Comparison of multiple typing methods for Aspergillus fumigatus

As part of studies on the spread of infections, risk factors and prevention, several typing methods were developed to investigate the epidemiology of Aspergillus fumigatus. In the present study, 52 clinical isolates of A. fumigatus from 12 airway specimens from patients with invasive aspergillosis (hospitalized in three different centres) were characterized by short tandem repeat (STR) typing and multilocus sequence typing (MLST). These isolates were previously typed by random amplified polymorphic DNA (RAPD), sequence-specific DNA polymorphism (SSDP), microsatellite polymorphism (MSP) and multilocus enzyme electrophoresis (MLEE). STR typing identified 30 genotypes and, for most patients, all isolates were grouped in one cluster of the unweighted pair group method with arithmetic mean dendrogram. Using MLST, 16 genotypes were identified among 50 isolates, while two isolates appeared untypeable. RAPD, MSP, SSDP and MLEE allowed identification of eight, 14, nine and eight genotypes, respectively. Combining the results of these methods led to the delineation of 25 genotypes and a similar clustering pattern as with STR typing. In general, STR typing led to similar results to the previous combination of RAPD, SSDP, MSP and MLEE, but had a higher resolution, whereas MLST was less discriminatory and resulted in a totally different clustering pattern. Therefore, this study suggests the use of STR typing for research concerning the local epidemiology of A. fumigatus, which requires a high discriminatory power

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ABSTRACT. Objective. Infections and thromboses are known complications of systemic lupus erythematosus (SLE). We investigated if infectious episodes in patients with SLE were followed by an increased risk of thrombotic events. Methods. A cohort of 571 patients with prevalent or incident SLE was followed for a mean of 8.9 ± 7.6 years. All episodes of hospitalized infections or episodes of cutaneous herpes zoster as well as arterial and venous thrombotic events were identified by retrospective chart review and prospective updating of a clinical database. For time-dependent analyses adjusted for age, sex, and ever-presence of antiphospholipid antibodies, thrombotic events were classified as occurring during the time at risk of 1 year after an infection or during the remaining control observation time. Infections and thromboses occur at an increased rate in patients with systemic lupus erythematosus (SLE) and, together with active SLE, are the most frequent causes of death in patients with SLE 1,2,3 . In general, acute infections have been recognized to be associated with the development of arterial thromboses, including myocardial infarction (MI) and stroke 4 . Also, the risk of MI and stroke after an acute respiratory tract infection is greater than after less severe urinary tract infection 5 . Large retrospective studies consistently find a 2-fold to 3-fold increase in the risk for acute coronary syndromes within 1-2 weeks after a respiratory infection, and this risk remains significant at 3 months 4 . It has been hypothesized that infections, in addition to eliciting systemic inflammatory responses, can also have direct inflammatory effects on atherosclerotic plaques and coronary arteries 4 . Studies have also demonstrated that there is a transient (up to 1 year) increased risk of venous thromboses [deep venous thrombosis (DVT) and pulmonary embolism (PE)] after respiratory infection 6,7 and urinary tract infection 7 in the general population. Clayton, et al found a 2.6-fold increased risk of DVT in the month following a respiratory infection persisting up to a year, as well as a 2.5-fold increased risk of PE for the same period 6 . We investigated whether infectious episodes in patients with SLE were followed by an increased risk of arterial and venous thrombotic events. MATERIALS AND METHODS Patients and procedures. Our SLE cohort was started and the majority of data (on 513 patients) were retrospectively collected in 1995 as part of previous study 8 . Patients were followed at several hospital centers in Denmark, including university hospitals that have specialized functions in diagnosing and treating SLE, and locally identified by means of a national disease coding system. Data collection on consecutive patients with SLE seen at one of the university hospitals is continuing, and we included further incident cases, resulting in data on 571 adult patients with SLE fulfilling the modified American College of Rheumatology (ACR) 1982 9 or 1997 10 classification criteria. The electronic SLE database includes basic demographics, SLE symptoms and dates of symptom onset, immunologi

Personal non-commercial use only

ABSTRACT. Objective. Infections and thromboses are known complications of systemic lupus erythematosus (SLE). We investigated if infectious episodes in patients with SLE were followed by an increased risk of thrombotic events. Methods. A cohort of 571 patients with prevalent or incident SLE was followed for a mean of 8.9 ± 7.6 years. All episodes of hospitalized infections or episodes of cutaneous herpes zoster as well as arterial and venous thrombotic events were identified by retrospective chart review and prospective updating of a clinical database. For time-dependent analyses adjusted for age, sex, and ever-presence of antiphospholipid antibodies, thrombotic events were classified as occurring during the time at risk of 1 year after an infection or during the remaining control observation time. Infections and thromboses occur at an increased rate in patients with systemic lupus erythematosus (SLE) and, together with active SLE, are the most frequent causes of death in patients with SLE 1,2,3 . In general, acute infections have been recognized to be associated with the development of arterial thromboses, including myocardial infarction (MI) and stroke 4 . Also, the risk of MI and stroke after an acute respiratory tract infection is greater than after less severe urinary tract infection 5 . Large retrospective studies consistently find a 2-fold to 3-fold increase in the risk for acute coronary syndromes within 1-2 weeks after a respiratory infection, and this risk remains significant at 3 months 4 . It has been hypothesized that infections, in addition to eliciting systemic inflammatory responses, can also have direct inflammatory effects on atherosclerotic plaques and coronary arteries 4 . Studies have also demonstrated that there is a transient (up to 1 year) increased risk of venous thromboses [deep venous thrombosis (DVT) and pulmonary embolism (PE)] after respiratory infection 6,7 and urinary tract infection 7 in the general population. Clayton, et al found a 2.6-fold increased risk of DVT in the month following a respiratory infection persisting up to a year, as well as a 2.5-fold increased risk of PE for the same period 6 . We investigated whether infectious episodes in patients with SLE were followed by an increased risk of arterial and venous thrombotic events. MATERIALS AND METHODS Patients and procedures. Our SLE cohort was started and the majority of data (on 513 patients) were retrospectively collected in 1995 as part of previous study 8 . Patients were followed at several hospital centers in Denmark, including university hospitals that have specialized functions in diagnosing and treating SLE, and locally identified by means of a national disease coding system. Data collection on consecutive patients with SLE seen at one of the university hospitals is continuing, and we included further incident cases, resulting in data on 571 adult patients with SLE fulfilling the modified American College of Rheumatology (ACR) 1982 9 or 1997 10 classification criteria. The electronic SLE database includes basic demographics, SLE symptoms and dates of symptom onset, immunologi

A new fireworm (Amphinomidae) from the Cretaceous of Lebanon identified from three-dimensionally preserved myoanatomy

© 2015 Parry et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The attached file is the published version of the article

Rapidly Decaying Supernova 2010X: A Candidate ".Ia" Explosion

We present the discovery, photometric and spectroscopic follow-up observations of SN 2010X (PTF 10bhp). This supernova decays exponentially with tau_d=5 days, and rivals the current recordholder in speed, SN 2002bj. SN 2010X peaks at M_r=-17mag and has mean velocities of 10,000 km/s. Our light curve modeling suggests a radioactivity powered event and an ejecta mass of 0.16 Msun. If powered by Nickel, we show that the Nickel mass must be very small (0.02 Msun) and that the supernova quickly becomes optically thin to gamma-rays. Our spectral modeling suggests that SN 2010X and SN 2002bj have similar chemical compositions and that one of Aluminum or Helium is present. If Aluminum is present, we speculate that this may be an accretion induced collapse of an O-Ne-Mg white dwarf. If Helium is present, all observables of SN 2010X are consistent with being a thermonuclear Helium shell detonation on a white dwarf, a ".Ia" explosion. With the 1-day dynamic-cadence experiment on the Palomar Transient Factory, we expect to annually discover a few such events.Comment: 6 pages, 5 figures; Minor Changes; Note correction in Fig 4 caption; published by ApJ

Increased ventral striatal volume in college-aged binge drinkers

BACKGROUND Binge drinking is a serious public health issue associated with cognitive, physiological, and anatomical differences from healthy individuals. No studies, however, have reported subcortical grey matter differences in this population. To address this, we compared the grey matter volumes of college-age binge drinkers and healthy controls, focusing on the ventral striatum, hippocampus and amygdala. METHOD T1-weighted images of 19 binge drinkers and 19 healthy volunteers were analyzed using voxel-based morphometry. Structural data were also covaried with Alcohol Use Disorders Identification Test (AUDIT) scores. Cluster-extent threshold and small volume corrections were both used to analyze imaging data. RESULTS Binge drinkers had significantly larger ventral striatal grey matter volumes compared to controls. There were no between group differences in hippocampal or amygdalar volume. Ventral striatal, amygdalar, and hippocampal volumes were also negatively related to AUDIT scores across groups. CONCLUSIONS Our findings stand in contrast to the lower ventral striatal volume previously observed in more severe forms of alcohol use disorders, suggesting that college-age binge drinkers may represent a distinct population from those groups. These findings may instead represent early sequelae, compensatory effects of repeated binge and withdrawal, or an endophenotypic risk factor

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

Background: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome- wide information on cytosine methylation. However, a profiling method that detects cytosine methylation state dispersed over the genome would allow high-throughput analysis of multiple plant samples with distinct epigenetic signatures. We use specific restriction endonucleases to enrich for cytosine coverage in a bisulfite and NGS-based profiling method, which was compared to whole-genome bisulfite sequencing of the same plant material. Methods: We established an effective methylome profiling method in plants, termed plant-reduced representation bisulfite sequencing (plant-RRBS), using optimized double restriction endonuclease digestion, fragment end repair, adapter ligation, followed by bisulfite conversion, PCR amplification and NGS. We report a performant laboratory protocol and a straightforward bioinformatics data analysis pipeline for plant-RRBS, applicable for any reference-sequenced plant species. Results: As a proof of concept, methylome profiling was performed using an Oryza sativa ssp. indica pure breeding line and a derived epigenetically altered line (epiline). Plant-RRBS detects methylation levels at tens of millions of cytosine positions deduced from bisulfite conversion in multiple samples. To evaluate the method, the coverage of cytosine positions, the intra-line similarity and the differential cytosine methylation levels between the pure breeding line and the epiline were determined. Plant-RRBS reproducibly covers commonly up to one fourth of the cytosine positions in the rice genome when using MspI-DpnII within a group of five biological replicates of a line. The method predominantly detects cytosine methylation in putative promoter regions and not-annotated regions in rice. Conclusions: Plant-RRBS offers high-throughput and broad, genome- dispersed methylation detection by effective read number generation obtained from reproducibly covered genome fractions using optimized endonuclease combinations, facilitating comparative analyses of multi-sample studies for cytosine methylation and transgenerational stability in experimental material and plant breeding populations

A Fokker-Planck formalism for diffusion with finite increments and absorbing boundaries

Gaussian white noise is frequently used to model fluctuations in physical systems. In Fokker-Planck theory, this leads to a vanishing probability density near the absorbing boundary of threshold models. Here we derive the boundary condition for the stationary density of a first-order stochastic differential equation for additive finite-grained Poisson noise and show that the response properties of threshold units are qualitatively altered. Applied to the integrate-and-fire neuron model, the response turns out to be instantaneous rather than exhibiting low-pass characteristics, highly non-linear, and asymmetric for excitation and inhibition. The novel mechanism is exhibited on the network level and is a generic property of pulse-coupled systems of threshold units.Comment: Consists of two parts: main article (3 figures) plus supplementary text (3 extra figures

Deficiency and Also Transgenic Overexpression of Timp-3 Both Lead to Compromised Bone Mass and Architecture In Vivo

Tissue inhibitor of metalloproteinases-3 (TIMP-3) regulates extracellular matrix via its inhibition of matrix metalloproteinases and membrane-bound sheddases. Timp-3 is expressed at multiple sites of extensive tissue remodelling. This extends to bone where its role, however, remains largely unresolved. In this study, we have used Micro-CT to assess bone mass and architecture, histological and histochemical evaluation to characterise the skeletal phenotype of Timp-3 KO mice and have complemented this by also examining similar indices in mice harbouring a Timp-3 transgene driven via a Col-2a-driven promoter to specifically target overexpression to chondrocytes. Our data show that Timp-3 deficiency compromises tibial bone mass and structure in both cortical and trabecular compartments, with corresponding increases in osteoclasts. Transgenic overexpression also generates defects in tibial structure predominantly in the cortical bone along the entire shaft without significant increases in osteoclasts. These alterations in cortical mass significantly compromise predicted tibial load-bearing resistance to torsion in both genotypes. Neither Timp-3 KO nor transgenic mouse growth plates are significantly affected. The impact of Timp-3 deficiency and of transgenic overexpression extends to produce modification in craniofacial bones of both endochondral and intramembranous origins. These data indicate that the levels of Timp-3 are crucial in the attainment of functionally-appropriate bone mass and architecture and that this arises from chondrogenic and osteogenic lineages