bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visceral leishmaniasis in a lung transplant recipient: usefulness of highly sensitive real‐time polymerase chain reaction for preemptive diagnosis
Authors: Opota O. , Balmpouzis Z. , Berutto C. , Kaiser‐Guignard J. , Greub G. , Aubert J.‐D. , Prod'hom G. , Manuel O. , Jaton K. 
Published: August 2016

AbstractWe report the case of a lung transplant recipient in whom the diagnosis of visceral leishmaniasis (VL) was made by detection of parasites in a peripheral blood smear when the parasite load already reached 8.9 × 103 parasites/mL. We demonstrated that the VL diagnosis could have been done months before the development of symptoms by the use of Leishmania‐specific real‐time polymerase chain reaction (PCR), suggesting the role of preemptive PCR‐based diagnosis in transplant recipients at risk for VL.
Fulminant Epstein–Barr virus‐associated hemophagocytic syndrome in a renal transplant patient and review of the literature
Authors: Romiopoulos I. , Pyrpasopoulou A. , Onoufriadis I. , Massa E. , Mouloudi E. , Kydona C. , Giasnetsova T. , Gerogianni N. , Myserlis G. , Solonaki F. , Nikodimopoulou M. , Mandala E. , Antachopoulos C. , Roilides E. 
Published: August 2016

AbstractWe describe a rare fulminant case of Epstein–Barr virus‐associated hemophagocytic syndrome (HPS) in a 37‐year‐old female renal transplant patient, indistinguishable from severe sepsis clinically and in the laboratory. HPS involves rapidly escalating immune system activation, resulting in a cytokine cascade, which can, especially in immunocompromised patients, lead to multi‐organ failure, and even death. Thirty‐two Herpesviridae‐associated HPS cases in renal transplant patients have been reported and are reviewed. Overall mortality is 47% (15/32 cases).
Incidence and outcomes of bloodstream infections among hematopoietic cell transplant recipients from species commonly reported to be in over‐the‐counter probiotic formulations
Authors: Cohen S.A. , Woodfield M.C. , Boyle N. , Stednick Z. , Boeckh M. , Pergam S.A. 
Published: August 2016

AbstractBackgroundProbiotic supplementation has been promoted for numerous health conditions; however, safety in immunosuppressed patients is unknown. We evaluated bloodstream infections (BSIs) caused by common probiotic organisms in hematopoietic cell transplant recipients.MethodsAll blood culture (BC) results from a cohort of hematopoietic cell transplant recipients transplanted at Fred Hutchinson Cancer Research Center in Seattle, Washington, between 2002 and 2011 were reviewed. Patients with at least 1 positive BC for common probiotic organisms (Lactobacillus species, Bifidobacterium species, Streptococcus thermophilus, and Saccharomyces species) within 1 year post hematopoietic cell transplantation (HCT) were considered cases. Data were collected from center databases, which contain archived laboratory data, patient demographics, and clinical summaries.ResultsA total of 19/3796 (0.5%) patients developed a BSI from one of these organisms within 1 year post HCT; no Bifidobacterium species or S. thermophilus were identified. Cases had a median age of 49 years (interquartile range [IQR]: 39–53), and the majority were allogeneic hematopoietic cell transplant recipients (14/19, 74%). Most positive BCs were Lactobacillus species (18/19) and occurred at a median of 84 days (IQR: 34–127) post transplant. The incidence rate of Lactobacillus bacteremia was 1.62 cases per 100,000 patient‐days; the highest rate occurred within 100 days post transplant (3.3 per 100,000 patient‐days). Eight patients (44%) were diagnosed with acute graft‐versus‐host disease of the gut prior to the development of bacteremia. No mortality was attributable to any of these infections.ConclusionOrganisms frequently incorporated in available over‐the‐counter probiotics are infrequent causes of bacteremia after HCT. Studies evaluating the use of probiotics among high‐risk patients are needed.
ABA‐dependent inhibition of the ubiquitin proteasome system during germination at high temperature in Arabidopsis
Authors: Chiu Rex Shun , Pan Shiyue , Zhao Rongmin , Gazzarrini Sonia 
Published: August 2016

SummaryDuring germination, endogenous and environmental factors trigger changes in the transcriptome, translatome and proteome to break dormancy. In Arabidopsis thaliana, the ubiquitin proteasome system (UPS) degrades proteins that promote dormancy to allow germination. While research on the UPS has focused on the identification of proteasomal substrates, little information is known about the regulation of its activity. Here we characterized the activity of the UPS during dormancy release and maintenance by monitoring protein ubiquitination and degradation of two proteasomal substrates: Suc‐LLVY‐AMC, a well characterized synthetic substrate, and FUSCA3 (FUS3), a dormancy‐promoting transcription factor degraded by the 26S proteasome. Our data indicate that proteasome activity and protein ubiquitination increase during imbibition at optimal temperature (21°C), and are required for seed germination. However, abscisic acid (ABA) and supraoptimal temperature (32°C) inhibit germination by dampening both protein ubiquitination and proteasome activity. Inhibition of UPS function by high temperature is reduced by the ABA biosynthesis inhibitor, fluridone, and in ABA biosynthetic mutants, suggesting that it is ABA dependent. Accordingly, inhibition of FUS3 degradation at 32°C is also dependent on ABA. Native gels show that inhibition of proteasome activity is caused by interference with the 26S/30S ratio as well as free 19S and 20S levels, impacting the proteasome degradation cycle. Transfer experiments show that ABA‐mediated inhibition of proteasome activity at 21°C is restricted to the first 2 days of germination, a time window corresponding to seed sensitivity to environmental and ABA‐mediated growth inhibition. Our data show that ABA and high temperature inhibit germination under unfavourable growth conditions by repressing the UPS.
The composition of surface wax on trichomes of Arabidopsis thaliana differs from wax on other epidermal cells
Authors: Hegebarth Daniela , Buschhaus Christopher , Wu May , Bird David , Jetter Reinhard 
Published: August 2016

SummaryTo protect plants against biotic and abiotic stress, the waxy cuticle must coat all epidermis cells. Here, two independent approaches addressed whether cell‐type‐specific differences exist between wax compositions on trichomes and other epidermal cells of Arabidopsis thaliana, possibly with different protection roles. First, the total waxes from a mutant lacking trichomes (gl1) were compared to waxes from wild type and a trichome‐rich mutant (cpc tcl1 etc1 etc3). In the stem wax, compounds with aliphatic chains longer than 31 carbons (derived from C32 precursors) increased in relative abundance in cpc tcl1 etc1 etc3 over gl1. Similarly, the leaf wax from the trichome‐rich mutant contained higher amounts of C32+ compounds as compared to gl1. Second, leaf trichomes were isolated, and their waxes were analyzed. The wax mixtures of the trichome‐rich mutant and the wild type were similar, comprising alkanes and alkenes as well as branched and unbranched primary alcohols. The direct analyses of trichome waxes confirmed that they contained relatively high concentrations of C32+ compounds, compared with the pavement cell wax inferred from analysis of gl1 leaves. Finally, the cell‐type‐specific wax compositions were put into perspective with expression patterns of wax biosynthesis genes in trichomes and pavement cells. Analyses of published transcriptome data (Marks et al., ) revealed that core enzymes involved in elongation of wax precursors to various carbon chain lengths are expressed differentially between epidermis cell types. By combining the chemical and gene expression data, we identified promising gene candidates involved in the formation of C32+ aliphatic chains.
Integrating metabolomics and transcriptomics data to discover a biocatalyst that can generate the amine precursors for alkamide biosynthesis
Authors: Rizhsky Ludmila , Jin Huanan , Shepard Michael R. , Scott Harry W. , Teitgen Alicen M. , Perera M. Ann , Mhaske Vandana , Jose Adarsh , Zheng Xiaobin , Crispin Matt , Wurtele Eve S. , Jones Dallas , Hur Manhoi , Góngora‐Castillo Elsa , Buell C. Robin , Minto Robert E. , Nikolau Basil J. 
Published: August 2016

SummaryThe Echinacea genus is exemplary of over 30 plant families that produce a set of bioactive amides, called alkamides. The Echinacea alkamides may be assembled from two distinct moieties, a branched‐chain amine that is acylated with a novel polyunsaturated fatty acid. In this study we identified the potential enzymological source of the amine moiety as a pyridoxal phosphate‐dependent decarboxylating enzyme that uses branched‐chain amino acids as substrate. This identification was based on a correlative analysis of the transcriptomes and metabolomes of 36 different E. purpurea tissues and organs, which expressed distinct alkamide profiles. Although no correlation was found between the accumulation patterns of the alkamides and their putative metabolic precursors (i.e., fatty acids and branched‐chain amino acids), isotope labeling analyses supported the transformation of valine and isoleucine to isobutylamine and 2‐methylbutylamine as reactions of alkamide biosynthesis. Sequence homology identified the pyridoxal phosphate‐dependent decarboxylase‐like proteins in the translated proteome of E. purpurea. These sequences were prioritized for direct characterization by correlating their transcript levels with alkamide accumulation patterns in different organs and tissues, and this multi‐pronged approach led to the identification and characterization of a branched‐chain amino acid decarboxylase, which would appear to be responsible for generating the amine moieties of naturally occurring alkamides.
Phase 3 evaluation of HP802‐247 in the treatment of chronic venous leg ulcers
Authors: Kirsner Robert S. , Vanscheidt Wolfgang , Keast David H. , Lantis John C. , Dove Cyaandi R. , Cazzell Shawn M. , Vartivarian Mher , Augustin Matthias , Marston William A. , McCoy Nicholas D. , Cargill D. Innes , Lee Tommy D. , Dickerson Jaime E. , Slade Herbert B. ,   for the HP802‐247 Study Group
Published: August 2016

AbstractIn 2012 we reported promising results from a phase 2 clinical trial of HP802‐247, a novel spray‐applied investigational treatment for chronic venous leg ulcers consisting of human, allogeneic fibroblasts and keratinocytes. We now describe phase 3 clinical testing of HP802‐247, its failure to detect efficacy, and subsequent investigation into the root causes of the failure. Two randomized, controlled trials enrolled a total of 673 adult outpatients at 96 centers in North America and Europe. The primary endpoint was the proportion of ulcers with confirmed closure at the end of 12 weeks of treatment. An investigation into the root cause for the failure of HP802‐247 to show efficacy in these two phase 3 trials was initiated immediately following the initial review of the North American trial results. Four hundred twenty‐one patients were enrolled in the North American (HP802‐247, 211; Vehicle 210) and 252 in the European (HP802‐247, 131; Vehicle 121) trials. No difference in proportion of closed ulcers at week 12 was observed between treatment groups for either the North American (HP802‐247, 61.1%; Vehicle 60.0%; p = 0.5896) or the European (HP802‐247, 47.0%; Vehicle 50.0%; p = 0.5348) trials. Thorough investigation found no likelihood that design or execution of the trials contributed to the failure. Variability over time during the trials in the clinical response implicated the quality of the cells comprising HP802‐247. Concordance between the two separate, randomized, controlled trials with distinct, nonoverlapping investigative sites and independent monitoring teams renders the possibility of a Type II error vanishingly small and provides strong credibility for the unexpected lack of efficacy observed. The most likely causative factors for the efficacy failure in phase 3 was phenotypic change in the cells (primarily keratinocytes) leading to batch to batch variability due to the age of the cell banks.
Mitochondria‐specific antioxidant supplementation does not influence endurance exercise training‐induced adaptations in circulating angiogenic cells, skeletal muscle oxidative capacity or maximal oxygen uptake
Authors: Shill Daniel D. , Southern W. Michael , Willingham T. Bradley , Lansford Kasey A. , McCully Kevin K. , Jenkins Nathan T. 
Published: August 2016

Key points
Reducing excessive oxidative stress, through chronic exercise or antioxidants, can decrease the negative effects induced by excessive amounts of oxidative stress. Transient increases in oxidative stress produced during acute exercise facilitate beneficial vascular training adaptations, but the effects of non‐specific antioxidants on exercise training‐induced vascular adaptations remain elusive.
Circulating angiogenic cells (CACs) are an exercise‐inducible subset of white blood cells that maintain vascular integrity.
We investigated whether mitochondria‐specific antioxidant (MitoQ) supplementation would affect the response to 3 weeks of endurance exercise training in CACs, muscle mitochondrial capacity and maximal oxygen uptake in young healthy men.
We show that endurance exercise training increases multiple CAC types, an adaptation that is not altered by MitoQ supplementation. Additionally, MitoQ does not affect skeletal muscle or whole‐body aerobic adaptations to exercise training.
These results indicate that MitoQ supplementation neither enhances nor attenuates endurance training adaptations in young healthy men.
AbstractAntioxidants have been shown to improve endothelial function and cardiovascular outcomes. However, the effects of antioxidants on exercise training‐induced vascular adaptations remain elusive. General acting antioxidants combined with exercise have not impacted circulating angiogenic cells (CACs). We investigated whether mitochondria‐specific antioxidant (MitoQ) supplementation would affect the response to 3 weeks of endurance exercise training on CD3+, CD3+/CD31+, CD14+/CD31+, CD31+, CD34+/VEGFR2+ and CD62E+ peripheral blood mononuclear cells (PBMCs), muscle mitochondrial capacity, and maximal oxygen uptake () in healthy men aged 22.1 ± 0.7 years, with a body mass index of 26.9 ± 0.9 kg m–2, and 24.8 ± 1.3% body fat. Analysis of main effects revealed that training induced 33, 105 and 285% increases in CD14+/CD31+, CD62E+ and CD34+/VEGFR2+ CACs, respectively, and reduced CD3+/CD31− PBMCs by 14%. There was no effect of MitoQ on CAC levels. Also independent of MitoQ supplementation, exercise training significantly increased quadriceps muscle mitochondrial capacity by 24% and by roughly 7%. In conclusion, endurance exercise training induced increases in multiple CAC types, and this adaptation is not modified by MitoQ supplementation. Furthermore, we demonstrate that a mitochondrial‐targeted antioxidant does not influence skeletal muscle or whole‐body aerobic adaptations to exercise training.
Building reaction kinetic models for amiloid fibril growth
Authors: Markov Svetoslav Marinov 
Published: August 2016

In this work weВ discuss some methodological aspects of the creation and formulation of mathematicalВ models describing the growth of species from the point of view of reaction kinetics. Our discussion is based on familiar examples of growth models such as logistic growth and enzyme kinetics. WeВ В propose several reaction networkВ modelsВ forВ the amiloid fibrillation processes in the citoplasm. The solutions of the models are sigmoidal functions graphically visualized usingВ the computer algebra system В Mathematica.
Reduction of Jet Impingement Noise by Addition of Swirl
Authors: Balakrishnan P. , Srinivasan K. 
Published: August 2016

Abstract
Experimental investigations are carried out with an objective of reducing impingement jet noise using coaxial swirl jets. Two nozzle-to-plate distances have been considered and the Mach number values ranged from 0.95 to 1.83. The vane angles of the coaxial swirlers ranged from 0 deg to 60 deg, corresponding to swirl numbers that ranged from weak to high. Flow visualization has also been conducted to understand the shock-cell structure for each case. The results indicate that swirl jets are highly efficient in the control of impingement noise. Transonic, screech, and impinging tones are completely eliminated by the swirl jets. A weak swirl seems efficient for lower Mach numbers while higher amounts of swirl are efficient at higher Mach numbers.
Carbon Catabolite Repression and Impranil Polyurethane Degradation in Pseudomonas protegens Strain Pf-5
Authors: Hung Chia-Suei , Zingarelli Sandra , Nadeau Lloyd J. , Biffinger Justin C. , Drake Carrie A. , Crouch Audra L. , Barlow Daniel E. , Russell John N. , Crookes-Goodson Wendy J. 
Published: August 2016

ABSTRACT

Polyester polyurethane (PU) coatings are widely used to help protect underlying structural surfaces but are susceptible to biological degradation. PUs are susceptible to degradation by
Pseudomonas
species, due in part to the degradative activity of secreted hydrolytic enzymes. Microorganisms often respond to environmental cues by secreting enzymes or secondary metabolites to benefit their survival. This study investigated the impact of exposing several
Pseudomonas
strains to select carbon sources on the degradation of the colloidal polyester polyurethane Impranil DLN (Impranil). The prototypic
Pseudomonas protegens
strain Pf-5 exhibited Impranil-degrading activities when grown in sodium citrate but not in glucose-containing medium. Glucose also inhibited the induction of Impranil-degrading activity by citrate-fed Pf-5 in a dose-dependent manner. Biochemical and mutational analyses identified two extracellular lipases present in the Pf-5 culture supernatant (PueA and PueB) that were involved in degradation of Impranil. Deletion of the
pueA
gene reduced Impranil-clearing activities, while
pueB
deletion exhibited little effect. Removal of both genes was necessary to stop degradation of the polyurethane. Bioinformatic analysis showed that putative Cbr/Hfq/Crc-mediated regulatory elements were present in the intergenic sequences upstream of both
pueA
and
pueB
genes. Our results confirmed that both PueA and PueB extracellular enzymes act in concert to degrade Impranil. Furthermore, our data showed that carbon sources in the growth medium directly affected the levels of Impranil-degrading activity but that carbon source effects varied among
Pseudomonas
strains. This study uncovered an intricate and complicated regulation of
P. protegens
PU degradation activity controlled by carbon catabolite repression.

IMPORTANCE
Polyurethane (PU) coatings are commonly used to protect metals from corrosion. Microbiologically induced PU degradation might pose a substantial problem for the integrity of these coatings. Microorganisms from diverse genera, including pseudomonads, possess the ability to degrade PUs via various means. This work identified two extracellular lipases, PueA and PueB, secreted by
P. protegens
strain Pf-5, to be responsible for the degradation of a colloidal polyester PU, Impranil. This study also revealed that the expression of the degradative activity by strain Pf-5 is controlled by glucose carbon catabolite repression. Furthermore, this study showed that the Impranil-degrading activity of many other
Pseudomonas
strains could be influenced by different carbon sources. This work shed light on the carbon source regulation of PU degradation activity among pseudomonads and identified the polyurethane lipases in
P. protegens
.
Multivalent Chromosomal Expression of the Clostridium botulinum Serotype A Neurotoxin Heavy-Chain Antigen and the Bacillus anthracis Protective Antigen in Lactobacillus acidophilus
Authors: O'Flaherty Sarah , Klaenhammer Todd R. 
Published: August 2016

ABSTRACT

Clostridium botulinum
and
Bacillus anthracis
produce potent toxins that cause severe disease in humans. New and improved vaccines are needed for both of these pathogens. For mucosal vaccine delivery using lactic acid bacteria, chromosomal expression of antigens is preferred over plasmid-based expression systems, as chromosomal expression circumvents plasmid instability and the need for antibiotic pressure. In this study, we constructed three strains of
Lactobacillus acidophilus
NCFM expressing from the chromosome (i) the nontoxic host receptor-binding domain of the heavy chain of
Clostridium botulinum
serotype A neurotoxin (BoNT/A-Hc), (ii) the anthrax protective antigen (PA), and (iii) both the BoNT/A-Hc and the PA. The BoNT/A-Hc vaccine cassette was engineered to contain the signal peptide from the S-layer protein A from
L. acidophilus
and a dendritic-cell-targeting peptide. A chromosomal region downstream of
lba0889
carrying a highly expressed enolase gene was selected for insertion of the vaccine cassettes. Western blot analysis confirmed the heterologous expression of the two antigens from plasmid and chromosome locations. Stability assays demonstrated loss of the vaccine cassettes from expression plasmids without antibiotic maintenance. RNA sequencing showed high expression of each antigen and that insertion of the vaccine cassettes had little to no effect on the transcription of other genes in the chromosome. This study demonstrated that chromosomal integrative recombinant strains are promising vaccine delivery vehicles when targeted into high-expression chromosomal regions. Levels of expression match high-copy-number plasmids and eliminate the requirement for antibiotic selective maintenance of recombinant plasmids.

IMPORTANCE
Clostridium botulinum
and
Bacillus anthracis
produce potent neurotoxins that pose a biochemical warfare concern; therefore, effective vaccines against these bacteria are required. Chromosomal expression of antigens is preferred over plasmid-based expression systems since expressing antigens from a chromosomal location confers an advantage to the vaccine strains by eliminating the antibiotic maintenance required for plasmids and negates issues with plasmid instability that would result in loss of the antigen. Lactic acid bacteria, including
Lactobacillus acidophilus
, have shown potential for mucosal vaccine delivery, as
L. acidophilus
is bile and acid tolerant, allowing transit through the gastrointestinal tract where cells interact with host epithelial and immune cells, including dendritic cells. In this study, we successfully expressed
C. botulinum
and
B. anthracis
antigens in the probiotic
L. acidophilus
strain NCFM. Both antigens were highly expressed individually or in tandem from the chromosome of
L. acidophilus
.