Early Indicators of Fatal Leptospirosis during the 2010 Epidemic in Puerto Rico

Background

Leptospirosis is a potentially fatal bacterial zoonosis that is endemic throughout the tropics and may be misdiagnosed as dengue. Delayed hospital admission of leptospirosis patients is associated with increased mortality.

Methodology/Principal Findings

During a concurrent dengue/leptospirosis epidemic in Puerto Rico in 2010, suspected dengue patients that tested dengue-negative were tested for leptospirosis. Fatal and non-fatal hospitalized leptospirosis patients were matched 1:1–3 by age. Records from all medical visits were evaluated for factors associated with fatal outcome. Among 175 leptospirosis patients identified (4.7 per 100,000 residents), 26 (15%) were fatal. Most patients were older males and had illness onset during the rainy season. Fatal case patients first sought medical care earlier than non-fatal control patients (2.5 vs. 5 days post-illness onset [DPO], p < 0.01), but less frequently first sought care at a hospital (52.4% vs. 92.2%, p < 0.01). Although fatal cases were more often diagnosed with leptospirosis at first medical visit (43.9% vs. 9.6%, p = 0.01), they were admitted to the hospital no earlier than non-fatal controls (4.5 vs. 6 DPO, p = 0.31). Cases less often developed fever (p = 0.03), but more often developed jaundice, edema, leg pain, hemoptysis, and had a seizure (p ≤ 0.03). Multivariable analysis of laboratory values from first medical visit associated with fatal outcome included increased white blood cell (WBC) count with increased creatinine (p = 0.001), and decreased bicarbonate with either increased WBC count, increased creatinine, or decreased platelet count (p < 0.001).

Conclusions/Significance

Patients with fatal leptospirosis sought care earlier, but were not admitted for care any earlier than non-fatal patients. Combinations of routine laboratory values predictive of fatal outcome should be considered in admission decision-making for patients with suspected leptospirosis.     

Ex Vivo Intestinal Sacs to Assess Mucosal Permeability in Models of Gastrointestinal Disease

The epithelial barrier is the first innate defense of the gastrointestinal tract and selectively regulates transport from the lumen to the underlying tissue compartments, restricting the transport of smaller molecules across the epithelium and almost completely prohibiting epithelial macromolecular transport. This selectivity is determined by the mucous gel layer, which limits the transport of lipophilic molecules and both the apical receptors and tight junctional protein complexes of the epithelium. In vitro cell culture models of the epithelium are convenient, but as a model, they lack the complexity of interactions between the microbiota, mucous-gel, epithelium and immune system. On the other hand, in vivo assessment of intestinal absorption or permeability may be performed, but these assays measure overall gastrointestinal absorption, with no indication of site specificity. Ex vivo permeability assays using "intestinal sacs" are a rapid and sensitive method of measuring either overall intestinal integrity or comparative transport of a specific molecule, with the added advantage of intestinal site specificity. Here we describe the preparation of intestinal sacs for permeability studies and the calculation of the apparent permeability (P_app)of a molecule across the intestinal barrier. This technique may be used as a method of assessing drug absorption, or to examine regional epithelial barrier dysfunction in animal models of gastrointestinal disease.     

Accounting for the nested nature of genetic variation across levels of organization improves our understanding of biodiversity and community ecology

Recent work has demonstrated that the presence or abundance of specific genotypes, populations, species and phylogenetic clades may influence community and ecosystem properties such as resilience or productivity. Many ecological studies, however, use simple linear models to test for such relationships, including species identity as the predictor variable and some measured trait or function as the response variable without accounting for the nestedness of genetic variation across levels of organization. This omission may lead to incorrect inference about which source of variation influences community and ecosystem properties. Here, we explicitly compare this common approach to alternative ways of modeling variation in trait data, using simulated trait data and empirical results of common‐garden trials using multiple levels of genetic variation within Eucalyptus, Populus and Picea. We show that: 1) when nested variation is ignored, an incorrect conclusion of species effect is drawn in up to 20% of cases; 2) overestimation of the species effect increases – up to 60% in some scenarios – as the nested term explains more of the variation; and 3) the sample sizes needed to overcome these potential problems associated with aggregating nested hierarchical variation may be impractically large. In common‐garden trials, incorporating nested models increased explanatory power twofold for mammal browsing rate in Eucalyptus, threefold for leaf area in Populus, and tenfold for branch number in Picea. Thoroughly measuring intraspecific variation and characterizing hierarchical genetic variation beyond the species level has implications for developing more robust theory in community ecology, managing invaded natural systems, and improving inference in biodiversity–ecosystem functioning research. Synthesis Until recently, ecologists acknowledged the ubiquity of within‐species trait variation, but paid scant attention to how much it affects communities and ecosystems. Here, the authors used simulated trait data and common‐garden studies to demonstrate that we ignore intraspecific trait variation at our peril. In both simulated and experimental systems, in many cases ignoring intraspecific variation led to incorrect statistical inferences and inflated the effect size of species identity. This study shows that ecologists must characterize hierarchically nested genetic and phenotypic variation to fully understand the links between individual traits, community structure and ecosystem functioning.     

Global agricultural intensification during climate change: a role for genomics

Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic‐assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.     

Odontocete occurrence in relation to changes in oceanography at a remote equatorial Pacific seamount

Seamounts are considered hot spots of biodiversity and can aggregate pelagic predators and their prey. Passive acoustic monitoring was conducted over 3 mo in 2012 to document the occurrence of odontocetes near a seamount chain in the central equatorial Pacific in relation to oceanographic changes over time. Beaked whale echolocation signals were most frequently encountered. The main beaked whale signal was an unknown type, BW38, which resembled signals produced by Blainville's beaked whales. It had high occurrence during high sea surface temperature and low sea surface salinity. Cuvier's beaked whales were the second most detected. They had an opposite pattern and were encountered more often when sea surface temperature was low and net primary productivity was high. Risso's dolphins and short‐finned pilot whales had high acoustic densities, and echolocated predominantly at night. Risso's dolphins occurred more often during low sea surface height deviation. False killer whales were less frequently detected and mostly occurred during the day. Sperm whale detections were fewer than expected and associated with high chlorophyll a. Short duration Kogiidae encounters occurred on average every third day. These types of long‐term site studies are an informative tool to comparatively assess species composition, relative abundance, and relationship to oceanographic changes.     

Comparison of black–white disparities in preterm birth between Canada and the United States

Background:

A higher risk of preterm birth among black women than among white women is well established in the United States. We compared differences in preterm birth between non-Hispanic black and white women in Canada and the US, hypothesizing that disparities would be less extreme in Canada given the different historical experiences of black populations and Canada’s universal health care system.

Methods:

Using data on singleton live births in Canada and the US for 2004–2006, we estimated crude and adjusted risk ratios and risk differences in preterm birth (< 37 wk) and very preterm birth (< 32 wk) among non-Hispanic black versus non-Hispanic white women in each country. Adjusted models for the US were standardized to the covariate distribution of the Canadian cohort.

Results:

In Canada, 8.9% and 5.9% of infants born to black and white mothers, respectively, were preterm; the corresponding figures in the US were 12.7% and 8.0%. Crude risk ratios for preterm birth among black women relative to white women were 1.49 (95% confidence interval [CI] 1.32 to 1.66) in Canada and 1.57 (95% CI 1.56 to 1.58) in the US (p value for heterogeneity [p_H] = 0.3). The crude risk differences for preterm birth were 2.94 (95% CI 1.91 to 3.96) in Canada and 4.63 (95% CI 4.56 to 4.70) in the US (p_H = 0.003). Adjusted risk ratios for preterm birth (p_H = 0.1) were slightly higher in Canada than in the US, whereas adjusted risk differences were similar in both countries. Similar patterns were observed for racial disparities in very preterm birth.

Interpretation:

Relative disparities in preterm birth and very preterm birth between non-Hispanic black and white women were similar in magnitude in Canada and the US. Absolute disparities were smaller in Canada, which reflects a lower overall risk of preterm birth in Canada than in the US in both black and white populations.In the United States, a higher risk of preterm birth among black women than among white women is well established.^1–3 This racial disparity is of great concern because preterm birth is a leading cause of perinatal mortality and is predictive of developmental problems and adverse health outcomes later in life.⁴ The underlying causes of the racial disparity in preterm birth in the US are not well understood, although research has suggested contributing roles for a wide range of factors, including socioeconomic disadvantage,⁵ poor neighbourhood conditions (e.g., poverty, crime),^5,6 lack of access to health care,⁷ psychosocial stress,⁸ racial discrimination⁹ and adverse health behaviours.¹⁰Rates of preterm birth have consistently been lower in Canada than in the US.^11,12 However, in contrast to the US, little is known about differences in rates by race or ethnicity in Canada. There is evidence that African-born and Caribbean-born women in the provinces of Quebec and Ontario have higher rates of preterm birth than Canadian-born women.^13–15 Although the magnitude of these differences is smaller than the disparity in preterm births between black and white women in the US,¹⁶ foreign-born black women in the US have been found to be at lower risk of preterm birth than US-born black women.^17,18In both Canada and the US, socioeconomic conditions at both individual and neighbourhood levels are important predictors of preterm birth.^19–21 Although the income gap between black and white people is markedly smaller in Canada than in the US,²² black populations in both countries have lower education levels, higher unemployment rates and a greater likelihood of living in low-quality neighbourhoods compared with white populations.²³ Canada and the US share similar social and economic influences, yet the historical experiences of black populations and the social welfare systems (e.g., universal health care) are quite different in the 2 countries. Black people constitute about 13% of the total US population, but only about 3% of the Canadian population.^24,25 The overwhelming majority of Canada’s black population are immigrants who entered the country after 1960 and their descendants, whereas more than 85% of black Americans can trace their ancestry 3 or more generations in the US, with most being descendants of slaves.²²The objectives of our study are twofold. First, using data from a new cohort linking birth registrations with information from the 2006 Canadian long-form census, we present Canada-wide estimates of differences in preterm birth rates between black and white populations. Second, we use comparable methodology to compare racial differences in preterm birth rates between Canada and the US. Given different historical experiences of black populations in the 2 countries, as well as Canada’s commitment to universal health care and its general perception as a more egalitarian society than the US,²² we hypothesized that we would observe smaller racial disparities in the rates in Canada than in the US.     

Structural Insight into Layer Gliding and Lattice Distortion in Layered Manganese Oxide Electrodes for Potassium‐Ion Batteries

Potassium‐ion batteries (PIBs) are an emerging, affordable, and environmentally friendly alternative to lithium‐ion batteries, with their further development driven by the need for suitably performing electrode materials capable of reversibly accommodating the relatively large K⁺. Layer‐structured manganese oxides are attractive as electrodes for PIBs, but suffer from structural instability and sluggish kinetics of K⁺ insertion/extraction, leading to poor rate capability. Herein, cobalt is successfully introduced at the manganese site in the K_xMnO₂ layered oxide electrode material and it is shown that with only 5% Co, the reversible capacity increases by 30% at 22 mA g^‐1 and by 92% at 440 mA g^‐1. In operando synchrotron X‐ray diffraction reveals that Co suppresses Jahn–Teller distortion, leading to more isotropic migration pathways for K⁺ in the interlayer, thus enhancing the ionic diffusion and consequently, rate capability. The detailed analysis reveals that additional phase transitions and larger volume change occur in the Co‐doped material as a result of layer gliding, with these associated with faster capacity decay, despite the overall capacity remaining higher than the pristine material, even after 500 cycles. These results assert the importance of understanding the detailed structural evolution that underpins performance that will inform the strategic design of electrode materials for high‐performance PIBs.     

Passiflora plastome sequencing reveals widespread genomic rearrangements

Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.