Comparison of fecal culture and F57 real-time polymerase chain reaction for the detection of Mycobacterium avium subspecies paratuberculosis in Swiss cattle herds with a history of paratuberculosis

BACKGROUND: Bovine paratuberculosis is an incurable chronic granulomatous enteritis caused by Mycobacterium avium subspecies paratuberculosis (MAP). The prevalence of MAP in the Swiss cattle population is hard to estimate, since only a few cases of clinical paratuberculosis are reported to the Swiss Federal Food Safety and Veterinary Office each year.Fecal samples from 1,339 cattle (855 animals from 12 dairy herds, 484 animals from 11 suckling cow herds, all herds with a history of sporadic paratuberculosis) were investigated by culture and real-time polymerase chain reaction (PCR) for shedding of MAP. RESULTS: By culture, MAP was detected in 62 of 445 fecal pools (13.9%), whereas PCR detected MAP in 9 of 445 pools (2.0%). All 186 samples of the 62 culture-positive pools were reanalyzed individually. By culture, MAP was grown from 59 individual samples (31.7%), whereas PCR detected MAP in 12 individual samples (6.5%), all of which came from animals showing symptoms of paratuberculosis during the study. Overall, MAP was detected in 10 out of 12 dairy herds (83.3%) and in 8 out of 11 suckling cow herds (72.7%). CONCLUSIONS: There is a serious clinically inapparent MAP reservoir in the Swiss cattle population. PCR cannot replace culture to identify individual MAP shedders but is suitable to identify MAP-infected herds, given that the amount of MAP shed in feces is increasing in diseased animals or in animals in the phase of transition to clinical disease

Characteristics and comprehensiveness of adult HIV care and treatment programmes in Asia-Pacific, sub-Saharan Africa and the Americas: results of a site assessment conducted by the International epidemiologic Databases to Evaluate AIDS (IeDEA) Collaboration

INTRODUCTION HIV care and treatment programmes worldwide are transforming as they push to deliver universal access to essential prevention, care and treatment services to persons living with HIV and their communities. The characteristics and capacity of these HIV programmes affect patient outcomes and quality of care. Despite the importance of ensuring optimal outcomes, few studies have addressed the capacity of HIV programmes to deliver comprehensive care. We sought to describe such capacity in HIV programmes in seven regions worldwide. METHODS Staff from 128 sites in 41 countries participating in the International epidemiologic Databases to Evaluate AIDS completed a site survey from 2009 to 2010, including sites in the Asia-Pacific region (n=20), Latin America and the Caribbean (n=7), North America (n=7), Central Africa (n=12), East Africa (n=51), Southern Africa (n=16) and West Africa (n=15). We computed a measure of the comprehensiveness of care based on seven World Health Organization-recommended essential HIV services. RESULTS Most sites reported serving urban (61%; region range (rr): 33-100%) and both adult and paediatric populations (77%; rr: 29-96%). Only 45% of HIV clinics that reported treating children had paediatricians on staff. As for the seven essential services, survey respondents reported that CD4+ cell count testing was available to all but one site, while tuberculosis (TB) screening and community outreach services were available in 80 and 72%, respectively. The remaining four essential services - nutritional support (82%), combination antiretroviral therapy adherence support (88%), prevention of mother-to-child transmission (PMTCT) (94%) and other prevention and clinical management services (97%) - were uniformly available. Approximately half (46%) of sites reported offering all seven services. Newer sites and sites in settings with low rankings on the UN Human Development Index (HDI), especially those in the President's Emergency Plan for AIDS Relief focus countries, tended to offer a more comprehensive array of essential services. HIV care programme characteristics and comprehensiveness varied according to the number of years the site had been in operation and the HDI of the site setting, with more recently established clinics in low-HDI settings reporting a more comprehensive array of available services. Survey respondents frequently identified contact tracing of patients, patient outreach, nutritional counselling, onsite viral load testing, universal TB screening and the provision of isoniazid preventive therapy as unavailable services. CONCLUSIONS This study serves as a baseline for on-going monitoring of the evolution of care delivery over time and lays the groundwork for evaluating HIV treatment outcomes in relation to site capacity for comprehensive care.

Where Empires Meet: Orientalism and Marginality at the Former Russo-British Frontier

This article explores the intersection of orientalism and marginality in two regions at the former Russo-British frontier between Central and South Asia. Focussing on Tajikistan’s Gorno-Badakhshan and Gilgit-Baltistan in today’s Pakistan, an analysis of historical and contemporary orientalist projections on and in the two border regions reveals changing modes of domination through the course of the twentieth century (British, Kashmiri, Pakistani and Russian, Soviet, Tajik). In this regard, different local experiences of “ colonial ” rule, both in Gorno-Badakhshan and Gilgit-Baltistan, challenge “ classical ” periodisations of colonial/postcolonial and colonial/socialist/postsocialist. This article furthermore maintains that processes of marginalisation in both regions can be interpreted as effects of imperial and Cold War contexts that have led to the establishment of the frontier. Thus, a central argument is that neither the status of the frontier between Central and South Asia as a stable entity, nor the periodisations that have conventionally been ascribed to the two regions as linear timelines can be taken for granted.

Palaeoenvironmental changes in Central Europe (NE Poland) during the last 6200 years reconstructed from a high-resolution multi-proxy peat archive

Peat deposits from an ombrotrophic bog (north-eastern Poland) were analysed to reconstruct peatland development and environmental changes. This paper presents reconstructions of hydrological changes and plant succession over the last 6000 years. The methods included the high-resolution analysis of plant macrofossils, pollen and testate amoebae, supported by radiocarbon dating. Three main phases were identified in the history of the bog and surrounding woodland vegetation: 4000–400 BC, 400 BC–AD 1700 and AD 1700–2011. Except for terrestrialisation and the fen-to-bog transition phase, the development of bog vegetation was mainly dependent on the climate until approximately AD 1700. The dominant taxon in Gązwa bog was Sphagnum fuscum/rubellum. Woodland development was significantly affected by human activity at several time periods. The most visible human activity, manifested by the decline of deciduous species, occurred ca. 350 BC, ca. AD 250, ca. AD 1350 and after AD 1700. These events correspond to phases of human settlement in the area. During 400–300 BC, the decline of deciduous trees, primarily Carpinus, coincided with an increase in indicators of human activity and fire frequency. At ca. AD 200, Carpinus and Tilia abundance decreased, corresponding to an increased importance of cereals (Secale and Triticum). Since ca. AD 1350, the impact of Teutonic settlement is apparent, and after AD 1700, deciduous forests largely disappeared.

An underestimated record breaking event – why summer 1540 was likely warmer than 2003

The heat of summer 2003 in Western and Central Europe was claimed to be unprecedented since the Middle Ages on the basis of grape harvest data (GHD) and late wood maximum density (MXD) data from trees in the Alps. This paper shows that the authors of these studies overlooked the fact that the heat and drought in Switzerland in 1540 likely exceeded the amplitude of the previous hottest summer of 2003, because the persistent temperature and precipitation anomaly in that year, described in an abundant and coherent body of documentary evidence, severely affected the reliability of GHD and tree-rings as proxy-indicators for temperature estimates. Spring–summer (AMJJ) temperature anomalies of 4.7 °C to 6.8 °C being significantly higher than in 2003 were assessed for 1540 from a new long Swiss GHD series (1444 to 2011). During the climax of the heat wave in early August the grapes desiccated on the vine, which caused many vine-growers to interrupt or postpone the harvest despite full grape maturity until after the next spell of rain. Likewise, the leaves of many trees withered and fell to the ground under extreme drought stress as would usually be expected in late autumn. It remains to be determined by further research whether and how far this result obtained from local analyses can be spatially extrapolated. Based on the temperature estimates for Switzerland it is assumed from a great number of coherent qualitative documentary evidence about the outstanding heat drought in 1540 that AMJJ temperatures were likely more extreme in neighbouring regions of Western and Central Europe than in 2003. Considering the significance of soil moisture deficits for record breaking heat waves, these results still need to be validated with estimated seasonal precipitation. It is concluded that biological proxy data may not properly reveal record breaking heat and drought events. Such assessments thus need to be complemented with the critical study of contemporary evidence from documentary sources which provide coherent and detailed data about weather extremes and related impacts on human, ecological and social systems.

Sources and contributions of wood smoke during winter in London: assessing local and regional influences

Determining the contribution of wood smoke to air pollution in large cities such as London is becoming increasingly important due to the changing nature of domestic heating in urban areas. During winter, biomass burning emissions have been identified as a major cause of exceedances of European air quality limits. The aim of this work was to quantify the contribution of biomass burning in London to concentrations of PM2:5 and determine whether local emissions or regional contributions were the main source of biomass smoke. To achieve this, a number of biomass burning chemical tracers were analysed at a site within central London and two sites in surrounding rural areas. Concentrations of levoglucosan, elemental carbon (EC), organic carbon (OC) and K+ were generally well correlated across the three sites. At all the sites, biomass burning was found to be a source of OC and EC, with the largest contribution of EC from traffic emissions, while for OC the dominant fraction included contributions from secondary organic aerosols, primary biogenic and cooking sources. Source apportionment of the EC and OC was found to give reasonable estimation of the total carbon from non-fossil and fossil fuel sources based upon comparison with estimates derived from 14C analysis. Aethalometer-derived black carbon data were also apportioned into the contributions frombiomass burning and traffic and showed trends similar to those observed for EC. Mean wood smoke mass at the sites was estimated to range from 0.78 to 1.0 μgm-3 during the campaign in January–February 2012. Measurements on a 160m tower in London suggested a similar ratio of brown to black carbon (reflecting wood burning and traffic respectively) in regional and London air. Peaks in the levoglucosan and K+ concentrations were observed to coincide with low ambient temperature, consistent with domestic heating as a major contributing local source in London. Overall, the source of biomass smoke in London was concluded to be a background regional source overlaid by contributions from local domestic burning emissions. This could have implications when considering future emission control strategies during winter and may be the focus of future work in order to better determine the contributing local sources.

Late Quaternary history of North Eurasian Norway spruce ( Picea abies ) and Siberian spruce ( Picea obovata ) inferred from macrofossils, pollen and cytoplasmic DNA variation

Aim We used combined palaeobotanical and genetic data to assess whether Norway spruce (Picea abies) and Siberian spruce (Picea obovata), two major components of the Eurasian boreal forests, occupied separate glacial refugia, and to test previous hypotheses on their distinction, geographical delimitation and introgression. Location The range of Norway spruce in northern Europe and Siberian spruce in northern Asia. Methods Pollen data and recently compiled macrofossil records were summarized for the Last Glacial Maximum (LGM), late glacial and Holocene. Genetic variation was assessed in 50 populations using one maternally (mitochondrial nad1) and one paternally (chloroplast trnT–trnL) inherited marker and analysed using spatial analyses of molecular variance (SAMOVA). Results Macrofossils showed that spruce was present in both northern Europe and Siberia at the LGM. Congruent macrofossil and pollen data from the late glacial suggested widespread expansions of spruce in the East European Plain, West Siberian Plain, southern Siberian mountains and the Baikal region. Colonization was largely completed during the early Holocene, except in the formerly glaciated area of northern Europe. Both DNA markers distinguished two highly differentiated groups that correspond to Norway spruce and Siberian spruce and coincide spatially with separate LGM spruce occurrences. The division of the mtDNA variation was geographically well defined and occurred to the east of the Ural Mountains along the Ob River, whereas the cpDNA variation showed widespread admixture. Genetic diversity of both DNA markers was higher in western than in eastern populations. Main conclusions North Eurasian Norway spruce and Siberian spruce are genetically distinct and occupied separate LGM refugia, Norway spruce on the East European Plain and Siberian spruce in southern Siberia, where they were already widespread during the late glacial. They came into contact in the basin of the Ob River and probably hybridized. The lower genetic diversity in the eastern populations may indicate that Siberian spruce suffered more from past climatic fluctuations than Norway spruce.

Material culture entanglements of early wetland sites in central Switzerland (4300-3850 BC)

In central Switzerland, the earliest wetland settlements with definitely attested finds and features date into the second half of the 5th millennium BC. Combining the information they have yielded with that from dryland sites, we can construct a detailed picture of material culture at the turn of the 5th to the 4th millennium. On this basis, the definition of clearly delimited archaeological cultures seems questionable, not only from a theoretical point of view. Similiarities and differences in the pottery show small-scale regional units defined via vessel forms as well as stylistic and technological aspects. Yet there are also inter-regional connections: roundbased vessels with opposing handles are typical for Lake Zurich, central and western Switzerland, the Valais and the central Rhône valley. In turn, ‘foreign‘ types such as shoulder-band beakers indicate regular connections between groups living in central Switzerland and those in Alsace and southern Germany. Are these beakers ‘imports‘ or locally produced items (‘imitations‘) indicating the adoption of ‘foreign‘ vessel types and concepts? This and similar material culture phenomena result in a picture of many material entanglements and problematise the kinds of relationships and mobility which might have existed. Our paper addresses these questions and discusses how and whether these interwoven connections changed in the early 4th millennium.

Early-Holocene afforestation processes in the lower subalpine belt of the Central Swiss Alps as inferred from macrofossil and pollen records

To reconstruct the vegetation history of the Upper Engadine, continuous sediment cores covering the past 11 800 years from Lej da Champfer and Lej da San Murezzan (Upper Engadine Valley, c. 1800 m a.s.l., southeastern Switzerland) have been analysed for pollen and plant macrofossils. The chronologies of the cores are based on 16 and 22 radiocarbon dates, respectively. The palaeobotanical records of both lakes are in agreement for the Holocene, but remarkable differences exist between the sites during the period 11 100 to 10 500 cal. BP, when Lej da Champfer was affected by re-sedimentation processes. Macrofossil data suggest that Holocene afforestation began at around 11400 cal. BP. A climatic deterioration, the Preboreal Oscillation, stopped and subsequently delayed the establishment of trees until c. 11000 cal. BP, when first Betula, then Pinus sylvestrislmugo, then Larix 300 years later, and finally Pinus cembra expanded within the lake catchment. Treeline was at c. 1500 m during the Younger Dryas (12 542- 11 550 cal. BP) in the Central Alps. Our results, along with other macrofossil studies from the Alps, suggest a nearly simultaneous afforestation (e.g., by Pinus sylvestris in the lower subalpine belt) between 1500 and 2340 m a.s.l. at around 11 400 to 11 300 cal. BP. We suggest that forest-limit species (e.g., Pinus cembra, Larix decidua) could expand faster at today's treeline (c. 2350 m a.s.l.), than 550 m lower. Earlier expansions at higher altitudes probably resulted from reduced competition with low-altitude trees (e.g. Pinus sylvestris) and herbaceous species. Comparison with other proxies such as oxygen isotopes, residual A14C, glacier fluctuations, and alpine climatic cooling phases suggests climatic sensitivity of vegetation during the early Holocene.

Middle to Late Holocene vegetation history of the Upper Engadine (Swiss Alps): the role of man and fire

o reconstruct the vegetation and fire history of the Upper Engadine, two continuous sediment cores from Lej da Champfèr and Lej da San Murezzan (Upper Engadine Valley, southeastern Switzerland) were analysed for pollen, plant macrofossils, charcoal and kerogen. The chronologies of the cores are based on 38 radiocarbon dates. Pollen and macrofossil data suggest a rapid afforestation with Betula, Pinus sylvestris, Pinus cembra, and Larix decidua after the retreat of the glaciers from the lake catchments 11,000 cal years ago. This vegetation type persisted until ca. 7300 cal b.p. (5350 b.c.) when Picea replaced Pinus cembra. Pollen indicative of human impact suggests that in this high-mountain region of the central Alps strong anthropogenic activities began during the Early Bronze Age (3900 cal b.p., 1950 b.c.). Local human settlements led to vegetational changes, promoting the expansion of Larix decidua and Alnus viridis. In the case of Larix, continuing land use and especially grazing after fire led to the formation of Larix meadows. The expansion of Alnus viridis was directly induced by fire, as evidenced by time-series analysis. Subsequently, the process of forest conversion into open landscapes continued for millennia and reached its maximum at the end of the Middle Ages at around 500 cal b.p. (a.d. 1450).