Five authors reply

We read with interest the comments offered by Drs. Hughes and Bradley (1) on our systematic review (2). Four single nucleotide polymorphisms (SNPs), rs9332739 and rs547154 in the complement component 2 gene (C2) and rs4151667 and rs641153 in the complement factor B gene (CFB), were pooled. Hughes and Bradley point out that we omitted the most common variant, rs12614. In fact, rs12614 is in high linkage disequilibrium (LD) with rs641153, which was included, and the major allele of both of these SNPs is in the range of 90% (population code, CEU, in the International HapMap Project (http://hapmap.ncbi.nlm.nih.gov/)). Moreover, our review was initiated in September 2010, at which point only 4 studies had published associations with rs12614, whereas 14 studies (n = 11,378) were available for rs641153. While it is true that both SNPs are better analyzed as a haplotype, these data were simply not available for pooling.
Hughes and Bradley also point out that we obtained and pooled new data that were not previously published. While it is recommended that contact with authors be completed as part of a comprehensive meta-analysis, we acknowledge that these additional data were not previously published and peer reviewed and, hence, do not have the same level of transparency. However, given that sample collections often increase over time and that the instrumentation for genotyping is continually improving, we thought that it would be advantageous to use the most recent information; this is a subjective decision.
We also agree that the allele frequencies given by Kaur et al. (3) were exactly opposite to those expected and were suggestive of strand flipping. However, we specifically queried this with the lead author on 2 separate occasions and were assured it was not.
Hughes and Bradley do make an interesting suggestion that SNPs in high LD should be used as a gauge of genotyping quality in HuGE reviews. This is an interesting idea but difficult to put into practice as the r2 parameter they propose as a measure of LD has some unusual properties. Although r2 is a measure of LD, it is also linked to the allele frequency; even small differences in allele frequencies between 2 linked SNPs can reduce the r2 dramatically. Wray (4) explored these effects and found that, at a baseline allele frequency of 10%, even a difference in allele frequency between 2 SNPs as small as 2% can drop the r2 value below 0.8. This degree of allele frequency difference is consistent with what could be expected for sampling error. Furthermore, when we look at 2 linked dialleleic SNPs, giving 4 possible haplotypes, the absence of 1 haplotype dramatically reduces r2, despite the 2 loci being in high LD as measured by D'. In fact, this is the situation for rs12614 and rs641153, where the low frequency of 1 haplotype means that the r2 is 0.01 but the D' is 1.
Hughes and Bradley also suggest consideration of genotype call rate restrictions as an inclusion criterion for metaanalysis. This would be more appropriate when focusing on genetic variants per se, as considered within the context of a genome-wide association study or other specific genetic analysis where large numbers of SNPs are evaluated (5).
The concerns raised by Hughes and Bradley reflect the limited ability of a meta-analysis based on summary data to tease out inconsistencies best identified at the individual level. We agree that SNPs in LD should be evaluated, but this will not necessarily be straightforward. A move to make genetic data sets publicly available, as in the Database of Genotypes and Phenotypes (http://www.ncbi.nlm.nih.gov/ gap), is a step in the right direction for greater transparency.

Retinal ultrastructural findings in cone degeneration

We studied an eye from a 73-year-old man with a sporadic type of retinal cone degeneration and choroidal melanoma. Histologic and ultrastructural studies of the nasal retina unaffected by the choroidal melanoma showed alterations at the outer retina predominantly involving the photoreceptors and retinal pigment epithelium. A wide spectrum of pathologic changes were observed, ranging from near normal retina showing only photoreceptor outer segment disease (distortion and kinking) to grossly pathologic regions where photoreceptor cell bodies were sparse and their outer segments absent. The retinal pigment epithelium in minimally affected regions of the retina showed an increased proportion of the melanin complement of the cell within complex granules. In severe disease, many cells showed only giant complex granules with no free melanin. Retinal pigment epithelial cell migration and relocation around blood vessels was also noted in severe disease.

Behaviour analysis and evidence-based education

Education has a powerful and long-term effect on people’s lives and therefore should be based on evidence of what works best. This assertion warrants a definition of what constitutes good research evidence. Two research designs that are often thought to come from diametrically opposed fields, single-subject research designs and randomised controlled-trials, are described and common features, such as the use of probabilistic assumptions and the aim of discovering causal relations are delineated. Differences between the two research designs are also highlighted and this is used as the basis to set out how these two research designs might better be used to complement one another. Recommendations for future action are made accordingly.

Myeloid cells expressing VEGF and arginase-1 following uptake of damaged retinal pigment epithelium suggests potential mechanism that drives the onset of choroidal angiogenesis in mice

Whilst data recognise both myeloid cell accumulation during choroidal neovascularisation (CNV) as well as complement activation, none of the data has presented a clear explanation for the angiogenic drive that promotes pathological angiogenesis. One possibility that is a pre-eminent drive is a specific and early conditioning and activation of the myeloid cell infiltrate. Using a laser-induced CNV murine model, we have identified that disruption of retinal pigment epithelium (RPE) and Bruch's membrane resulted in an early recruitment of macrophages derived from monocytes and microglia, prior to angiogenesis and contemporaneous with lesional complement activation. Early recruited CD11b(+) cells expressed a definitive gene signature of selective inflammatory mediators particularly a pronounced Arg-1 expression. Accumulating macrophages from retina and peripheral blood were activated at the site of injury, displaying enhanced VEGF expression, and notably prior to exaggerated VEGF expression from RPE, or earliest stages of angiogenesis. All of these initial events, including distinct VEGF (+) Arg-1(+) myeloid cells, subsided when CNV was established and at the time RPE-VEGF expression was maximal. Depletion of inflammatory CCR2-positive monocytes confirmed origin of infiltrating monocyte Arg-1 expression, as following depletion Arg-1 signal was lost and CNV suppressed. Furthermore, our in vitro data supported a myeloid cell uptake of damaged RPE or its derivatives as a mechanism generating VEGF (+) Arg-1(+) phenotype in vivo. Our results reveal a potential early driver initiating angiogenesis via myeloid-derived VEGF drive following uptake of damaged RPE and deliver an explanation of why CNV develops during any of the stages of macular degeneration and can be explored further for therapeutic gain.

Development and single laboratory validation of an optical biosensor assay for tetrodotoxin detection as a tool to combat emerging risks in European seafood

Tetrodotoxin (TTX) is a potent neurotoxin emerging in European waters due to increasing ocean temperatures. Its detection in seafood is currently performed as a consequence of using the Association of Analytical Communities (AOAC) mouse bioassay (MBA) for paralytic shellfish poisoning (PSP) toxins, but TTX is not monitored routinely in Europe. Due to ethical and performance-related issues associated with this bioassay, the European Commission has recently published directives extending procedures that may be used for official PSP control. An AOAC-accredited high-performance liquid chromatography (HPLC) method has now been accepted by the European Union as a first action screening method for PSP toxins to replace the MBA. However, this AOAC HPLC method is not capable of detecting TTX, so this potent toxin would be undetected; thereby, a separate method of analysis is required. Surface plasmon resonance (SPR) optical biosensor technology has been proven as a potential alternative screening method to detect PSP toxins in seafood. The addition of a similar SPR inhibition assay for TTX would complement the PSP assay in removing the MBA. The present report describes the development and single laboratory validation in accordance with AOAC and IUPAC guidelines of an SPR method to be used as a rapid screening tool to detect TTX in the sea snail Charonia lampas lampas, a species which has been implicated in 2008 in the first case of human TTX poisoning in Europe. As no current regulatory limits are set for TTX in Europe, single laboratory validation was undertaken using those for PSP toxins at 800 µg/kg. The decision limit (CCa) was 100 µg/kg, with the detection capability (CCß) found to be =200 µg/kg. Repeatability and reproducibility were assessed at 200, 400, and 800 µg/kg and showed relative standard deviations of 8.3, 3.8, and 5.4 % and 7.8, 8.3, and 3.7 % for both parameters at each level, respectively. At these three respective levels, the recovery of the assay was 112, 98, and 99 %.

Analysis of IL6 Signal Transduction Model using Reduced Rank Regression

This work presents the application of reduced rank regression to the field of systems biology. A computational approach is used to investigate the mechanisms of the janus-associated kinases/signal transducers and transcription factors (JAK/STAT) and mitogen activated protein kinases (MAPK) signal transduction pathways in hepatic cells stimulated by interleukin-6. The results obtained identify the contribution of individual reactions to the dynamics of the model. These findings are compared to previously available results from sensitivity analysis of the model which focused on the parameters involved and their effect. This application of reduced rank regression allows for an understanding of the individual reaction terms involved in the modelled signal transduction pathways and has the benefit of being computationally inexpensive. The obtained results complement existing findings and also confirm the importance of several protein complexes in the MAPK pathway which hints at benefits that can be achieved by further refining the model.

Justice for Victims before the International Criminal Court

Many prosecutors and commentators have praised the victim provisions at the International Criminal Court (ICC) as 'justice for victims', which for the first time include participation, protection and reparations. This book critically examines the role of victims in international criminal justice, drawing from human rights, victimology, and best practices in transitional justice.

Drawing on field research in Northern Uganda, Luke Moffet explores the nature of international crimes and assesses the role of victims in the proceedings of the ICC, paying particular attention to their recognition, participation, reparations and protection. The book argues that because of the criminal nature and structural limitations of the ICC, justice for victims is symbolic, requiring State Parties to complement the work of the Court to address victims' needs.

In advancing an innovative theory of justice for victims, and in offering solutions to current challenges, the book will be of great interest and use to academics, practitioners and students engaged in victimology, the ICC, transitional justice, or reparations.

Frequency Filtering of Torsional Alfvén Waves by Chromospheric Magnetic Field

In this Letter, we demonstrate how the observation of broadband frequency propagating torsional Alfvén waves in chromospheric magnetic flux tubes can provide valuable insight into their magnetic field structure. By implementing a full nonlinear three-dimensional magnetohydrodynamic numerical simulation with a realistic vortex driver, we demonstrate how the plasma structure of chromospheric magnetic flux tubes can act as a spatially dependent frequency filter for torsional Alfvén waves. Importantly, for solar magnetoseismology applications, this frequency filtering is found to be strongly dependent on magnetic field structure. With reference to an observational case study of propagating torsional Alfvén waves using spectroscopic data from the Swedish Solar Telescope, we demonstrate how the observed two-dimensional spatial distribution of maximum power Fourier frequency shows a strong correlation with our forward model. This opens the possibility of beginning an era of chromospheric magnetoseismology, to complement the more traditional methods of mapping the magnetic field structure of the solar chromosphere.

Treatment of choroidal neovascularisation secondary to membranoproliferative glomerulonephritis type II with intravitreal ranibizumab

Membranoproliferative glomerulonephritis type II (MPGN II) is characterised by electron-dense deposits of complement components in the glomerular basement membrane and retinal pigment epithelium. Approximately, 10% of affected individuals develop serious ocular complications similar to age-related macular degeneration such as choroidal neovascularisation (CNV), which has been managed with photocoagulation or photodynamic therapy; however, these treatments can impact visual acuity. We report the case of a 42-year-old woman with MPGN II presenting with decreased visual acuity and paracentral scotoma in her left eye due to an extrafoveal choroidal neovascular membrane (growth of new vessels under the retina). The patient was successfully treated with intravitreal ranibizumab (Lucentis) with restoration of visual function. This case highlights the successful management of CNV secondary to MPGN II with the antivascular endothelial growth factor agent ranibizumab and emphasises the importance of early referral of patients with MPGN II who are reporting of visual 'distortion'.

Proteomic analysis reveals oxidative stress response as the main adaptative physiological mechanism in cows under different production systems

Three groups of cows representing three ranges of welfare in the production system were included in the study: two groups of Bruna dels Pirineus beef cattle maintained under different management systems (good and semiferal conditions) and a group of Alberes cows, a breed that lives in the mountains (hardest conditions).

In order to identify new stress/welfare biomarkers, serum from Bruna cows living in both environments was subjected to DIGE labelling, two-dimensional electrophoresis and MALDI-MS or ion trap MS. Identification was achieved for 15 proteins, which mainly belonged to three biological functions, the oxidative stress pathway (glutathione peroxidase (GPx) and paraoxonase (PON-1)), the acute phase protein family (Heremans Schmid glycoprotein alpha2 (α2-HSG)) and the complement system.

Biological validation included the Alberes breed. GPx and PON-1 were validated by an enzymatic assay and found to be higher and lower, respectively, in cows living in hard conditions. α2-HSG was validated by ELISA and found to be reduced in hard conditions. Other biomarkers of the redox status were also altered by living conditions: protein carbonyl content, superoxide dismutase (SOD) and glutathione reductase (GR).

Our results show that changes in the redox system are the main adaptation of cows living in challenging environmental conditions. This article is part of a Special Issue entitled: “Farm animal proteomics”.

Origin of British and Irish mammals: disparate post-glacial colonisation and species introductions

Global climate changes during the Quaternary reveal much about broader evolutionary effects of environmental change. Detailed regional studies reveal how evolutionary lineages and novel communities and ecosystems, emerge through glacial bottlenecks or from refugia. There have been significant advances in benthic imaging and dating, particularly with respect to the movements of the British (Scottish) and Irish ice sheets and associated changes in sea level during and after the Last Glacial Maximum (LGM). Ireland has been isolated as an island for approximately twice as long as Britain with no evidence of any substantial, enduring land bridge between these islands after ca 15 kya. Recent biogeographical studies show that Britain's mammal community is akin to those of southern parts of Scandinavia, The Netherlands and Belgium, but the much lower mammal species richness of Ireland is unique and needs explanation. Here, we consider physiographic, archaeological, phylogeographical i.e. molecular genetic, and biological evidence comprising ecological, behavioural and morphological data, to review how mammal species recolonized western Europe after the LGM with emphasis on Britain and, in particular, Ireland. We focus on why these close neighbours had such different mammal fauna in the early Holocene, the stability of ecosystems after LGM subject to climate change and later species introductions.

There is general concordance of archaeological and molecular genetic evidence where data allow some insight into history after the LGM. Phylogeography reveals the process of recolonization, e.g. with respect to source of colonizers and anthropogenic influence, whilst archaeological data reveal timing more precisely through carbon dating and stratigraphy. More representative samples and improved calibration of the ‘molecular clock’ will lead to further insights with regards to the influence of successive glaciations. Species showing greatest morphological, behavioural and ecological divergence in Ireland in comparison to Britain and continental Europe, were also those which arrived in Ireland very early in the Holocene either with or without the assistance of people. Cold tolerant mammal species recolonized quickly after LGM but disappeared, potentially as a result of a short period of rapid warming. Other early arrivals were less cold tolerant and succumbed to the colder conditions during the Younger Dryas or shortly after the start of the Holocene (11.5 kya), or the area of suitable habitat was insufficient to sustain a viable population especially in larger species. Late Pleistocene mammals in Ireland were restricted to those able to colonize up to ca 15 kya, probably originating from adjacent areas of unglaciated Britain and land now below sea level, to the south and west (of Ireland). These few, early colonizers retain genetic diversity which dates from before the LGM. Late Pleistocene Ireland, therefore, had a much depleted complement of mammal species in comparison to Britain.

Mammal species, colonising predominantly from southeast and east Europe occupied west Europe only as far as Britain between ca 15 and 8 kya, were excluded from Ireland by the Irish and Celtic Seas. Smaller species in particular failed to colonise Ireland. Britain being isolated as an island from ca. 8 kya has similar species richness and composition to adjacent lowland areas of northwest continental Europe and its mammals almost all show strongest genetic affinity to populations in neighbouring continental Europe with a few retaining genotypes associated with earlier, western lineages.

The role of people in the deliberate introduction of mammal species and distinct genotypes is much more significant with regards to Ireland than Britain reflecting the larger species richness of the latter and its more enduring land link with continental Europe. The prime motivation of early people in moving mammals was likely to be resource driven but also potentially cultural; as elsewhere, people exploring uninhabited places introduced species for food and the materials they required to survive. It is possible that the process of introduction of mammals to Ireland commenced during the Mesolithic and accelerated with Neolithic people. Irish populations of these long established, introduced species show some unique genetic variation whilst retaining traces of their origins principally from Britain but in some cases, Scandinavia and Iberia. It is of particular interest that they may retain genetic forms now absent from their source populations. Further species introductions, during the Bronze and late Iron Ages, and Viking and Norman invasions, follow the same pattern but lack the time for genetic divergence from their source populations. Accidental introductions of commensal species show considerable genetic diversity based on numerous translocations along the eastern Atlantic coastline. More recent accidental and deliberate introductions are characterised by a lack of genetic diversity other than that explicable by more than one introduction.

The substantial advances in understanding the postglacial origins and genetic diversity of British and Irish mammals, the role of early people in species translocations, and determination of species that are more recently introduced, should inform policy decisions with regards to species and genetic conservation. Conservation should prioritise early, naturally recolonizing species and those brought in by early people reflecting their long association with these islands. These early arrivals in Britain and Ireland and associated islands show genetic diversity that may be of value in mitigating anthropogenic climate change across Europe. In contrast, more recent introductions are likely to disturb ecosystems greatly, lead to loss of diversity and should be controlled. This challenge is more severe in Ireland where the number and proportion of invasive species from the 19th century to the present has been greater than in Britain.

Topology synthesis of three-legged spherical parallel manipulators employing Lie group theory

Driven by the requirements of the bionic joint or tracking equipment for the spherical parallel manipulators (SPMs) with three rotational degrees-of-freedom (DoFs), this paper carries out the topology synthesis of a class of three-legged SPMs employing Lie group theory. In order to achieve the intersection of the displacement subgroups, the subgroup characteristics and operation principles are defined in this paper. Mainly drawing on the Lie group theory, the topology synthesis procedure of three-legged SPMs including four stages and two functional blocks is proposed, in which the assembly principles of three legs are defined. By introducing the circular track, a novel class of three-legged SPMs is synthesized, which is the important complement to the existing SPMs. Finally, four typical examples are given to demonstrate the finite displacements of the synthesized three-legged SPMs.

Synchronous records of pCO2 and Δ14C suggest rapid, ocean-derived pCO2 fluctuations at the onset of Younger Dryas

Just before the onset of the Younger Dryas (YD) cold event, several stomatal proxy-based pCO2 records have shown a sharp increase in atmospheric CO2 concentration (pCO2) of between ca 50 and 100 ppm, followed by a rapid decrease of similar or even larger magnitude. Here we compare one of these records, a high-resolution pCO2 record from southern Sweden, with the IntCal13 record of radiocarbon (Δ14C). The two records show broadly synchronous fluctuations at the YD onset. Specifically, the IntCal13 record documents decreasing Δ14C just before the YD onset when pCO2 peaks, consistent with a source of “old” CO2 from the deep ocean. We propose that this fluctuation occurred due to a major ocean flushing event. The cause of the flushing event remains speculative but could be related to the hypothesis of the glacial ocean as a thermobaric capacitor. We confirm that the earth system can produce such large multi-decadal timescale fluctuations in pCO2 through simulating an artificial ocean flushing event with the GENIE Earth System Model. We suggest that sharp transitions of pCO2 may have remained undetected so far in ice cores due to inter-firn gas exchange and time-averaging. The stomatal proxy record is a powerful complement to the ice core records for the study of rapid climate change.

Realising Justice for victims before the International Criminal Court

The International Criminal Court (ICC) has been celebrated for its innovative victim provisions, which enable victims to participate in proceedings, avail of protection measures and assistance, and to claim reparations. The impetus for incorporating victim provisions within the ICC, came from victims’ dissatisfaction with the ad hoc tribunals in providing them with more meaningful and tangible justice.1 The International Criminal Tribunals for the former Yugoslavia and Rwanda (ICTY/R) only included victim protection measures, with no provisions for victims to participate in proceedings nor to claim reparations at them. Developments in domestic and international law, in particular human rights such as the 1985 UN Declaration on Justice for Victims and the UN Guidelines on Remedy and Reparations, and transitional justice mechanisms, such as truth commissions and reparations bodies, have helped to expand the notion of justice for international crimes to be more attuned to victims as key stakeholders in dealing with such crimes.

With the first convictions secured at the ICC and the victim participation and reparation regime taking form, it is worth evaluating the extent to which these innovative provisions have translated into justice for victims. The first part of this paper outlines what justice for victims of international crimes entails, drawing from victimology and human rights. The second section surveys the extent to which the ICC has incorporated justice for victims, in procedural and substantive terms, before concluding in looking beyond the Court to how state parties can complement the ICC in achieving justice for victims. This paper argues that while much progress has been made to institutionalise justice for victims within the Court, there is much more progress needed to evolve and develop justice for victims within the ICC to avoid dissatisfaction of past tribunals.

Data Mapping for Unreliable Memories

Future digital signal processing (DSP) systems must provide robustness on algorithm and application level to the presence of reliability issues that come along with corresponding implementations in modern semiconductor process technologies. In this paper, we address this issue by investigating the impact of unreliable memories on general DSP systems. In particular, we propose a novel framework to characterize the effects of unreliable memories, which enables us to devise novel methods to mitigate the associated performance loss. We propose to deploy specifically designed data representations, which have the capability of substantially improving the system reliability compared to that realized by conventional data representations used in digital integrated circuits, such as 2's-complement or sign-magnitude number formats. To demonstrate the efficacy of the proposed framework, we analyze the impact of unreliable memories on coded communication systems, and we show that the deployment of optimized data representations substantially improves the error-rate performance of such systems.