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1.  Interacting effects of age, density, and weather on survival and current reproduction for a large mammal 
Ecology and Evolution  2014;4(19):3851-3860.
Individual-based study of natural populations allows for accurate and precise estimation of fitness components and the extent to which they might vary with ecological conditions. By tracking the fates of all 701 horses known to have lived on Sable Island, Canada, from 2009 to 2013 (where there is no predation, human interference, or interspecific competition for food), we present a detailed analysis of structured population dynamics with focus on interacting effects of intraspecific competition and weather on reproduction and survival. Annual survival of adult females (0.866 ± 0.107 [ ± SE]) was lower than that of 3-year-olds (0.955 ± 0.051), although annual fecundity (producing a foal in a year that was observed during our census) was higher in adults (0.616 ± 0.023) compared to 3-year-olds (0.402 ± 0.054). Milder winters and lower densities during gestation increased fecundity. Density negatively impacted survival for all age and sex categories; however, highest adult female survival was observed during high-density years coupled with a harsh winter, the result expected if pregnancy loss during winter or loss of foals in spring improved survival. Three-year-old females, which reproduced at lower rates, experienced higher survival than adults. Our results contrast with a previous study of feral horses that suggested recently feral ungulates might be artificially selected to reproduce even when costs to survival are high. In part, this may be because of the comparably long history of feralization (250 years; at least 25 generations) for Sable Island horses.
doi:10.1002/ece3.1250
PMCID: PMC4301048  PMID: 25614799
Density dependence; density independence; feral horses; life history theory; reproduction; survival
2.  Molecular Identification of Isolated Fungi from Unopened Containers of Greek Yogurt by DNA Sequencing of Internal Transcribed Spacer Region 
Pathogens  2014;3(3):499-509.
In our previous study, we described the development of an internal transcribed spacer (ITS)1 sequencing method, and used this protocol in species-identification of isolated fungi collected from the manufacturing areas of a compounding company known to have caused the multistate fungal meningitis outbreak in the United States. In this follow-up study, we have analyzed the unopened vials of Greek yogurt from the recalled batch to determine the possible cause of microbial contamination in the product. A total of 15 unopened vials of Greek yogurt belonging to the recalled batch were examined for the detection of fungi in these samples known to cause foodborne illness following conventional microbiological protocols. Fungi were isolated from all of the 15 Greek yogurt samples analyzed. The isolated fungi were genetically typed by DNA sequencing of PCR-amplified ITS1 region of rRNA gene. Analysis of data confirmed all of the isolated fungal isolates from the Greek yogurt to be Rhizomucor variabilis. The generated ITS1 sequences matched 100% with the published sequences available in GenBank. In addition, these yogurt samples were also tested for the presence of five types of bacteria (Salmonella, Listeria, Staphylococcus, Bacillus and Escherichia coli) causing foodborne disease in humans, and found negative for all of them.
doi:10.3390/pathogens3030499
PMCID: PMC4243425  PMID: 25438008
nucleotide sequencing; rapid identification; foodborne disease
3.  Genetic Characterization of Fungi Isolated from the Environmental Swabs collected from a Compounding Center Known to Cause Multistate Meningitis Outbreak in United States Using ITS Sequencing 
Pathogens  2014;3(3):732-742.
A multistate fungal meningitis outbreak started in September of 2012 which spread in 20 states of the United States. The outbreak has been fatal so far, and has affected 751 individuals with 64 deaths among those who received contaminated spinal injections manufactured by a Compounding Center located in Massachusetts. In a preliminary study, Food and Drug Administration (FDA) investigated the outbreak in collaboration with Centers for Disease Control and Prevention (CDC), state and local health departments, and identified four fungal and several bacterial contaminations in the recalled unopened injection vials. This follow-up study was carried out to assess DNA sequencing of the ITS1 region of rRNA gene for rapid identification of fungal pathogens during public health outbreak investigations. A total of 26 environmental swabs were collected from several locations at the manufacturing premises of the Compounding Center known to have caused the outbreak. The swab samples were initially examined by conventional microbiologic protocols and a wide range of fungal species were recovered. Species-identification of these microorganisms was accomplished by nucleotide sequencing of ITS1 region of rRNA gene. Analysis of data confirmed 14 additional fungal species in the swabs analyzed.
doi:10.3390/pathogens3030732
PMCID: PMC4243438  PMID: 25438021
genetic marker; fungal meningitis; microbiological indicators; rapid detection
4.  Pulmonary Manifestations of the Pre-Engraftment Syndrome after Umbilical Cord Blood Transplantation 
Annals of hematology  2013;93(5):847-854.
Pre-engraftment syndrome (PES) is a condition occurring after umbilical cord blood transplantation (UCBT) characterized by fever and erythematous skin rash prior to neutrophil engraftment. We sought to determine the incidence and characterize the pulmonary manifestations of PES.
A retrospective review of patients who underwent UCBT at the University of Kansas Medical Center over a 5 year period was performed. Data collected included patient baseline characteristics, presence of PES, pulmonary findings, treatments and survival.
Forty-four patients underwent UCBT with 22 of those patients developing PES. Full-intensity myeloablative conditioning regimen was found to be a risk factor for development of PES. Of those 22 patients, 13 had resting hypoxemia. The most common radiographic findings included diffuse ground glass opacities with pleural effusions. Fifteen patients with PES received corticosteroids, of which twelve had improvement in fevers and rash. These patients had a trend towards worse mortality than those not receiving corticosteroids. There was a non-significant trend towards worse survival in patients with PES and hypoxemia compared to those without hypoxemia.
PES is a common complication following cord blood transplantation, with hypoxemia being present in over half of patients with PES. Hypoxemia with PES and treatment with corticosteroids may portend a worse prognosis.
doi:10.1007/s00277-013-1981-0
PMCID: PMC4109706  PMID: 24346710
Immunocompromised; pre-engraftment syndrome; respiratory failure; umbilical cord blood transplantation
5.  Idiopathic granulomatous hypophysitis: a systematic review of 82 cases in the literature 
Pituitary  2013;17(4):357-365.
Idiopathic granulomatous hypophysitis (IGH) is a rare inflammatory disease of the pituitary. There is debate in the scientific literature as to whether IGH represents a continuum of disease with lymphocytic hypophysitis or has a distinct pathogenesis. Due to the rare nature of the disease, previous descriptions have been limited to single case reports or small series. In the present study, a systematic review of the literature was performed for cases of IGH. 82 cases met inclusion criteria. Data was gathered on IGH clinical aspects, in order to elucidate any associations useful in determining pathogenesis, appropriate clinical treatment, or prognosis. Univariate and multivariate analysis was performed on available data. Female sex was significantly associated with IGH (p < 0.0001). Fever (p = 0.002), nausea or vomiting at presentation (p = 0.031), and histological evidence of necrosis (p = 0.022) correlated with reduced time to presentation. Panhypopituitarism at presentation predicted need for long term hormone replacement (p = 0.014). Hyperprolactinaemia (p = 0.032), normal gonadal (p = 0.037) and thyroid axes (p = 0.001) were associated with reduced likelihood of long-term hormone replacement. Anorexia (p = 0.017), cold intolerance (p = 0.046), and fatigue (p = 0.0033) were associated with death from IGH. Patients who had excisional surgery alone trended towards increased rates of symptom resolution, compared with patients who received corticosteroids as an adjunct to excisional surgery (p = 0.11). This article details the first systematic review of IGH, and presents evidence for a female predilection of the disease. Implications for pathogenesis, and a suggested clinical approach are discussed. An online disease registry has been established to facilitate further IGH research.
doi:10.1007/s11102-013-0510-4
PMCID: PMC4085501  PMID: 23990347
Hypophysitis; Granulomatous; Lymphocytic; Systematic review
6.  Association of bronchoalveolar lavage yield with chest computed tomography findings and symptoms in immunocompromised patients 
Annals of Thoracic Medicine  2013;8(3):153-159.
INTRODUCTION:
Fiber-optic bronchoscopy (FOB) with bronchoalveolar lavage (BAL) is a common procedure performed in immunocompromised patients with undiagnosed pulmonary pathology. Identifying patients with the highest potential diagnostic yield may help to avoid morbidity in patients unlikely to benefit from the procedure. We sought to determine which patient factors, specifically chest computed tomography (CT) findings, affected diagnostic yield of BAL.
METHODS:
Retrospective chart review of immunocompromised patients who underwent FOB with BAL from 01/01/2010 to 12/31/2011 at an academic medical center was performed. The lung lobe lavaged, characteristics of pulmonary infiltrate on radiograph, patient symptoms, and diagnostic yield were collected. A positive diagnostic yield was defined as a positive microbiological culture, finding on cytopathologic staining, diffuse alveolar hemorrhage, alveolar eosinophilia or a positive immunologic or nucleic acid assay.
RESULTS:
The overall diagnostic yield was 52.6%. Infiltrates that were predominantly reticular or nodular by CT had a lower diagnostic yield than predominantly consolidated, ground-glass, or tree-in-bud infiltrates (36.5% vs. 61.2%, P = 0.0058). The diagnostic yield was significantly improved in patients with both fever and chest symptoms compared to patients without symptoms (61.3% vs. 29.6%, P = 0.0066).
CONCLUSION:
CT findings of reticular and nodular infiltrates portend a worse diagnostic yield from BAL than those that are alveolar in nature. Symptomatic patients are more likely to have diagnostic FOB with BAL than asymptomatic patients.
doi:10.4103/1817-1737.114302
PMCID: PMC3731857  PMID: 23922610
Bronchoscopy; computed tomography; immunodeficiency; respiratory infection; respiratory symptoms
7.  Hepcidin in anemia of chronic heart failure 
American journal of hematology  2011;86(1):107-109.
Anemia is a common finding among patients with chronic heart failure. Although co-morbidities, such as kidney failure, might contribute to the pathogenesis of anemia, many patients with heart failure do not have any other obvious etiology for their anemia. We investigated whether anemia in heart failure is associated with an elevation in hepcidin concentration.
We used time-of-flight mass spectrometry to measure hepcidin concentration in urine and serum samples of patients with heart failure and in control subjects. We found that the concentration of hepcidin was lower in urine samples of patients with heart failure compared to those of control subjects. Serum hepcidin was also reduced in heart failure but was not significantly lower than that in controls. There were no significant differences between hepcidin levels in patients with heart failure and anemia compared to patients with heart failure and normal hemoglobin. We concluded that hepcidin probably does not play a major role in pathogenesis of anemia in patients with chronic heart failure.
doi:10.1002/ajh.21902
PMCID: PMC3076004  PMID: 21080339
Anemias; Cytokines; Iron
8.  An in vitro study comparing a peripherally inserted central catheter to a conventional central venous catheter: no difference in static and dynamic pressure transmission 
BMC Anesthesiology  2010;10:18.
Background
Early goal directed therapy improves survival in patients with septic shock. Central venous pressure (CVP) monitoring is essential to guide adequate resuscitation. Use of peripherally inserted central catheters (PICC) is increasing, but little data exists comparing a PICC to a conventional CVP catheter. We studied the accuracy of a novel PICC to transmit static and dynamic pressures in vitro.
Methods
We designed a device to generate controlled pressures via a column of water allowing simultaneous measurements from a PICC and a standard triple lumen catheter. Digital transducers were used to obtain all pressure readings. Measurements of static pressures over a physiologic range were recorded using 5Fr and 6Fr dual lumen PICCs. Additionally, random repetitive pressure pulses were applied to the column of water to simulate physiologic intravascular pressure variations. The resultant PICC and control waveforms were recorded simultaneously.
Results
Six-hundred thirty measurements were made using the 5 Fr and 6 Fr PICCs. The average bias determined by Bland-Altman plot was 0.043 mmHg for 5 Fr PICC and 0.023 mmHg for 6 Fr PICC with a difference range of 1.0 to -1.0. The correlation coefficient for both catheters was 1.0 (p-value < 0.001). Dynamic pressure waveforms plotted simultaneously between PICC and control revealed equal peaks and troughs.
Conclusion
In vitro, no static or dynamic pressure differences were found between the PICC and a conventional CVP catheter. Clinical studies are required to assess whether the novel PICC has bedside equivalence to conventional catheters when measuring central venous pressures.
doi:10.1186/1471-2253-10-18
PMCID: PMC2964716  PMID: 20939919
9.  Phytoliths in woody plants from the Miombo woodlands of Mozambique 
Annals of Botany  2009;104(1):91-113.
Background and Aims
There are no descriptions of phytoliths produced by plants from the ‘Zambezian’ zone, where Miombo woodlands are the dominant element of the largest single phytochorion in sub-Saharan Africa. The preservation of phytoliths in fossil records of Africa makes phytoliths a tool to study early plant communities. Paleo-ethnobotanical interpretation of phytoliths relies on the comparison of ancient types with morphotypes extracted from living reference collections.
Methods
Phytoliths were extracted from plant samples representing 41 families, 77 genera and 90 species through sonic cleaning, dry ashing and acid treatment; and phytoliths thus extracted were quantified. For each species, an average of 216 phytoliths were counted. The percentage of each morphotype identified per species was calculated, and types were described according to the descriptors from the International Code for Phytolith Nomenclature. Phytolith assemblages were subject to discriminant analysis, cluster analysis and principal component analysis.
Key Results
Phytoliths were grouped into 57 morphotypes (two were articulated forms and 55 were discrete shapes), and provide a reference collection of phytolith assemblages produced by Miombo woody species. Common and unique morphotypes are described and taxonomic and grouping variables are looked into from a statistical perspective.
Conclusions
The first quantitative taxonomy of phytoliths from Miombos is presented here, including new types and constituting the most extensive phytolith key for any African ecoregion. Evidence is presented that local woody species are hypervariable silica producers and their phytolith morphotypes are highly polymorphic. The taxonomic significance of these phytoliths is largely poor, but there are important exceptions that include the morphotypes produced by members from >10 families and orders. The typical phytolithic signal that would allow scientists to identify ancient woodlands of ‘Zambezian’ affiliation comprises only half of the original number of phytoliths originally produced and might favour the more resilient blocky, cylindroid, globular and tabular forms.
doi:10.1093/aob/mcp097
PMCID: PMC2706725  PMID: 19429923
Africa; Mozambique; Niassa; Miombo; phytolith analysis; reference collection; quantitative methods; principal component analysis; cluster analysis; discriminant analysis
10.  Convalescent Pulmonary Dysfunction Following Hantavirus Pulmonary Syndrome in Panama and the United States 
Lung  2010;188(5):387-391.
The objective of this study was to document persistent pulmonary symptoms and pulmonary function abnormalities in adults surviving hantavirus pulmonary syndrome (HPS). Acute infection by most hantaviruses result in mortality rates of 25–35%, while in Panama the mortality rate of 10% is contrasted by an unusually high incidence. In all types of HPS, the viral prodrome, cardiopulmonary phase due to massive pulmonary capillary leak syndrome, and spontaneous diuresis are followed by a convalescent phase with exertional dyspnea for 3–4 weeks, but the frequency of persistent symptoms is not known. In this observational study of a convenience sample, 14 survivors of HPS caused by Choclo virus infection in Panama and 9 survivors of HPS caused by Sin Nombre virus infection in New Mexico completed a questionnaire and pulmonary function tests up to 8 years after infection. In both groups, exertional dyspnea persisted for 1–2 years after acute infection in 43% (Panama) and 77% (New Mexico) of survivors surveyed. Reduction in midexpiratory flows (FEF25–75%), increased residual volume (RV), and reduced diffusion capacity (DLCO/VA) also were common in both populations; but the severity of reduced expiratory flow did not correlate with exertional dyspnea. Symptoms referable to previous hantavirus infection had resolved within 3 years of acute infection in most but not all patients in the Panama group. Temporary exertional dyspnea and reduced expiratory flow are common in early convalescence after HPS but resolves in almost all patients.
doi:10.1007/s00408-010-9245-4
PMCID: PMC2939327  PMID: 20524006
Hantavirus; Pneumonia; Pulmonary function test

Results 1-10 (10)