The East African contribution to the formalisation of the soil catena concept

The concept of the soil catena was first explicitly formalised by Geoffrey Milne and his colleagues in East Africa in the 1930s. It has been widely adopted and applied in soil survey and continues to be of great value in soil and other field sciences The concept characterises widespread patterns in which distinctive associations of soils and vegetation are consistently located in specific slope positions. The formalisation of the concept in an area well outside the mainstream of soil research appears to have been due to the combination of highly visible recurrent patterns of red slope soils overlooking dark valley clays in East Africa’s extensive savannahs, together with a group of receptive and collaborative soil scientists working in a supportive institutional environment. The concept is often attributed to Geoffrey Milne, the group’s coordinator, but we show that several colleagues and friends also contributed. We summarise some of the early soil catenas characterised by Milne and his colleagues in Uganda, Kenya and Tanganyika Territory (now Tanzania). Even at the beginning, it was appreciated that the catena was not universally applicable and that heterogeneity of parent materials can override catenary patterns. The catena was quickly and widely adopted in soil science, and this diffusion has led to some broadening of the definition, and several types of soil pattern are now designated as catenas. The concept has also spread beyond soil science and is used by ecologists, geomorphologists and hydrologists amongst others. It continues to be a paradigm of great explicative and educational power in soil science and ecology

The contributions of C. F. Charter to tropical soil survey and classification

Cecil Charter had taught botany and biology in China and Antigua for five years, when in 1931 he was engaged to conduct a soil survey of the sugarcane-growing areas of Antigua. This was followed by similar surveys elsewhere in the Caribbean. In 1944, he joined the West African Cacao Research Institute in the Gold Coast (now Ghana) to carry out soil investigations in the forest zones of West Africa. In 1949 he moved to organise the soil survey unit in the Gold Coast Department of Agriculture, and, in 1951, to found and direct the new Soil and Land Use Survey Department. He rapidly built up a highly professional unit that produced many practical and useful reports of high quality. He based the surveys on ecological principles, selecting river basins as mapping regions. In the initial absence of qualified soil scientists, he subdivided the soil survey process and trained school leavers as technicians for separate tasks. Teams of these technicians examined soils, vegetation and land use at regular intervals on regularly-spaced traverses cut across the topography. Charter’s contributions to soil science included his recognition of non-residual tropical soils formed in material brought to the surface by soil fauna and treefall. Also, he differentiated between highly acidic upland Oxysols in high-rainfall areas, which he considered unsuitable for cocoa cultivation, and less acidic Ochrosols, which were more suitable. Based on farmers’ experience and his ecological background, he differentiated between forest, thicket and savannah soils within these groups. He strongly advocated genetic and contextual classification of tropical soils

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

Background: Chromosome-level assemblies are indispensable for accurate gene prediction, synteny assessment, and understanding higher-order genome architecture. Reference and draft genomes of key helminth species have been published, but little is yet known about the biology of their chromosomes. Here, we present the complete genome of the tapeworm Hymenolepis microstoma, providing a reference quality, end-to-end assembly that represents the first fully assembled genome of a spiralian/lophotrochozoan, revealing new insights into chromosome evolution. Results: Long-read sequencing and optical mapping data were added to previous short-read data enabling complete re-assembly into six chromosomes, consistent with karyology. Small genome size (169 Mb) and lack of haploid variation (1 SNP/3.2 Mb) contributed to exceptionally high contiguity with only 85 gaps remaining in regions of low complexity sequence. Resolution of repeat regions reveals novel gene expansions, micro-exon genes, and spliced leader trans-splicing, and illuminates the landscape of transposable elements, explaining observed length differences in sister chromatids. Syntenic comparison with other parasitic flatworms shows conserved ancestral linkage groups indicating that the H. microstoma karyotype evolved through fusion events. Strikingly, the assembly reveals that the chromosomes terminate in centromeric arrays, indicating that these motifs play a role not only in segregation, but also in protecting the linear integrity and full lengths of chromosomes. Conclusions: Despite strong conservation of canonical telomeres, our results show that they can be substituted by more complex, species-specific sequences, as represented by centromeres. The assembly provides a robust platform for investigations that require complete genome representation

Spatial variation in spring arrival patterns of Afro‐Palaearctic bird migration across Europe

Aim: Geographical patterns of migrant species arrival have been little studied, despite their relevance to global change responses. Here, we quantify continent-wide inter-specific variation in spatio-temporal patterns of spring arrival of 30 common migrant bird species and relate these to species characteristics and environmental conditions.Location: EuropeTime period: 2010-2019Major taxa studied: Birds, 30 speciesMethods: Using citizen science data from EuroBirdPortal, we modelled arrival phenology for 30 Afro-Palearctic migrant species across Europe to extract start and duration of species arrival at a 400 km square resolution. We related inter and intra-specific variation in arrival and duration to species characteristics and temperature at the start of the growing season (green-up) .Results: Spatial variation in start of arrival times indicates it took on average 1.6 days for the leading migratory front to move northwards by 100 km (range: 0.6—2.5 days). There was a major gradient in arrival phenology, from species which arrived earlier, least synchronously, in colder temperatures and progressed slowly northwards to species which arrived later, most synchronously and in warmer temperatures, and advanced quickly through Europe. The slow progress of early arrivers suggests that temperature limits their northward advance; this group included Aerial Insectivores and species wintering north of the Sahel. For the late arrivers, which included species wintering further south, seasonal resource availability in Africa may delay their arrival into Europe.Main conclusions: We found support for the green-wave hypothesis applying widely to migratory landbirds. Species arrival phenologies are linked to ecological differences between taxa, such as diet, and wintering location. Understanding these differences informs predictions of species’ sensitivity to global change. Publishing these arrival phenologies will facilitate further research and have additional conservation benefits such as informing designation of hunting seasons. Our methods are applicable to any taxa with repeated occurrence data across large scales. Key words: phenology, European-African migrants, bird migration, spring arrival, spatial variation, intraspecific and interspecific variation, EuroBirdPortal, citizen scientists, complete lists and casual record

Estimating age-dependent survival from age-aggregated ringing data - extending the use of historical records

Bird ring-recovery data have been widely used to estimate demographic parameters such as survival probabilities since the mid-twentieth century. However, while the total number of birds ringed each year is usually known, historical information on age at ringing is often not available. A standard ring-recovery model, for which information on age at ringing is required, cannot be used when historical data are incomplete. We develop a new model to estimate agedependent survival probabilities from such historical data when age at ringing is not recorded; we call this the historical data model. This new model provides an extension to the model of Robinson (2010) by estimating the proportion of the ringed birds marked as juveniles as an additional parameter. We conduct a simulation study to examine the performance of the historical data model and compare it with other models including the standard and conditional ringrecovery models. Simulation studies show that the approach of Robinson (2010) can cause bias in parameter estimates. In contrast, the historical data model yields similar parameter estimates to the standard model. Parameter redundancy results show that the newly developed historical data model is comparable to the standard ring-recovery model, in terms of which parameters can be estimated, and has fewer identifiability issues than the conditional model. We illustrate the new proposed model using Blackbird and Sandwich Tern data. The new historical data model allows us to make full use of historical data and estimate the same parameters as the standard model with incomplete data and in doing so, detect potential changes in demographic parameters further back in time

QCD with dynamical Wilson fermions

We present results from a study of QCD with two flavors of Wilson fermions using the hybrid Monte Carlo algorithm, which incorporates the effects of fermion loops exactly. We evaluate the performance of the algorithm and its potential for large-scale computations. We argue that in the best case the algorithm slows down as V^(5/4)mq^(-13/4) at a fixed gauge coupling. We present improved algorithms for calculating the inverse and the determinant of the Wilson fermion operator. Results for the finite-temperature transition on 4×6^3 and 6×8^3 lattices are presented at β=5.2-5.6. We also give Wilson loop expectation values obtained on 84 lattices at β=5.3 for six values of κ. The data show evidence for screening in the qq̅ potential. Lastly, on comparing Wilson and staggered-fermion results we find that β=5.3 is far from the scaling region

Tissue proteomic analysis identifies mechanisms and stages of immunopathology in fatal COVID-19

Funding: This work was funded by UK Research and Innovation (UKRI) (Coronavirus Disease [COVID-19] Rapid Response Initiative; MR/V028790/1 to C.D.L., D.A.D., and J.A.H.), LifeArc (through the University of Edinburgh STOPCOVID funding award, to K.D, D.A.D., C.D.L), The Chief Scientist Office (RARC-19 Funding Call, ‘Inflammation in Covid-19: Exploration of Critical Aspects of Pathogenesis; COV/EDI/20/10’ to D.A.D, C.D.L, C.D.R, J.K.B and D.J.H), and Medical Research Scotland (CVG-1722- 2020 to DAD, CDL, CDR, JKB, and DJH). C.D.L is funded by a Wellcome Trust Clinical Career Development Fellowship (206566/Z/17/Z). J.K.B. and C.D.R. are supported by the Medical Research Council (grant MC_PC_19059) as part of the ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC-4C). C.D.R. is supported by an Edinburgh Clinical Academic Track (ECAT)/Wellcome Trust PhD Training Fellowship for Clinicians award (214178/Z/18/Z). J.A.H. is supported by the U.S. Food and Drug Administration (contract 75F40120C00085, Characterization of severe coronavirus infection in humans and model systems for medical countermeasure development and evaluation’). G.C.O is funded by an NRS Clinician award. N.N.G. is funded by a Pathological Society Award. A.R.A. is supported by a Cancer Research UK Clinician Scientist Fellowship award (A24867).Immunopathology occurs in the lung and spleen in fatal COVID-19, involving monocytes/macrophages and plasma cells. Anti-inflammatory therapy reduces mortality but additional therapeutic targets are required. We aimed to gain mechanistic insight into COVID-19 immunopathology by targeted proteomic analysis of pulmonary and splenic tissues. Lung parenchymal and splenic tissue was obtained from 13 post-mortem examinations of patients with fatal COVID-19. Control tissue was obtained from cancer resection samples (lung) and deceased organ donors (spleen). Protein was extracted from tissue by phenol extraction. Olink® multiplex immunoassay panels were used for protein detection and quantification. Proteins with increased abundance in the lung included MCP-3, antiviral TRIM21 and pro-thrombotic TYMP. OSM and EN-RAGE/S100A12 abundance was correlated, and associated with inflammation severity. Unsupervised clustering identified ‘early viral’ and ‘late inflammatory’ clusters with distinct protein abundance profiles, and differences in illness duration prior to death and presence of viral RNA. In the spleen, lymphocyte chemotactic factors and CD8A were decreased in abundance, and pro-apoptotic factors were increased. B-cell receptor signalling pathway components and macrophage colony stimulating factor (CSF-1) were also increased. Additional evidence for a sub-set of host factors (including DDX58, OSM, TYMP, IL-18, MCP-3 and CSF-1) was provided by overlap between (i) differential abundance in spleen and lung tissue, (ii) meta-analysis of existing datasets, and (iii) plasma proteomic data. This proteomic analysis of lung parenchymal and splenic tissue from fatal COVID-19 provides mechanistic insight into tissue anti-viral responses, inflammation and disease stages, macrophage involvement, pulmonary thrombosis, splenic B-cell activation and lymphocyte depletion.Publisher PDFPeer reviewe

Evaluation of Pneumococcal Load in Blood by Polymerase Chain Reaction for the Diagnosis of Pneumococcal Pneumonia in Young Children in the PERCH Study.

BACKGROUND.: Detection of pneumococcus by lytA polymerase chain reaction (PCR) in blood had poor diagnostic accuracy for diagnosing pneumococcal pneumonia in children in 9 African and Asian sites. We assessed the value of blood lytA quantification in diagnosing pneumococcal pneumonia. METHODS.: The Pneumonia Etiology Research for Child Health (PERCH) case-control study tested whole blood by PCR for pneumococcus in children aged 1-59 months hospitalized with signs of pneumonia and in age-frequency matched community controls. The distribution of load among PCR-positive participants was compared between microbiologically confirmed pneumococcal pneumonia (MCPP) cases, cases confirmed for nonpneumococcal pathogens, nonconfirmed cases, and controls. Receiver operating characteristic analyses determined the "optimal threshold" that distinguished MCPP cases from controls. RESULTS.: Load was available for 290 of 291 cases with pneumococcal PCR detected in blood and 273 of 273 controls. Load was higher in MCPP cases than controls (median, 4.0 × 103 vs 0.19 × 103 copies/mL), but overlapped substantially (range, 0.16-989.9 × 103 copies/mL and 0.01-551.9 × 103 copies/mL, respectively). The proportion with high load (≥2.2 log10 copies/mL) was 62.5% among MCPP cases, 4.3% among nonconfirmed cases, 9.3% among cases confirmed for a nonpneumococcal pathogen, and 3.1% among controls. Pneumococcal load in blood was not associated with respiratory tract illness in controls (P = .32). High blood pneumococcal load was associated with alveolar consolidation on chest radiograph in nonconfirmed cases, and with high (>6.9 log10 copies/mL) nasopharyngeal/oropharyngeal load and C-reactive protein ≥40 mg/L (both P < .01) in nonconfirmed cases but not controls. CONCLUSIONS.: Quantitative pneumococcal PCR in blood has limited diagnostic utility for identifying pneumococcal pneumonia in individual children, but may be informative in epidemiological studies

Is Higher Viral Load in the Upper Respiratory Tract Associated With Severe Pneumonia? Findings From the PERCH Study.

BACKGROUND.: The etiologic inference of identifying a pathogen in the upper respiratory tract (URT) of children with pneumonia is unclear. To determine if viral load could provide evidence of causality of pneumonia, we compared viral load in the URT of children with World Health Organization-defined severe and very severe pneumonia and age-matched community controls. METHODS.: In the 9 developing country sites, nasopharyngeal/oropharyngeal swabs from children with and without pneumonia were tested using quantitative real-time polymerase chain reaction for 17 viruses. The association of viral load with case status was evaluated using logistic regression. Receiver operating characteristic (ROC) curves were constructed to determine optimal discriminatory viral load cutoffs. Viral load density distributions were plotted. RESULTS.: The mean viral load was higher in cases than controls for 7 viruses. However, there was substantial overlap in viral load distribution of cases and controls for all viruses. ROC curves to determine the optimal viral load cutoff produced an area under the curve of <0.80 for all viruses, suggesting poor to fair discrimination between cases and controls. Fatal and very severe pneumonia cases did not have higher viral load than less severe cases for most viruses. CONCLUSIONS.: Although we found higher viral loads among pneumonia cases than controls for some viruses, the utility in using viral load of URT specimens to define viral pneumonia was equivocal. Our analysis was limited by lack of a gold standard for viral pneumonia