The genetic legacy of the expansion of Bantu-speaking peoples in Africa

The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.

aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow

Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.

Human adaptation to arsenic in Bolivians living in the Andes

Humans living in the Andes Mountains have been historically exposed to arsenic from natural sources, including drinking water. Enzymatic methylation of arsenic allows it to be excreted more efficiently by the human body. Adaptation to high-arsenic environments via enhanced methylation and excretion of arsenic was first reported in indigenous women in the Argentinean Andes, but whether adaptation to arsenic is a general phenomenon across native populations from the Andes Mountains remains unclear. Therefore, we evaluated whether adaptation to arsenic has occurred in the Bolivian Andes by studying indigenous groups who belong to the Aymara-Quechua and Uru ethnicities and have lived in the Bolivian Andes for generations. Our population genetics methods, including genome-wide selection scans based on linkage disequilibrium patterns and allele frequency differences, in combination with targeted and whole-genome sequencing and genotype-phenotype association analyses, detected signatures of positive selection near the gene encoding arsenite methyltransferase (AS3MT), the main arsenic methylating enzyme. This was among the strongest selection signals (top 0.5% signals via locus-specific branch length and extended haplotype homozygosity tests) at a genome-wide level in the Bolivian study groups. We found a large haplotype block of 676 kb in the AS3MT region and identified candidate functional variants for further analysis. Moreover, our analyses revealed associations between AS3MT variants and the fraction of mono-methylated arsenic in urine and showed that the Bolivian study groups had the highest frequency of alleles associated with more efficient arsenic metabolism reported so far. Our data support the idea that arsenic exposure has been a driver for human adaptation to tolerate arsenic through more efficient arsenic detoxification in different Andean populations.

Phenotyping calcium and contraction in a zebrafish model of phospholamban R9C mutation

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Ministry of Science, Innovation and Universities, Spain by Consejería de Educación, Cultura y Deportes. Junta de Comunidades de Castilla-La Mancha.

Background

Phospholamban regulates SERCA2a pump activity by reducing its calcium affinity in the heart. Under β-adrenergic stimulation, protein kinase A (PKA) phosphorylates phospholamban attenuating its inhibitory effect on SERCA2a. The phospholamban mutation Arg 9 to Cys (R9C) was firstly identified in an American family with ventricular dilatation and premature death, and subsequently in a cohort of dilated cardiomyopathy patients in South Africa. Emerging evidence suggests that phospholamban R9C is a loss-of-function mutation with autosomal dominant inheritance. In vitro studies revealed that it enhances pentamer assembly by disulfide bridge formation, reducing the availability of phospholamban monomers to regulate SERCA2a.

Purpose

The present study aimed to investigate defects in Ca2+ handling and cardiac function of phospholamban R9C mutation in an in vivo zebrafish model.

Methods

We generated transgenic zebrafish lines overexpressing phospholamban wild-type (TgPLNwt) and phospholamban R9C (TgPLNR9C) in the heart of zebrafish. To measure calcium kinetics in 3 day-old larvae, TgPLNwt and TgPLNR9C fish were outcrossed with transgenic zebrafish lines expressing the fluorescent calcium biosensor mCyRFP1-GCaMP6f (TgRFP-GcaMP6f) and the bioluminescence calcium biosensor GFP-Aequorin (TgGA) in the heart.

Results

Overexpression of phospholamban wild-type and R9C did not alter the heart rate compared to sibling larvae, and no differences were observed in the upstroke and recovery time of the calcium transients.  However, atrial and ventricular calcium transient amplitude were higher in TgPLNR9C larvae with respect to TgPLNwt larvae. Contractile force of the heart, assessed as the fractional shortening, increased in TgPLNR9C larvae compared to siblings and TgPLNwt. Furthermore, stroke volume and cardiac output were also higher in TgPLNR9C larvae. Bioluminescence experiments were performed to estimate the average calcium levels in the heart. We found that TgPLNR9C larvae showed higher calcium levels than sibling and TgPLNwt larvae. To evaluate the responsiveness to β-adrenergic stimulation, larvae were treated with the β-agonist isoproterenol. Calcium transient amplitude and contractile force increased in sibling and TgPLNwt larvae after treatment. However, this response was absent in TgPLNR9C larvae, suggesting that they were hyper-stimulated in basal conditions, displaying amplitude and contractile force similar to sibling and TgPLNwt larvae treated with isoproterenol.

Conclusion

TgPLNR9C larvae exhibited aberrant calcium handling in the heart with higher calcium levels and contractility, consistent with a lack of inhibition of SERCA2a. Consequently, TgPLNR9C larvae did not respond to β-adrenergic stimulation. These results were consistent with previous in vitro studies carried out in cardiomyocites infected with phospholamban R9C and highlighted the pathological defects of phospholamban R9C at early stages of the disease.

Calcium, contraction, and hemodynamic alterations induced by arrhythmogenic drugs in the zebrafish larvae

Funding Acknowledgements

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): MCIN/AEI/ 10.13039/501100011033 and “ERDF A way of making Europe” by the European Union

Background

Ca2+ ion is pivotal in excitation-contraction coupling. The dysregulation of Ca2+ fluxes is at the core of inherited and acquired arrhythmias. In recent years zebrafish have become an attractive vertebrate model to study heart development, cardiotoxicity, and heart diseases. We recently reported that the transgenic zebrafish line Tg(myl7:Twitch-4) expressing the ratiometric Ca2+ indicator Twitch-4 in the heart, allowed imaging Ca2+ transients (CaT) simultaneously with heart contraction in zebrafish larvae, thus maintaining the physiological mechano-electrical feedback.

Purpose

This study aimed to detect subtle disturbances in Ca2+ cycling, contractility, and hemodynamics induced by arrhythmogenic drugs in zebrafish larvae.

Methods

We have used the zebrafish transgenic line Tg(myl7:Twitch-4) and a custom software to acquire and analyze fluorescence emission ratio images of the heart. Larvae of 3- and 5-days post-fertilization (dpf) were incubated with arrhythmogenic drugs, and their effects on the systolic and diastolic Ca2+ and the CaT amplitude in the atrium and ventricle were determined. As the ventricular diameter was assessed in the same fluorescence images, a simultaneous, real-time, measurement of contraction correlated with Ca2+ was obtained. The systolic and diastolic areas, measured independently, were used to estimate hemodynamic parameters.

Results

Dofetilide caused time-dependent bradycardia and ultimately a 2:1 arrhythmia in 3 and 5 dpf larvae, with an increase in the CaT amplitude. the ejection fraction and the stroke volume increased, but the cardiac output decreased due to the low heart rate (2:1 arrhythmia). The T-type Ca2+ channel antagonist ML218 induced bradycardia and decreased systolic and diastolic Ca2+ levels in 3 dpf larvae, but the CaT amplitude did not change. Interestingly, some larvae (3 out of 14) displayed a progressive lengthening of the time between the start of atrial and ventricular CaT, analogous to increased PR interval of the electrocardiogram, until a ventricular systole failed. This is reminiscent of a second-degree atrioventricular block in humans. At higher ML218 concentration, a 2:1 arrhythmia was observed and increased ventricular CaT amplitude in all larvae.

Conclusions

We characterized Ca2+ changes induced by arrhythmogenic drugs and correlated them with contractility and hemodynamic parameters. The zebrafish line Tg(myl7:Twitch-4) allowed investigating drug-induced arrhythmias in this animal model with unprecedented detail. This transgenic line will serve to screen cardiotoxicity during drug development and to study conduction and rhythm defects in zebrafish, and their correlation with human disease.

Male-biased migration from East Africa introduced pastoralism into southern Africa

BACKGROUND

Hunter-gatherer lifestyles dominated the southern African landscape up to ~ 2000 years ago, when herding and farming groups started to arrive in the area. First, herding and livestock, likely of East African origin, appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agro-pastoralist expansion that introduced West African-related genetic ancestry into the area. Present-day Khoekhoe-speaking Namaqua (or Nama in short) pastoralists show high proportions of East African admixture, linking the East African ancestry with Khoekhoe herders. Most other historical Khoekhoe populations have, however, disappeared over the last few centuries and their contribution to the genetic structure of present-day populations is not well understood. In our study, we analyzed genome-wide autosomal and full mitochondrial data from a population who trace their ancestry to the Khoekhoe-speaking Hessequa herders from the southern Cape region of what is now South Africa.

RESULTS

We generated genome-wide data from 162 individuals and mitochondrial DNA data of a subset of 87 individuals, sampled in the Western Cape Province, South Africa, where the Hessequa population once lived. Using available comparative data from Khoe-speaking and related groups, we aligned genetic date estimates and admixture proportions to the archaeological proposed dates and routes for the arrival of the East African pastoralists in southern Africa. We identified several Afro-Asiatic-speaking pastoralist groups from Ethiopia and Tanzania who share high affinities with the East African ancestry present in southern Africa. We also found that the East African pastoralist expansion was heavily male-biased, akin to a pastoralist migration previously observed on the genetic level in ancient Europe, by which Pontic-Caspian Steppe pastoralist groups represented by the Yamnaya culture spread across the Eurasian continent during the late Neolithic/Bronze Age.

CONCLUSION

We propose that pastoralism in southern Africa arrived through male-biased migration of an East African Afro-Asiatic-related group(s) who introduced new subsistence and livestock practices to local southern African hunter-gatherers. Our results add to the understanding of historical human migration and mobility in Africa, connected to the spread of food-producing and livestock practices.

The performance of common SNP arrays in assigning African mitochondrial haplogroups

Background

Mitochondrial haplogroup assignment is an important tool for forensics and evolutionary genetics. African populations are known to display a high diversity of mitochondrial haplogroups. In this research we explored mitochondrial haplogroup assignment in African populations using commonly used genome-wide SNP arrays.

Results

We show that, from eight commonly used SNP arrays, two SNP arrays outperform the other arrays when it comes to the correct assignment of African mitochondrial haplogroups. One array enables the recognition of 81% of the African mitochondrial haplogroups from our compiled dataset of full mitochondrial sequences. Other SNP arrays were able to assign 4–62% of the African mitochondrial haplogroups present in our dataset. We also assessed the performance of available software for assigning mitochondrial haplogroups from SNP array data.

Conclusions

These results provide the first cross-checked quantification of mitochondrial haplogroup assignment performance from SNP array data. Mitochondrial haplogroup frequencies inferred from most common SNP arrays used for human population analysis should be considered with caution.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-021-01000-2.

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

Philippine Ayta possess the highest level of Denisovan ancestry in the world

Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world-∼30%-40% greater than that of Australians and Papuans-consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.

Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens

The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.

Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences

Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.

Patterns of African and Asian admixture in the Afrikaner population of South Africa

BACKGROUND

The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%.

RESULTS

To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population.

CONCLUSIONS

While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.

Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations

Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as “Khoe-San” populations and have a long history in southern Africa. Their ancestors were largely isolated up until ∼2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx’a-language family (ǂHoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.

Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait

Background

Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt.

Results

Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake.

Conclusions

Our findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

Surgical repair versus conservative treatment and subacromial decompression for the treatment of rotator cuff tears

Aims

The purpose of this study was to compare the effectiveness of surgical repair to conservative treatment and subacromial decompression for the treatment of chronic/degenerative tears of the rotator cuff.

Materials and Methods

PubMed, Cochrane database, and Medline were searched for randomized controlled trials published until March 2018. Included studies were assessed for methodological quality, and data were extracted for statistical analysis. The systematic review was conducted following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines.

Results

Six studies were included. Surgical repair resulted in a statistically significantly better Constant–Murley Score (CMS) at one year compared with conservative treatment (mean difference 6.15; p = 0.002) and subacromial decompression alone (mean difference 5.81; p = 0.0004). In the conservatively treated group, 11.9% of patients eventually crossed over to surgical repair.

Conclusion

The results of this review show that surgical repair results in significantly improved outcomes when compared with either conservative treatment or subacromial decompression alone for degenerative rotator cuff tears in older patients. However, the magnitude of the difference in outcomes between surgery and conservative treatment may be small and the ‘success rate’ of conservative treatment may be high, allowing surgeons to be judicious in choosing those patients who are most likely to benefit from surgery. Cite this article: Bone Joint J 2019;101-B:1100–1106.

Silk flow-diverter stent for the treatment of complex intracranial aneurysms: A one-year follow-up multicenter study

Background Flow-diverter stents have been successfully used in the treatment of complex aneurysms with limited therapeutic alternatives. We report our experience using the Silk flow diverter (SFD; Balt Extrusion, Montmorency, France) for the treatment of complex aneurysms in four Argentine centers. Methods We conducted a retrospective review of 246 consecutive patients who were treated with the SFD at four Argentine centers between January 2009 and January 2017. The patient and aneurysm characteristics, as well as the details of the procedure, were analyzed. The angiographic and clinical findings were recorded during and immediately after the procedure and at 12-month follow-up. Results Angiography follow-up at 12 months was possible in 235 patients (95.5%) with 282 aneurysms. A total of 265 aneurysms (93.9%) presented with complete occlusion of the aneurysmal sac (class 1) and 17 aneurysms (6.1%) presented with partial occlusion (class 2). The 12-month clinical follow-up showed 11 patients with major events (seven, scale 2; five, scale 3; and two, scale 4). The morbidity and mortality rates were 4.2% (11/289) and 2.1% (5/289), respectively. Conclusions The treatment of aneurysms with the SFD was associated with a low rate of complications and a high percentage of aneurysmal occlusion. These findings suggest that SFD is an effective and safe alternative in the endovascular treatment of complex aneurysms.

Business Process Modelling is an Essential Part of a Requirements Analysis

To perform a requirements analysis of the barriers to conducting research linking of primary care, genetic and cancer data.

We extended our initial data-centric approach to include socio-culturalandbusinessrequirements.Wecreatedreferencemodels of core data requirements common to most studies using unified modelling language (UML), dataflow diagrams (DFD) and business process modelling notation (BPMN). We conducted a stakeholder analysis and constructed DFD and UML diagrams for use cases based on simulated research studies. We used research output as a sensitivity analysis.

Differences between the reference model and use cases identified study specific data requirements. The stakeholder analysis identified: tensions, changes in specification, some indifference from data providers and enthusiastic informaticians urging inclusion of socio-cultural context. We identified requirements to collect information at three levels: microdata items, which need to be semantically interoperable, meso-the medical record and data extraction, and macro-the health system and socio-cultural issues. BPMN clarified complex business requirements among data providers and vendors; and additional geographical requirements for patients to be represented in both linked datasets. High quality research output was the norm for most repositories.

Reference models provide high-level schemata of the core data requirements. However, business requirements’ modelling identifies stakeholder issues and identifies what needs to be addressed to enable participation.

Key Concepts to Assess the Readiness of Data for International Research: Data Quality, Lineage and Provenance, Extraction and Processing Errors, Traceability, and Curation

To define the key concepts which inform whether a system for collecting, aggregating and processing routine clinical data for research is fit for purpose.

Literature review and shared experiential learning from research using routinely collected data. We excluded socio-cultural issues, and privacy and security issues as our focus was to explore linking clinical data.

Six key concepts describe data: (1) Data quality: the core Overarching concept – Are these data fit for purpose? (2) Data provenance: defined as how data came to be; incorporating the concepts of lineage and pedigree. Mapping this process requires metadata. New variables derived during data analysis have their own provenance. (3) Data extraction errors and (4) Data processing errors, which are the responsibility of the investigator extracting the data but need quantifying. (5) Traceability: the capability to identify the origins of any data cell within the final analysis table essential for good governance, and almost impossible without a formal system of metadata; and (6) Curation: storing data and look-up tables in a way that allows future researchers to carry out further research or review earlier findings.

There are common distinct steps in processing data; the quality of any metadata may be predictive of the quality of the process. Outputs based on routine data should include a review of the process from data origin to curation and publish information about their data provenance and processing method.

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500–6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east–west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

The Scandinavian peninsula was the last part of Europe to be colonized after the Last Glacial Maximum. The migration routes, cultural networks, and the genetic makeup of the first Scandinavians remain elusive and several hypotheses exist based on archaeology, climate modeling, and genetics. By analyzing the genomes of early Scandinavian hunter-gatherers, we show that their migrations followed two routes: one from the south and another from the northeast along the ice-free Norwegian Atlantic coast. These groups met and mixed in Scandinavia, creating a population more diverse than contemporaneous central and western European hunter-gatherers. As northern Europe is associated with cold and low light conditions, we investigated genomic patterns of adaptation to these conditions and genes known to be involved in skin pigmentation. We demonstrate that Mesolithic Scandinavians had higher levels of light pigmentation variants compared to the respective source populations of the migrations, suggesting adaptation to low light levels and a surprising signal of genetic continuity in TMEM131, a gene that may be involved in long-term adaptation to the cold.

How 3D patient-specific instruments improve accuracy of pelvic bone tumour resection in a cadaveric study

OBJECTIVES

To assess the accuracy of patient-specific instruments (PSIs) versus standard manual technique and the precision of computer-assisted planning and PSI-guided osteotomies in pelvic tumour resection.

METHODS

CT scans were obtained from five female cadaveric pelvises. Five osteotomies were designed using Mimics software: sacroiliac, biplanar supra-acetabular, two parallel iliopubic and ischial. For cases of the left hemipelvis, PSIs were designed to guide standard oscillating saw osteotomies and later manufactured using 3D printing. Osteotomies were performed using the standard manual technique in cases of the right hemipelvis. Post-resection CT scans were quantitatively analysed. Student's t-test and Mann-Whitney U test were used.

RESULTS

Compared with the manual technique, PSI-guided osteotomies improved accuracy by a mean 9.6 mm (p < 0.008) in the sacroiliac osteotomies, 6.2 mm (p < 0.008) and 5.8 mm (p < 0.032) in the biplanar supra-acetabular, 3 mm (p < 0.016) in the ischial and 2.2 mm (p < 0.032) and 2.6 mm (p < 0.008) in the parallel iliopubic osteotomies, with a mean linear deviation of 4.9 mm (p < 0.001) for all osteotomies. Of the manual osteotomies, 53% (n = 16) had a linear deviation > 5 mm and 27% (n = 8) were > 10 mm. In the PSI cases, deviations were 10% (n = 3) and 0 % (n = 0), respectively. For angular deviation from pre-operative plans, we observed a mean improvement of 7.06° (p < 0.001) in pitch and 2.94° (p < 0.001) in roll, comparing PSI and the standard manual technique.

CONCLUSION

In an experimental study, computer-assisted planning and PSIs improved accuracy in pelvic tumour resections, bringing osteotomy results closer to the parameters set in pre-operative planning, as compared with standard manual techniques.Cite this article: A. Sallent, M. Vicente, M. M. Reverté, A. Lopez, A. Rodríguez-Baeza, M. Pérez-Domínguez, R. Velez. How 3D patient-specific instruments improve accuracy of pelvic bone tumour resection in a cadaveric study. Bone Joint Res 2017;6:577-583. DOI: 10.1302/2046-3758.610.BJR-2017-0094.R1.

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.

Seizures and electroencephalography findings in 61 patients with fetal alcohol spectrum disorders

Fetal alcohol spectrum disorders (FASD) cause neurodevelopmental abnormalities. However, publications about epilepsy and electroencephalographic features are scarce. In this study, we prospectively performed electroencephalography (EEG) and brain magnetic resonance (MR) imaging in 61 patients with diagnosis of FASD. One patient had multiple febrile seizures with normal EEGs. Fourteen children showed EEG anomalies, including slow background activity and interictal epileptiform discharges, focal and/or generalized, and 3 of them had epilepsy. In one patient, seizures were first detected during the EEG recording and one case had an encephalopathy with electrical status epilepticus during slow sleep (ESES). Focal interictal discharges in our patients did not imply the presence of underlying visible focal brain lesions in the neuroimaging studies, such as cortical dysplasia or polymicrogyria. However, they had nonspecific brain MR abnormalities, including corpus callosum hypoplasia, vermis hypoplasia or cavum septum pellucidum. The latter was significantly more frequent in the group with EEG abnormal findings (p < 0.01).

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations

Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.

Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa

Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000–5000 years, reaching different parts of southern Africa 1200–2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu speakers. During their expansion, Bantu speakers would have come into contact with diverse local populations, such as the Khoisan hunter-gatherers and pastoralists of southern Africa, with whom they may have intermarried. In this study, we analyze complete mtDNA genome sequences from over 900 Bantu-speaking individuals from Angola, Zambia, Namibia, and Botswana to investigate the demographic processes at play during the last stages of the Bantu expansion. Our results show that most of these Bantu-speaking populations are genetically very homogenous, with no genetic division between speakers of Eastern and Western Bantu languages. Most of the mtDNA diversity in our dataset is due to different degrees of admixture with autochthonous populations. Only the pastoralist Himba and Herero stand out due to high frequencies of particular L3f and L3d lineages; the latter are also found in the neighboring Damara, who speak a Khoisan language and were foragers and small-stock herders. In contrast, the close cultural and linguistic relatives of the Herero and Himba, the Kuvale, are genetically similar to other Bantu-speakers. Nevertheless, as demonstrated by resampling tests, the genetic divergence of Herero, Himba, and Kuvale is compatible with a common shared ancestry with high levels of drift, while the similarity of the Herero, Himba, and Damara probably reflects admixture, as also suggested by linguistic analyses.

Evaluation of risk factors for vancomycin-resistant Enterococcus bacteremia among previously colonized hematopoietic stem cell transplant patients

BACKGROUND

Hematopoietic stem cell transplantation (HSCT) recipients colonized with vancomycin-resistant Enterococcus (VRE) may have an increased risk of developing VRE bacteremia. Identification of risk factors for the development of subsequent VRE bacteremia among colonized HSCT recipients is necessary to predict which patients may benefit the most from receiving anti-VRE antibiotic therapy as part of an initial antimicrobial regimen when gram-positive bacteremia is suspected.

METHODS

This study was a retrospective chart review conducted from May 2008 to May 2011. Adult HSCT patients admitted to the hospital found to have positive VRE surveillance cultures were included. A multivariate analysis was completed to identify risk factors for the development of VRE bacteremia in the study population.

RESULTS

Of 152 patients, 19 (13%) patients developed subsequent VRE bacteremia. Risk factors identified for patients with current VRE colonization for VRE bacteremia were the utilization of vancomycin subsequent to VRE surveillance culture positivity (P = 0.017), prolonged duration of neutropenia (P = 0.001), immunosuppression (P < 0.001), and timing of first VRE surveillance screen positivity at week 1 (P = 0.005). A history of VRE colonization on a prior admission was not an independent risk factor for bacteremia in HSCT patients (P = 1.0). HSCT patients with VRE bacteremia had a 30-day all-cause inpatient mortality rate of 29% (P = 0.001).

CONCLUSION

HSCT patients receiving immunosuppressive therapy, who have been exposed to vancomycin subsequent to surveillance culture positivity, have had prolonged neutropenia of >30 days, or first surveillance culture positive at week 1 of admission are potential candidates for early implementation of anti-VRE therapy when a gram-positive bacteremia is suspected.

Membrane reconstitution of FtsZ-ZipA complex inside giant spherical vesicles made of E. coli lipids: large membrane dilation and analysis of membrane plasticity

During the division process of Escherichia coli, the globular protein FtsZ is early recruited at the constriction site. The Z-ring, based on FtsZ filaments associated to the inner cell membrane, has been postulated to exert constriction forces. Membrane anchoring is mediated by ZipA, an essential transmembrane protein able to specifically bind FtsZ. In this work, an artificial complex of FtsZ-ZipA has been reconstituted at the inner side of spherical giant unilamellar vesicles made of E. coli lipids. Under these conditions, FtsZ polymerization, triggered when a caged GTP analogue is UV-irradiated, was followed by up to 40% vesicle inflation. The homogeneous membrane dilation was accompanied by the visualization of discrete FtsZ assemblies at the membrane. Complementary rheological data revealed enhanced elasticity under lateral dilation. This explains why vesicles can undergo large dilations in the regime of mechanical stability. A mechanical role for FtsZ polymers as promoters of membrane softening and plasticization is hypothesized.

Cucumber anaphylaxis in a latex-sensitized patient

We report the case of a 76-year-old woman who experienced dizziness, vomiting, dyspnea, thoracic erythema, and vaginal itching within 5 minutes of eating cucumber. She had been diagnosed 3 months earlier with papaya urticaria and latex sensitization. The results of skin prick tests were positive for cucumber, watermelon, papaya, and latex and negative for melon and profilin extracts. ImmunoCAP for latex-specific serum immunoglobulin (Ig) E was positive. Cucumber-specific serum IgE was negative. Immunoblot analysis using patient serum revealed a 30- to 32-kDa protein band in the cucumber (peel) and papaya extracts. Immunoblot inhibition with latex extract demonstrated inhibition of the band in both extracts. Immunoblot inhibition with cucumber-papaya and papaya-cucumber revealed inhibition of the same band in the cucumber and papaya extracts, respectively. We present a case of IgE-mediated allergy to cucumber and papaya. Our results strongly suggest that the allergen(s) implicated are associated with latex sensitization. To our knowledge, this is the first report of cucumber-latex and cucumber-papaya cross-reactivity.

Monitoring influenza activity in Europe with Google Flu Trends: comparison with the findings of sentinel physician networks - results for 2009-10

The number of Internet searches has recently been used by Google to estimate the influenza incidence in the United States. We examined the correlation between the Google Flu Trends tool and sentinel networks estimates in several European countries during the 2009 influenza A(H1N1) pandemic and found a good correlation between estimates and peak incidence timing, with the highest peaks in countries where Internet is most frequently used for health-related searching. Although somehow limited, Google could be a valuable tool for syndromic surveillance.

Fracturas en el plano coronal del húmero distal

Son lesiones que comprenden las fracturas del cóndilo y/o de la tróclea humeral. Suponen el 1% de las fracturas del codo y el 6% de las fracturas del húmero distal. Las más frecuentes son las fracturas del cóndilo humeral tipo I según la clasificación de Bryan y Morrey. Analizamos 16 casos de este tipo de lesiones tratadas con reducción abierta y osteosíntesis con tornillos y valoramos los resultados funcionales. Obtuvimos la consolidación en el 100 % de los casos con ausencia de dolor o dolor leve. El 87,5 % de los casos presentaron una movilidad activa en flexión entre 120º y 140º, en extensión de –10º a –30º. Prono-supinación completa en 15 casos y un déficit de pronación de 60º y de supinación de 50º en un caso. El 100 % volvieron a su actividad laboral sin restricciones en 11 semanas. En el seguimiento (11,3 meses de media, rango: 4-29), 2 pacientes (12,5%), necesitaron de cirugía por rigidez articular (artrolisis abierta). No hubo ningún caso de necrosis avascular. Subrayamos la importancia de obtener una reducción anatómica suficientemente estable, siendo la osteosíntesis abierta el mejor método para conseguirlo y así permitir la movilización precoz del codo y una la correcta recuperación funcional.

Carotid bifurcation atherosclerosis in the over-65s: a prevalence study

AIM

The aim of this study was to determine the prevalence of carotid stenosis (CS) in the over-65 population segment residing in a catchment area (Gijón) served by the Asturias Health Service (Spain) as a necessary step in planning medical care for treating cerebrovascular disease in the elderly.

METHODS

In this descriptive transversal study, 232 subjects (114 men and 118 women) randomly chosen from health card data underwent colour-flow duplex scanning of the supra-aortic trunks.

RESULTS

The prevalence of CS in this sample was 21.5%. When stratified by sex and age (65-74 and >75 years of age), the CS rate was 5 points higher in the older than in the younger group, and 4 points higher among males (23.6%) than among females (19.2%).

CONCLUSION

Approximately one in every 5 subjects over 65 years of age presents with CS; CS prevalence was higher in the over-75s and among males, although the differences were not statistically significant.