bluuebunny/crossref_metadata_2025_split huggingface dataset:
Image‐based reconstruction of three‐dimensional myocardial infarct geometry for patient‐specific modeling of cardiac electrophysiology
Authors: Ukwatta Eranga , Arevalo Hermenegild , Rajchl Martin , White James , Pashakhanloo Farhad , Prakosa Adityo , Herzka Daniel A. , McVeigh Elliot , Lardo Albert C. , Trayanova Natalia A. , Vadakkumpadan Fijoy 
Published: July 2015

Purpose:Accurate three‐dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient‐specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two‐dimensional (2D) late‐gadolinium enhanced cardiac magnetic resonance (LGE‐CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE‐CMR images has been lacking. The purpose of this study was to address this need.Methods:The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low‐resolution (Lo‐res) clinical LGE‐CMR images. Their methodology employed the so‐called logarithm of odds (LogOdds) function to implicitly represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high‐resolution (Hi‐res) LGE‐CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi‐res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method.Results:The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo‐ECGs.Conclusions:The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo‐res clinical 2D LGE‐CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations.
Pathogenic Enteric Viruses and Microbial Indicators during Secondary Treatment of Municipal Wastewater
Authors: Montazeri Naim , Goettert Dorothee , Achberger Eric C. , Johnson Crystal N. , Prinyawiwatkul Witoon , Janes Marlene E. 
Published: July 2015

ABSTRACT

Pathogenic enteric viruses are responsible for a wide range of infections in humans, with diverse symptoms. Raw and partially treated wastewaters are major sources of environmental contamination with enteric viruses. We monitored a municipal secondary wastewater treatment plant (New Orleans, LA) on a monthly basis for norovirus (NoV) GI and GII and enterovirus serotypes using multiplex reverse transcription-quantitative PCR (RT-qPCR) and microbial indicators of fecal contamination using standard plating methods. Densities of indicator bacteria (enterococci, fecal coliforms, and
Escherichia coli
) did not show monthly or seasonal patterns. Norovirus GII was more abundant than GI and, along with enterovirus serotypes, increased in influent during fall and spring. The highest NoV GI density in influent was in the fall, reaching an average of 4.0 log
10
genomic copies/100 ml. Norovirus GI removal (0.95 log
10
) was lower than that for GII, enterovirus serotypes, and male-specific coliphages (1.48 log
10
) or for indicator bacteria (4.36 log
10
), suggesting higher resistance of viruses to treatment. Male-specific coliphages correlated with NoV GII densities in influent and effluent (
r
= 0.48 and 0.76, respectively) and monthly removal, indicating that male-specific coliphages can be more reliable than indicator bacteria to monitor norovirus GII load and microbial removal. Dominant norovirus genotypes were classified into three GI genotypes (GI.1, GI.3, and GI.4) and four GII genotypes (GII.3, GII.4, GII.13, and GII.21), dominated by GI.1 and GII.4 strains. Some of the seasonal and temporal patterns we observed in the pathogenic enteric viruses were different from those of epidemiological observations.
Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems
Authors: Shaw Jennifer L. A. , Monis Paul , Weyrich Laura S. , Sawade Emma , Drikas Mary , Cooper Alan J. 
Published: July 2015

ABSTRACT

Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as
Nitrospira
, were detected.
Burkholderiales
were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs.
Most of the Dominant Members of Amphibian Skin Bacterial Communities Can Be Readily Cultured
Authors: Walke Jenifer B. , Becker Matthew H. , Hughey Myra C. , Swartwout Meredith C. , Jensen Roderick V. , Belden Lisa K. 
Published: July 2015

ABSTRACT

Currently, it is estimated that only 0.001% to 15% of bacteria in any given system can be cultured by use of commonly used techniques and media, yet culturing is critically important for investigations of bacterial function. Despite this situation, few studies have attempted to link culture-dependent and culture-independent data for a single system to better understand which members of the microbial community are readily cultured. In amphibians, some cutaneous bacterial symbionts can inhibit establishment and growth of the fungal pathogen
Batrachochytrium dendrobatidis
, and thus there is great interest in using these symbionts as probiotics for the conservation of amphibians threatened by
B. dendrobatidis
. The present study examined the portion of the culture-independent bacterial community (based on Illumina amplicon sequencing of the 16S rRNA gene) that was cultured with R2A low-nutrient agar and whether the cultured bacteria represented rare or dominant members of the community in the following four amphibian species: bullfrogs (
Lithobates catesbeianus
), eastern newts (
Notophthalmus viridescens
), spring peepers (
Pseudacris crucifer
), and American toads (
Anaxyrus americanus
). To determine which percentage of the community was cultured, we clustered Illumina sequences at 97% similarity, using the culture sequences as a reference database. For each amphibian species, we cultured, on average, 0.59% to 1.12% of each individual's bacterial community. However, the average percentage of bacteria that were culturable for each amphibian species was higher, with averages ranging from 2.81% to 7.47%. Furthermore, most of the dominant operational taxonomic units (OTUs), families, and phyla were represented in our cultures. These results open up new research avenues for understanding the functional roles of these dominant bacteria in host health.
The Pseudomonas aeruginosa Isohexenyl Glutaconyl Coenzyme A Hydratase (AtuE) Is Upregulated in Citronellate-Grown Cells and Belongs to the Crotonase Family
Authors: Poudel Nirmal , Pfannstiel Jens , Simon Oliver , Walter Nadine , Papageorgiou Anastassios C. , Jendrossek Dieter 
Published: July 2015

ABSTRACT

Pseudomonas aeruginosa
is one of only a few
Pseudomonas
species that are able to use acyclic monoterpenoids, such as citronellol and citronellate, as carbon and energy sources. This is achieved by the acyclic terpene utilization pathway (Atu), which includes at least six enzymes (AtuA, AtuB, AtuCF, AtuD, AtuE, AtuG) and is coupled to a functional leucine-isovalerate utilization (Liu) pathway. Here, quantitative proteome analysis was performed to elucidate the terpene metabolism of
P. aeruginosa
. The proteomics survey identified 187 proteins, including AtuA to AtuG and LiuA to LiuE, which were increased in abundance in the presence of citronellate. In particular, two hydratases, AtuE and the PA4330 gene product, out of more than a dozen predicted in the
P. aeruginosa
proteome showed an increased abundance in the presence of citronellate. AtuE (isohexenyl-glutaconyl coenzyme A [CoA] hydratase; EC 4.2.1.57) most likely catalyzes the hydration of the unsaturated distal double bond in the isohexenyl-glutaconyl-CoA thioester to yield 3-hydroxy-3-isohexenyl-glutaryl-CoA. Determination of the crystal structure of AtuE at a 2.13-Å resolution revealed a fold similar to that found in the hydratase (crotonase) superfamily and provided insights into the nature of the active site. The AtuE active-site architecture showed a significantly broader cavity than other crotonase superfamily members, in agreement with the need to accommodate the branched isoprenoid unit of terpenes. Glu139 was identified to be a potential catalytic residue, while the backbone NH groups of Gly116 and Gly68 likely form an oxyanion hole. The present work deepens the understanding of terpene metabolism in
Pseudomonas
and may serve as a basis to develop new strategies for the biotechnological production of terpenoids.
Effectiveness of Natural Antifungal Compounds in Controlling Infection by Grapevine Trunk Disease Pathogens through Pruning Wounds
Authors: Cobos Rebeca , Mateos Rosa María , Álvarez-Pérez José Manuel , Olego Miguel Angel , Sevillano Silvia , González-García Sandra , Garzón-Jimeno Enrique , Coque Juan José R. 
Published: July 2015

ABSTRACTGrapevine trunk fungal pathogens, such asDiplodia seriataandPhaeomoniella chlamydospora, can infect plants through pruning wounds. They cause grapevine trunk diseases and are involved in grapevine decline. Accordingly, the protection of pruning wounds is crucial for the management of grapevine trunk diseases. The efficacy of different natural antifungals in inhibiting the growth of several fungi causing grapevine trunk diseases was evaluatedin vitro. The fungi showing greaterin vitroefficacy were tested on autoclaved grape wood assays againstD. seriataandP. chlamydospora. Based on results from these assays, chitosan oligosaccharide, vanillin, and garlic extract were selected for further evaluation on pruning wounds inoculated withD. seriataandP. chlamydosporain field trials. A significant decrease in plant mortality was observed after 2 years of growth in the plants treated with the different natural antifungals compared to the mortality rate observed in infected plants that were not treated with antifungals. Also, the infection rate for the inoculated pathogens was significantly reduced in plants treated with the selected natural antifungals. Therefore, natural antifungals represent a promising alternative for disease control and could provide significant economic benefits for the grape-growing industry.
The Enterobacterium Trabulsiella odontotermitis Presents Novel Adaptations Related to Its Association with Fungus-Growing Termites
Authors: Sapountzis Panagiotis , Gruntjes Thijs , Otani Saria , Estevez James , da Costa Rafael R. , Plunkett Guy , Perna Nicole T. , Poulsen Michael 
Published: July 2015

ABSTRACT

Fungus-growing termites rely on symbiotic microorganisms to help break down plant material and to obtain nutrients. Their fungal cultivar,
Termitomyces
, is the main plant degrader and food source for the termites, while gut bacteria complement
Termitomyces
in the degradation of foodstuffs, fixation of nitrogen, and metabolism of amino acids and sugars. Due to the community complexity and because these typically anaerobic bacteria can rarely be cultured, little is known about the physiological capabilities of individual bacterial members of the gut communities and their associations with the termite host. The bacterium
Trabulsiella odontotermitis
is associated with fungus-growing termites, but this genus is generally understudied, with only two described species. Taking diverse approaches, we obtained a solid phylogenetic placement of
T. odontotermitis
among the
Enterobacteriaceae
, investigated the physiology and enzymatic profiles of
T. odontotermitis
isolates, determined the localization of the bacterium in the termite gut, compared draft genomes of two
T. odontotermitis
isolates to those of their close relatives, and examined the expression of genes relevant to host colonization and putative symbiont functions. Our findings support the hypothesis that
T. odontotermitis
is a facultative symbiont mainly located in the paunch compartment of the gut, with possible roles in carbohydrate metabolism and aflatoxin degradation, while displaying adaptations to association with the termite host, such as expressing genes for a type VI secretion system which has been demonstrated to assist bacterial competition, colonization, and survival within hosts.
Bartonella Infection among Cats Adopted from a San Francisco Shelter, Revisited
Authors: Fleischman Drew A. , Chomel Bruno B. , Kasten Rickie W. , Stuckey Matthew J. , Scarlet Jennifer , Liu Hongwei , Boulouis Henri-Jean , Haddad Nadia , Pedersen Niels C. 
Published: July 2015

ABSTRACT

Bartonella
infection among cats from shelters can pose a health risk to adopters.
Bartonella henselae
is the most common species, with
B. clarridgeiae
and
B. koehlerae
being less common. The lower rates of infection by the latter species may reflect their rarity or an inefficiency of culture techniques. To assess the incidence of infection, blood cultures, serology, and PCR testing were performed on 193 kittens (6 to 17 weeks old) and 158 young adult cats (5 to 12 months old) from a modern regional shelter. Classical
B. henselae
culture medium was compared to a medium supplemented with insect cell growth factors.
Bartonella
colonies were isolated from 115 (32.8%) animals, including 50 (25.9%) kittens and 65 (41.1%) young adults. Therefore, young adults were twice as likely to be culture positive as kittens. Enhanced culture methods did not improve either the isolation rate or species profile.
B. henselae
was isolated from 40 kittens and 55 young adults, while
B. clarridgeiae
was cultured from 10 animals in each group.
B. koehlerae
was detected in one young adult by PCR only.
B. henselae
genotype II was more commonly isolated from young adults, and genotype I was more frequently isolated from kittens. Kittens were 4.7 times more likely to have a very high bacterial load than young adults. A significantly higher incidence of bacteremia in the fall and winter than in the spring and summer was observed.
Bartonella
antibodies were detected in 10% (19/193) of kittens and 46.2% (73/158) of young adults, with culture-positive kittens being 9.4 times more likely to be seronegative than young adults.
Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins
Authors: Hartard C. , Rivet R. , Banas S. , Gantzer C. 
Published: July 2015

ABSTRACT
F-specific RNA bacteriophages (FRNAPH) have been widely studied as tools for evaluating fecal or viral pollution in water. It has also been proposed that they can be used to differentiate human from animal fecal contamination. While FRNAPH subgroup I (FRNAPH-I) and FRNAPH-IV are often associated with animal pollution, FRNAPH-II and -III prevail in human wastewater. However, this distribution is not absolute, and variable survival rates in these subgroups lead to misinterpretation of the original distribution. In this context, we studied FRNAPH distribution in urban wastewater and animal feces/wastewater. To increase the specificity, we partially sequenced the genomes of phages of urban and animal origins. The persistence of the genomes and infectivity were also studied, over time in wastewater and during treatment, for each subgroup. FRNAPH-I genome sequences did not show any specific urban or animal clusters to allow development of molecular tools for differentiation. They were the most resistant and as such may be used as fecal or viral indicators. FRNAPH-II's low prevalence and low sequence variability in animal stools, combined with specific clusters formed by urban strains, allowed differentiation between urban and animal pollution by using a specific reverse transcription-PCR (RT-PCR) method. The subgroup's resistance over time was comparable to that of FRNAPH-I, but its surface properties allowed higher elimination rates during activated-sludge treatment. FRNAPH-III's low sequence variability in animal wastewater and specific cluster formation by urban strains also allowed differentiation by using a specific RT-PCR method. Nevertheless, its low resistance restricted it to being used only for recent urban pollution detection. FRNAPH-IV was too rare to be used.
Analysis of the Aspergillus fumigatus Biofilm Extracellular Matrix by Solid-State Nuclear Magnetic Resonance Spectroscopy
Authors: Reichhardt Courtney , Ferreira Jose A. G. , Joubert Lydia-Marie , Clemons Karl V. , Stevens David A. , Cegelski Lynette 
Published: July 2015

ABSTRACT

Aspergillus fumigatus
is commonly responsible for lethal fungal infections among immunosuppressed individuals.
A. fumigatus
forms biofilm communities that are of increasing biomedical interest due to the association of biofilms with chronic infections and their increased resistance to antifungal agents and host immune factors. Understanding the composition of microbial biofilms and the extracellular matrix is important to understanding function and, ultimately, to developing strategies to inhibit biofilm formation. We implemented a solid-state nuclear magnetic resonance (NMR) approach to define compositional parameters of the
A. fumigatus
extracellular matrix (ECM) when biofilms are formed in RPMI 1640 nutrient medium. Whole biofilm and isolated matrix networks were also characterized by electron microscopy, and matrix proteins were identified through protein gel analysis. The
13
C NMR results defined and quantified the carbon contributions in the insoluble ECM, including carbonyls, aromatic carbons, polysaccharide carbons (anomeric and nonanomerics), aliphatics, etc. Additional
15
N and
31
P NMR spectra permitted more specific annotation of the carbon pools according to C-N and C-P couplings. Together these data show that the
A. fumigatus
ECM produced under these growth conditions contains approximately 40% protein, 43% polysaccharide, 3% aromatic-containing components, and up to 14% lipid. These fundamental chemical parameters are needed to consider the relationships between composition and function in the
A. fumigatus
ECM and will enable future comparisons with other organisms and with
A. fumigatus
grown under alternate conditions.
Severe Community-Acquired Pneumonia with Bacteremia Caused by Herbaspirillum aquaticum or Herbaspirillum huttiense in an Immune-Competent Adult
Authors: Regunath Hariharan , Kimball Joanna , Smith L. Patrick , Salzer William 
Published: July 2015

ABSTRACT

Herbaspirillum
spp. are Gram-negative bacteria that inhabit soil and water. Infections caused by these organisms have been reported in immunocompromised hosts. We describe severe community-acquired pneumonia and bacteremia caused by
Herbaspirillum aquaticum
or
H. huttiense
in an immunocompetent adult male.