A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations

We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region.     

Single Versus Multiple Sources of Introduced Populations Identified With Molecular Markers: A Case Study of a Freshwater Fish

The presence of a widespread exotic raises the question as to whether the successful invasion can be attributed to spread after a single introduction or is the product of multiple introductions. The plains killifish, Fundulus zebrinus, is native to the western Great Plains of the United States but is also found throughout the Colorado River basin. We surveyed five introduced populations for genetic variation in allozymes and mitochondrial DNA (mtDNA) in order to compare the genetic structure of these populations with those from across the native range. Our survey revealed two genetically distinct stocks of introduced F. zebrinus, one in the San Juan and one in the Yampa and Colorado drainages. Each stock corresponds to at least one unique introduction event. In addition, data available from a genetic survey of the native range allowed us to identify the sources of these introduced populations. The combination of allozyme and mtDNA data for the San Juan population indicated that the most probable source for this population was the Pecos drainage of New Mexico and Texas. The Yampa and Colorado populations seem to be derived from the western Arkansas drainage, although the allozyme data indicated that another nearby drainage(s) might have also served as a source for the Colorado population.     

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture,Training Population Composition,Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite,Tropical Rice Breeding Lines

Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute''s (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.     

Multiple Sclerosis and CCSVI: A Population-Based Case Control Study

Background

Chronic cerebrospinal venous insufficiency (CCSVI) has been associated to multiple sclerosis (MS).

Objective

To evaluate the possible association between CCSVI and MS, using a population-based control design.

Methods

A random cohort of 148 incident MS patients were enrolled in the study. We have also studied 20 patients with clinically isolated syndrome (CIS), 40 patients with other neurological diseases (OND), and 172 healthy controls. Transcranial (TCC) and Echo Color Doppler (ECD) were carried out in 380 subjects. A subject was considered CCSVI positive if ≥2 venous hemodynamic criteria were fulfilled.

Results

CCSVI was present in 28 (18.9%) of the MS patients, in 2 (10%) of CIS patients, in 11 (6.4%) of the controls, and in 2 (5%) of the OND patients. A significant association between MS and CCSVI was found with an odds ratio of 3.41 (95% confidence interval 1.63–7.13; p = 0.001). CCSVI was significantly more frequent among MS subjects with a disease duration longer than 144 months (26.1% versus 12.6% of patients with duration shorter than 144 months; p = 0.03) and among patients with secondary progressive (SP) and primary progressive (PP) forms (30.2% and 29.4, respectively) than in patients with relapsing remitting (RR) MS (14.3%). A stronger association was found considering SP and PP forms (age adjusted OR = 4.7; 95% CI 1.83–12.0, p = 0.001); the association was weaker with the RR patients (age adjusted OR = 2.58; 95%CI 1.12–5.92; p = 0.02) or not significant in CIS group (age adjusted OR = 2.04; 95%CI 0.40–10.3; p = 0.4).

Conclusions

A higher frequency of CCSVI has been found in MS patients; it was more evident in patients with advanced MS, suggesting that CCSVI could be related to MS disability.     

Accuracy of Lightweight Satellite Telemetry: A Case Study in the Iberian Peninsula

Abstract: Here we provide the first assessment of the accuracy of lightweight satellite transmitters (<80 g) under actual operating conditions and the performance of the Argos system in southern Europe. To estimate transmitter accuracy we used transmitters equipped with a Global Positioning System (GPS) and compared the location estimates provided by Argos with the estimates provided by the GPS. Using the 68th percentile to define the accuracy of locations estimates, observed accuracy was 4 km for Location Class (LC) 1, 15 km for LC 0, 20 km for LC A, and 59 km for LC B, which is in line with estimates reported by other authors. Yet, the error of the remaining 32% of the data ranged between 4 km and 11 km, 15 km and 217 km, 20 km and 145 km, and 59 km and 493 km, respectively, suggesting that using the 68th percentile to estimate accuracies might give misleading confidence on the accuracy of location estimates. Using the 90th percentile is probably more appropriate. Less than 10% of the locations we obtained corresponded to the more accurate LCs (3, 2, and 1), with Argos failing to provide a position estimate in 45% of the attempts. The low number of high-quality location estimates is likely a consequence of the electromagnetic interference reported for our study area, rather than a defect of the Platform Transmitter Terminals (PTTs), which under good conditions of signal reception seem to be as reliable as heavier ones. The recent advent of lightweight GPS transmitters overrides most of these problems. Yet, whereas the smallest Argos-GPS PTTs weigh 30 g, which restricts their use to animals weighting > 1,000 g, conventional PTTs can be as small as 9.5 g, allowing their use with animals weighting 250-300 g.     

Atrophy and Other Potential Factors Affecting Long Term Deep Brain Stimulation Response: A Case Series

Objective

To describe three DBS cases which presented with new side effects or loss of benefit from stimulation after long-term follow-up and to discuss the potential contributing factors.

Methods

A University of Florida (UF) database (INFORM) search was performed, identifying three patients, two Parkinson''s disease (PD) and one Essential Tremor (ET), with an unexpected change in long-term programming thresholds as compared to initial evaluation. Clinical follow-up, programming, imaging studies, and lead measurements were reviewed. The UF Institutional Review Board (IRB) approved this study.

Results

A substantial increase in the 3^rd ventricular width (120%), Evans index (6%), ventricular index (5%), and cella media index (17%) was uncovered. A change in thresholds across lead contacts with a decrease in current densities as well as a relative lateral change of lead location was also observed. Hardware-related complications, lead migration, and impedance variability were not identified.

Conclusions

Potential factors contributing to long-term side effects should be examined during a DBS troubleshooting assessment. Clinicians should be aware that in DBS therapy there is delivery of electricity to a changing brain, and atrophy may possibly affect DBS programming settings as part of long-term follow-up.     

The Genome Response to Artificial Selection: A Case Study in Dairy Cattle

Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways and regions which were affected by this selection. After analyzing the population structure, we estimated F_ST within and across the three breeds for each SNP under a pure drift model. We further considered two different strategies to evaluate the effect of selection at the genome level. First, smoothing F_ST values over each chromosome with a local variable bandwidth kernel estimator allowed identifying 13 highly significant regions subjected to strong and/or recent positive selection. Some of them contained genes within which causal variants with strong effect on milk production traits (GHR) or coloration (MC1R) have already been reported. To go further in the interpretation of the observed signatures of selection we subsequently concentrated on the annotation of differentiated genes defined according to the F_ST value of SNPs localized close or within them. To that end we performed a comprehensive network analysis which suggested a central role of somatotropic and gonadotropic axes in the response to selection. Altogether, these observations shed light on the antagonism, at the genome level, between milk production and reproduction traits in highly producing dairy cows.     

Dog Ownership in the West Indies: A Case Study From the Bahamas

ABSTRACT

Results from several studies in The Bahamas, which included 511 interviews with residents and data on 776 dogs, are reported. The composition and characteristics of the dog population are described. The majority of dogs, both owned and unowned, are local mongrels called “potcakes.” The median age of the dog population is three years. Potcakes are given a lower level of health care than dogs considered to resemble a recognised breed. Many dogs have no place in the household and are able to roam. The dynamics of the owned and unowned dog populations are derived, and abandoned dogs are shown to sustain the free-roaming population. The free-roaming dog population breeds throughout the year but it has a breeding cycle longer than six months, which is probably caused by its ill health. Despite the nuisance caused by unowned dogs, residents are tolerant towards them, and over half the households feed dogs they do not own. The changes in pet ownership required to increase the welfare of dogs are discussed.     

The Accuracy of Computerized Adaptive Testing in Heterogeneous Populations: A Mixture Item-Response Theory Analysis

Background

Computerized adaptive testing (CAT) utilizes latent variable measurement model parameters that are typically assumed to be equivalently applicable to all people. Biased latent variable scores may be obtained in samples that are heterogeneous with respect to a specified measurement model. We examined the implications of sample heterogeneity with respect to CAT-predicted patient-reported outcomes (PRO) scores for the measurement of pain.

Methods

A latent variable mixture modeling (LVMM) analysis was conducted using data collected from a heterogeneous sample of people in British Columbia, Canada, who were administered the 36 pain domain items of the CAT-5D-QOL. The fitted LVMM was then used to produce data for a simulation analysis. We evaluated bias by comparing the referent PRO scores of the LVMM with PRO scores predicted by a “conventional” CAT (ignoring heterogeneity) and a LVMM-based “mixture” CAT (accommodating heterogeneity).

Results

The LVMM analysis indicated support for three latent classes with class proportions of 0.25, 0.30 and 0.45, which suggests that the sample was heterogeneous. The simulation analyses revealed differences between the referent PRO scores and the PRO scores produced by the “conventional” CAT. The “mixture” CAT produced PRO scores that were nearly equivalent to the referent scores.

Conclusion

Bias in PRO scores based on latent variable models may result when population heterogeneity is ignored. Improved accuracy could be obtained by using CATs that are parameterized using LVMM.     

Risk Factors for Obstetric Fistula in Western Uganda: A Case Control Study

Introduction

Two million women worldwide are living with genital fistula with an annual incidence of 50,000–100,000 women. Risk factors for obstetric fistula are context bound. Studies from other countries show variation in the risk factors for obstetric fistula. This study was conducted to identify risk factors for obstetric fistula in western Ugandan context.

Methods

A case control study comparing background factors of women with obstetric fistula (cases) and women without fistula (controls) was conducted in western Uganda. Data was collected using face-to-face interviews. Univariate, bivariate and multivariate analysis was conducted using Stata 12.

Results

Altogether, 420 respondents (140 cases and 280 controls) participated in the study. Duration of labour was used to form the product terms when assessing for interaction and confounding since it was one the most significant factors at bivariate level with a narrow confidence interval and was hence considered the main predictor. After adjusting for interaction and confounding, significant risk factors associated with development of obstetric fistula in western Uganda were: Caesarean section (adjusted odds ratio [AOR]  = 13.30, 95% CI  = 6.74–26.39), respondent height of 150 cm or less (AOR  = 2.63, 95% CI  = 1.35–5.26), baby weight of 3.5 kg or more (AOR  = 1.52, 95% CI  = 1.15–1.99), prolonged labour (AOR  = 1.06, 95% CI  = 1.04–1.08. A quarter of the fistulas had resulted from iatrogenic complication during caesarean section. Compared to no education, post primary level of education was protective against obstetric fistula (AOR  = 0.31, 95% CI  = 0.13–0.72) and there was no difference between respondents without education and those with primary level education.

Conclusions

Surgeons contribute to a big proportion (25%) of fistula cases hence caesarean section being a risk factor in this region. Other risk factors include; prolonged labour, weight of the baby of 3.5 kg or more, respondent height of 150 cm or less (short stature), and low or no education are risk factors for obstetric fistula in western Ugandan.     

Ecological Praxis and Blackwater Ecosystems: A Case Study From the Brazilian Amazon

This article explores how anthropogenic modifications of soil condition human adaptive processes on the Amazonian uplands. The occurrence of black earth (a nutrient-rich anthrosol) in nutrient-poor blackwater environments and its cultivation by contemporary residents provide a unique opportunity for understanding the ecological praxis of Amazonian groups. Two years of ethnographic, ethnoscientific, and agronomic research among caboclo residents of the Lower Rio Negro and Rio Urubú confirm that unique cognitive and behavioral orientations characterize black earth and adjacent environments. When compared with cognitive and behavioral orientations to these two environments in distant blackwater regions, data suggest that political-economic, technological, cultural, and ecological factors have had~a strong influence on the trajectory of human-environmental interactions. Data in large part illustrate the utility of historical ecological models, yet point to an interactive role of diverse histories in shaping the range of human responses.     

森林土壤氮素可利用性的影响因素研究综述

近几十年来 ,人类对木材、纤维和其他森林资源需求的急剧增加 ,对森林的集约化经营管理成为必然趋势。由于大部分森林生态系统缺乏Ｎ素 ,因此施肥成为经济有效的途径。但是 ,由于森林中的Ｎ肥利用效率低于农业系统 ,且Ｎ肥生产成本较高 ,易造成环境中多余Ｎ素的污染 ,所以需要更有效的经营管理方法。要改进这类方法 ,则必须很好地理解全球各种森林生态系统的Ｎ素循环和Ｎ素可利用性[3 1] 。可利用性养分 (ａｖａｉｌａｂｌｅｎｕｔｒｉｅｎｔ)是指土壤中易被植物吸收同化的养分元素或化合物的数量[4 0 ] ,可以理解为植物利用土壤中易吸收和…     

鹅掌楸配子选择与雄性繁殖适合度

在多父本等量花粉混合授粉的交配实验设计基础上, 利用SSR分子标记对其子代进行父本分析, 研究鹅掌楸的配子选择与雄性繁殖适合度。参试亲本为鹅掌楸2个种的5个单株（鹅掌楸（Liriodendron chinense）2株, 即FY和LS; 北美鹅掌楸（L. tulipifera）3株, 即LYS、MSL和NK）。结果表明： 鹅掌楸的配子选择个体间差异较大。作为母本, NK和LYS倾向于选择异种雄配子, 而MSL和LS则倾向于选择同种雄配子; 在同种雄配子的选择中, NK、LYS和LS倾向于自交, 而MSL则倾向于异交。以北美鹅掌楸为母本时, 北美鹅掌楸与鹅掌楸的雄性繁殖贡献率分别为45.5%和54.5%, 北美鹅掌楸的雄性繁殖适合度为鹅掌楸的0.556倍。以鹅掌楸为母本时, 二者的繁殖贡献率分别为15.6%和84.4%, 北美鹅掌楸的雄性繁殖适合度为鹅掌楸的0.123倍。总体上看, 鹅掌楸的雄性繁殖适合度高于北美鹅掌楸, 鹅掌楸与北美鹅掌楸均表现为自交亲和。     

鹅掌楸配子选择与雄性繁殖适合度

在多父本等量花粉混合授粉的交配实验设计基础上, 利用SSR分子标记对其子代进行父本分析, 研究鹅掌楸的配子选择与雄性繁殖适合度。参试亲本为鹅掌楸2个种的5个单株(鹅掌楸(Liriodendron chinense)2株, 即FY和LS; 北美鹅掌楸(L. tulipifera)3株, 即LYS、MSL和NK)。结果表明: 鹅掌楸的配子选择个体间差异较大。作为母本, NK和LYS倾向于选择异种雄配子, 而MSL和LS则倾向于选择同种雄配子; 在同种雄配子的选择中, NK、LYS和LS倾向于自交, 而MSL则倾向于异交。以北美鹅掌楸为母本时, 北美鹅掌楸与鹅掌楸的雄性繁殖贡献率分别为45.5%和54.5%, 北美鹅掌楸的雄性繁殖适合度为鹅掌楸的0.556倍。以鹅掌楸为母本时, 二者的繁殖贡献率分别为15.6%和84.4%, 北美鹅掌楸的雄性繁殖适合度为鹅掌楸的0.123倍。总体上看, 鹅掌楸的雄性繁殖适合度高于北美鹅掌楸, 鹅掌楸与北美鹅掌楸均表现为自交亲和。     

From Serbia with Hate: A Case Study in Globalization, Trauma, and Language

This article analyzes a set of five postcards, purchased from a street stand in Belgrade, the capital of Yugoslavia, shortly after the NATO bombing of the country took place in the spring of 1999. While the postcards obviously serve as protests against the bombing, as well as testimonies of the nation-wide trauma caused by it, they also reveal a careful negotiation between representations of trauma — keeping it displaced enough to avoid vicarious traumatization for individual survivors, but focused enough to translate it into a part of the national Serb identity and relying on the symbolism available in historical public narratives. However, since all the postcards analyzed here use English language in one form or another, they can also be read as peculiar interpretations of globalization on a local level. The article is an examination of the function of English, both in the negotiation of private/public trauma as described above, and its role in the complex reconfiguration of the phenomenon of globalization as embedded with local meaning given the context of the narrative within the Serbian popular culture. While these pop culture artifacts offer an assurance to the Serb national spirit, they also express a multifaceted national take on globalization visible in the use of English as the language of the Western ‘enemy’. Overall,the postcards can be read as a curious traumatic figuration of postmodernism which seems to be battling modernism in Belgrade's streets, while the Serb nationalism faces off with the global world in the realm of the imaginary.     

Risk Factors for Colorectal Cancer in Patients with Multiple Serrated Polyps: A Cross-Sectional Case Series from Genetics Clinics

Background

Patients with multiple serrated polyps are at an increased risk for developing colorectal cancer (CRC). Recent reports have linked cigarette smoking with the subset of CRC that develops from serrated polyps. The aim of this work therefore was to investigate the association between smoking and the risk of CRC in high-risk genetics clinic patients presenting with multiple serrated polyps.

Methods and Findings

We identified 151 Caucasian individuals with multiple serrated polyps including at least 5 outside the rectum, and classified patients into non-smokers, current or former smokers at the time of initial diagnosis of polyposis. Cases were individuals with multiple serrated polyps who presented with CRC. Controls were individuals with multiple serrated polyps and no CRC. Multivariate logistic regression was performed to estimate associations between smoking and CRC with adjustment for age at first presentation, sex and co-existing traditional adenomas, a feature that has been consistently linked with CRC risk in patients with multiple serrated polyps. CRC was present in 56 (37%) individuals at presentation. Patients with at least one adenoma were 4 times more likely to present with CRC compared with patients without adenomas (OR = 4.09; 95%CI 1.27 to 13.14; P = 0.02). For females, the odds of CRC decreased by 90% in current smokers as compared to never smokers (OR = 0.10; 95%CI 0.02 to 0.47; P = 0.004) after adjusting for age and adenomas. For males, there was no relationship between current smoking and CRC. There was no statistical evidence of an association between former smoking and CRC for both sexes.

Conclusion

A decreased odds for CRC was identified in females with multiple serrated polyps who currently smoke, independent of age and the presence of a traditional adenoma. Investigations into the biological basis for these observations could lead to non-smoking-related therapies being developed to decrease the risk of CRC and colectomy in these patients.