Pertactin-deficient Bordetella pertussis isolates in Poland—a country with whole-cell pertussis primary vaccination

The introduction of pertussis vaccination in the 1950s resulted in a significant decrease in the incidence of disease. However, since the 1990s many highly vaccinated countries have observed the re-emergence of the disease. One of the causes of this phenomenon might be related to the adaptation of Bordetella pertussis to vaccination. The purpose of the presented study was an investigation of the emergence and spread of vaccine antigen-deficient B. pertussis isolates in Poland and genomic characterization of the currently circulating pathogen population using PFGE, MLVA and MAST. The results revealed that all tested isolates expressed Ptx, FHA and ACT antigens but 15.4% (4/26) of isolates from 2010 to 2016 were Prn-deficient. Moreover, one TcfA-deficient isolate was collected in 2015. The genotyping showed a genetic distinction between the isolates circulating in 2010–2016 and isolates from previous periods. The majority of currently circulating isolates belonged to PFGE group IV (96.2%), type MT27 (73.1%), and carried ptxA1-ptxC2-ptxP3-prn2-tcfA2-fim2-1-fim3-1 alleles (61.5%). The unique genetic structure of the B. pertussis population in Poland has changed since 2010 and became similar to that observed in countries with aP vaccination. This could be a result of increasing use of aP vaccines (60% of primary vaccination in 2013) over wP vaccines, which have been broadly used for primary vaccination in Poland for decades.     

Whole Genome Sequencing of Field Isolates Provides Robust Characterization of Genetic Diversity in Plasmodium vivax

Background

An estimated 2.85 billion people live at risk of Plasmodium vivax transmission. In endemic countries vivax malaria causes significant morbidity and its mortality is becoming more widely appreciated, drug-resistant strains are increasing in prevalence, and an increasing number of reports indicate that P. vivax is capable of breaking through the Duffy-negative barrier long considered to confer resistance to blood stage infection. Absence of robust in vitro propagation limits our understanding of fundamental aspects of the parasite''s biology, including the determinants of its dormant hypnozoite phase, its virulence and drug susceptibility, and the molecular mechanisms underlying red blood cell invasion.

Methodology/Principal Findings

Here, we report results from whole genome sequencing of five P. vivax isolates obtained from Malagasy and Cambodian patients, and of the monkey-adapted Belem strain. We obtained an average 70–400 X coverage of each genome, resulting in more than 93% of the Sal I reference sequence covered by 20 reads or more. Our study identifies more than 80,000 SNPs distributed throughout the genome which will allow designing association studies and population surveys. Analysis of the genome-wide genetic diversity in P. vivax also reveals considerable allele sharing among isolates from different continents. This observation could be consistent with a high level of gene flow among parasite strains distributed throughout the world.

Conclusions

Our study shows that it is feasible to perform whole genome sequencing of P. vivax field isolates and rigorously characterize the genetic diversity of this parasite. The catalogue of polymorphisms generated here will enable large-scale genotyping studies and contribute to a better understanding of P. vivax traits such as drug resistance or erythrocyte invasion, partially circumventing the lack of laboratory culture that has hampered vivax research for years.     

Efficient, chemoselective synthesis of immunomicelles using single-domain antibodies with a C-terminal thioester

Background  

Classical bioconjugation strategies for generating antibody-functionalized nanoparticles are non-specific and typically result in heterogeneous compounds that can be compromised in activity. Expression systems based on self-cleavable intein domains allow the generation of recombinant proteins with a C-terminal thioester, providing a unique handle for site-specific conjugation using native chemical ligation (NCL). However, current methods to generate antibody fragments with C-terminal thioesters require cumbersome refolding procedures, effectively preventing application of NCL for antibody-mediated targeting and molecular imaging.     

Ultrasound enhanced prehospital thrombolysis using microbubbles infusion in patients with acute ST elevation myocardial infarction: Rationale and design of the Sonolysis study

Background

The CONSORT Statement provides recommendations for reporting randomized controlled trials. We assessed the extent to which leading medical journals that publish reports of randomized trials incorporate the CONSORT recommendations into their journal and editorial processes.

Methods

This article reports on two observational studies. Study 1: We examined the online version of 'Instructions to Authors' for 165 high impact factor medical journals and extracted all text mentioning the CONSORT Statement or CONSORT extension papers. Any mention of the International Committee of Medical Journal Editors (ICMJE) or clinical trial registration were also sought and extracted. Study 2: We surveyed the editor-in-chief, or editorial office, for each of the 165 journals about their journal's endorsement of CONSORT recommendations and its incorporation into their editorial and peer-review processes.

Results

Study 1: Thirty-eight percent (62/165) of journals mentioned the CONSORT Statement in their online 'Instructions to Authors'; of these 37% (23/62) stated this was a requirement, 63% (39/62) were less clear in their recommendations. Very few journals mentioned the CONSORT extension papers. Journals that referred to CONSORT were more likely to refer to ICMJE guidelines (RR 2.16; 95% CI 1.51 to 3.08) and clinical trial registration (RR 3.67; 95% CI 2.36 to 5.71) than those journals which did not. Study 2: Thirty-nine percent (64/165) of journals responded to the on-line survey, the majority were journal editors. Eighty-eight percent (50/57) of journals recommended authors comply with the CONSORT Statement; 62% (35/56) said they would require this. Forty-one percent (22/53) reported incorporating CONSORT into their peer-review process and 47% (25/53) into their editorial process. Eighty-one percent (47/58) reported including CONSORT in their 'Instructions to Authors' although there was some inconsistency when cross checking information on the journal's website. Sixty-nine percent (31/45) of journals recommended authors comply with the CONSORT extension for cluster trials, 60% (27/45) for harms and 42% (19/45) for non-inferiority and equivalence trials. Few journals mentioned these extensions in their 'Instructions to Authors'.

Conclusion

Journals should be more explicit in their recommendations and expectations of authors regarding the CONSORT Statement and related CONSORT extensions papers.     

Humans and elephants as treefall drivers in African savannas

Humans have played a major role in altering savanna structure and function, and growing land‐use pressure will only increase their influence on woody cover. Yet humans are often overlooked as ecological components. Both humans and the African elephant Loxodonta africana alter woody vegetation in savannas through removal of large trees and activities that may increase shrub cover. Interactive effects of both humans and elephants with fire may also alter vegetation structure and composition. Here we capitalize on a macroscale experimental opportunity – brought about by the juxtaposition of an elephant‐mediated landscape, human‐utilized communal harvesting lands and a nature reserve fenced off from both humans and elephants – to investigate the influence of humans and elephants on height‐specific treefall dynamics. We surveyed 6812 ha using repeat, airborne high resolution Light Detection and Ranging (LiDAR) to track the fate of 453 685 tree canopies over two years. Human‐mediated biennial treefall rates were 2–3.5 fold higher than the background treefall rate of 1.5% treefall ha^–1, while elephant‐mediated treefall rates were 5 times higher at 7.6% treefall ha^–1 than the control site. Model predictors of treefall revealed that human or elephant presence was the most important variable, followed by the interaction between geology and fire frequency. Treefall patterns were spatially heterogeneous with elephant‐driven treefall associated with geology and surface water, while human patterns were related to perceived ease of access to wood harvesting areas and settlement expansion. Our results show humans and elephants utilize all height classes of woody vegetation, and that large tree shortages in a heavily utilized communal land has transferred treefall occurrence to shorter vegetation. Elephant‐ and human‐dominated landscapes are tied to interactive effects that may hinder tree seedling survival which, combined with tree loss in the landscape, may compromise woodland sustainability.     

Assessing the frequency and drivers of early‐greening in broad‐leaved woodlands along a latitudinal gradient in southern Africa

Savannas are the only deciduous system where new leaf flush pre‐empts the onset of suitable conditions for growth, a phenological phenomenon known as early‐greening. Limited understanding of the frequency and drivers of the occurrence of early‐greening in southern African savanna trees exists. We aimed to estimate the frequency of early‐greening events across southern Africa and investigated potential environmental drivers of green‐up. We selected and compared seven broad‐leaved woodland sites where Burkea africana was a dominant species using remotely sensed data along a latitudinal gradient from South Africa to Zambia. Normalized difference vegetation index (NDVI) values were extracted from the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite imagery at each site from January 2002 to June 2014. Using an austral year (July 1st–June 30th), early‐greening was recorded if the green‐up start date occurred prior to the onset date of seasonal rainfall. A latitudinal gradient of early‐green‐up was detected across southern Africa (R² = 0.74) with the two most northerly (Zambian) sites showing the earliest and most consistent green‐up start dates (3 October ± 5.34 days). A strong latitudinal gradient was observed between the variability in the amount of rainfall in the first 6 months of green‐up and the green‐up start dates across southern Africa (R² = 0.92). Photoperiod appeared to play a role in areas where the onset of rainfall commenced late into the austral year. Mean maximum temperatures recorded 10 days prior to green‐up start dates suggested a potential threshold of about 35°C, which could drive early‐greening in the absence of rainfall. Correlations between the proportion of early‐greening years and the above mentioned environmental factors indicated that rainfall variability had the strongest influence over the observed phenological gradient (R² = 0.96). Understanding early‐greening in complex savanna systems is a vital step in furthering predictive phenological models under changing climatic conditions.     

Survival of <Emphasis Type="Italic">Listeria monocytogenes</Emphasis> in Wilted and Additive-Treated Grass Silage

Grass was field-dried to 3 different dry matter (DM) levels (200, 430 and 540 g/kg) and inoculated with 10⁶–10⁷ cfu/g of a Listeria monocytogenes strain sharing a phagovar occasionally involved in food-borne outbreaks of listeriosis. Formic acid (3 ml/kg) or lactic acid bacteria (8·10⁵/g) with cellulolytic enzymes were applied only to forages with low and intermediate DM levels. Forages were ensiled in laboratory silos (1700 ml) and were stored at 25°C for 30 or 90 days. After 90 days of storage, L. monocytogenes could not be detected in any silo, except one with the high dry matter grass without additive. After 30 days of storage, between 10² and 10⁶ cfu L. monocytogenes/g silage were isolated from the untreated silages. Increasing the DM content from 200 to 540 g/kg did not reduce listeria counts possibly because of the lower production of fermentation acids (higher pH). In silages treated with additives, counts of L. monocytogenes were always lower than in silages without additive. In wet silages (DM 200 g/kg) both additives were effective, but in the wilted silages (DM 430 g/kg) only the bacterial additive reduced listeria counts below detection level. Listeria counts were highly correlated to silage pH (r = 0.92), the concentration of lactic acid (r = -0.80) and the pooled amount of undissociated acids (r = -0.83).     

Plant resources used for subsistence in tsehlanyane and bokong in lesotho

The communities of Tsehlanyane and Bokong depend on subsistence agriculture and harvesting natural resources for a variety of needs, mainly firewood, handcrafts, medicine, food, construction, and socio-cultural amenities. They have done so since time immemorial and are singularly responsible for the good conservation value that the area represents. The area has the longest history of conservation championed by a local traditional authority in Lesotho. From December 1999 to March 2000 we conducted a survey that was aimed at making an inventory of resources, on which people rely, that will be affected by the establishment of a biosphere reserve linking the Tsehlanyane National Park and the Bokong Nature Reserve. In the survey, 149 households were sampled representing a sampling intensity of 19% in both communities. One hundred forty-seven species of plants were mentioned, falling into 51 families with the most commonly used families being Asteraceae, Liliaceae sens. lat. and Poaceae. The study also revealed that tenurial rights on these resources are communal and usufructuary and are increasingly being undermined by commercialization that relegate resources to an open access system. The study identified six main use categories, namely, firewood, handcrafts, medicinals, wild fruits, wild vegetables, and miscellaneous uses. Finally, the study demonstrated that ethnobotanical knowledge is widely held in Lesotho with the traditional doctors being the major repositories     

A model of modes of attention and inattention for artificial perception

This paper considers several aspects of natural visual attention and its link to wider notions of awareness, natural and artificial, in the context of foveated vision. It builds on a theory of abductive perception; a formal definition for an artificial or robot perceptual system, using objects represented as feature clouds. It proposes a broad, but unifying approach to several aspects of visual attention in the light of this, including autonomic eye gaze movements, aspects of secondary and covert attention, and exogenous (sense driven) and endogenous (task driven) attention. Modes of attentional lapse, commonly referred to as inattentional blindness and change blindness, are also discussed in the context of the model presented.