MHC-correlated preferences in diestrous female horses (Equus caballus).

Genes of the major histocompatibility complex (MHC) have been shown to influence communication in many vertebrates, possibly with context-specific MHC-correlated reactions. Here we test for MHC-linked female preferences in the polygynous horse (Equus caballus) by repeatedly exposing 19 mares to a group of seven sexually experienced stallions. Each mare was tested four times during two consecutive reproductive cycles, twice during estrus and twice during diestrus. Male plasma testosterone concentrations were determined from weekly blood samples, and equine leukocyte antigen (ELA) class I and II alleles were determined serologically at the end of the experiments. Perception of male attractiveness was strongly dependent on estrous cycle: mean preference scores did not correlate for mares in diestrus and estrus and varied more during estrus than during diestrus. We found elevated female interests for MHC-dissimilar stallions, but only during diestrus, not during estrus. Female preferences were not significantly predicted by mean male testosterone plasma concentrations. However, testosterone concentrations changed during the 11 weeks of the experiment. By the end of the experiment, average testosterone concentration was significantly correlated to the average number of MHC alleles the stallions shared with the mares. We conclude that the MHC affects female preferences for stallions, but non-MHC linked male characteristics can overshadow effects of the MHC during estrus

On the use of multilayer Laue lenses with X-ray Free Electron Lasers

Multilayer Laue lenses were used for the first time to focus x-rays from an X-ray Free Electron Laser (XFEL). In an experiment, which was performed at the European XFEL, we demonstrated focusing to a spot size of a few tens of nanometers. A series of runs in which the number of pulses per train was increased from 1 to 2, 3, 4, 5, 6, 7, 10, 20 and 30 pulses per train, all with a pulse separation of 3.55 us, was done using the same set of lenses. The increase in the number of pulses per train was accompanied with an increase of x-ray intensity (transmission) from 9% to 92% at 5 pulses per train, and then the transmission was reduced to 23.5 % when the pulses were increased further. The final working condition was 30 pulses per train and 23.5% transmission. Only at this condition we saw that the diffraction efficiency of the MLLs changed over the course of a pulse train, and this variation was reproducible from train to train. We present the procedure to align and characterize these lenses and discuss challenges working with the pulse trains from this unique x-ray source

Survival prediction from clinico-genomic models - a comparative study

<p>Abstract</p> <p>Background</p> <p>Survival prediction from high-dimensional genomic data is an active field in today's medical research. Most of the proposed prediction methods make use of genomic data alone without considering established clinical covariates that often are available and known to have predictive value. Recent studies suggest that combining clinical and genomic information may improve predictions, but there is a lack of systematic studies on the topic. Also, for the widely used Cox regression model, it is not obvious how to handle such combined models.</p> <p>Results</p> <p>We propose a way to combine classical clinical covariates with genomic data in a clinico-genomic prediction model based on the Cox regression model. The prediction model is obtained by a simultaneous use of both types of covariates, but applying dimension reduction only to the high-dimensional genomic variables. We describe how this can be done for seven well-known prediction methods: variable selection, unsupervised and supervised principal components regression and partial least squares regression, ridge regression, and the lasso. We further perform a systematic comparison of the performance of prediction models using clinical covariates only, genomic data only, or a combination of the two. The comparison is done using three survival data sets containing both clinical information and microarray gene expression data. Matlab code for the clinico-genomic prediction methods is available at <url>http://www.med.uio.no/imb/stat/bmms/software/clinico-genomic/</url>.</p> <p>Conclusions</p> <p>Based on our three data sets, the comparison shows that established clinical covariates will often lead to better predictions than what can be obtained from genomic data alone. In the cases where the genomic models are better than the clinical, ridge regression is used for dimension reduction. We also find that the clinico-genomic models tend to outperform the models based on only genomic data. Further, clinico-genomic models and the use of ridge regression gives for all three data sets better predictions than models based on the clinical covariates alone.</p

Benchmarking Yield for Sustainable Intensification of Oil Palm Production in Indonesia using PALMSIM

The physiological oil palm growth model PALMSIM can be used to estimate yield ceilings that provide benchmarks for sustainable intensification of oil palm production, either by expansion of cultivation to degraded sites or by increasing production from areas under cultivation. This is demonstrated using two case studies. In the first case study, PALMSIM estimates of water-limited yield for Kalimantan was overlaid onto a recently published map showing degraded sites potentially suitable for oil palm cultivation. A large proportion (35.6%; or 115,300 km2) of the identified areas fell into the potential productivity range of 35 to 40 tonnes FFB per hectare. In the second case study, PALMSIM was used to estimate potential yield for six plantation sites in Indonesia where best management practices (BMP) were assessed for yield intensification by the International Plant Nutrition Institute (IPNI) Southeast Asia Program (SEAP) and its collaborating plantation partners. Potential yields are generally higher in Sumatra than in Kalimantan due to higher solar radiation. Water deficit was a problem at two sites. The gap between water-limited yield and actual yield differs from location to location, and therefore requires a site-specific analysis. In these two case studies, the scope for sustainable intensification at regional and at plantation level was explored in a quantitative manner - a novel approach to oil palm production

Regaining momentum for international climate policy beyond Copenhagen

The 'Copenhagen Accord' fails to deliver the political framework for a fair, ambitious and legally-binding international climate agreement beyond 2012. The current climate policy regime dynamics are insufficient to reflect the realities of topical complexity, actor coalitions, as well as financial, legal and institutional challenges in the light of extreme time constraints to avoid 'dangerous' climate change of more than 2°C. In this paper we analyze these stumbling blocks for international climate policy and discuss alternatives in order to regain momentum for future negotiations

The Butterfly Fauna Of The Italian Maritime Alps:Results Of The &#171;Edit&#187; Project

Bonelli, Simona, Barbero, Francesca, Casacci, Luca Pietro, Cerrato, Cristiana, Balletto, Emilio (2015): The butterfly fauna of the Italian Maritime Alps: results of the EDIT project. Zoosystema 37 (1): 139-167, DOI: 10.5252/z2015n1a6, URL: http://dx.doi.org/10.5252/z2015n1a

Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX

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