Probable endometrial tuberculosis in a patient with rhupus

Endometrial tuberculosis (TB) is an uncommon manifestation of disseminated TB. Rhupus is the coexistence of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). We describe a case of endometrial TB in rhupus patient an immunosuppressed.

Contribution

We describe an uncommon presentation of disseminated TB, endometrial TB, in a rare rheumatic disease, rhupus. A high index of suspicion for TB is imperative in immunocompromised patients presenting with chronic urogenital symptoms especially in an endemic area.

Osteoporosis in Black South Africans With Rheumatoid Arthritis

Background Osteoporosis is a common comorbidity associated with rheumatoid arthritis (RA). The aim of this study was to determine the risk factors and possible predictors of osteoporosis in black patients with RA. Methods A retrospective study of 120 randomly selected RA patients attending an arthritis clinic in Johannesburg, South Africa, was carried out, in which 60 patients were with and 60 without osteoporosis. The demographics, disease activity, American College of Rheumatology (ACR) functional status, treatment, and dual-energy X-ray absorptiometry (DEXA) characteristics were compared. Statistical analysis was performed using SPSS version 25.0 (IBM Corp, Armonk, NY). Bivariate comparisons of demographic factors, disease factors, and T-scores between patients with and without osteoporosis were performed, using two-sided t-tests for continuous variables and chi-squared tests for categorical variables. Possible predictors of osteoporosis were subsequently entered into a multivariate logistic regression model with osteoporosis being the dependent variable. The level of significance for all analyses was set at p < 0.05. Results The median (IQR) age of the overall cohort was 67 (61.0, 72.8) years, the majority (95.5%) were female, of which 97.4% were postmenopausal. The mean disease duration from diagnosis to the DEXA was 8.6 ± 6.2 years. Rheumatoid factor (RF) positivity was 89.2% and anti-cyclic citrullinated peptide (ACCP) positivity was 82.7%. The median (IQR) for disease activity score 28 swollen and tender joint count using the erythrocyte sedimentation rate (DAS-28 ESR) was 3.4 (2.8-4.7) and the median (IQR) for ESR was 41 (22, 64.3) mm/h. There were significantly more patients treated with triple therapy in the no osteoporosis group, 38 (63.3%), than in the osteoporosis group, 21 (35%) (p = 0.00). The ACR functional class was significantly worse in the RA patients with osteoporosis than in the RA patients without osteoporosis [median (IQR), 2 (2, 3) vs 2 (1, 2), (p = 0.03)], respectively. Conclusion This study found that a worse ACR functional class was significantly associated with osteoporosis. In addition, the use of triple therapy had a protective effect. Early recognition of the risk factors for osteoporosis should be sought, with prompt preventative measures, screening, and treatment.

Geo-epidemiology of autoantibodies in rheumatoid arthritis: comparison between four ethnically diverse populations

BACKGROUND

Rheumatoid arthritis (RA) occurs across the globe in different ethnic populations. Most RA patients harbor anti-modified protein antibodies (AMPA); however, it is unclear whether differences exist in autoantibody responses at different geographic locations and between different ethnic groups, which could provide new clues regarding factors underlying autoantibody development. We therefore investigated AMPA prevalence and association with HLA DRB1 alleles and smoking in four ethnically diverse populations on four different continents.

METHODS

Anti-carbamylated (anti-CarP), anti-malondialdehyde acetaldehyde (anti-MAA), and anti-acetylated protein antibodies (anti-AcVim) IgG were determined in anti-citrullinated protein antibody-positive Dutch (NL, n = 103), Japanese (JP, n = 174), First Nations Peoples in Canada (FN, n = 100), and black South African (SA, n = 67) RA patients. Ethnicity-matched local healthy controls were used to calculate cut-offs. Risk factors associated with AMPA seropositivity in each cohort were identified using logistic regression.

RESULTS

Median AMPA levels were higher in First Nations Peoples in Canada and especially South African patients, as reflected by percentage seropositivity: NL, JP, FN, and SA: anti-CarP: 47%, 43%, 58%, and 76% (p < 0.001); anti-MAA: 29%, 22%, 29%, and 53% (p < 0.001); and anti-AcVim: 20%, 17%, 38%, and 28% (p < 0.001). Total IgG levels also differed markedly, and when autoantibody levels were normalized to total IgG, differences between cohorts became less pronounced. Although there were some associations with AMPA and HLA risk alleles and smoking, none was consistent across all four cohorts.

CONCLUSIONS

AMPA against various post-translational modifications could consistently be detected on different continents across ethnically diverse RA populations. Differences in AMPA levels corresponded to differences in total serum IgG levels. This suggests that, despite differences in risk factors, a common pathway may be involved in AMPA development across geographic locations and ethnicities.

Clinical spectrum and outcomes of idiopathic inflammatory myopathies in South Africans

Background

Idiopathic inflammatory myopathies (IIM) are rare diseases for which there is a paucity of data in Africa. We undertook a retrospective records review of clinical and laboratory features of patients with IIM attending a tertiary service in Gauteng, South Africa.

Materials and methods

Case records of patients seen between January 1990 and December 2019 and fulfilling the Bohan and Peter criteria for IIM were reviewed for demographics, clinical features, special investigations and drug therapy.

Results

Of 94 patients included in the study, 65 (69.1%) had dermatomyositis (DM) and 29 (30.9%) had polymyositis (PM). Overall, the mean (SD) age at presentation and disease duration were 41.5 (13.6) and 5.9 (6.2) years, respectively. 88 (93.6%) were Black Africans. The most common cutaneous features in DM patients were Gottron's lesions (72.3%) and abnormal cuticular overgrowth (67.7%). Dysphagia was the most common extra-muscular feature (31.9%), more so in PM than DM (p = 0.02). Creatine kinase, total leucocyte count and CRP were similarly higher in PM than DM patients (p = 0.006, 0.002, and 0.01, respectively). Anti-nuclear and anti-Jo-1 antibodies were positive in 62.2 and 20.4% of patients tested, respectively, the latter significantly more in PM than DM patients (OR = 5.1, p = 0.03) and more likely to be positive with ILD (p = 0.001). Corticosteroids were prescribed in all patients, 89.4% had additional immunosuppressive drugs and 6.4% required intensive/high care. Malignancies occurred in three patients, all of whom had DM. There were seven known deaths.

Conclusion

The present study provides further insights into the spectrum of clinical features of IIM, especially cutaneous features of DM, anti-Jo-1 antibodies and associated ILD, in a cohort of predominantly black African patients.

A genome-wide association study for rheumatoid arthritis replicates previous HLA and non-HLA associations in a cohort from South Africa

The complex pathogenesis of rheumatoid arthritis (RA) is not fully understood, with few studies exploring the genomic contribution to RA in patients from Africa. We report a genome-wide association study (GWAS) of South-Eastern Bantu-Speaking South Africans (SEBSSAs) with seropositive RA (n = 531) and population controls (n = 2653). Association testing was performed using PLINK (logistic regression assuming an additive model) with sex, age, smoking and the first three principal components as covariates. The strong association with the Human Leukocyte Antigen (HLA) region, indexed by rs602457 (near HLA-DRB1), was replicated. An additional independent signal in the HLA region represented by the lead SNP rs2523593 (near the HLA-B gene; Conditional P-value = 6.4 × 10-10) was detected. Although none of the non-HLA signals reached genome-wide significance (P < 5 × 10-8), 17 genomic regions showed suggestive association (P < 5 × 10-6). The GWAS replicated two known non-HLA associations with MMEL1 (rs2843401) and ANKRD55 (rs7731626) at a threshold of P < 5 × 10-3 providing, for the first time, evidence for replication of non-HLA signals for RA in sub-Saharan African populations. Meta-analysis with summary statistics from an African-American cohort (CLEAR study) replicated three additional non-HLA signals (rs11571302, rs2558210 and rs2422345 around KRT18P39-NPM1P33, CTLA4-ICOS and AL645568.1, respectively). Analysis based on genomic regions (200 kb windows) further replicated previously reported non-HLA signals around PADI4, CD28 and LIMK1. Although allele frequencies were overall strongly correlated between the SEBSSA and the CLEAR cohort, we observed some differences in effect size estimates for associated loci. The study highlights the need for conducting larger association studies across diverse African populations to inform precision medicine-based approaches for RA in Africa.

Comorbidities in Black South Africans with established rheumatoid arthritis

Objective

Comorbidities contribute both to morbidity and mortality in rheumatoid arthritis (RA). The aim of the current study was to investigate the prevalence and spectrum of comorbidities in South Africans with established RA.

Methods

A retrospective, consecutive case record review of 500 Black South African patients with established disease of ≥5 years attending a tertiary rheumatology service was performed. Common comorbidities including those listed in the Charlson Comorbidity Score (CCS) were documented.

Results

Most patients, 463 known alive (AG) and 37 known deceased (DG), were female (87%). Mean (SD) age and disease duration were 60 (11.1) and 10.7 (5.0) years respectively, and 98% had ≥1 comorbidities. Median CCS was 2, significantly higher in DG than AG (4 vs 2, P < .0001). Despite hypertension (70%) and hypercholesterolemia (47%) being the commonest comorbidities overall and type 2 diabetes (T2D) occurring in 15.4%, clinical cardiovascular events were rare (0.6%). Peptic ulcer disease (odds ratio [OR] = 8.67), congestive cardiac failure (OR = 7.09), serious infections (OR = 7.02) and tuberculosis (OR = 2.56) were significantly more common in DG than AG. Multivariate analysis showed that American College of Rheumatology functional class 3/4 was associated with increased risk for serious infections (OR = 3.84) and tuberculosis (OR = 2.10).

Conclusion

Despite the high burden of cardiometabolic comorbidities in South Africans with established RA, cardiovascular events were rare. Serious infections and tuberculosis, both associated with severe functional disability, are a major cause of morbidity and mortality.

Phenotype and treatment of elderly onset compared with younger onset rheumatoid arthritis patients in international daily practice

OBJECTIVE

To identify possible differences in baseline characteristics, initial treatment and treatment response between RA patient subgroups based on age at disease onset.

METHODS

Daily practice data from the worldwide METEOR registry were used. Patients (7912) were stratified into three age-groups (age at disease diagnosis <45 years, 45-65 years, >65 years). Initial treatment was compared between the different age-groups. With Cox regression analyses the effect of age-group on time-to-switch from first to second treatment was investigated, and with linear mixed models differences in response to treatment (DAS and HAQ) between the age-groups were assessed, after correction for potential confounders.

RESULTS

The >65 years age-group included more men, and more seronegative RA with somewhat higher inflammatory markers. Initial treatment choices differed only slightly between the age-groups, and the time-to-switch from initial treatment to the next was similar. DAS and HAQ improvement were dependent on the age-group, reflected by a significant interaction between age-group and outcome. The stratified analysis showed a difference of -0.02 and -0.05 DAS points and, -0.01 and 0.02 HAQ points per month in the <45 and 45-65 years age-groups as compared with the >65 year age group, a difference that did not seem clinically relevant.

CONCLUSION

In this international study on worldwide clinical practice, patients with RA onset >65 years include more men and seronegative arthritis, and were initially treated slightly differently than younger patients. We observed no clinically relevant differences in timing of a next treatment step, or response to treatment measured by DAS and HAQ.

Patterns and outcomes of admissions to the medical acute care unit of a tertiary teaching hospital in South Africa

BACKGROUND

A Medical Acute Care Unit (MACU) was established at Chris Hani Baragwanath Academic Hospital (CHBAH) to provide comprehensive medical specialist care to the patients presenting with acute medical emergencies. Improved healthcare delivery systems at the MACU may result in shorter hospital stays, better outcomes, and less mortality.

OBJECTIVES

The study's objective was to describe the demographics, diagnoses, disease patterns, and outcomes, including patient's mortality, admitted to the MACU at CHBAH.

METHODS

Records of 200 patients admitted, between March 2015 to August 2015, to the MACU at CHBAH were reviewed. Patient demographics, diagnosis at admission, duration of stay, and outcomes were documented. Patients transferred to the medical ward, the Intensive Care Unit (ICU), or discharge. The leading causes of mortality were documented.

RESULTS

Of the 200 patients, 59% were females. The patients' mean age was 46 (17.2) years, and the mean duration of stay at the MACU was 1.45 (1.25) days. Non-communicable diseases accounted for 76% of admissions. The most frequently diagnosed conditions included: diabetic ketoacidosis acidosis (DKA) and hyperosmolar non-ketotic (HONK) (17.5%), non-accidental self-poisoning (16%), hypertensive emergencies (9.5%), decompensated cardiac failure (8%) and ischemic heart disease (7%). Infectious diseases comprised 14% of the diagnoses, of which cases of pneumonia were the most common (5%). Most patients (77.5%) were transferred to medical wards, 12% to ICU, while 10% demised at the MACU. The leading causes of death included sepsis (25%), DKA/HONK (20%), non-accidental self-poisoning (10%), and cardiac failure (10%).

CONCLUSION

Non-communicable diseases, particularly diabetic emergencies, were the leading causes of admission to the MACU at CHBAH. During the study period, high rates of case improvement, patient discharge, shorter hospital stay, and less mortality were observed. The leading cause of mortality was sepsis related.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Impact of the combined presence of erosions and ACPA on rheumatoid arthritis disease activity over time: results from the METEOR registry

Objective

To investigate associations between baseline presence of erosions and/or anti-citrullinated protein antibodies (ACPA) on functional ability, disease activity and treatment survival over time.

Methods

Real life data from newly diagnosed rheumatoid arthritis patients were identified in the international METEOR registry. Patients were grouped according to presence/absence of ACPA and/or erosions at baseline. Associations between the presence of ACPA and/or erosions (four groups) with the change of Disease Activity Score (DAS) and Health Assessment Questionnaire (HAQ) over time were assessed using linear mixed models during maximum 6 or maximum 12 months from baseline. Treatment survival was assessed using multiple failure-times Cox regression.

Results

Data were included from 701 ACPA‒/erosions‒, 334 ACPA‒/erosions+, 1585 ACPA+/erosions‒ and 1993 ACPA+/erosions+ patients. We found statistically significant differences in DAS and HAQ change over time between the four groups, both after maximum follow-up durations of 6 and of 12 months, but after stratification differences proved small and not clinically meaningful. Patients in the ACPA‒/erosions‒ group were less likely to switch treatment compared with the ACPA+/erosions‒ reference group (p<0.001). The other two ACPA/erosions groups did not differ from the reference group.

Conclusions

In this analysis of worldwide real life data, we found statistically significant, but clinically irrelevant differences in treatment response to initial disease modifying anti-rheumatic drug therapies as measured by DAS and HAQ in ACPA‒/erosions‒, ACPA‒/erosions+, ACPA+/erosions‒ and ACPA+/erosions+ rheumatoid arthritis patients. However, after maximum follow-up durations of 6 and 12 months all groups had a similar response to initial treatment, but with a lower likelihood to switch treatment for ACPA‒/erosions‒ patients during the first year of follow-up.

HLA-DRB1 Amino Acid Positions and Residues Associated with Antibody-positive Rheumatoid Arthritis in Black South Africans

OBJECTIVE

To investigate the association of specific amino acid positions, residues, and haplotypes of HLA-DRB1 in black South Africans with autoantibody-positive rheumatoid arthritis (RA).

METHODS

High-resolution HLA-DRB1 genotyping was performed in 266 black South Africans with autoantibody-positive RA and 362 ethnically and geographically matched controls. The alleles were converted to specific amino acid residues at polymorphic sites for downstream analyses. Logistic regression models were used to test whether variability at site, specific amino acid residues, and haplotypes (constructed from positions 11, 71, and 74) were associated with RA.

RESULTS

Of the 29 amino acid positions examined, positions 11, 13, and 33 (permutation p = 3.4^e-26, 1.2^e-27, and 2.1^e-28, respectively) showed the strongest association with RA. Univariate analyses of individual amino acid residues showed valine at position 11 (OR 5.1, 95% CI 3.7-7.0) and histidine at position 13 (OR 6.1, 95% CI 4.2-8.6) conferred the highest risk. The valine containing haplotypes of position 11, 71, 74, V_K_A conferred the most risk (OR 4.52, 95% CI 2.68-7.61) and conversely the haplotype with serine at this position, S_K_R, conferred the most protection (OR 0.83, 95% CI 0.61-1.15).

CONCLUSION

Autoantibody-positive RA in black South Africans is associated with histidine at position 13 and valine at position 11 of HLA-DRB1, and haplotypes with valine at position 11 conferred the highest risk; conversely, serine at position 11 conveyed protection.

Inequity in access to bDMARD care and how it influences disease outcomes across countries worldwide: results from the METEOR-registry

Objective

To establish in a global setting the relationships between countries’ socioeconomic status (SES), measured biological disease modifying antirheumatic drug (bDMARD)-usage and disease outcomes. To assess if prescription and reimbursement rules and generic access to medication relates to a countries’ bDMARD-usage.

Methods

Data on disease activity and drug use from countries that had contributed at least 100 patients were extracted from the METEOR database. Mean disease outcomes of all available patients at the final visit were calculated on a per-country basis. A questionnaire was sent to at least two rheumatologists per country inquiring about DMARD-prices, access to treatment and valid regulations for prescription and reimbursement.

Results

Data from 20 379 patients living in 12 different countries showed that countries’ SES was positively associated with measured disease activity (meanDAS28), but not always with physical functioning (HAQ-score). A lower country’s SES, stricter rules for prescription and reimbursement of bDMARDs as well as worse affordability of bDMARDs were associated with lower bDMARD-usage. bDMARD-usage was negatively associated with disease activity (although not with physical functioning), but the association was moderate at best.

Conclusions

Disease activity in patients with rheumatoid arthritis as well as bDMARD-usage varies across countries worldwide. The (negative) relationship between countries’ bDMARD-usage and level of disease activity is complex and under the influence of many factors, including—but not limited to—countries’ SES, affordability of bDMARDs and valid prescription and reimbursement rules for bDMARDs.

Sex-associated Treatment Differences and Their Outcomes in Rheumatoid Arthritis: Results from the METEOR Register

OBJECTIVE

To assess differences in initial treatment and treatment response in male and female patients with rheumatoid arthritis (RA) in daily clinical practice.

METHODS

The proportion of patients with RA starting different antirheumatic treatments (disease-modifying antirheumatic drugs; DMARD) and the response to treatment were compared in the international, observational METEOR register. All visits from start of the first DMARD until the first DMARD switch or the end of followup were selected. The effect of sex on time to switch from first to second treatment was calculated using Cox regression. Linear mixed model analyses were performed to assess whether men and women responded differently to treatments, as measured by Disease Activity Score (DAS) or Health Assessment Questionnaire.

RESULTS

Women (n = 4393) more often started treatment with hydroxychloroquine, as monotherapy or in combination with methotrexate (MTX) or a glucocorticoid, and men (n = 1142) more often started treatment with MTX and/or sulfasalazine. Time to switch DMARD was shorter for women than for men. Women had a statistically significantly higher DAS over time than men (DAS improvement per year β -0.69, 95% CI -0.75 to -0.62 for men and -0.58, 95% CI -0.62 to -0.55 for women). Subanalyses per DMARD group showed for the conventional synthetic DMARD combination therapy a slightly greater decrease in DAS over time in men (-0.89, 95% CI -1.07 to -0.71) compared to women (-0.59, 95% CI -0.67 to -0.51), but these difference between the sexes were clinically negligible.

CONCLUSION

This worldwide observational study suggests that in daily practice, men and women with RA are prescribed different initial treatments, but there were no differences in response to treatment between the sexes.

Evaluation of the joint distribution at disease presentation of patients with rheumatoid arthritis: a large study across continents

Background

Genetic and environmental risk factors for rheumatoid arthritis (RA) are population dependent and may affect disease expression. Therefore, we studied tender and swollen joint involvement in patients newly diagnosed with RA in four countries and performed a subanalysis within countries to assess whether the influence of autoantibody positivity affected disease expression.

Methods

Patients with symptom duration <2 years fulfilling the American College of Rheumatology/European League Against Rheumatism 2010 RA classification criteria were selected from METEOR (Measurement of Efficacy of Treatment in the Era of Outcome in Rheumatology), an international observational database, and the Dutch Leiden Early Arthritis Clinic. Indian (n=947), Mexican (n=141), South African (n=164) and Dutch (n=947) autoantibody-positive and negative patients with RA, matched by symptom duration, were studied for swollen and tender joint distribution.

Results

Between countries, the reported distribution of swollen joint distribution differed, with more knee synovitis in Mexico, South Africa and India compared with the Netherlands (37%, 36%, 30% and 13%) and more elbow (29%, 23%, 7%, 7%) and shoulder synovitis (21%, 11%, 0%, 1%) in Mexico and South Africa compared with India and the Netherlands.

Since the number of autoantibody-negative patients in Mexico and South Africa was limited, Indian and Dutch autoantibody-positive and negative patients with RA were compared. The number of swollen and tender joints was higher in autoantibody-negative patients, but the overall distribution of involved joints was similar.

Conclusion

Joint involvement at diagnosis does not differ between autoantibody-positive and negative patients with RA in India and the Netherlands. However, joint involvement is reported differently across countries. More research is needed whether these differences are cultural and/or pathogenetic.

Disseminated fungal infection in an HIV-infected patient due to Aureobasidium pullulans

In South Africa, novel fungal pathogens have emerged as an important cause of disease in HIV-infected individuals. The clinical presentation is characteristically prolonged, insidious and the diagnosis elusive, often being made post mortem. We report an HIV-infected individual with a systemic mycosis due to Aureobasidium pullulans, a ubiquitous dematiaceous mould which has not been described in HIV-infected individuals.

Immunochip identifies novel, and replicates known, genetic risk loci for rheumatoid arthritis in black South Africans

The aim of this study was to identify genetic variants associated with rheumatoid arthritis (RA) risk in black South Africans. Black South African RA patients (n = 263) were compared with healthy controls (n = 374). Genotyping was performed using the Immunochip, and four-digit high-resolution human leukocyte antigen (HLA) typing was performed by DNA sequencing of exon 2. Standard quality control measures were implemented on the data. The strongest associations were in the intergenic region between the HLA-DRB1 and HLA-DQA1 loci. After conditioning on HLA-DRB1 alleles, the effect in the rest of the extended major histocompatibility (MHC) diminished. Non-HLA single nucleotide polymorphisms (SNPs) in the intergenic regions LOC389203|RBPJ, LOC100131131|IL1R1, KIAA1919|REV3L, LOC643749|TRAF3IP2, and SNPs in the intron and untranslated regions (UTR) of IRF1 and the intronic region of ICOS and KIAA1542 showed association with RA (p < 5 × 10(-5)). Of the SNPs previously associated with RA in Caucasians, one SNP, rs874040, locating to the intergenic region LOC389203|RBPJ was replicated in this study. None of the variants in the PTPN22 gene was significantly associated. The seropositive subgroups showed similar results to the overall cohort. The effects observed across the HLA region are most likely due to HLA-DRB1, and secondary effects in the extended MHC cannot be detected. Seven non-HLA loci are associated with RA in black South Africans. Similar to Caucasians, the intergenic region between LOC38920 and RBPJ is associated with RA in this population. The strong association of the R620W variant of the PTPN22 gene with RA in Caucasians was not replicated since this variant was monomorphic in our study, but other SNP variants of the PTPN22 gene were also not associated with RA in black South Africans, suggesting that this locus does not play a major role in RA in this population.

Genetic diversity in black South Africans from Soweto

Background

Due to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap and 1000 Genomes Projects. Notably excluded, however, is the southern Africa region, which is inhabited predominantly by southeastern Bantu-speakers, currently suffering under the dual burden of infectious and non-communicable diseases. Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure. Here, we present the most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg).

Results

Participants were typed for ~4.3 million SNPs using the Illumina Omni5 beadchip. PCA and ADMIXTURE plots were used to compare the observed variation with that seen in selected populations worldwide. Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources. To assess the suitability of our sample as representative of Sowetans, we compared our results to participants in a larger rheumatoid arthritis case–control study. The control group showed good clustering with our sample, but among the cases were individuals who demonstrated notable admixture.

Conclusions

Sowetan population structure appears unique compared to other black Africans, and may have clinical implications. Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme.

Linear-Response and Real-Time Time-Dependent Density Functional Theory Studies of Core-Level Near-Edge X-Ray Absorption

We discuss our implementation and application of time-dependent density functional theory (TDDFT) to core-level near-edge absorption spectroscopy, using both linear-response (LR) and real-time (RT) approaches. We briefly describe our restricted excitation window TDDFT (REW-TDDFT) approach for core excitations, which has also been reported by other groups. This is followed by a detailed discussion of real-time TDDFT techniques tailored to core excitations, including obtaining spectral information through delta-function excitation, postprocessing time-dependent signals, and resonant excitation through quasi-monochromatic excitation. We present results for the oxygen K-edge of water and carbon monoxide; the carbon K-edge of carbon monoxide; the ruthenium L3-edge for the hexaamminerutheium(III) ion, including scalar relativistic corrections via the zeroth order regular approximation (ZORA); and the carbon and fluorine K-edges for a series of fluorobenzenes. In all cases, the calculated spectra are found to be in reasonable agreement with experimental results, requiring only a uniform shift ranging from -4 eV to +19 eV, i.e., on the order of a few percent of the excitation energy. Real-time TDDFT visualization of excited state charge densities is used to visually examine the nature of each excitation, which gives insight into the effects of atoms bound to the absorbing center.

Excited-State Studies of Polyacenes: A Comparative Picture Using EOMCCSD, CR-EOMCCSD(T), Range-Separated (LR/RT)-TDDFT, TD-PM3, and TD-ZINDO

The low-lying excited states (La and Lb) of polyacenes from naphthalene to heptacene (N = 2-7) are studied using various time-dependent computational approaches. We perform high-level excited-state calculations using equation of motion coupled cluster with singles and doubles (EOMCCSD) and completely renormalized equation of motion coupled cluster with singles, doubles, and perturbative triples (CR-EOMCCSD(T)) and use these results to evaluate the performance of various range-separated exchange-correlation functionals within linear-response (LR) and real-time (RT) time-dependent density functional theories (TDDFT). As has been reported recently, we find that the range-separated family of functionals addresses the well-documented TDDFT failures in describing these low-lying singlet excited states to a large extent and are as about as accurate as results from EOMCCSD on average. Real-time TDDFT visualization shows that the excited state charged densities are consistent with the predictions of the perimeter free electron orbital (PFEO) model. This corresponds to particle-on-a-ring confinement, which leads to the well-known red-shift of the excitations with acene length. We also use time-dependent semiempirical methods like TD-PM3 and TD-ZINDO, which are capable of handling very large systems. Once reparametrized to match the CR-EOMCCSD(T) results, TD-ZINDO becomes roughly as accurate as range-separated TDDFT, which opens the door to modeling systems such as large molecular assemblies.

Prediction of electronic excited states of adsorbates on metal surfaces from first principles

We present the first ab initio prediction of localized electronic excited states in a periodically infinite condensed phase, a heretofore intractable goal. In particular, we examined local excitations within a CO molecule adsorbed on Pd(111). The calculation allows a configuration interaction treatment of a local region, while its interaction with the extended condensed phase is described via an embedding potential obtained from periodic density functional theory. Our work lays the foundation of a microscopic understanding of photochemistry and spectroscopy on metal surfaces.

Long live vinylidene! A new view of the H(2)C=C: --> HC triple bond CH rearrangement from ab initio molecular dynamics

We present complete active space self-consistent field (CASSCF) ab initio molecular dynamics (AIMD) simulations of the preparation of the metastable species vinylidene, and its subsequent, highly exothermic isomerization to acetylene, via electron removal from vinylidene anion (D(2)C=C(-) --> D(2)C=C: --> DC triple bond CD). After equilibrating vinylidene anion-d(2) at either 600 +/- 300 K (slightly below the isomerization barrier) or 1440 K +/- 720 K (just above the isomerization barrier), we remove an electron to form a vibrationally excited singlet vinylidene-d(2) and follow its dynamical evolution for 1.0 ps. Remarkably, we find that none of the vinylidenes equilibrated at 600 K and only 20% of the vinylidenes equilibrated at 1440 K isomerized, suggesting average lifetimes >1 ps for vibrationally excited vinylidene-d(2). Since the anion and neutral vinylidene are structurally similar, and yet extremely different geometrically from the isomerization transition state (TS), neutral vinylidene is not formed near the TS so that it must live until it has sufficient instantaneous kinetic energy in the correct vibrational mode(s). The origin of the delay is explained via both orbital rearrangement and intramolecular vibrational energy redistribution (IVR) effects. Unique signatures of the isomerization dynamics are revealed in the anharmonic vibrational frequencies extracted from the AIMD, which should be observable by ultrafast vibrational spectroscopy and in fact are consistent with currently available experimental spectra. Most interestingly, of those trajectories that did isomerize, every one of them violated conventional transition-state theory by recrossing back to vinylidene multiple times, against conventional notions that expect highly exothermic reactions to be irreversible. The dynamical motion responsible for the multiple barrier recrossings involves strong mode-coupling between the vinylidene CD(2) rock and a local acetylene DCC bend mode that has been recently observed experimentally. The multiple barrier recrossings can be used, via a generalized definition of lifetime, to reconcile extremely disparate experimental estimates of vinylidene's lifetime (differing by at least 6 orders of magnitude). Last, a caveat: These results are constrained by the approximations inherent in the simulation (classical nuclear motion, neglect of rotation-vibration coupling, and restriction to C(s) symmetry); refinement of these predictions may be necessary when more exact simulations someday become feasible.