Influence of Geographical Origin and Ethnicity on Mortality in Patients on Antiretroviral Therapy in Canada, Europe, and the United States

Our objective was to assess differences in all-cause mortality, as well as AIDS and non-AIDS death rates, among patients started on antiretroviral therapy (ART) according to their geographical origin and ethnicity/race in Europe, Canada, and the United States. METHODS: This was a collaboration of 19 cohort studies of human immunodeficiency virus-positive subjects who have initiated ART (ART Cohort Collaboration) between 1998 and 2009. Adjusted mortality hazard ratios (AHRs) were estimated using Cox regression. A competing risk framework was used to estimate adjusted subdistribution hazard ratios for AIDS and non-AIDS mortality. RESULTS: Of 46 648 European patients, 16.3% were from sub-Saharan Africa (SSA), 5.1% Caribbean and Latin America, 1.6% North Africa and Middle East, and 1.7% Asia/West; of 1371 patients from Canada, 14.9% were First Nations and 22.4% migrants, and of 7742 patients from North America, 55.5% were African American and 6.6% Hispanic. Migrants from SSA (AHR, 0.79; 95% confidence interval [CI], .68-.92) and Asia/West (AHR, 0.62; 95% CI, .41-.92) had lower mortality than Europeans; these differences appeared mainly attributable to lower non-AIDS mortality. Compared with white Canadians, mortality in Canadian First Nations people (AHR, 1.48; 95% CI, .96-2.29) was higher, both for AIDS and non-AIDS mortality rates. Among US patients, when compared with whites, African Americans had higher AIDS and non-AIDS mortality, and hazard ratios for all-cause mortality increased with time on ART. CONCLUSIONS: The lower mortality observed in migrants suggests "healthy migrant" effects, whereas the higher mortality in First Nations people and African Americans in North America suggests social inequality gaps. KEYWORDS: HIV infection, antiretroviral therapy, ethnic minorities, migrants Comment in Addressing disparities in HIV mortality: antiretroviral therapy is necessary but not sufficient. [Clin Infect Dis. 2013]

Noble gas, CFC and other geochemical evidence for the age and origin of the Bath thermal waters, UK

The city of Bath is a World Heritage site and its thermal waters, the Roman Baths and new spa development rely on undisturbed flow of the springs (45 °C). The current investigations provide an improved understanding of the residence times and flow regime as basis for the source protection. Trace gas indicators including the noble gases (helium, neon, argon, krypton and xenon) and chlorofluorocarbons (CFCs), together with a more comprehensive examination of chemical and stable isotope tracers are used to characterise the sources of the thermal water and any modern components. It is shown conclusively by the use of 39Ar that the bulk of the thermal water has been in circulation within the Carboniferous Limestone for at least 1000 years. Other stable isotope and noble gas measurements confirm previous findings and strongly suggest recharge within the Holocene time period (i.e. the last 12 kyr). Measurements of dissolved 85Kr and chlorofluorocarbons constrain previous indications from tritium that a small proportion (<5%) of the thermal water originates from modern leakage into the spring pipe passing through Mesozoic valley fill underlying Bath. This introduces small amounts of O2 into the system, resulting in the Fe precipitation seen in the King’s Spring. Silica geothermometry indicates that the water is likely to have reached a maximum temperature of between 69–99 °C, indicating a most probable maximum circulation depth of ∼3 km, which is in line with recent geological models. The rise to the surface of the water is sufficiently indirect that a temperature loss of >20 °C is incurred. There is overwhelming evidence that the water has evolved within the Carboniferous Limestone formation, although the chemistry alone cannot pinpoint the geometry of the recharge area or circulation route. For a likely residence time of 1–12 kyr, volumetric calculations imply a large storage volume and circulation pathway if typical porosities of the limestone at depth are used, indicating that much of the Bath-Bristol basin must be involved in the water storage.

Adherence to host extracellular matrix and serum components by Enterococcus faecium isolates of diverse origin.

Enterococcus faecium has emerged as an important cause of nosocomial infections over the last two decades. We recently demonstrated collagen type I (CI) as a common adherence target for some E. faecium isolates and a significant correlation was found to exist between acm-mediated CI adherence and clinical origin. Here, we evaluated 60 diverse E. faecium isolates for their adherence to up to 15 immobilized host extracellular matrix and serum components. Adherence phenotypes were most commonly observed to fibronectin (Fn) (20% of the 60 isolates), fibrinogen (17%) and laminin (Ln) (13%), while only one or two of the isolates adhered to collagen type V (CV), transferrin or lactoferrin and none to the other host components tested. Adherence to Fn and Ln was almost exclusively restricted to clinical isolates, especially the endocarditis-enriched nosocomial genogroup clonal complex 17 (CC17). Thus, the ability to adhere to Fn and Ln, in addition to CI, may have contributed to the emergence and adaptation of E. faecium, in particular CC17, as a nosocomial pathogen.

The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants.

The 'Mycoplasma mycoides cluster' comprises the ruminant pathogens Mycoplasma mycoides subsp. mycoides the causative agent of contagious bovine pleuropneumonia (CBPP), Mycoplasma capricolum subsp. capripneumoniae the agent of contagious caprine pleuropneumonia (CCPP), Mycoplasma capricolum subsp. capricolum, Mycoplasma leachii and Mycoplasma mycoides subsp. capri. CBPP and CCPP are major livestock diseases and impact the agricultural sector especially in developing countries through reduced food-supply and international trade restrictions. In addition, these diseases are a threat to disease-free countries. We used a multilocus sequence typing (MLST) approach to gain insights into the demographic history of and phylogenetic relationships among the members of the 'M. mycoides cluster'. We collected partial sequences from seven housekeeping genes representing a total of 3,816 base pairs from 118 strains within this cluster, and five strains isolated from wild Caprinae. Strikingly, the origin of the 'M. mycoides cluster' dates to about 10,000 years ago, suggesting that the establishment and spread of the cluster coincided with livestock domestication. In addition, we show that hybridization and recombination may be important factors in the evolutionary history of the cluster.

Acculturation and cultural identity of immigrant youth: The impact of courses in the language and culture of origin

Career choices in the fields of science, technology, engineering, and mathematics (STEM) are favoured by men and often avoided by women; on the other hand, women tend to choose fields such as the social sciences. This not only leads to a shortage of employees with STEM degrees, but also reinforces the prejudice that certain (personality) characteristics are ‘typically female’ or ‘typically male’. Career orientation motives of young women and men can have important implications for gender (a-)typical career choices. However, there is little empirical research on the correlates of career orientation motives in young women in the field of STEM. This study seeks to address this gap by outlining the components of career orientation motives and showing relationships among them. Therefore, our results provide insight into the circumstances and conditions that are associated with academic and career choices.

Nuclear markers reveal unexpected genetic variation and a Congolese-Nilotic origin of the Lake Victoria cichlid species flock

Phylogenetic analyses based on mitochondrial (mt) DNA have indicated that the cichlid species flock of the Lake Victoria region is derived from a single ancestral species found in East African rivers, closely related to the ancestor of the Lake Malawi cichlid species flock. The Lake Victoria flock contains ten times less mtDNA variation than the Lake Malawi radiation, consistent with current estimates of the ages of the lakes. We present results of a phylogenetic investigation using nuclear (amplified fragment length polymorphism) markers and a wider coverage of riverine haplochromines. We demonstrate that the Lake Victoria–Edward flock is derived from the morphologically and ecologically diverse cichlid genus Thoracochromis from the Congo and Nile, rather than from the phenotypically conservative East African Astatotilapia. This implies that the ability to express much of the morphological diversity found in the species flock may by far pre–date the origin of the flock. Our data indicate that the nuclear diversity of the Lake Victoria–Edward species flock is similar to that of the Lake Malawi flock, indicating that the genetic diversity is considerably older than the 15 000 years that have passed since the lake began to refill. Most of this variation is manifested in trans–species polymorphisms, indicating very recent cladogenesis from a genetically very diverse founder stock. Our data do not confirm strict monophyly of either of the species flocks, but raise the possibility that these flocks have arisen from hybrid swarms.

Tracing the origin of Arctic driftwood

Arctic environments, where surface temperatures increase and sea ice cover and permafrost depth decrease, are very sensitive to even slight climatic variations. Placing recent environmental change of the high-northern latitudes in a long-term context is, however, complicated by too short meteorological observations and too few proxy records. Driftwood may represent a unique cross-disciplinary archive at the interface of marine and terrestrial processes. Here, we introduce 1445 driftwood remains from coastal East Greenland and Svalbard. Macroscopy and microscopy were applied for wood anatomical classification; a multi-species subset was used for detecting fungi; and information on boreal vegetation patterns, circumpolar river systems, and ocean current dynamics was reviewed and evaluated. Four conifer (Pinus, Larix, Picea, and Abies) and three deciduous (Populus, Salix, and Betula) genera were differentiated. Species-specific identification also separated Pinus sylvestris and Pinus sibirica, which account for ~40% of all driftwood and predominantly originate from western and central Siberia. Larch and spruce from Siberia or North America represents ~26% and ~18% of all materials, respectively. Fungal colonization caused different levels of driftwood staining and/or decay. Our results demonstrate the importance of combining wood anatomical knowledge with insight on boreal forest composition for successfully tracing the origin of Arctic driftwood. To ultimately reconstruct spatiotemporal variations in ocean currents, and to better quantify postglacial uplift rates, we recommend consideration of dendrochronologically dated material from many more circumpolar sites.

Origin and evolution of reactive and noble gases dissolved in matrix pore water

Reactive and noble gases dissolved in matrix pore water of low permeable crystalline bedrock were successfully extracted and characterized for the fist time based on drillcore samples from the Olkiluoto investigation site (SW Finland). Interaction between matrix pore water and fracture groundwater occurs predominately by diffusion. Changes in the chemical and isotopic composition of gases dissolved in fracture groundwater are transmitted and preserved in the pore water. Absolute concentrations, their ratios and the stable carbon isotope signature of hydrocarbon gases dissolved in pore water give valuable indications about the evolution of these gases in the nearby-flowing fracture groundwaters. Inert noble gases dissolved in matrix pore water and their isotopes combined with their in-situ production and accumulation rates deliver information about the residence time of pore water.

The long non-coding RNA NEAT1 is increased in IUGR placentas, leading to potential new hypotheses of IUGR origin/development.

INTRODUCTION Intrauterine Growth Restriction (IUGR) is a multifactorial disease defined by an inability of the fetus to reach its growth potential. IUGR not only increases the risk of neonatal mortality/morbidity, but also the risk of metabolic syndrome during adulthood. Certain placental proteins have been shown to be implicated in IUGR development, such as proteins from the GH/IGF axis and angiogenesis/apoptosis processes. METHODS Twelve patients with term IUGR pregnancy (birth weight < 10th percentile) and 12 CTRLs were included. mRNA was extracted from the fetal part of the placenta and submitted to a subtraction method (Clontech PCR-Select cDNA Subtraction). RESULTS One candidate gene identified was the long non-coding RNA NEAT1 (nuclear paraspeckle assembly transcript 1). NEAT1 is the core component of a subnuclear structure called paraspeckle. This structure is responsible for the retention of hyperedited mRNAs in the nucleus. Overall, NEAT1 mRNA expression was 4.14 (±1.16)-fold increased in IUGR vs. CTRL placentas (P = 0.009). NEAT1 was exclusively localized in the nuclei of the villous trophoblasts and was expressed in more nuclei and with greater intensity in IUGR placentas than in CTRLs. PSPC1, one of the three main proteins of the paraspeckle, co-localized with NEAT1 in the villous trophoblasts. The expression of NEAT1_2 mRNA, the long isoform of NEAT1, was only modestly increased in IUGR vs. CTRL placentas. DISCUSSION/CONCLUSION The increase in NEAT1 and its co-localization with PSPC1 suggests an increase in paraspeckles in IUGR villous trophoblasts. This could lead to an increased retention of important mRNAs in villous trophoblasts nuclei. Given that the villous trophoblasts are crucial for the barrier function of the placenta, this could in part explain placental dysfunction in idiopathic IUGR fetuses.

CHROMOSOMAL ORIGIN OF DM-DNA

Double minutes (dm) are small chromatin particles of 0.3 microns diameter found only in the metaphase cells of human and murine tumors. Dm are unique cytogenetic structures since their numbers per cell show wide variation. At cell division, dm are retained despite the lack of centromeres. In squash preparations, dm show clustering often in association with chromosomes. Human carcinoma cell line SW613-S18 was found to have large numbers of dm and biological characteristics favorable for mitotic synchronization and chromosome isolation experiments.^ S18 cells were synchronized to mitosis with metabolic and mitotic blocking compounds. Mitotic cells were lysed to release chromosomes and dm from the mitotic spindle and the resulting suspensions were fractionated to enrich for dm. The DNA in enriched fractions was characterized. The reassociation kinetics of dm-DNA driven with placental human DNA was similar to the reassociation curve of labeled placental DNA under similar conditions. In situ hybridization of dm-DNA to tumor and normal metaphase cells showed grain localization over the entire karyotype. Dm-DNA was shown by pulse chase DNA replication experiments to replicate during early and mid S-phase of the cell cycle, but not in late S-phase. In addition, BrdUrd incorporation studies showed that dm-DNA replicates only once during the S-phase. Premature chromosome condensation studies suggest the basis of numerical heterogeneity of dm is nondisjunction, not anomalous or unscheduled DNA replication.^ These data and previous cytochemical banding studies of dm in SW613-S18 indicate that dm-DNA is chromosomal in origin. No evidence of gene amplification was found in the DNA reassociation data. It is likely that dm-DNA represents the pale-staining G-band regions of the human karyotype in this cell line. ^

Molecular epidemiology of Bacillus anthracis: determining the correct origin

We analyzed and compared strains of Bacillus anthracis isolated from husbandry and industrial anthrax cases in Switzerland between 1952 and 1981 with published data using multiple-locus variable-number tandem repeat analysis. Strains isolated from autochthonous cases of anthrax in cattle belong to genotype B2, together with strains from continental Europe, while human B. anthracis strains clustered with genotype A4. These strains could be traced back to outbreaks of human anthrax that occurred between 1978 and 1981 in a factory processing cashmere wool from the Indian subcontinent. We interpret the worldwide occurrence of B. anthracis strains of cluster A4 to be due to the extensive global trade of untreated cashmere wool during the last century.

The origin of oriented lakes: evidence from the Bolivian Amazon

The presence of hundreds of rectangular and oriented lakes is one of the most striking characteristics of the Llanos de Moxos (LM) landscape in the Bolivian Amazon. Oriented lakes also occur in the Arctic coastal plains of Russia, Alaska and Canada and along the Atlantic Coastal Plain from northeast Florida to southeast New Jersey and along the coast of northeast Brazil. Many different mechanisms have been proposed for their formation. In the LM, Plafker's (1964) tectonic model, in which subsidence results from the propagation of bedrock faults through the foreland sediments, is the most accepted. However, this model has not been verified. Here, we present new results from stratigraphic transects across the borders of three rectangular and oriented lakes in the LM. A paleosol buried under mid-Holocene sediments is used as a stratigraphic marker to assess the vertical displacement of sediments on both sides of the alleged faults. Our results show that there is no vertical displacement and, therefore, that Plafker's model can be ruled out. We suggest that, among all the proposed mechanisms behind lake formation, the combined action of wind and waves is the most likely. The evidence from the LM provides new hints for the formation of oriented lakes worldwide.