fenics_ice 1.0: A framework for quantifying initialisation uncertainty for time-dependent ice-sheet models

Mass loss due to dynamic changes in ice sheets is a significant contributor to sea level rise, and this contribution is expected to increase in the future. Numerical codes simulating the evolution of ice sheets can potentially quantify this future contribution. However, the uncertainty inherent in these models propagates into projections of sea level rise is and hence crucial to understand. Key variables of ice sheet models, such as basal drag or ice stiffness, are typically initialized using inversion methodologies to ensure that models match present observations. Such inversions often involve tens or hundreds of thousands of parameters, with unknown uncertainties and dependencies. The computationally intensive nature of inversions along with their high number of parameters mean traditional methods such as Monte Carlo are expensive for uncertainty quantification. Here we develop a framework to estimate the posterior uncertainty of inversions and project them onto sea level change projections over the decadal timescale. The framework treats parametric uncertainty as multivariate Gaussian and exploits the equivalence between the Hessian of the model and the inverse covariance of the parameter set. The former is computed efficiently via algorithmic differentiation, and the posterior covariance is propagated in time using a time-dependent model adjoint to produce projection error bars. This work represents an important step in quantifying the internal uncertainty of projections of ice sheet models.</p

Law Libraries and Laboratories: The Legacies of Langdell and His Metaphor

Law Librarians and others have often referred to Harvard Law School Dean C.C. Langdell’s statements that the law library is the lawyer’s laboratory. Professor Danner examines the context of what Langdell through his other writings, the educational environment at Harvard in the late nineteenth century, and the changing perceptions of university libraries generally. He then considers how the “laboratory metaphor” has been applied by librarians and legal scholars during the twentieth century and into the twenty-first. The article closes with thoughts on Langdell’s legacy for law librarians and the usefulness of the laboratory metaphor

Understanding Urban Demand for Wild Meat in Vietnam: Implications for Conservation Actions

Vietnam is a significant consumer of wildlife, particularly wild meat, in urban restaurant settings. To meet this demand, poaching of wildlife is widespread, threatening regional and international biodiversity. Previous interventions to tackle illegal and potentially unsustainable consumption of wild meat in Vietnam have generally focused on limiting supply. While critical, they have been impeded by a lack of resources, the presence of increasingly organised criminal networks and corruption. Attention is, therefore, turning to the consumer, but a paucity of research investigating consumer demand for wild meat will impede the creation of effective consumer-centred interventions. Here we used a mixed-methods research approach comprising a hypothetical choice modelling survey and qualitative interviews to explore the drivers of wild meat consumption and consumer preferences among residents of Ho Chi Minh City, Vietnam. Our findings indicate that demand for wild meat is heterogeneous and highly context specific. Wild-sourced, rare, and expensive wild meat-types are eaten by those situated towards the top of the societal hierarchy to convey wealth and status and are commonly consumed in lucrative business contexts. Cheaper, legal and farmed substitutes for wild-sourced meats are also consumed, but typically in more casual consumption or social drinking settings. We explore the implications of our results for current conservation interventions in Vietnam that attempt to tackle illegal and potentially unsustainable trade in and consumption of wild meat and detail how our research informs future consumer-centric conservation actions

First Record of the Coffee Berry Borer, Hypothenemus hampei (Ferrari, 1867), on the Hawaiian Island of Lanai (Coleoptera: Curculionidae: Scolytinae)

A survey for scolytine bark and ambrosia beetles undertaken on the entomologically understudied Hawaiian island of Lanai revealed for the first time the presence there of the coffee berry borer, Hypothenemus hampei (Ferrari, 1867), a serious exotic pest of cultivated coffee. Lanai is chronologically the fourth Hawaiian island on which H. hampei has been found, following its initial detection on the island of Hawaii, followed by Oahu then Maui. We present the new records from Lanai in detail, together with a map of collecting sites and photographs of an adult specimen, demonstrating that the beetle is now widespread on Lanai, occurring at high and low elevations, and in both mesic and xeric environments

AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data.

Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples. AMULET has high precision, estimated via donor-based multiplexing, and high recall, estimated via simulated multiplets, compared to alternatives and identifies multiplets most effectively when a certain read depth of 25K median valid reads per nucleus is achieved

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

Proteomic and transcriptomic data from wild-type and laboratory-evolved strains of Escherichia coli are consistent with predicted pathway usage from optimal growth rate solutions.In laboratory-evolved strains, there is an upregulation of the pathways in the computed optimal growth states, and downregulation of non-functional pathways.Known regulatory mechanisms are only partially responsible for altered metabolic pathway activity

Increased B Cell ADAM10 in Allergic Patients and Th2 Prone Mice

ADAM10, as the sheddase of the low affinity IgE receptor (CD23), promotes IgE production and thus is a unique target for attenuating allergic disease. Herein, we describe that B cell levels of ADAM10, specifically, are increased in allergic patients and Th2 prone WT mouse strains (Balb/c and A/J). While T cell help augments ADAM10 expression, Balb WT B cells exhibit increased ADAM10 in the naïve state and even more dramatically increased ADAM10 after anti-CD40/IL4 stimulation compared C57 (Th1 prone) WT B cells. Furthermore, ADAM17 and TNF are reduced in allergic patients and Th2 prone mouse strains (Balb/c and A/J) compared to Th1 prone controls. To further understand this regulation, ADAM17 and TNF were studied in C57Bl/6 and Balb/c mice deficient in ADAM10. C57-ADAM10B-/- were more adept at increasing ADAM17 levels and thus TNF cleavage resulting in excess follicular TNF levels and abnormal secondary lymphoid tissue architecture not noted in Balb-ADAM10B-/-. Moreover, the level of B cell ADAM10 as well as Th context is critical for determining IgE production potential. Using a murine house dust mite airway hypersensitivity model, we describe that high B cell ADAM10 level in a Th2 context (Balb/c WT) is optimal for disease induction including bronchoconstriction, goblet cell metaplasia, mucus, inflammatory cellular infiltration, and IgE production. Balb/c mice deficient in B cell ADAM10 have attenuated lung and airway symptoms compared to Balb WT and are actually most similar to C57 WT (Th1 prone). C57-ADAM10B-/- have even further reduced symptomology. Taken together, it is critical to consider both innate B cell levels of ADAM10 and ADAM17 as well as Th context when determining host susceptibility to allergic disease. High B cell ADAM10 and low ADAM17 levels would help diagnostically in predicting Th2 disease susceptibility; and, we provide support for the use ADAM10 inhibitors in treating Th2 disease

The Sample Analysis at Mars Investigation and Instrument Suite

The Sample Analysis at Mars (SAM) investigation of the Mars Science Laboratory(MSL) addresses the chemical and isotopic composition of the atmosphere and volatilesextracted from solid samples. The SAM investigation is designed to contribute substantiallyto the mission goal of quantitatively assessing the habitability of Mars as an essentialstep in the search for past or present life on Mars. SAM is a 40 kg instrument suite locatedin the interior of MSLs Curiosity rover. The SAM instruments are a quadrupole massspectrometer, a tunable laser spectrometer, and a 6-column gas chromatograph all coupledthrough solid and gas processing systems to provide complementary information on thesame samples. The SAM suite is able to measure a suite of light isotopes and to analyzevolatiles directly from the atmosphere or thermally released from solid samples. In additionto measurements of simple inorganic compounds and noble gases SAM will conducta sensitive search for organic compounds with either thermal or chemical extraction fromsieved samples delivered by the sample processing system on the Curiosity rovers roboticarm

C5 deficiency and C5a or C5aR blockade protects against cerebral malaria

Experimental infection of mice with Plasmodium berghei ANKA (PbA) provides a powerful model to define genetic determinants that regulate the development of cerebral malaria (CM). Based on the hypothesis that excessive activation of the complement system may confer susceptibility to CM, we investigated the role of C5/C5a in the development of CM. We show a spectrum of susceptibility to PbA in a panel of inbred mice; all CM-susceptible mice examined were found to be C5 sufficient, whereas all C5-deficient strains were resistant to CM. Transfer of the C5-defective allele from an A/J (CM resistant) onto a C57BL/6 (CM-susceptible) genetic background in a congenic strain conferred increased resistance to CM; conversely, transfer of the C5-sufficient allele from the C57BL/6 onto the A/J background recapitulated the CM-susceptible phenotype. The role of C5 was further explored in B10.D2 mice, which are identical for all loci other than C5. C5-deficient B10.D2 mice were protected from CM, whereas C5-sufficient B10.D2 mice were susceptible. Antibody blockade of C5a or C5a receptor (C5aR) rescued susceptible mice from CM. In vitro studies showed that C5a-potentiated cytokine secretion induced by the malaria product P. falciparum glycosylphosphatidylinositol and C5aR blockade abrogated these amplified responses. These data provide evidence implicating C5/C5a in the pathogenesis of CM

Non-standard embedding and five-branes in heterotic M-Theory

We construct vacua of M-theory on S^1/Z_2 associated with Calabi-Yau three-folds. These vacua are appropriate for compactification to N=1 supersymmetry theories in both four and five dimensions. We allow for general E_8 x E_8 gauge bundles and for the presence of five-branes. The five-branes span the four-dimensional uncompactified space and are wrapped on holomorphic curves in the Calabi-Yau space. Properties of these vacua, as well as of the resulting low-energy theories, are discussed. We find that the low-energy gauge group is enlarged by gauge fields that originate on the five-brane world-volumes. In addition, the five-branes increase the types of new E_8 x E_8 breaking patterns allowed by the non-standard embedding. Characteristic features of the low-energy theory, such as the threshold corrections to the gauge kinetic functions, are significantly modified due to the presence of the five-branes, as compared to the case of standard or non-standard embeddings without five-branes.Comment: 34 pages, Latex 2e with amsmath, typos removed, factors corrected, refs improve