Designing a Suite of Models to Explore Critical Zone Function

Critical Zone; weathering; hydrology; ecology; watershedsThe Critical Zone (CZ) incorporates all aspects of the earth's environment from the vegetation canopy to the bottom of groundwater. CZ researchers target processes that cross timescales from that of water fluxes (milliseconds to decades) to that of the evolution of landforms (thousands to tens of millions of years). Conceptual and numerical models are used to investigate the important fluxes: water, energy, solutes, carbon, nitrogen, and sediments. Depending upon the questions addressed, these models must calculate the distribution of landforms, regolith structure and chemistry, biota, and the chemistry of water, solutes, sediments, and soil atmospheres. No single model can accomplish all these objectives. We are designing a group of models or model capabilities to explore the CZ and testing them at the Susquehanna Shale Hills CZ Observatory. To examine processes over different timescales, we establish the core hydrologic fluxes using the Penn State Integrated Hydrologic Model (PIHM) – and then augment PIHM with simulation modules. For example, most land-atmosphere models currently do not incorporate an accurate representation of the geologic subsurface. We are exploring what aspects of subsurface structure must be accurately modelled to simulate water, carbon, energy, and sediment fluxes accurately. Only with a suite of modeling tools will we learn to forecast – earthcast -- the future CZ

Designing a Suite of Models to Explore Critical Zone Function

Critical Zone; weathering; hydrology; ecology; watershedsThe Critical Zone (CZ) incorporates all aspects of the earth's environment from the vegetation canopy to the bottom of groundwater. CZ researchers target processes that cross timescales from that of water fluxes (milliseconds to decades) to that of the evolution of landforms (thousands to tens of millions of years). Conceptual and numerical models are used to investigate the important fluxes: water, energy, solutes, carbon, nitrogen, and sediments. Depending upon the questions addressed, these models must calculate the distribution of landforms, regolith structure and chemistry, biota, and the chemistry of water, solutes, sediments, and soil atmospheres. No single model can accomplish all these objectives. We are designing a group of models or model capabilities to explore the CZ and testing them at the Susquehanna Shale Hills CZ Observatory. To examine processes over different timescales, we establish the core hydrologic fluxes using the Penn State Integrated Hydrologic Model (PIHM) – and then augment PIHM with simulation modules. For example, most land-atmosphere models currently do not incorporate an accurate representation of the geologic subsurface. We are exploring what aspects of subsurface structure must be accurately modelled to simulate water, carbon, energy, and sediment fluxes accurately. Only with a suite of modeling tools will we learn to forecast – earthcast -- the future CZ

Influence of weather and endogenous cycles on spatiotemporal yield variation in oil palm

Oil palm is the major source of vegetable oil in the world and Indonesia is the main palm oil producing country. There is limited knowledge on the factors accounting for spatial and temporal variation in fresh fruit bunches (FFB) yield. Here we investigated relationships between weather and endogenous factors with FFB yield and its components (bunch number and individual bunch weight) using data collected from well-managed plantations in Indonesia. The database included many sites and years (total of 136 block-years observations), portraying a wide range of FFB yield and environmental conditions. We used average annual values to detect spatial variations in yield associated with weather, and monthly values to detect temporal yield variations in yield associated with weather and endogenous cycles. We found that water stress was the key factor accounting for the spatial and/or temporal variation in FFB yield. Our analysis also highlights the importance of vapor pressure deficit (VPD) as a stress factor in oil palm, with this study being the first to demonstrate the negative relationship between yield and VPD and yield and water-use efficiency at the block level. Meteorological anomalies during the bunch failure, anthesis, and sex differentiation periods had the largest impact on yield. Besides climate factors, we confirmed the existence of endogenous yield cycles, with high-yield cycles typically followed by low-yield cycles and vice versa. Our findings extend current knowledge about sources of variation in oil palm yield, providing useful information to describe oil palm production environments and improve oil palm modeling and yield forecasting.Fil: Monzon, Juan Pablo. Universidad de Nebraska - Lincoln; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; ArgentinaFil: Jabloun, Mohamed. University of Agriculture Wageningen; Países BajosFil: Cock, James. Centro Internacional de Agricultura Tropical; ColombiaFil: Caliman, Jean Pierre. Smart Research Institute; IndonesiaFil: Couëdel, Antoine. Universidad de Nebraska - Lincoln; Estados UnidosFil: Donough, Christopher R.. Universidad de Nebraska - Lincoln; Estados UnidosFil: Vui, Philip Ho Vun. Wilmar International; IndonesiaFil: Lim, Ya Li. Universidad de Nebraska - Lincoln; Estados UnidosFil: Mathews, Joshua. Research Centre Pt Bumitama Gunajaya Agro; IndonesiaFil: Oberthür, Thomas. Mohammed Vi Polytechnic University; MarruecosFil: Prabowo, Noto E.. Jln. A. Yani No. 2; IndonesiaFil: Rattalino Edreira, Juan Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad de Nebraska - Lincoln; Estados UnidosFil: Sidhu, Manjit. Tebing Tinggi Deli; IndonesiaFil: Slingerland, Maja A.. University of Agriculture Wageningen; Países BajosFil: Sugianto, Hendra. Universidad de Nebraska - Lincoln; Estados UnidosFil: Grassini, Patricio. Universidad de Nebraska - Lincoln; Estados Unido

Fostering a climate-smart intensification for oil palm

Oil palm production in Indonesia illustrates the intense pressure that exists worldwide to convert natural ecosystems to agricultural production. Oil palm production has increased because of expansion of cultivated area rather than due to average-yield increases. We used a data-rich modelling approach to investigate how intensification on existing plantations could help Indonesia meet palm oil demand while preserving fragile ecosystems. We found that average current yield represents 62% and 53% of the attainable yield in large and smallholder plantations, respectively. Narrowing yield gaps via improved agronomic management, together with a limited expansion that excludes fragile ecosystems, would save 2.6 million hectares of forests and peatlands and avoid 732 MtCO2e compared with following historical trends in yield and land use. Fine-tuning policy to promote intensification, along with investments in agricultural research and development, can help reconcile economic and environmental goals

Shortening harvest interval, reaping benefits? A study on harvest practices in oil palm smallholder farming systems in Indonesia

CONTEXT: Smallholders are responsible for a large share of global palm oil production. Yet, in Indonesia, the main palm oil producing country, smallholders’ yields remain low. Better management practices, including short harvest interval (HI, the number of days between two harvest rounds), could help to raise smallholder yields. However, at present, HI is long in smallholder fields and the drivers underlying this phenomenon are poorly understood. OBJECTIVE: We explored agronomic, socio-economic, and institutional factors that underlie harvesting practices in independent oil palm smallholder farming systems in Indonesia to assess scope for sustainable intensification through shorter HI and reduced harvest losses. METHODS: Combining methods from agronomy and anthropology, we followed harvest interval of 950 farmers in six representative locations across Indonesia via farmer diaries over a period of two years to establish a correlation with yield. To quantify this relationship, we conducted post-harvest field measurements, and to explain which underlying factors impact HI we did qualitative interviews and surveys. RESULTS AND CONCLUSIONS: The HI of smallholders in our study ranged from 10 to 39 days (average: 17-d). Half of the farmers followed long HI (\u3e16-d). Key factors impacting HI include annual fresh fruit bunch (FFB) yield, total palm area per farmer, trusted labor availability, plantation accessibility, and FFB price. Farmers responded to low yield by prolonging HI to increase labor productivity and optimize labor and transportation costs. SIGNIFICANCE: This study contributes to a better understanding of the relation between HI and yield in smallholder farming systems, by uncovering how socio-economic and institutional factors sometimes override agronomic considerations. Long HI can potentially lead to harvest loss from loose fruits and missed bunches, and reduce oil quality from overripe bunches. However, to obtain the benefits of shorter HI requires collective action and incentives along the supply chain to streamline the harvest and sale process

The Synergistic Effect of SAHA and Parthenolide in MDA-MB231 Breast Cancer Cells

The sesquiterpene lactone Parthenolide (PN) exerted a cytotoxic effect on MDA-MB231 cells, a triple-negative breast cancer (TNBC) cell line, but its effectiveness was scarce when employed at low doses. This represents an obstacle for a therapeutic utilization of PN. In order to overcome this difficulty we associated to PN the suberoylanilide hydroxamic acid (SAHA), an histone deacetylase inhibitor. Our results show that SAHA synergistically sensitized MDA-MB231 cells to the cytotoxic effect of PN. It is noteworthy that treatment with PN alone stimulated the survival pathway Akt/mTOR and the consequent nuclear translocation of Nrf2, while treatment with SAHA alone induced autophagic activity. However, when the cells were treated with SAHA/PN combination, SAHA suppressed PN effect on Akt/mTOR/Nrf2 pathway, while PN reduced the prosurvival autophagic activity of SAHA. In addition SAHA/PN combination induced GSH depletion, fall in Δψm, release of cytochrome c, activation of caspase 3 and apoptosis. Finally we demonstrated that combined treatment maintained both hyperacetylation of histones H3 and H4 induced by SAHA and down-regulation of DNMT1 expression induced by PN. Inhibition of the DNA-binding activity of NF-kB, which is determined by PN, was also observed after combined treatment. In conclusion, combination of PN to SAHA inhibits the cytoprotective responses induced by the single compounds, but does not alter the mechanisms leading to the cytotoxic effects. Taken together our results suggest that this combination could be a candidate for TNBC therapy. J. Cell. Physiol. 230: 1276-1289, 2015

One-Sided Position-Dependent Smoothness-Increasing Accuracy-Conserving (SIAC) Filtering Over Uniform and Non-Uniform Meshes

In this paper, we introduce a new position-dependent Smoothness-Increasing Accuracy-Conserving (SIAC) filter that retains the benefits of position dependence while ameliorating some of its shortcomings. As in the previous position-dependent filter, our new filter can be applied near domain boundaries, near a discontinuity in the solution, or at the interface of different mesh sizes; and as before, in general, it numerically enhances the accuracy and increases the smoothness of approximations obtained using the discontinuous Galerkin (dG) method. However, the previously proposed position-dependent one-sided filter had two significant disadvantages: (1) increased computational cost (in terms of function evaluations), brought about by the use of $4k+1$ central B-splines near a boundary (leading to increased kernel support) and (2) increased numerical conditioning issues that necessitated the use of quadruple precision for polynomial degrees of $k\ge 3$ for the reported accuracy benefits to be realizable numerically. Our new filter addresses both of these issues --- maintaining the same support size and with similar function evaluation characteristicsas the symmetric filter in a way that has better numerical conditioning --- making it, unlike its predecessor, amenable for GPU computing. Our new filter was conceived by revisiting the original error analysis for superconvergence of SIAC filters and by examining the role of the B-splines and their weights in the SIAC filtering kernel. We demonstrate, in the uniform mesh case, that our new filter is globally superconvergent for $k=1$ and superconvergent in the interior (e.g., region excluding the boundary) for $k\ge2$. Furthermore, we present the first theoretical proof of superconvergence for postprocessing over smoothly varying meshes, and explain the accuracy-order conserving nature of this new filter when applied to certain non-uniform meshes cases. We provide numerical examples supporting our theoretical results and demonstrating that our new filter, in general, enhances the smoothness and accuracy of the solution. Numerical results are presented for solutions of both linear and nonlinear equation solved on both uniform and non-uniform one- and two-dimensional meshes

B-cell-specific checkpoint molecules that regulate anti-tumour immunity.

The role of B cells in anti-tumour immunity is still debated and, accordingly, immunotherapies have focused on targeting T and natural killer cells to inhibit tumour growth1,2. Here, using high-throughput flow cytometry as well as bulk and single-cell RNA-sequencing and B-cell-receptor-sequencing analysis of B cells temporally during B16F10 melanoma growth, we identified a subset of B cells that expands specifically in the draining lymph node over time in tumour-bearing mice. The expanding B cell subset expresses the cell surface molecule T cell immunoglobulin and mucin domain 1 (TIM-1, encoded by Havcr1) and a unique transcriptional signature, including multiple co-inhibitory molecules such as PD-1, TIM-3, TIGIT and LAG-3. Although conditional deletion of these co-inhibitory molecules on B cells had little or no effect on tumour burden, selective deletion of Havcr1 in B cells both substantially inhibited tumour growth and enhanced effector T cell responses. Loss of TIM-1 enhanced the type 1 interferon response in B cells, which augmented B cell activation and increased antigen presentation and co-stimulation, resulting in increased expansion of tumour-specific effector T cells. Our results demonstrate that manipulation of TIM-1-expressing B cells enables engagement of the second arm of adaptive immunity to promote anti-tumour immunity and inhibit tumour growth

PTEN deficiency: a role in mammary carcinogenesis

The PTEN gene is often mutated in primary human tumors and cell lines, but the low rate of somatic PTEN mutation in human breast cancer has led to debate over the role of this tumor suppressor in this disease. The involvement of PTEN in human mammary oncogenesis has been implicated from studies showing that germline PTEN mutation in Cowden disease predisposes to breast cancer, the frequent loss of heterozygosity at the PTEN locus, and reduced PTEN protein levels in sporadic breast cancers. To assay the potential contribution of PTEN loss in breast tumor promotion, Li et al. [1] crossed Pten heterozygous mice with mouse mammary tumor virus-Wnt-1 transgenic (Wnt-1 TG, Pten+/-) mice. Mammary ductal carcinoma developed earlier in Wnt-1 TG, Pten+/- mice than in mice bearing either genetic change alone, and showed frequent loss of the remaining wild-type PTEN allele. These data indicate a role for PTEN in breast tumorigenesis in an in vivo model