Farmers’ spending on variable inputs tends to maximise crop yields, not profit

We estimate the marginal returns to spending on Crop Variable Inputs (CVI) (such as fertilizers and crop protection), to explore whether observed spending maximises physical or economic returns to farmers. Data are taken from the Farm Business Survey for 2004-2013, where gross margins and input spending are available, in over 10,300 crops of conventional winter wheat or oilseed rape in England and Wales. Marginal spending on CVIs generate financial returns significantly less than £1 per marginal pound spent. This suggests that expenditure on CVIs exceeds an economic optimum that would maximise profit. However marginal physical products (crop yields) are positive, but small and significantly different from zero. This suggests that, on average, farmers approximately maximise yields. These results hold across a wide range of alternative economic models and two crop species. Similar results have been reported in estimations for Indian grain production and for maize in China. In practice, farmers are making decisions on input use in advance of having information on a variety of factors, including future yield, product quality and price, making it difficult to optimise input levels according to expected profit. Farmers may be consistently optimistic, prefer to avoid risk, or deliberately seek to maximise yields. Some farmers may put on the standard recommended application irrespective of input or expected output price. It is also possible that advice may sometimes aim to maximise yield, influenced by an incentive to encourage greater sales. Excessive input use both reduces private profits and is a cause of environmental damage. There are thus potential private as well as social benefits to be gained from optimising levels of input use

Recurrent Gaussian processes

We define Recurrent Gaussian Processes (RGP) models, a general family of Bayesian nonparametric models with recurrent GP priors which are able to learn dynamical patterns from sequential data. Similar to Recurrent Neural Networks (RNNs), RGPs can have different formulations for their internal states, distinct inference methods and be extended with deep structures. In such context, we propose a novel deep RGP model whose autoregressive states are latent, thereby performing representation and dynamical learning simultaneously. To fully exploit the Bayesian nature of the RGP model we develop the Recurrent Variational Bayes (REVARB) framework, which enables efficient inference and strong regularization through coherent propagation of uncertainty across the RGP layers and states. We also introduce a RGP extension where variational parameters are greatly reduced by being reparametrized through RNN-based sequential recognition models. We apply our model to the tasks of nonlinear system identification and human motion modeling. The promising obtained results indicate that our RGP model maintains its highly flexibility while being able to avoid overfitting and being applicable even when larger datasets are not available

On the persistence of supplementary resources in biomedical publications

BACKGROUND: Providing for long-term and consistent public access to scientific data is a growing concern in biomedical research. One aspect of this problem can be demonstrated by evaluating the persistence of supplementary data associated with published biomedical papers. METHODS: We manually evaluated 655 supplementary data links extracted from PubMed abstracts published 1998–2005 (Method 1) as well as a further focused subset of 162 full-text manuscripts published within three representative high-impact biomedical journals between September and December 2004 (Method 2). RESULTS: For Method 1 we found that since 2001, only 71 – 92% of supplementary data were still accessible via the links provided, with 93% of these inaccessible links occurring where supplementary data was not stored with the publishing journal. Of the manuscripts evaluated in Method 2, we found that only 83% of these links were available approximately a year after publication, with 55% of these inaccessible links were at locations outside the journal of publication. CONCLUSION: We conclude that if supplemental data is required to support the publication, journals policies must take-on the responsibility to accept and store such data or require that it be maintained with a credible independent institution or under the terms of a strategic data storage plan specified by the authors. We further recommend that publishers provide automated systems to ensure that supplementary links remain persistent, and that granting bodies such as the NIH develop policies and funding mechanisms to maintain long-term persistent access to these data

Statistical validation of the criteria for symptom remission in schizophrenia: Preliminary findings

<p>Abstract</p> <p>Background</p> <p>Published methods for assessing remission in schizophrenia are variable and none have been definitively validated or standardized. Andreasen et al (2005) suggest systematic operational criteria using eight PANSS items for which patients must score ≤ 3 (mild) for at least six months.</p> <p>Methods</p> <p>Using data from a one year, multi-site clinical trial (n = 675) remission criteria were compared to total PANSS scores and other endpoints and demonstrate excellent agreement with overall clinical status.</p> <p>Results</p> <p>Compared to total PANSS score of 60 points and other criteria, at time points > 6 months (8 and 12 months) the specificity of the remission criteria was 85%, i.e. of the patients who had a total score >60, 85% were classified as "not in remission." Sensitivity was also very high; 75% of patients with scores of <60 were classified as "in remission."Patients who dropped out of the trial were more likely not to be in remission prior to dropping out.</p> <p>Conclusion</p> <p>These findings indicate that the remission criteria are both sensitive and specific indicators of clinical status. Additional analyses are required to determine if remission status predicts other outcomes, such as employment, independent living, and prognosis.</p

Selective expansion of viral variants following experimental transmission of a reconstituted feline immunodeficiency virus quasispecies

Following long-term infection with virus derived from the pathogenic GL8 molecular clone of feline immunodeficiency virus (FIV), a range of viral variants emerged with distinct modes of interaction with the viral receptors CD134 and CXCR4, and sensitivities to neutralizing antibodies. In order to assess whether this viral diversity would be maintained following subsequent transmission, a synthetic quasispecies was reconstituted comprising molecular clones bearing envs from six viral variants and its replicative capacity compared in vivo with a clonal preparation of the parent virus. Infection with either clonal (Group 1) or diverse (Group 2) challenge viruses, resulted in a reduction in CD4+ lymphocytes and an increase in CD8+ lymphocytes. Proviral loads were similar in both study groups, peaking by 10 weeks post-infection, a higher plateau (set-point) being achieved and maintained in study Group 1. Marked differences in the ability of individual viral variants to replicate were noted in Group 2; those most similar to GL8 achieved higher viral loads while variants such as the chimaeras bearing the B14 and B28 Envs grew less well. The defective replication of these variants was not due to suppression by the humoral immune response as virus neutralising antibodies were not elicited within the study period. Similarly, although potent cellular immune responses were detected against determinants in Env, no qualitative differences were revealed between animals infected with either the clonal or the diverse inocula. However, in vitro studies indicated that the reduced replicative capacity of variants B14 and B28 in vivo was associated with altered interactions between the viruses and the viral receptor and co-receptor. The data suggest that viral variants with GL8-like characteristics have an early, replicative advantage and should provide the focus for future vaccine development

The characteristic blue spectra of accretion disks in quasars as uncovered in the infrared

Quasars are thought to be powered by supermassive black holes accreting surrounding gas. Central to this picture is a putative accretion disk which is believed to be the source of the majority of the radiative output. It is well known, however, that the most extensively studied disk model -- an optically thick disk which is heated locally by the dissipation of gravitational binding energy -- is apparently contradicted by observations in a few major respects. In particular, the model predicts a specific blue spectral shape asymptotically from the visible to the near-infrared, but this is not generally seen in the visible wavelength region where the disk spectrum is observable. A crucial difficulty was that, toward the infrared, the disk spectrum starts to be hidden under strong hot dust emission from much larger but hitherto unresolved scales, and thus has essentially been impossible to observe. Here we report observations of polarized light interior to the dust-emiting region that enable us to uncover this near-infrared disk spectrum in several quasars. The revealed spectra show that the near-infrared disk spectrum is indeed as blue as predicted. This indicates that, at least for the outer near-infrared-emitting radii, the standard picture of the locally heated disk is approximately correct. The model problems at shorter wavelengths should then be directed toward a better understanding of the inner parts of the revealed disk. The newly uncovered disk emission at large radii, with more future measurements, will also shed totally new light on the unanswered critical question of how and where the disk ends.Comment: published in Nature, 24 July 2008 issue. Supplementary Information can be found at http://www.mpifr-bonn.mpg.de/div/ir-interferometry/suppl_info.pdf Published version can be accessed from http://www.nature.com/nature/journal/v454/n7203/pdf/nature07114.pd

Interleukin 7 from Maternal Milk Crosses the Intestinal Barrier and Modulates T- Cell Development in Offspring

Background Breastfeeding protects against illnesses and death in hazardous environments, an effect partly mediated by improved immune function. One hypothesis suggests that factors within milk supplement the inadequate immune response of the offspring, but this has not been able to account for a series of observations showing that factors within maternally derived milk may supplement the development of the immune system through a direct effect on the primary lymphoid organs. In a previous human study we reported evidence suggesting a link between IL-7 in breast milk and the thymic output of infants. Here we report evidence in mice of direct action of maternally-derived IL-7 on T cell development in the offspring. Methods and Findings  We have used recombinant IL-7 labelled with a fluorescent dye to trace the movement in live mice of IL-7 from the stomach across the gut and into the lymphoid tissues. To validate the functional ability of maternally derived IL- 7 we cross fostered IL-7 knock-out mice onto normal wild type mothers. Subsets of thymocytes and populations of peripheral T cells were significantly higher than those found in knock-out mice receiving milk from IL-7 knock-out mothers. Conclusions/Significance Our study provides direct evidence that interleukin 7, a factor which is critical in the development of T lymphocytes, when maternally derived can transfer across the intestine of the offspring, increase T cell production in the thymus and support the survival of T cells in the peripheral secondary lymphoid tissue