Geographical trends in research: a preliminary analysis on authors' affiliations

In the last decade, research literature reached an enormous volume with an unprecedented current annual increase of 1.5 million new publications. As research gets ever more global and new countries and institutions, either from academia or corporate environment, start to contribute with their share, it is important to monitor this complex scenario and understand its dynamics. We present a study on a conference proceedings dataset extracted from Springer Nature Scigraph that illustrates insightful geographical trends and highlights the unbalanced growth of competitive research institutions worldwide. Results emerged from our micro and macro analysis show that the distributions among countries of institutions and papers follow a power law, and thus very few countries keep producing most of the papers accepted by high-tier conferences. In addition, we found that the annual and overall turnover rate of the top 5, 10 and 25 countries is extremely low, suggesting a very static landscape in which new entries struggle to emerge. Finally, we highlight the presence of an increasing gap between the number of institutions initiating and overseeing research endeavours (i.e. first and last authors' affiliations) and the total number of institutions participating in research. As a consequence of our analysis, the paper also discusses our experience in working with affiliations: an utterly simple matter at first glance, that is instead revealed to be a complex research and technical challenge yet far from being solved

A Trial of a 7-Valent Pneumococcal Conjugate Vaccine in HIV-Infected Adults.

BACKGROUND: Streptococcus pneumoniae is a leading and serious coinfection in adults with human immunodeficiency virus (HIV) infection, particularly in Africa. Prevention of this disease by vaccination with the current 23-valent polysaccharide vaccine is suboptimal. Protein conjugate vaccines offer a further option for protection, but data on their clinical efficacy in adults are needed. METHODS: In this double-blind, randomized, placebo-controlled clinical efficacy trial, we studied the efficacy of a 7-valent conjugate pneumococcal vaccine in predominantly HIV-infected Malawian adolescents and adults who had recovered from documented invasive pneumococcal disease. Two doses of vaccine were given 4 weeks apart. The primary end point was a further episode of pneumococcal infection caused by vaccine serotypes or serotype 6A. RESULTS: From February 2003 through October 2007, we followed 496 patients (of whom 44% were male and 88% were HIV-seropositive) for 798 person-years of observation. There were 67 episodes of pneumococcal disease in 52 patients, all in the HIV-infected subgroup. In 24 patients, there were 19 episodes that were caused by vaccine serotypes and 5 episodes that were caused by the 6A serotype. Of these episodes, 5 occurred in the vaccine group and 19 in the placebo group, for a vaccine efficacy of 74% (95% confidence interval [CI], 30 to 90). There were 73 deaths from any cause in the vaccine group and 63 in the placebo group (hazard ratio in the vaccine group, 1.18; 95% CI, 0.84 to 1.66). The number of serious adverse events within 14 days after vaccination was significantly lower in the vaccine group than in the placebo group (3 vs. 17, P=0.002), and the number of minor adverse events was significantly higher in the vaccine group (41 vs. 13, P=0.003). CONCLUSIONS: The 7-valent pneumococcal conjugate vaccine protected HIV-infected adults from recurrent pneumococcal infection caused by vaccine serotypes or serotype 6A. (Current Controlled Trials number, ISRCTN54494731.) Copyright 2010 Massachusetts Medical Society

Central America Field Epidemiology Training Program (CA FETP): a pathway to sustainable public health capacity development

The Central America Field Epidemiology Training Program (CA FETP) is a public health capacity-building training programme aimed at developing high-caliber field epidemiologists at various levels of the public health system. It began in 2000 as part of the effort to rebuild public health infrastructure in six Central American and Caribbean countries following the devastation of Hurricanes Mitch and Georges in late 1998. Since then, the CA FETP has evolved from one regional training programme managed by CDC to several national FETPs with each country assuming ownership of its domestic programme. The curriculum is competency-based, and is divided into a three-tiered training pyramid that corresponds to the needs at the local, district and central levels of the health system. Trainees at each tier spend about 20% of their time in the classroom and 80% in the field implementing what they have learned while being mentored by graduates of the programme. FETP trainees have responded to multiple natural disasters and conducted hundreds of investigations including surveillance evaluations, outbreak responses and planned studies. Also graduates of the CA FETP are assuming influential positions in their respective ministries. As countries meet the challenge of institutionalizing their programmes, the CA FETP concept will increasingly be recognized as a model for sustainable public health capacity development

Detergent and sanitizer stresses decrease the thermal resistance of Enterobacter sakazakii in infant milk formula

Infant milk formula has been identified as a potential source of Enterobacter sakazakii. This bacterium can cause a severe form of neonatal meningitis and necrotizing entercolitis. This study determined the effect of acid, alkaline, chlorine and ethanol stresses on the thermal inactivation of E. sakazakii in infant milk formula. Stressed cells were mixed with reconstituted powdered infant milk formula (PIMF) at temperatures between 52 and 58°C for various time periods or mixed with PFMF prior to reconstitution with water at temperatures between 50 and 100°C. The D- and z-values of the cells were determined using linear regression analysis. Detergent and sanitizer stresses decreased the thermal resistance of E. sakazakii in powdered and reconstituted infant milk formula. The values for Z)- acid, alkaline, chlorine and ethanol stressed E. sakazakii at 52-58°C were 14.57-0.54, 12.07-0.37, 10.08-0.40 and 11.61-0.50 min, respectively. The values of alkaline, chlorine and ethanol stressed cells were significantly lower than those of unstressed cells. Only the z-value (4.4°C) of ethanol stressed E. sakazakii was significantly different than that of unstressed cells (4.12°C). Reconstitution at 60°C did not significantly reduce the number of pre-stressed E. sakazakii cells compared with unstressed control cells, whereas significant decreases were obtained at 70°C. Using water at 70°C during the preparation of reconstituted PIMF before feeding infants, may be a suitable and applicable means of reducing the risk of E. sakazakii in the formula. The results of this study may be of use to regulatory agencies, infant milk producers and infant caregivers to design heating processes to eliminate E. sakazakii that may be present in infant milk formula

Adaptation of the carbamoyl-phosphate synthetase (CPS) enzyme in an extremophile fish

Tetrapods and fish have adapted distinct carbamoyl-phosphate synthase (CPS) enzymes to initiate the ornithine urea cycle during the detoxification of nitrogenous wastes. We report evidence that in the ureotelic subgenus of extremophile fish Oreochromis Alcolapia, CPS III has undergone convergent evolution and adapted its substrate affinity to ammonia which is typical of terrestrial vertebrate CPS I. Unusually, unlike in other vertebrates, the expression of CPS III in Alcolapia is localised to the skeletal muscle and is activated in the myogenic lineage during early embryonic development with expression remaining in mature fish. We propose that adaptation in Alcolapia included both convergent evolution of CPS function to that of terrestrial vertebrates, as well as changes in development mechanisms redirecting CPS III gene expression to the skeletal muscle

Interplay of Mre11 Nuclease with Dna2 plus Sgs1 in Rad51-Dependent Recombinational Repair

The Mre11/Rad50/Xrs2 complex initiates IR repair by binding to the end of a double-strand break, resulting in 5′ to 3′ exonuclease degradation creating a single-stranded 3′ overhang competent for strand invasion into the unbroken chromosome. The nuclease(s) involved are not well understood. Mre11 encodes a nuclease, but it has 3′ to 5′, rather than 5′ to 3′ activity. Furthermore, mutations that inactivate only the nuclease activity of Mre11 but not its other repair functions, mre11-D56N and mre11-H125N, are resistant to IR. This suggests that another nuclease can catalyze 5′ to 3′ degradation. One candidate nuclease that has not been tested to date because it is encoded by an essential gene is the Dna2 helicase/nuclease. We recently reported the ability to suppress the lethality of a dna2Δ with a pif1Δ. The dna2Δ pif1Δ mutant is IR-resistant. We have determined that dna2Δ pif1Δ mre11-D56N and dna2Δ pif1Δ mre11-H125N strains are equally as sensitive to IR as mre11Δ strains, suggesting that in the absence of Dna2, Mre11 nuclease carries out repair. The dna2Δ pif1Δ mre11-D56N triple mutant is complemented by plasmids expressing Mre11, Dna2 or dna2K1080E, a mutant with defective helicase and functional nuclease, demonstrating that the nuclease of Dna2 compensates for the absence of Mre11 nuclease in IR repair, presumably in 5′ to 3′ degradation at DSB ends. We further show that sgs1Δ mre11-H125N, but not sgs1Δ, is very sensitive to IR, implicating the Sgs1 helicase in the Dna2-mediated pathway

Synergistic Embryotoxicity of Polycyclic Aromatic Hydrocarbon Aryl Hydrocarbon Receptor Agonists with Cytochrome P4501A Inhibitors in Fundulus heteroclitus

Widespread contamination of aquatic systems with polycyclic aromatic hydrocarbons (PAHs) has led to concern about effects of PAHs on aquatic life. Some PAHs have been shown to cause deformities in early life stages of fish that resemble those elicited by planar halogenated aromatic hydrocarbons (pHAHs) that are agonists for the aryl hydrocarbon receptor (AHR). Previous studies have suggested that activity of cytochrome P4501A, a member of the AHR gene battery, is important to the toxicity of pHAHs, and inhibition of CYP1A can reduce the early-life-stage toxicity of pHAHs. In light of the effects of CYP1A inhibition on pHAH-derived toxicity, we explored the impact of both model and environmentally relevant CYP1A inhibitors on PAH-derived embryotoxicity. We exposed Fundulus heteroclitus embryos to two PAH-type AHR agonists, β-naphthoflavone and benzo(a)pyrene, and one pHAH-type AHR agonist, 3,3′,4,4′,5-pentachlorobiphenyl (PCB-126), alone and in combination with several CYP1A inhibitors. In agreement with previous studies, coexposure of embryos to PCB-126 with the AHR antagonist and CYP1A inhibitor α-naphthoflavone decreased frequency and severity of deformities compared with embryos exposed to PCB-126 alone. In contrast, embryos coexposed to the PAHs with each of the CYP1A inhibitors tested were deformed with increased severity and frequency compared with embryos dosed with PAH alone. The mechanism by which inhibition of CYP1A increased embryotoxicity of the PAHs tested is not understood, but these results may be helpful in elucidating mechanisms by which PAHs are embryotoxic. Additionally, these results call into question additive models of PAH embryotoxicity for environmental PAH mixtures that contain both AHR agonists and CYP1A inhibitors

Effects of high relative humidity and dry purging on VOCs obtained during breath sampling on common sorbent tubes.

BACKGROUND:Offline breath analysis by GC-MS requires the use of sorbent traps to concentrate and store volatile compounds. The selection of which sorbent to use and best practices for managing water retention are important considerations to allow for reproducible, untargeted, biomarker discovery in water saturated breath samples. OBJECTIVE:To assess three commonly used sorbent materials for their use in breath volatile sampling and determine how the high relative humidity inherent in such samples effects the capture of volatile compounds of interest. METHODS:TenaxGR, TenaxTA/Carbograph1TD and TenaxTA/Carbograph5TD tubes were selected as they are the most commonly used sorbents in the breath sampling literature. The recovery of 29 compounds in a standard mix loaded using high humidity gas was tested for each sorbent and compared to loading in dry gas. Water retention and dry purge rates were determined. Finally, breath samples were sampled simultaneously on to each sorbent type using the ReCIVA and analysed by TD-GC-MS. RESULTS:All three sorbents exhibited acceptable reproducibility when loaded with the standard mix in dry gas. Loading the standard mix in humid gas led to reduced recovery of compounds based on their chemical properties. Dry purging performance for each sorbent material was assessed and was shown to be 1.14, 1.13 and 0.89 mg H2O min-1for TenaxGR, TenaxTA/Carbograph1TD and TenaxTA/Carbograph5TD respectively. A comparison of breath profiles on different sorbents showed differences in background artefacts (sulfur dioxide, cyclopenten-1-one and 3-nonene) and endogenous breath compounds (2-methyl-furan and furfural). CONCLUSIONS:High relative humidity during sampling reduces the ability of sorbent tubes to capture volatile compounds and could impact method detection limits during breath sampling. Sufficient water to impair accurate analysis was retained on all tubes. Minimal differences were observed between sorbent materials when used to sample breath, however, suggestions are provided for sorbent selection for future studies

Exploring the expression of cardiac regulators in a vertebrate adapted to an extreme environment: the cichlid fish Oreochromis (Alcolapia) alcalica

Although it is widely accepted that the cellular and molecular mechanisms of vertebrate cardiac development are evolutionarily conserved, this is on the basis of data from only a few model organisms suited to laboratory studies. Here, we investigate gene expression during cardiac development in the extremophile, non-model fish species, Oreochromis (Alcolapia) alcalica. We first characterise the early development of O. alcalica and observe extensive vascularisation across the yolk prior to hatching. We further investigate heart development by identifying and cloning O. alcalica orthologues of conserved cardiac transcription factors gata4, tbx5, and mef2c for analysis by in situ hybridisation. Expression of these three key cardiac developmental regulators also reveals other aspects of O. alcalica development, as these genes are expressed in developing blood, limb, eyes, and muscle, as well as the heart. Our data support the notion that O. alcalica is a direct-developing vertebrate that shares the highly conserved molecular regulation of the vertebrate body plan. However, the expression of gata4 in O. alcalica reveals interesting di erences in the development of the circulatory system distinct from that of the well-studied zebrafish. Understanding the development of O. alcalica embryos is an important step towards providing a model for future research into the adaptation to extreme conditions; this is particularly relevant given that anthropogenic-driven climate change will likely result in more freshwater organisms being exposed to less favourable conditions