bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of infection and sepsis in the Brazilian Network for Surveillance of Severe Maternal Morbidity
Authors: Pfitscher L. C. , Cecatti J. G. , Haddad S. M. , Parpinelli M. A. , Souza J. P. , Quintana S. M. , Surita F. G. , Costa M. L. ,   the Brazilian Network for Surveillance of Severe Maternal Morbidity Study Group
Published: November 2015

AbstractObjectiveTo identify the burden of severe infection within the Brazilian Network for Surveillance of Severe Maternal Morbidity and factors associated with worse maternal outcomes.MethodsThis was a multicentre cross‐sectional study involving 27 referral maternity hospitals in Brazil. WHO′s standardised criteria for potentially life‐threatening conditions and maternal near miss were used to identify cases through prospective surveillance and the main cause of morbidity was identified as infection or other causes (hypertension, haemorrhage or clinical/surgical). Complications due to infection were compared to complications due to the remaining causes of morbidity. Factors associated with a severe maternal outcome were assessed for the cases of infection.ResultsA total of 502 (5.3%) cases of maternal morbidity were associated with severe infection vs. 9053 cases (94.7%) with other causes. Considering increased severity of cases, infection was responsible for one‐fourth of all maternal near miss (23.6%) and nearly half (46.4%) of maternal deaths, with a maternal near miss to maternal death ratio three times (2.8:1) that of cases without infection (7.8:1) and a high mortality index (26.3%). Within cases of infection, substandard care was present in over one half of the severe maternal outcome cases. Factors independently associated with worse maternal outcomes were HIV/AIDS, hysterectomy, prolonged hospitalisation, intensive care admission and delays in medical care.ConclusionsInfection is an alarming cause of maternal morbidity and mortality and timely diagnosis and adequate management are key to improving outcomes during pregnancy. Delays should be addressed, risk factors identified, and specific protocols of surveillance and care developed for use during pregnancy.
MYBD employed by HY5 increases anthocyanin accumulation via repression of MYBL2 in Arabidopsis
Authors: Nguyen Nguyen Hoai , Jeong Chan Young , Kang Geun‐Ho , Yoo Sang‐Dong , Hong Suk‐Whan , Lee Hojoung 
Published: November 2015

SummaryPhotomorphogenesis is an essential program in plant development. This process is effected by the balanced cooperation of many factors under light and dark conditions. In a previous study, we showed that MYB hypocotyl elongation‐related (MYBH) is involved in cell elongation. To expand our understanding of MYBH function, we performed a yeast two‐hybrid assay and identified an MYB‐like Domain transcription factor (MYBD). In this study, we investigated the function of MYBD, which is an MYBH homolog involved in anthocyanin accumulation. MYBD expression increased in response to light or cytokinin, and MYBD enhanced anthocyanin biosynthesis via repression of MYBL2, which encodes a transcription factor that has a negative effect on this process. In addition, MYBD binding in vivo to the MYBL2 promoter and the lower level of histone H3K9 acetylation at the upstream region of MYBL2 in MYBD over‐expressing plants in comparison with wild‐type plants imply that MYBD represses MYBL2 expression via an epigenetic mechanism. HY5 directly binds to the MYBD promoter, which indicates that MYBD acts on HY5‐downstream in light‐ or cytokinin‐triggered signaling pathways, leading to anthocyanin accumulation. Our results suggest that, although MYBD and MYBH are homologs, they act in opposite ways during plant photomorphogenesis, and these functions should be examined in further studies.
Characterisation of a Novel Pulsating Heat Pipe Cooler for Power Electronics at Extreme Ambient Temperatures
Authors: Torresin Daniele , Habert Mathieu , Mounier Violette , Agostini Francesco , Agostini Bruno 
Published: November 2015

A compact and low cost pulsating heat pipe cooler (PHP) based on automotive technology is presented. This technology uses numerous aluminium MultiPort Extruded (MPE) tubes with capillary sized channels disposed in parallel to achieve the desired compactness. The sub-channels of the MPEs are connected in a serpentine manner by means of fluid distribution elements integrated in the evaporator and condenser manifolds. This configuration enables the oscillation of liquid slugs and elongated bubbles between the evaporator and the condenser areas.
In the present paper the experimental results of an open loop type PHP with refrigerants fluids R134a and R245fa are presented. Tests have been carried out for air temperatures ranging between −60 and 60 °C at a fixed air flow rate of 480 m3/h and heat loads from 3 to 13 W/cm2. The experimental results show the different thermo-physical properties effect of the two tested fluids on the cooler performances: R134a is more adapted to low saturation temperature than R245fa and the contrary has been observed at high saturation temperatures. This is due to the fact that R245fa reaches its viscous limit at low temperatures while at high temperatures R134a reaches its critical temperature.
Condensation Heat Transfer Characteristics on the Outside of Horizontal Smooth, Herringbone and Enhanced Surface 1EHT Tubes
Authors: Zhou Xiao-peng , Kukulka David J. , Li Jing , Sun Jian-Jun , Li Wei 
Published: November 2015

Heat transfer enhancement plays an important role in improving energy efficiency and developing high performance thermal systems. Phase-change heat transfer processes take place in thermal systems; typically heat transfer enhanced tubes are used in these systems and they are designed to increase heat transfer coefficients in evaporation and condensation. Enhanced heat transfer tubes are widely used in refrigeration and air-conditioning applications in order to reduce cost and create a smaller footprint of the application.
Microfins, roughness and dimples are often incorporated into the inner surface of tubes in order to enhance heat transfer performance. Under many conditions, enhanced surface tubes can recover more energy and provide the opportunity to advance the design of many heat transfer products.
Convective condensation heat transfer and pressure loss characteristics were investigated for R410A on the outside of: (i) a smooth tube (outer diameter 12.7 mm); (ii) an external herringbone tube (fin root diameter 12.7 mm); and (iii) the 1EHT tube (outer diameter 12.7 mm) for very low mass fluxes. Data was obtained for values of mass flux ranging from 8 to 50 kg/(m2 s); at a saturation temperature of 318 K; with an inlet quality of 0.8 (±0.05) and an outlet quality of 0.1 (±0.05). In a comparison of heat transfer at a low mass flux, both the 1EHT tube and the herringbone tube did not perform as well as the smooth tube. And it’s difficult to analyze the reason for this strange phenomenon.
Electrowetting on Dielectric (EWOD) Assisted Droplet Desiccation
Authors: Greyson Marcette , Dunning Peter D. , Schertzer Michael J. 
Published: November 2015

Abstract
Lab-on-a-chip (LOAC) devices are emerging technologies that aim to perform all of the laboratory functions of traditional diagnostic tests on single microchips. Microarrays are one promising type of LOAC device that consist of an array of droplets for testing tens to thousands of samples simultaneously. Microarrays are commonly used in gene sequencing, pathogen detection, determining microbial resistances, and conducting enzyme-linked immunosorbent assays (ELISAs). As droplets in these arrays dry, the majority of material within the droplet is deposited around the periphery. This phenomenon is referred to as the coffee stain effect. The non-uniform depositions left by this effect can result in variation of fluorescence intensity measurements in automated vision systems. A means of producing more uniform particle depositions for the microscopy analysis would allow for more accurate test results.
One promising method for suppression of the coffee stain effect involves the use of electrowetting on dielectric (EWOD). EWOD devices apply an electrokinetic force at the three-phase contact line to manipulate the shape of a droplet interface. The Mugele group has already begun investigating EWOD’s effects on the coffee stain effect and found that an AC voltage applied to droplets on EWOD devices can suppress the coffee stain effect and produce smaller, more uniform droplet deposition patterns.
This work presents (i) a method to characterize the deposition pattern left by a desiccated droplet as a function of radial position and (ii) a discussion of the microfabrication technique used to create devices to perform EWOD assisted desiccation for both AC and DC voltages.
Iron Modulates Butyrate Production by a Child Gut Microbiota
In Vitro
Authors: Dostal Alexandra , Lacroix Christophe , Bircher Lea , Pham Van Thanh , Follador Rainer , Zimmermann Michael Bruce , Chassard Christophe 
Published: November 2015

ABSTRACT

The aim of this study was to investigate the effect of iron (Fe) availability on butyrate production in the complex bacterial ecosystem of the human gut. Hence, different Fe availabilities were mimicked in an
in vitro
colonic fermentation model (the polyfermenter intestinal model called PolyFermS) inoculated with immobilized gut microbiota from a child and in batch cultures of the butyrate producer
Roseburia intestinalis
. Shifts in the microbial community (16S rRNA sequencing and quantitative PCR), metabolic activity (high-performance liquid chromatography), and expression of genes involved in butyrate production were assessed. In the PolyFermS, moderate Fe deficiency resulted in a 1.4-fold increase in butyrate production and a 5-fold increase in butyryl-coenzyme A (CoA):acetate CoA-transferase gene expression, while very strong Fe deficiency significantly decreased butyrate concentrations and butyrate-producing bacteria compared with the results under normal Fe conditions. Batch cultures of
R. intestinalis
grown in a low-Fe environment preferentially produced lactate and had reduced butyrate and hydrogen production, in parallel with upregulation of the lactate dehydrogenase gene and downregulation of the pyruvate:ferredoxin-oxidoreductase gene. In contrast, under high-Fe conditions,
R. intestinalis
cultures showed enhanced butyrate and hydrogen production, along with increased expression of the corresponding genes, compared with the results under normal-Fe conditions. Our data reveal the strong regulatory effect of Fe on gut microbiota butyrate producers and on the concentrations of butyrate, which contributes to the maintenance of host gut health.

IMPORTANCE
Fe deficiency is one of the most common nutritional deficiencies worldwide and can be corrected by Fe supplementation. In this
in vitro
study, we show that environmental Fe concentrations in a continuous gut fermentation model closely mimicking a child's gut microbiota strongly affect the composition of the gut microbiome and its metabolic activity, particularly butyrate production. The differential expression of genes involved in the butyrate production pathway under different Fe conditions and the enzyme cofactor role of Fe explain the observed modulation of butyrate production. Our data reveal that the level of dietary Fe reaching the colon affects the microbiome, and its essential function of providing the host with beneficial butyrate.
RNA Futile Cycling in Model Persisters Derived from MazF Accumulation
Authors: Mok Wendy W. K. , Park Junyoung O. , Rabinowitz Joshua D. , Brynildsen Mark P. 
Published: November 2015

ABSTRACT

Metabolism plays an important role in the persister phenotype, as evidenced by the number of strategies that perturb metabolism to sabotage this troublesome subpopulation. However, the absence of techniques to isolate high-purity populations of native persisters has precluded direct measurement of persister metabolism. To address this technical challenge, we studied
Escherichia coli
populations whose growth had been inhibited by the accumulation of the MazF toxin, which catalyzes RNA cleavage, as a model system for persistence. Using chromosomally integrated, orthogonally inducible promoters to express MazF and its antitoxin MazE, bacterial populations that were almost entirely tolerant to fluoroquinolone and β-lactam antibiotics were obtained upon MazF accumulation, and these were subjected to direct metabolic measurements. While MazF model persisters were nonreplicative, they maintained substantial oxygen and glucose consumption. Metabolomic analysis revealed accumulation of all four ribonucleotide monophosphates (NMPs). These results are consistent with a MazF-catalyzed RNA futile cycle, where the energy derived from catabolism is dissipated through continuous transcription and MazF-mediated RNA degradation. When transcription was inhibited, oxygen consumption and glucose uptake decreased, and nucleotide triphosphates (NTPs) and NTP/NMP ratios increased. Interestingly, the MazF-inhibited cells were sensitive to aminoglycosides, and this sensitivity was blocked by inhibition of transcription. Thus, in MazF model persisters, futile cycles of RNA synthesis and degradation result in both significant metabolic demands and aminoglycoside sensitivity.

IMPORTANCE
Metabolism plays a critical role in controlling each stage of bacterial persistence (shutdown, stasis, and reawakening). In this work, we generated an
E. coli
strain in which the MazE antitoxin and MazF toxin were artificially and independently inducible, and we used this strain to generate model persisters and study their metabolism. We found that even though growth of the model persisters was inhibited, they remained highly metabolically active. We further uncovered a futile cycle driven by continued transcription and MazF-mediated transcript degradation that dissipated the energy derived from carbon catabolism. Interestingly, the existence of this futile cycle acted as an Achilles’ heel for MazF model persisters, rendering them vulnerable to killing by aminoglycosides.
Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone
Authors: Forde Brian M. , Phan Minh-Duy , Gawthorne Jayde A. , Ashcroft Melinda M. , Stanton-Cook Mitchell , Sarkar Sohinee , Peters Kate M. , Chan Kok-Gan , Chong Teik Min , Yin Wai-Fong , Upton Mathew , Schembri Mark A. , Beatson Scott A. 
Published: November 2015

ABSTRACT

Escherichia coli
sequence type 131 (ST131) is a clone of uropathogenic
E. coli
that has emerged rapidly and disseminated globally in both clinical and community settings. Members of the ST131 lineage from across the globe have been comprehensively characterized in terms of antibiotic resistance, virulence potential, and pathogenicity, but to date nothing is known about the methylome of these important human pathogens. Here we used single-molecule real-time (SMRT) PacBio sequencing to determine the methylome of
E. coli
EC958, the most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081 methylated adenines in the genome of EC958 discovered three
m6
A methylation motifs that have not been described previously. Subsequent SMRT sequencing of isogenic knockout mutants identified the two type I methyltransferases (MTases) and one type IIG MTase responsible for
m6
A methylation of novel recognition sites. Although both type I sites were rare, the type IIG sites accounted for more than 12% of all methylated adenines in EC958. Analysis of the distribution of MTase genes across 95 ST131 genomes revealed their prevalence is highly conserved within the ST131 lineage, with most variation due to the presence or absence of mobile genetic elements on which individual MTase genes are located.

IMPORTANCE
DNA modification plays a crucial role in bacterial regulation. Despite several examples demonstrating the role of methyltransferase (MTase) enzymes in bacterial virulence, investigation of this phenomenon on a whole-genome scale has remained elusive until now. Here we used single-molecule real-time (SMRT) sequencing to determine the first complete methylome of a strain from the multidrug-resistant
E. coli
sequence type 131 (ST131) lineage. By interrogating the methylome computationally and with further SMRT sequencing of isogenic mutants representing previously uncharacterized MTase genes, we defined the target sequences of three novel ST131-specific MTases and determined the genomic distribution of all MTase target sequences. Using a large collection of 95 previously sequenced ST131 genomes, we identified mobile genetic elements as a major factor driving diversity in DNA methylation patterns. Overall, our analysis highlights the potential for DNA methylation to dramatically influence gene regulation at the transcriptional level within a well-defined
E. coli
clone.
Cryptococcus gattii in the Age of Whole-Genome Sequencing
Authors: Meyer Wieland 
Published: November 2015

ABSTRACT

Cryptococcus gattii
, the sister species of
Cryptococcus neoformans
, is an emerging pathogen which gained importance in connection with the ongoing cryptococcosis outbreak on Vancouver Island. Many molecular studies have divided this species into for major lineages: VGI, VGII, VGIII, and VGIV. This commentary summarizes the whole-genome sequencing (WGS) studies that have been carried out with this species, re-emphasizing the phylogenetic relationships, showing chromosomal rearrangements between those four groups, and identifying VGII as ancestral population within
C. gattii
. In addition, WGS specific to VGII, containing the Vancouver Island outbreak genotypes and those from the Pacific Northwest region of the United States, has placed the origin of this lineage within South America and identified specific genes responsible for either brain or lung infection. It also showed, that many genotypes are spread across a number of different continents, as has been previously shown by multilocus sequence typing (MLST). In addition, it showed that recombination occurs more frequently between mitochondrial than nuclear genomes.
Posttranslational Modification of HOIP Blocks Toll-Like Receptor 4-Mediated Linear-Ubiquitin-Chain Formation
Authors: Bowman James , Rodgers Mary A. , Shi Mude , Amatya Rina , Hostager Bruce , Iwai Kazuhiro , Gao Shou-Jiang , Jung Jae U. 
Published: November 2015

ABSTRACT
Linear ubiquitination is an atypical posttranslational modification catalyzed by the linear-ubiquitin-chain assembly complex (LUBAC), containing HOIP, HOIL-1L, and Sharpin. LUBAC facilitates NF-κB activation and inflammation upon receptor stimulation by ligating linear ubiquitin chains to critical signaling molecules. Indeed, linear-ubiquitination-dependent signaling is essential to prevent pyogenic bacterial infections that can lead to death. While linear ubiquitination is essential for intracellular receptor signaling upon microbial infection, this response must be measured and stopped to avoid tissue damage and autoimmunity. While LUBAC is activated upon bacterial stimulation, the mechanisms regulating LUBAC activity in response to bacterial stimuli have remained elusive. We demonstrate that LUBAC activity itself is downregulated through ubiquitination, specifically, ubiquitination of the catalytic subunit HOIP at the carboxyl-terminal lysine 1056. Ubiquitination of Lys1056 dynamically altered HOIP conformation, resulting in the suppression of its catalytic activity. Consequently, HOIP Lys1056-to-Arg mutation led not only to persistent LUBAC activity but also to prolonged NF-κB activation induced by bacterial lipopolysaccharide-mediated Toll-like receptor 4 (TLR4) stimulation, whereas it showed no effect on NF-κB activation induced by CD40 stimulation. This study describes a novel posttranslational regulation of LUBAC-mediated linear ubiquitination that is critical for specifically directing TLR4-mediated NF-κB activation.

IMPORTANCE
Posttranslational modification of proteins enables cells to respond quickly to infections and immune stimuli in a tightly controlled manner. Specifically, covalent modification of proteins with the small protein ubiquitin is essential for cells to initiate and terminate immune signaling in response to bacterial and viral infection. This process is controlled by ubiquitin ligase enzymes, which themselves must be regulated to prevent persistent and deleterious immune signaling. However, how this regulation is achieved is poorly understood. This paper reports a novel ubiquitination event of the atypical ubiquitin ligase HOIP that is required to terminate bacterial lipopolysaccharide (LPS)-induced TLR4 immune signaling. Ubiquitination causes the HOIP ligase to undergo a conformational change, which blocks its enzymatic activity and ultimately terminates LPS-induced TLR4 signaling. These findings provide a new mechanism for controlling HOIP ligase activity that is vital to properly regulate a proinflammatory immune response.
What's in a name? The challenge of describing interventions in systematic reviews: analysis of a random sample of reviews of non-pharmacological stroke interventions
Authors: Hoffmann Tammy C , Walker Marion F , Langhorne Peter , Eames Sally , Thomas Emma , Glasziou Paul 
Published: November 2015

ObjectiveTo assess, in a sample of systematic reviews of non-pharmacological interventions, the completeness of intervention reporting, identify the most frequently missing elements, and assess review authors’ use of and beliefs about providing intervention information.DesignAnalysis of a random sample of systematic reviews of non-pharmacological stroke interventions; online survey of review authors.Data sources and study selectionThe Cochrane Library and PubMed were searched for potentially eligible systematic reviews and a random sample of these assessed for eligibility until 60 (30 Cochrane, 30 non-Cochrane) eligible reviews were identified.Data collectionIn each review, the completeness of the intervention description in each eligible trial (n=568) was assessed by 2 independent raters using the Template for Intervention Description and Replication (TIDieR) checklist. All review authors (n=46) were invited to complete a survey.ResultsMost reviews were missing intervention information for the majority of items. The most incompletely described items were: modifications, fidelity, materials, procedure and tailoring (missing from all interventions in 97%, 90%, 88%, 83% and 83% of reviews, respectively). Items that scored better, but were still incomplete for the majority of reviews, were: ‘when and how much’ (in 31% of reviews, adequate for all trials; in 57% of reviews, adequate for some trials); intervention mode (in 22% of reviews, adequate for all trials; in 38%, adequate for some trials); and location (in 19% of reviews, adequate for all trials). Of the 33 (71%) authors who responded, 58% reported having further intervention information but not including it, and 70% tried to obtain information.ConclusionsMost focus on intervention reporting has been directed at trials. Poor intervention reporting in stroke systematic reviews is prevalent, compounded by poor trial reporting. Without adequate intervention descriptions, the conduct, usability and interpretation of reviews are restricted and therefore, require action by trialists, systematic reviewers, peer reviewers and editors.