FRAIR: an R package for fitting and comparing consumer functional responses

This is the author accepted manuscript. The final version is available from Wiley / British Ecological Society via the DOI in this record.1.Consumer‐resource interactions (i.e. the functional response) underpin decades of ecological advancements. However, selecting, fitting and comparing functional response models using appropriate methods remains a non‐trivial endeavour. 2.The R package frair provides tools for selecting and differentiating various forms of consumer functional response models, a consistent interface for fitting and visualising response curves, and a selection of statistically robust methods for comparing fitted parameters. 3.Using real data from crustacean predator‐prey systems, we demonstrate the utility of frair, highlighting best practice and common analytical mistakes.Pūnaha Hihiko Vision Mātauranga Capability.European Union INTERREG IVA Programme and Department of Environment, Northern Ireland (DOENI)Natural Environment Research Counci

Derandomized Construction of Combinatorial Batch Codes

Combinatorial Batch Codes (CBCs), replication-based variant of Batch Codes introduced by Ishai et al. in STOC 2004, abstracts the following data distribution problem: $n$ data items are to be replicated among $m$ servers in such a way that any $k$ of the $n$ data items can be retrieved by reading at most one item from each server with the total amount of storage over $m$ servers restricted to $N$. Given parameters $m, c,$ and $k$, where $c$ and $k$ are constants, one of the challenging problems is to construct $c$-uniform CBCs (CBCs where each data item is replicated among exactly $c$ servers) which maximizes the value of $n$. In this work, we present explicit construction of $c$-uniform CBCs with $\Omega(m^{c-1+{1 \over k}})$ data items. The construction has the property that the servers are almost regular, i.e., number of data items stored in each server is in the range $[{nc \over m}-\sqrt{{n\over 2}\ln (4m)}, {nc \over m}+\sqrt{{n \over 2}\ln (4m)}]$. The construction is obtained through better analysis and derandomization of the randomized construction presented by Ishai et al. Analysis reveals almost regularity of the servers, an aspect that so far has not been addressed in the literature. The derandomization leads to explicit construction for a wide range of values of $c$ (for given $m$ and $k$) where no other explicit construction with similar parameters, i.e., with $n = \Omega(m^{c-1+{1 \over k}})$, is known. Finally, we discuss possibility of parallel derandomization of the construction

The experience of sleep for women with borderline personality disorder: An occupational perspective

Introduction: Sleep difficulties are prevalent in borderline personality disorder (BPD); however, the experience of sleep for individuals with a diagnosis of BPD has not been considered from an occupational therapy perspective. Method: This study adopted a qualitative methodology. Semi-structured interviews were utilised to explore how sleep is experienced by four women with a diagnosis of BPD, in an inpatient setting. Interviews were recorded and transcribed verbatim. Findings: Through thematic analysis four themes were identified: ‘there isn’t a proper pattern or structure to my sleeps’, ‘sleep is getting away for me’, ‘before I came in [to the unit] my life-work balance was all chaotic’ and ‘I know the routine, but it doesn’t really seem to affect me’. These findings described the variety of problems experienced by participants in regards to sleep and the implications of sleep difficulties on occupational performance and participation. Conclusion: Women with BPD on an inpatient unit experienced a variety of sleep difficulties which impact on their ability to engage in occupations. Sleep and sleep difficulties should be explicitly addressed by occupational therapists and sleep interventions should be individually tailored; further research is required to examine occupational therapy interventions for sleep

The impact of ocean acidification on the functional morphology of foraminifera

This work was supported by the NERC UK Ocean Acidification Research Programme grant NE/H017445/1. WENA acknowledges NERC support (NE/G018502/1). DMP received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland). MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.Culturing experiments were performed on sediment samples from the Ythan Estuary, N. E. Scotland, to assess the impacts of ocean acidification on test surface ornamentation in the benthic foraminifer Haynesina germanica. Specimens were cultured for 36 weeks at either 380, 750 or 1000 ppm atmospheric CO2. Analysis of the test surface using SEM imaging reveals sensitivity of functionally important ornamentation associated with feeding to changing seawater CO2 levels. Specimens incubated at high CO2 levels displayed evidence of shell dissolution, a significant reduction and deformation of ornamentation. It is clear that these calcifying organisms are likely to be vulnerable to ocean acidification. A reduction in functionally important ornamentation could lead to a reduction in feeding efficiency with consequent impacts on this organism’s survival and fitness.Publisher PDFPeer reviewe

Fibrinogen is not elevated in the cerebrospinal fluid of patients with multiple sclerosis

<p>Abstract</p> <p>Background</p> <p>Elevated plasma fibrinogen levels are a well known finding in acute infectious diseases, acute stroke and myocardial infarction. However its role in the cerebrospinal fluid (CSF) of acute and chronic central (CNS) and peripheral nervous system (PNS) diseases is unclear.</p> <p>Findings</p> <p>We analyzed CSF and plasma fibrinogen levels together with routine parameters in patients with multiple sclerosis (MS), acute inflammatory diseases of the CNS (bacterial and viral meningoencephalitis, BM and VM) and PNS (Guillain-Barré syndrome; GBS), as well as in non-inflammatory neurological controls (OND) in a total of 103 patients. Additionally, MS patients underwent cerebral MRI scans at time of lumbar puncture.</p> <p>CSF and plasma fibrinogen levels were significantly lower in patients with MS and OND patients as compared to patients with BM, VM and GBS. There was a close correlation between fibrinogen levels and albumin quotient (rho = 0.769, <it>p </it>< 0.001) which strongly suggests passive transfer of fibrinogen through the blood-CSF-barrier during acute inflammation. Hence, in MS, the prototype of chronic neuroinflammation, CSF fibrinogen levels were not elevated and could not be correlated to clinical and neuroradiological outcome parameters.</p> <p>Conclusions</p> <p>Although previous work has shown clear evidence of the involvement of fibrinogen in MS pathogenesis, this is not accompanied by increased fibrinogen in the CSF compartment.</p

Determinants of parasite distribution in Arctic charr populations: catchment structure versus dispersal potential

Parasite distribution patterns in lotic catchments are driven by the combined influences of unidirectional water flow and the mobility of the most mobile host. However, the importance of such drivers in catchments dominated by lentic habitats are poorly understood. We examined parasite populations of Arctic charr Salvelinus alpinus from a series of linear-connected lakes in northern Norway to assess the generality of lotic-derived catchment-scale parasite assemblage patterns. Our results demonstrated that the abundance of most parasite taxa increased from the upper to lower catchment. Allogenic taxa (piscivorous birds as final host) were present throughout the entire catchment, whereas their autogenic counterparts (charr as final hosts) demonstrated restricted distributions, thus supporting the theory that the mobility of the most mobile host determines taxa-specific parasite distribution patterns. Overall, catchment-wide parasite abundance and distribution patterns in this lentic-dominated system were in accordance with those reported for lotic systems. Additionally, our study highlighted that upper catchment regions may be inadequate reservoirs to facilitate recolonization of parasite communities in the event of downstream environmental perturbations

Future climate effects on suitability for growth of oil palms in Malaysia and Indonesia

The production of palm oil (PO) is highly profitable. The economies of the principal producers, Malaysia and Indonesia, and others, benefit considerably. Climate change (CC) will most likely have an impact on the distribution of oil palms (OP) (Elaeis guineensis). Here we present modelled CC projections with respect to the suitability of growing OP, in Malaysia and Indonesia. A process-oriented niche model of OP was developed using CLIMEX to estimate its potential distribution under current and future climate scenarios. Two Global Climate Models (GCMs), CSIRO-Mk3.0 and MIROC-H, were used to explore the impacts of CC under the A1B and A2 scenarios for 2030, 2070 and 2100. Decreases in climatic suitability for OP in the region were gradual by 2030 but became more pronounced by 2100. These projections imply that OP growth will be affected severely by CC, with obvious implications to the economies of (a) Indonesia and Malaysia and (b) the PO industry, but with potential benefits towards reducing CC. A possible remedial action is to concentrate research on development of new varieties of OP that are less vulnerable to CC.The Portuguese-based authors thank the FCT Strategic Project of UID/BIO/04469/2013 unit, the project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462) and the Project "BioEnv - Biotechnology and Bioengineering for a sustainable world", REF. NORTE-07-0124-FEDER-000048, co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER

Out of Mind, Out of Sight: Language Affects Perceptual Vividness in Memory

We examined whether language affects the strength of a visual representation in memory. Participants studied a picture, read a story about the depicted object, and then selected out of two pictures the one whose transparency level most resembled that of the previously presented picture. The stories contained two linguistic manipulations that have been demonstrated to affect concept availability in memory, i.e., object presence and goal-relevance. The results show that described absence of an object caused people to select the most transparent picture more often than described presence of the object. This effect was not moderated by goal-relevance, suggesting that our paradigm tapped into the perceptual quality of representations rather than, for example, their linguistic availability. We discuss the implications of these findings within a framework of grounded cognition

Synergies for Improving Oil Palm Production and Forest Conservation in Floodplain Landscapes

Lowland tropical forests are increasingly threatened with conversion to oil palm as global demand and high profit drives crop expansion throughout the world’s tropical regions. Yet, landscapes are not homogeneous and regional constraints dictate land suitability for this crop. We conducted a regional study to investigate spatial and economic components of forest conversion to oil palm within a tropical floodplain in the Lower Kinabatangan, Sabah, Malaysian Borneo. The Kinabatangan ecosystem harbours significant biodiversity with globally threatened species but has suffered forest loss and fragmentation. We mapped the oil palm and forested landscapes (using object-based-image analysis, classification and regression tree analysis and on-screen digitising of high-resolution imagery) and undertook economic modelling. Within the study region (520,269 ha), 250,617 ha is cultivated with oil palm with 77% having high Net-Present-Value (NPV) estimates ($413/ha?yr–$637/ha?yr); but 20.5% is under-producing. In fact 6.3% (15,810 ha) of oil palm is commercially redundant (with negative NPV of $-299/ha?yr-$-65/ha?yr) due to palm mortality from flood inundation. These areas would have been important riparian or flooded forest types. Moreover, 30,173 ha of unprotected forest remain and despite its value for connectivity and biodiversity 64% is allocated for future oil palm. However, we estimate that at minimum 54% of these forests are unsuitable for this crop due to inundation events. If conversion to oil palm occurs, we predict a further 16,207 ha will become commercially redundant. This means that over 32,000 ha of forest within the floodplain would have been converted for little or no financial gain yet with significant cost to the ecosystem. Our findings have globally relevant implications for similar floodplain landscapes undergoing forest transformation to agriculture such as oil palm. Understanding landscape level constraints to this crop, and transferring these into policy and practice, may provide conservation and economic opportunities within these seemingly high opportunity cost landscapes