Combining Biophysical and Price Simulations to Assess the Economics of Long-Term Crop Rotations

Biophysical simulation models (e.g. APSIM) using historical rainfall data are increasingly being used to provide yield and other data on crop rotations in various regions of Australia. However, to analyse the economics of these rotations it is desirable to incorporate the other main driver of profitability, price variation. Because the context was that APSIM was being used to simulate an existing trial site being monitored by a farmer group Gross Margin output was considered most appropriate. Long-run rotational gross margins were calculated for the various rotations with yields (and other physical outputs) derived from APSIM simulations over a period of 100+ years and prices simulated in @Risk based on subjective triangular price distributions elicited from farmers in the group. Rotations included chickpeas, cotton, lucerne, sorghum, wheat and different lengths of fallow. Output presented to the farmers included mean annual gross margins and distributions of gross margins presented as probability distributions, cumulative probability distributions and box and whisker plots. Cotton rotations were the most profitable but had greater declines in soil fertility and greater drainage out of the root zone.Crop Production/Industries,

Combining biophysical and price simulations to assess the economics of long-term crop rotations

Long-run rotational gross margins were calculated with yields derived from biophysical simulations in APSIM over a period of 100+ years and prices simulated in @Risk based on subjective triangular price distributions elicited from the Jimbour Plains farmer group. Rotations included chickpeas, cotton, lucerne, sorghum, wheat and different lengths of fallow. Output presented to the farmers included mean annual GMs and distributions of GMs with box and whisker plots found to be suitable. Mean-standard deviation and first and second-degree stochastic dominance efficiency measures were also calculated. Including lucerne in the rotations improved some sustainability indicators but reduced profitability.Crop Production/Industries, Farm Management,

Inverse Magnetoresistance of Molecular Junctions

We present calculations of spin-dependent electron transport through single organic molecules bridging pairs of iron nanocontacts. We predict the magnetoresistance of these systems to switch from positive to negative with increasing applied bias for both conducting and insulating molecules. This novel inverse magnetoresistance phenomenon is robust, does not depend on the presence of impurities, and is unique to molecular and atomic nanoscale magnetic junctions. Its physical origin is identified and its relevance to experiment and to potential technological applications is discussed.Comment: 5 pages, 3 figures; published version Phys. Rev.

Development and application of two novel monoclonal antibodies against overexpressed CD26 and integrin α3 in human pancreatic cancer.

Monoclonal antibody (mAb) technology is an excellent tool for the discovery of overexpressed cell surface tumour antigens and the development of targeting agents. Here, we report the development of two novel mAbs against CFPAC-1 human pancreatic cancer cells. Using ELISA, flow cytometry, immunoprecipitation, mass spectrometry, Western blot and immunohistochemistry, we found that the target antigens recognised by the two novel mAbs KU44.22B and KU44.13A, are integrin α3 and CD26 respectively, with high levels of expression in human pancreatic and other cancer cell lines and human pancreatic cancer tissue microarrays. Treatment with naked anti-CD26 mAb KU44.13A did not have any effect on the growth and migration of cancer cells nor did it induce receptor downregulation. In contrast, treatment with anti-integrin α3 mAb KU44.22B inhibited growth in vitro of Capan-2 cells, increased migration of BxPC-3 and CFPAC-1 cells and induced antibody internalisation. Both novel mAbs are capable of detecting their target antigens by immunohistochemistry but not by Western blot. These antibodies are excellent tools for studying the role of integrin α3 and CD26 in the complex biology of pancreatic cancer, their prognostic and predictive values and the therapeutic potential of their humanised and/or conjugated versions in patients whose tumours overexpress integrin α3 or CD26

Enhanced effect of checkpoint inhibitors when given after or together with IMM-101: significant responses in four advanced melanoma patients with no additional major toxicity

Background The use of checkpoint inhibitors (ipilimumab, pembrolizumab, nivolumab) has revolutionised the treatment of metastatic melanoma. However still more than the half the patients do not respond to single-agent immunotherapy. This has led to the development of combining these agents in an attempt to enhance the anti-cancer activity. More than 300 different studies with 15 different drug doses are currently ongoing. Combining different checkpoint inhibitors (CPIs) does indeed lead to an increase in response rate, but this is associated with significant toxicity. IMM-101 is a heat killed Mycobacterium preparation which induces marked immune modulation and little systemic toxicity. It has been reported as having activity in melanoma as single agent and in pancreatic cancer in combination with gemcitabine, the latter in a randomised study. Methods Here we report the effect of adding CPIs to 3 patients who had previously been on IMM-101, either as a trial or a named patient programme and a patient who received the IMM-101 together with nivolumab. Results All 4 patients had rapid and very good responses, three of them maintained over 18 months with no significant additional toxicity. Conclusions The rapid and complete clinical responses seen in these patients may suggest that IMM-101 is activating a complementary pathway which is synergistic with CPI treatment

Gemcitabine alters the proteasome composition and immunopeptidome of tumour cells

The antigenic makeup of tumour cells can have a profound effect on the progression of cancer and success of immunotherapies. Therefore, one strategy to improve the efficacy of cancer treatments is to augment the antigens displayed by tumours. The present study explores how the recognition of tumour cells may be altered by non-cytotoxic concentrations of gemcitabine (GEM). Testing a panel of chemotherapeutics in human cancer cell lines in vitro, it was found that GEM increased surface expression of HLA-A,B,C and that underlying this were specific increases in β-2-microglobulin and immunoproteasome subunit proteins. Furthermore, the peptide antigen repertoire displayed on HLA class I was altered, revealing a number of novel antigens, many of which that were derived from proteins involved in the DNA-damage response. Changes in the nature of the peptide antigens eluted from HLA-A,B,C after GEM treatment consisted of amino acid anchor-residue modifications and changes in peptide length which rendered peptides likely to favour alternative HLA-alleles and increased their predicted immunogenicity. Signalling through the MAPK/ERK and NFκB/RelB pathways was associated with these changes. These data may explain observations made in previous in vivo studies, advise as to which antigens should be used in future vaccination protocols and reinforce the idea that chemotherapy and immunotherapy could be used in combination

Theoretical Study of Spin-dependent Electron Transport in Atomic Fe Nanocontacts

We present theoretical predictions of spintronic transport phenomena that should be observable in ferromagnetic Fe nanocontacts bridged by chains of Fe atoms. We develop appropriate model Hamiltonians based on semi-empirical considerations and the known electronic structure of bulk Fe derived from ab initio density functional calculations. Our model is shown to provide a satisfactory description of the surface properties of Fe nano-clusters as well as bulk properties. Lippmann-Schwinger and Green's function techniques are used together with Landauer theory to predict the current, magneto-resistance, and spin polarization of the current in Fe nanocontacts bridged by atomic chains under applied bias. Unusual device characteristics are predicted including negative magneto-resistance and spin polarization of the current, as well as spin polarization of the current for anti-parallel magnetization of the Fe nanocontacts under moderate applied bias. We explore the effects that stretching the atomic chain has on the magneto-resistance and spin polarization and predict a cross-over regime in which the spin polarization of the current for parallel magnetization of the contacts switches from negative to positive. We find resonant transmission due to dangling bond formation on tip atoms as the chain is stretched through its breaking point to play an important role in spin-dependent transport in this regime. The physical mechanisms underlying the predicted phenomena are discussed.Comment: 13 pages, 6 figures, Accepted for publication in Physical Review

Suite2p: beyond 10,000 neurons with standard two-photon microscopy

Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p: a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons

Supernatants from lymphocytes stimulated with Bacillus Calmette-Guerin can modify the antigenicity of tumours and stimulate allogeneic T-cell responses

BACKGROUND: Reduced expression of class 1 human leucocyte antigens (HLA1) is often a mechanism by which tumours evade surveillance by the host immune system. This is often associated with an immune function that is unable to mount appropriate responses against disease, which can result in a state that favours carcinogenesis. METHODS: In the current study, we have explored the effects of Bacillus Calmette-Guerin (BCG) on the cytokine output of leucocytes, which is a key determinant in generating antitumour action, and have also assessed the effect of these cytokine cocktails on HLA1 expression in solid tumour cell lines. RESULTS: BCG potently activated a broad range of leucocytes, and also enhanced the production of cytokines that were Th(1)-predominant. Supernatants from BCG-treated leucocytes significantly increased the expression of HLA1 on the surface of cancer cell lines, which correlated with increased cytolytic T-cell activity. We also showed that the increased HLA1 expression was associated with activation of intracellular signalling pathways, which was triggered by the increases in the Th(1)-cytokines interferon-γ and tumour necrosis factor-α, as counteracting their effects negated the enhancement. CONCLUSION: These studies reaffirm the role of BCG as a putative immunotherapy through their cytokine-modifying effects on leucocytes and their capacity to enhance tumour visibility