Interior Point Methods and Preconditioning for PDE-Constrained Optimization Problems Involving Sparsity Terms

PDE-constrained optimization problems with control or state constraints are challenging from an analytical as well as numerical perspective. The combination of these constraints with a sparsity-promoting $\rm L^1$ term within the objective function requires sophisticated optimization methods. We propose the use of an Interior Point scheme applied to a smoothed reformulation of the discretized problem, and illustrate that such a scheme exhibits robust performance with respect to parameter changes. To increase the potency of this method we introduce fast and efficient preconditioners which enable us to solve problems from a number of PDE applications in low iteration numbers and CPU times, even when the parameters involved are altered dramatically

Does Faux Pas Detection in Adult Autism Reflect Differences in Social Cognition or Decision-Making Abilities?

43 typically-developed adults and 35 adults with ASD performed a cartoon faux pas test. Adults with ASD apparently over-detected faux pas despite good comprehension abilities, and were generally slower at responding. Signal detection analysis demonstrated that the ASD participants had significantly greater difficulty detecting whether a cartoon depicted a faux pas and showed a liberal response bias. Test item analysis demonstrated that the ASD group were not in agreement with a reference control group (n = 69) about which non-faux pas items were most difficult. These results suggest that the participants with ASD had a primary problem with faux pas detection, but that there is another factor at work, possibly compensatory, that relates to their choice of a liberal response criterion

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

Environmental DNA (eDNA ) analysis is a rapid, cost‐effective, non‐invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species‐specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and “metabarcoding” have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA . We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real‐time quantitative PCR (qPCR ) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using high‐throughput sequencing technology. With qPCR and a detection threshold of 1 of 12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4 of 12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species‐specific surveys

Deep forecasting of translational impact in medical research.

The value of biomedical research-a $1.7 trillion annual investment-is ultimately determined by its downstream, real-world impact, whose predictability from simple citation metrics remains unquantified. Here we sought to determine the comparative predictability of future real-world translation-as indexed by inclusion in patents, guidelines, or policy documents-from complex models of title/abstract-level content versus citations and metadata alone. We quantify predictive performance out of sample, ahead of time, across major domains, using the entire corpus of biomedical research captured by Microsoft Academic Graph from 1990-2019, encompassing 43.3 million papers. We show that citations are only moderately predictive of translational impact. In contrast, high-dimensional models of titles, abstracts, and metadata exhibit high fidelity (area under the receiver operating curve [AUROC] > 0.9), generalize across time and domain, and transfer to recognizing papers of Nobel laureates. We argue that content-based impact models are superior to conventional, citation-based measures and sustain a stronger evidence-based claim to the objective measurement of translational potential

Spectral reflectance of whale skin above the sea surface: a proposed measurement protocol

Great whales have been detected using very-high-resolution satellite imagery, suggesting this technology could be used to monitor whales in remote areas. However, the application of this method to whale studies is at an early developmental stage and several technical factors need to be addressed, including capacity for species differentiation and the maximum depth of detection in the water column. Both require knowledge of the spectral reflectance of the various whale species just above the sea surface, as when whales bodies break the surface of the water to breath, log or breach, there is, theoretically, no sea water between the whale’s skin and the satellite sensor. Here we tested whether such reflectance could be measured on dead whale tissue. We measured the spectral reflectance of fresh integument collected during the bowhead subsistence harvest, and of thawed integument samples from various species obtained following strandings and stored at -20°C. We show that fresh and thawed samples of whale integument have different spectral properties. The reflectance of fresh samples was higher than the reflectance of thawed samples, as integument appears to darken after death and with time, even under frozen conditions. In this study, we present the first whale reflectance estimates (without the influence of sea water and for dead tissue). These provide a baseline for additional work, needed to advance the use of satellite imagery to monitor whales and facilitate their conservation.MAVA Foundation, B B Roberts Fund, Cambridge Philosophical Society, Prescott Stranding Grants

In Vivo Assessment of Arsenic Bioavailability in Rice and Its Significance for Human Health Risk Assessment

BACKGROUND: Millions of people worldwide consume arsenic-contaminated rice; however, little is known about the uptake and bioavailability of arsenic species after arsenic-contaminated rice ingestion. OBJECTIVES: In this study, we assessed arsenic speciation in greenhouse-grown and supermarket-bought rice, and determined arsenic bioavailability in cooked rice using an in vivo swine model. RESULTS: In supermarket-bought rice, arsenic was present entirely in the inorganic form compared to greenhouse-grown rice (using irrigation water contaminated with sodium arsenate), where most (~ 86%) arsenic was present as dimethylarsinic acid (organic arsenic). Because of the low absolute bioavailability of dimethylarsinic acid and the high proportion of dimethylarsinic acid in greenhouse-grown rice, only 33 ± 3% (mean ± SD) of the total rice-bound arsenic was bioavailable. Conversely, in supermarket-bought rice cooked in water contaminated with sodium arsenate, arsenic was present entirely in the inorganic form, and bioavailability was high (89 ± 9%). CONCLUSIONS: These results indicate that arsenic bioavailability in rice is highly dependent on arsenic speciation, which in turn can vary depending on rice cultivar, arsenic in irrigation water, and the presence and nature of arsenic speciation in cooking water. Arsenic speciation and bioavailability are therefore critical parameters for reducing uncertainties when estimating exposure from the consumption of rice grown and cooked using arsenic-contaminated water

Alkali activation of vitreous calcium aluminosilicate derived from glass fiber waste

The properties and microstructure of alkali-activated (AA) vitreous calcium aluminosilicate (VCAS) are presented in this paper. VCAS is manufactured from a by-product of the glass fiber industry and has been activated using NaOH and KOH solutions. The microstructure and mechanical properties of AA VCAS pastes and mortars are reported. The results show that depending on the type and concentration of hydroxide solution used, mortar samples with compressive strengths up to 77 MPa can be formed after curing for three days at 65 °C. The research demonstrates the potential of VCAS to produce AA cements and the importance of alkali type and concentration in optimizing properties and microstructure.Mitsuuchi Tashima, M.; Soriano Martinez, L.; Borrachero Rosado, MV.; Monzó Balbuena, JM.; Cheeseman, CR.; Paya Bernabeu, JJ. (2012). Alkali activation of vitreous calcium aluminosilicate derived from glass fiber waste. Journal of Sustainable Cement-Based Materials. 1(3):83-93. doi:10.1080/21650373.2012.742610S839313Mahasenan N, Smith S, Humphreys K. The cement industry and global climate change: current and potential future cement industry CO2emissions. Greenhouse Gas Control Technologies – 6th International Conference. Oxford: Pergamon; 2003. p. 995–1000.Schneider, M., Romer, M., Tschudin, M., & Bolio, H. (2011). Sustainable cement production—present and future. Cement and Concrete Research, 41(7), 642-650. doi:10.1016/j.cemconres.2011.03.019WBCSD – World Business Council for Sustainable Development. Cement industry energy and CO2performance – Getting numbers right. Edited by WBCSD, Geneva-Switzerland (ISBN 978-3-940388-48-3). 2009.Shi, C., Jiménez, A. F., & Palomo, A. (2011). New cements for the 21st century: The pursuit of an alternative to Portland cement. Cement and Concrete Research, 41(7), 750-763. doi:10.1016/j.cemconres.2011.03.016Duxson, P., Fernández-Jiménez, A., Provis, J. L., Lukey, G. C., Palomo, A., & van Deventer, J. S. J. (2006). Geopolymer technology: the current state of the art. Journal of Materials Science, 42(9), 2917-2933. doi:10.1007/s10853-006-0637-zFernández-Jiménez, A., Palomo, A., & Criado, M. (2005). Microstructure development of alkali-activated fly ash cement: a descriptive model. Cement and Concrete Research, 35(6), 1204-1209. doi:10.1016/j.cemconres.2004.08.021Hossain, A. B., Shirazi, S. A., Persun, J., & Neithalath, N. (2008). Properties of Concrete Containing Vitreous Calcium Aluminosilicate Pozzolan. Transportation Research Record: Journal of the Transportation Research Board, 2070(1), 32-38. doi:10.3141/2070-05Neithalath, N., Persun, J., & Hossain, A. (2009). Hydration in high-performance cementitious systems containing vitreous calcium aluminosilicate or silica fume. Cement and Concrete Research, 39(6), 473-481. doi:10.1016/j.cemconres.2009.03.006Tashima MM, Soriano L, Borrachero MV, Monzó J, Payá J. Effect of curing time on the microstructure and mechanical strength development of alkali activated nbinders based on vitreous calcium aluminosilicate (VCAS). Bull. Mater. Sci. in press.Hemmings RT, Nelson RD, Graves PL, Cornelius BJ. White pozzolan composition and blended cements containing same. Patent US6776838. 2004.Provis, J. L., Lukey, G. C., & van Deventer, J. S. J. (2005). Do Geopolymers Actually Contain Nanocrystalline Zeolites? A Reexamination of Existing Results. Chemistry of Materials, 17(12), 3075-3085. doi:10.1021/cm050230iCriado, M., Fernández-Jiménez, A., de la Torre, A. G., Aranda, M. A. G., & Palomo, A. (2007). An XRD study of the effect of the SiO2/Na2O ratio on the alkali activation of fly ash. Cement and Concrete Research, 37(5), 671-679. doi:10.1016/j.cemconres.2007.01.013Rees, C. A., Provis, J. L., Lukey, G. C., & van Deventer, J. S. J. (2007). In Situ ATR-FTIR Study of the Early Stages of Fly Ash Geopolymer Gel Formation. Langmuir, 23(17), 9076-9082. doi:10.1021/la701185gLee, W. K. W., & van Deventer, J. S. J. (2003). Use of Infrared Spectroscopy to Study Geopolymerization of Heterogeneous Amorphous Aluminosilicates. Langmuir, 19(21), 8726-8734. doi:10.1021/la026127eGarcía-Lodeiro, I., Fernández-Jiménez, A., Blanco, M. T., & Palomo, A. (2007). FTIR study of the sol–gel synthesis of cementitious gels: C–S–H and N–A–S–H. Journal of Sol-Gel Science and Technology, 45(1), 63-72. doi:10.1007/s10971-007-1643-6Barbosa VFF. Sintese e caracterização de polissialatos (Synthesis and characterization of polysialates) [PhD thesis] (in Portuguese). Instituto Militar de Engenharia. Rio de Janeiro - Brazil. 190 p. 1999.Bernal, S. A., Rodríguez, E. D., Mejía de Gutiérrez, R., Gordillo, M., & Provis, J. L. (2011). Mechanical and thermal characterisation of geopolymers based on silicate-activated metakaolin/slag blends. Journal of Materials Science, 46(16), 5477-5486. doi:10.1007/s10853-011-5490-zBoccaccini, A. R., Bücker, M., Bossert, J., & Marszalek, K. (1997). Glass matrix composites from coal flyash and waste glass. Waste Management, 17(1), 39-45. doi:10.1016/s0956-053x(97)00035-4Kourti, I., Rani, D. A., Deegan, D., Boccaccini, A. R., & Cheeseman, C. R. (2010). Production of geopolymers using glass produced from DC plasma treatment of air pollution control (APC) residues. Journal of Hazardous Materials, 176(1-3), 704-709. doi:10.1016/j.jhazmat.2009.11.089Lampris, C., Lupo, R., & Cheeseman, C. R. (2009). Geopolymerisation of silt generated from construction and demolition waste washing plants. Waste Management, 29(1), 368-373. doi:10.1016/j.wasman.2008.04.007Wu, H.-C., & Sun, P. (2007). New building materials from fly ash-based lightweight inorganic polymer. Construction and Building Materials, 21(1), 211-217. doi:10.1016/j.conbuildmat.2005.06.052Kourti, I., Amutha Rani, D., Boccaccini, A. R., & Cheeseman, C. R. (2011). Geopolymers from DC Plasma–Treated Air Pollution Control Residues, Metakaolin, and Granulated Blast Furnace Slag. Journal of Materials in Civil Engineering, 23(6), 735-740. doi:10.1061/(asce)mt.1943-5533.000017

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development is ongoing, with strong commercial interest, and new uses are continually being discovered. General applications of eDNA and guidelines for best practice in freshwater systems have been established, but habitat-specific assessments are lacking. Ponds are highly diverse, yet understudied systems that could benefit from eDNA monitoring. However, eDNA applications in ponds and methodological constraints specific to these environments remain unaddressed. Following a stakeholder workshop in 2017, researchers combined knowledge and expertise to review these applications and challenges that must be addressed for the future and consistency of eDNA monitoring in ponds. The greatest challenges for pond eDNA surveys are representative sampling, eDNA capture, and potential PCR inhibition. We provide recommendations for sampling, eDNA capture, inhibition testing, and laboratory practice, which should aid new and ongoing eDNA projects in ponds. If implemented, these recommendations will contribute towards an eventual broad standardisation of eDNA research and practice, with room to tailor workflows for optimal analysis and different applications. Such standardisation will provide more robust, comparable, and ecologically meaningful data to enable effective conservation and management of pond biodiversity

Brachytherapy for rhabdomyosarcoma: Survey of international clinical practice and development of guidelines.

BACKGROUND AND PURPOSE: The purpose of this study was to address the lack of published data on the use of brachytherapy in pediatric rhabdomyosarcoma by describing current practice as starting point to develop consensus guidelines. MATERIALS AND METHODS: An international expert panel on the treatment of pediatric rhabdomyosarcoma comprising 24 (pediatric) radiation oncologists, brachytherapists and pediatric surgeons met for a Brachytherapy Workshop hosted by the European paediatric Soft tissue Sarcoma Study Group (EpSSG). The panel's clinical experience, the results of a previously distributed questionnaire, and a review of the literature were presented. RESULTS: The survey indicated the most common use of brachytherapy to be in combination with tumor resection, followed by brachytherapy as sole local therapy modality. HDR was increasingly deployed in pediatric practice, especially for genitourinary sites. Brachytherapy planning was mostly by 3D imaging based on CT. Recommendations for patient selection, treatment requirements, implant technique, delineation, dose prescription, dose reporting and clinical management were defined. CONCLUSIONS: Consensus guidelines for the use of brachytherapy in pediatric rhabdomyosarcoma have been developed through multicenter collaboration establishing the basis for future work. These have been adopted for the open EpSSG overarching study for children and adults with Frontline and Relapsed RhabdoMyoSarcoma (FaR-RMS)

Age-related changes in global motion coherence: conflicting haemodynamic and perceptual responses

Our aim was to use both behavioural and neuroimaging data to identify indicators of perceptual decline in motion processing. We employed a global motion coherence task and functional Near Infrared Spectroscopy (fNIRS). Healthy adults (n = 72, 18-85) were recruited into the following groups: young (n = 28, mean age = 28), middle-aged (n = 22, mean age = 50), and older adults (n = 23, mean age = 70). Participants were assessed on their motion coherence thresholds at 3 different speeds using a psychophysical design. As expected, we report age group differences in motion processing as demonstrated by higher motion coherence thresholds in older adults. Crucially, we add correlational data showing that global motion perception declines linearly as a function of age. The associated fNIRS recordings provide a clear physiological correlate of global motion perception. The crux of this study lies in the robust linear correlation between age and haemodynamic response for both measures of oxygenation. We hypothesise that there is an increase in neural recruitment, necessitating an increase in metabolic need and blood flow, which presents as a higher oxygenated haemoglobin response. We report age-related changes in motion perception with poorer behavioural performance (high motion coherence thresholds) associated with an increased haemodynamic response