 15 ± 0.5 kPa and dynamic modulus of 20 ± 0.5 kPa for whole prostates, and a sensitivity of up to 80% with slightly lower specificity was achieved on diagnosis of prostate cancer using a combination of mechanical measures. This assessment did not take into account some obvious factors such as edge effects, overlap and clinical significance of the cancer, all of which would improve performance. The device, as currently configured, is immediately deployable in vivo. A number of improvements are also identified which could improve the sensitivity and specificity in future embodiments of the probe

Natural drivers of multidecadal Arctic sea ice variability over the last millennium

This is the final version. Available from Nature Research via the DOI in this record.The climate varies due to human activity, natural climate cycles, and natural events external to the climate system. Understanding the different roles played by these drivers of variability is fundamental to predicting near-term climate change and changing extremes, and to attributing observed change to anthropogenic or natural factors. Natural drivers such as large explosive volcanic eruptions or multidecadal cycles in ocean circulation occur infrequently and are therefore poorly represented within the observational record. Here we turn to the first high-latitude annually-resolved and absolutely dated marine record spanning the last millennium, and the Paleoclimate Modelling Intercomparison Project (PMIP) Phase 3 Last Millennium climate model ensemble spanning the same time period, to examine the influence of natural climate drivers on Arctic sea ice. We show that bivalve oxygen isotope data are recording multidecadal Arctic sea ice variability and through the climate model ensemble demonstrate that external natural drivers explain up to third of this variability. Natural external forcing causes changes in sea-ice mediated export of freshwater into areas of active deep convection, affecting the strength of the Atlantic Meridional Overturning Circulation (AMOC) and thereby northward heat transport to the Arctic. This in turn leads to sustained anomalies in sea ice extent. The models capture these positive feedbacks, giving us improved confidence in their ability to simulate future sea ice in in a rapidly evolving Arctic.Natural Environment Research Council (NERC)Natural Environment Research Council (NERC)Natural Environment Research Council (NERC)Leverhulme TrustAustralian Research CouncilEuropean Union’s Horizon 202

Reassessing the association: Evaluation of a polyalanine deletion variant of RUNX2 in non‐syndromic sagittal and metopic craniosynostosis

The RUNT‐related transcription factor RUNX2 plays a critical role in osteoblast differentiation, and alterations to gene dosage cause distinct craniofacial anomalies. Uniquely amongst the RUNT‐related family, vertebrate RUNX2 encodes a polyglutamine/polyalanine repeat (Gln23‐Glu‐Ala17 in humans), with the length of the polyalanine component completely conserved in great apes. Surprisingly, a frequent 6‐amino acid deletion polymorphism, p.(Ala84_Ala89)del, occurs in humans (termed 11A allele), and a previous association study (Cuellar et al. Bone 137:115395;2020) reported that the 11A variant was significantly more frequent in non‐syndromic sagittal craniosynostosis (nsSag; allele frequency [AF] = 0.156; 95% confidence interval [CI] 0.126–0.189) compared to non‐syndromic metopic craniosynostosis (nsMet; AF = 0.068; 95% CI 0.045–0.098). However, the gnomAD v.2.1.1 control population used by Cuellar et al. did not display Hardy–Weinberg equilibrium, hampering interpretation. To re‐examine this association, we genotyped the RUNX2 11A polymorphism in 225 individuals with sporadic nsSag as parent–child trios and 164 singletons with sporadic nsMet, restricting our analysis to individuals of European ancestry. We compared observed allele frequencies to the non‐transmitted alleles in the parent–child trios, and to the genome sequencing data from gnomAD v.4, which display Hardy–Weinberg equilibrium. Observed AFs (and 95% CI) were 0.076 (0.053–0.104) in nsSag and 0.082 (0.055–0.118) in nsMet, compared with 0.062 (0.042–0.089) in non‐transmitted parental alleles and 0.065 (0.063–0.067) in gnomAD v.4.0.0 non‐Finnish European control genomes. In summary, we observed a non‐significant excess, compared to gnomAD data, of 11A alleles in both nsSag (relative risk 1.18, 95% CI 0.83–1.67) and nsMet (relative risk 1.29, 95% CI 0.87–1.92), but we did not replicate the much higher excess of RUNX2 11A alleles in nsSag previously reported (p = 0.0001)

Separating Forced from Chaotic Climate Variability over the Past Millennium

Reconstructions of past climate show notable temperature variability over the past millennium, with relatively warm conditions during the Medieval Climate Anomaly (MCA) and a relatively cold Little Ice Age (LIA). Multimodel simulations of the past millennium are used together with a wide range of reconstructions of Northern Hemispheric mean annual temperature to separate climate variability from 850 to 1950 CE into components attributable to external forcing and internal climate variability. External forcing is found to contribute significantly to long-term temperature variations irrespective of the proxy reconstruction, particularly from 1400 onward. Over the MCA alone, however, the effect of forcing is only detectable in about half of the reconstructions considered, and the response to forcing in the models cannot explain the warm conditions around 1000 CE seen in some reconstructions. The residual from the detection analysis is used to estimate internal variability independent from climate modeling, and it is found that the recent observed 50- and 100-yr hemispheric temperature trends are substantially larger than any of the internally generated trends even using the large residuals over the MCA. Variations in solar output and explosive volcanism are found to be the main drivers of climate change from 1400 to 1900, but for the first time a significant contribution from greenhouse gas variations to the cold conditions during 1600-1800 is also detected. The proxy reconstructions tend to show a smaller forced response than is simulated by the models. This discrepancy is shown, at least partly, to be likely associated with the difference in the response to large volcanic eruptions between reconstructions and model simulations

The PMIP4 contribution to CMIP6 – Part 2: two interglacials, scientific objective and experimental design for Holocene and last interglacial simulations

Two interglacial epochs are included in the suite of Paleoclimate Modeling Intercomparison Project (PMIP4) simulations in the Coupled Model Intercomparison Project (CMIP6). The experimental protocols for Tier 1 simulations of the mid-Holocene (midHolocene, 6000 years before present) and the Last Interglacial (lig127k, 127,000 years before present) are described here. These equilibrium simulations are designed to examine the impact of changes in orbital forcing at times when atmospheric greenhouse gas levels were similar to those of the preindustrial period and the continental configurations were almost identical to modern. These simulations test our understanding of the interplay between radiative forcing and atmospheric circulation, and the connections among large-scale and regional climate changes giving rise to phenomena such as land-sea contrast and high-latitude amplification in temperature changes, and responses of the monsoons, as compared to today. They also provide an opportunity, through carefully designed additional CMIP6 Tier 2 and Tier 3 sensitivity experiments of PMIP4, to quantify the strength of atmosphere, ocean, cryosphere, and land-surface feedbacks. Sensitivity experiments are proposed to investigate the role of freshwater forcing in triggering abrupt climate changes within interglacial epochs. These feedback experiments naturally lead to a focus on climate evolution during interglacial periods, which will be examined through transient experiments. Analyses of the sensitivity simulations will also focus on interactions between extratropical and tropical circulation, and the relationship between changes in mean climate state and climate variability on annual to multi-decadal timescales. The comparative abundance of paleoenvironmental data and of quantitative climate reconstructions for the Holocene and Last Interglacial make these two epochs ideal candidates for systematic evaluation of model performance, and such comparisons will shed new light on the importance of external feedbacks (e.g., vegetation, dust) and the ability of state-of-the-art models to simulate climate changes realistically