bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation and calibration of mobile phones for noise monitoring application
Authors: Ventura Raphaël , Mallet Vivien , Issarny Valérie , Raverdy Pierre-Guillaume , Rebhi Fadwa
Published: November 2017

The increasing number and quality of sensors integrated in mobile phones have paved the way for sensing schemes driven by city dwellers. The sensing quality can drastically depend on the mobile phone, and appropriate calibration strategies are needed. This paper evaluates the quality of noise measurements acquired by a variety of Android phones. The Ambiciti application was developed so as to acquire a larger control over the acquisition process. Pink and narrowband noises were used to evaluate the phones' accuracy at levels ranging from background noise to 90 dB(A) inside the lab. Conclusions of this evaluation lead to the proposition of a calibration strategy that has been embedded in Ambiciti and applied to more than 50 devices during public events. A performance analysis addressed the range, accuracy, precision, and reproducibility of measurements. After identification and removal of a bias, the measurement error standard deviation is below 1.2 dB(A) within a wide range of noise levels [45 to 75 dB(A)], for 12 out of 15 phones calibrated in the lab. In the perspective of citizens-driven noise sensing, in situ experiments were carried out, while additional tests helped to produce recommendations regarding the sensing context (grip, orientation, moving speed, mitigation, frictions, wind).
Generation of 1/f noise from a broken-symmetry model for the arbitrary absolute pitch of musical melodies
Authors: Grant Martin , Faghihi Niloufar
Published: November 2017

A model is presented to generate power spectrum noise with intensity proportional to 1/f  as a function of frequency f. The model arises from a broken-symmetry variable, which corresponds to absolute pitch, where fluctuations occur in an attempt to restore that symmetry, influenced by interactions in the creation of musical melodies.
glnA
Truncation in Salmonella enterica Results in a Small Colony Variant Phenotype, Attenuated Host Cell Entry, and Reduced Expression of Flagellin and SPI-1-Associated Effector Genes
Authors: Aurass Philipp , Düvel Juliane , Karste Susanne , Nübel Ulrich , Rabsch Wolfgang , Flieger Antje
Published: November 2017

Many pathogenic bacteria use sophisticated survival strategies to overcome harsh environmental conditions. One strategy is the formation of slow-growing subpopulations termed small colony variants (SCVs). Here we characterize an SCV that spontaneously emerged from an axenic
Salmonella enterica
serovar Typhimurium water culture. We found that the SCV harbored a frameshift mutation in the glutamine synthetase gene
glnA
, leading to an ∼90% truncation of the corresponding protein. Glutamine synthetase, a central enzyme in nitrogen assimilation, converts glutamate and ammonia to glutamine. Glutamine is an important nitrogen donor that is required for the synthesis of cellular compounds. The internal glutamine pool serves as an indicator of nitrogen availability in
Salmonella
. In our study, the SCV and a constructed
glnA
knockout mutant showed reduced growth rates, compared to the wild type. Moreover, the SCV and the
glnA
mutant displayed attenuated entry into host cells and severely reduced levels of exoproteins, including flagellin and several
Salmonella
pathogenicity island 1 (SPI-1)-dependent secreted virulence factors. We found that these proteins were also depleted in cell lysates, indicating their diminished synthesis. Accordingly, the SCV and the
glnA
mutant had severely decreased expression of flagellin genes, several SPI-1 effector genes, and a class 2 motility gene (
flgB
). However, the expression of a class 1 motility gene (
flhD
) was not affected. Supplementation with glutamine or genetic reversion of the
glnA
truncation restored growth, cell entry, gene expression, and protein abundance. In summary, our data show that
glnA
is essential for the growth of
S. enterica
and controls important motility- and virulence-related traits in response to glutamine availability.

IMPORTANCE
Salmonella enterica
serovar Typhimurium is a significant pathogen causing foodborne infections. Here we describe an
S
. Typhimurium small colony variant (SCV) that spontaneously emerged from a long-term starvation experiment in water. It is important to study SCVs because (i) SCVs may arise spontaneously upon exposure to stresses, including environmental and host defense stresses, (ii) SCVs are slow growing and difficult to eradicate, and (iii) only a few descriptions of
S. enterica
SCVs are available. We clarify the genetic basis of the SCV described here as a frameshift mutation in the glutamine synthetase gene
glnA
, leading to glutamine auxotrophy. In
Salmonella
, internal glutamine limitation serves as a sign of external nitrogen deficiency and is thought to regulate cell growth. In addition to exhibiting impaired growth, the SCV showed reduced host cell entry and reduced expression of SPI-1 virulence and flagellin genes.
Temporal Stability of Escherichia coli Concentrations in Waters of Two Irrigation Ponds in Maryland
Authors: Pachepsky Yakov , Kierzewski Rachel , Stocker Matthew , Sellner Kevin , Mulbry Walter , Lee Hoonsoo , Kim Moon
Published: November 2017

Fecal contamination of water sources is an important water quality issue for agricultural irrigation ponds.
Escherichia coli
concentrations are commonly used to evaluate recreational and irrigation water quality. We hypothesized that there may exist temporally stable spatial patterns of
E. coli
concentrations across ponds, meaning that some areas mostly have higher and other areas mostly lower than average concentrations of
E. coli
. To test this hypothesis, we sampled two irrigation ponds in Maryland at nodes of spatial grids biweekly during the summer of 2016. Environmental covariates—temperature, turbidity, conductivity, pH, dissolved oxygen, chlorophyll
a
, and nutrients—were measured in conjunction with
E. coli
concentrations. Temporal stability was assessed using mean relative differences between measurements in each location and averaged measurements across ponds. Temporally stable spatial patterns of
E. coli
concentrations and the majority of environmental covariates were expressed for both ponds. In the pond interior, larger relative mean differences in chlorophyll
a
corresponded to smaller mean relative differences in
E. coli
concentrations, with a Spearman's rank correlation coefficient of 0.819. Turbidity and ammonium concentrations were the two other environmental covariates with the largest positive correlations between their location ranks and the
E. coli
concentration location ranks. Tenfold differences were found between geometric mean
E. coli
concentrations in locations that were consistently high or consistently low. The existence of temporally stable patterns of
E. coli
concentrations can affect the results of microbial water quality assessment in ponds and should be accounted for in microbial water quality monitoring design.

IMPORTANCE
The microbial quality of water in irrigation water sources must be assessed to prevent the spread of microbes that can cause disease in humans because of produce consumption. The microbial quality of irrigation water is evaluated based on concentrations of
Escherichia coli
as the indicator organism. Given the high spatial and temporal variability of
E. coli
concentrations in irrigation water sources, recommendations are needed on where and when samples of water have to be taken for microbial analysis. This work demonstrates the presence of a temporally stable spatial pattern in the distributions of
E. coli
concentrations across irrigation ponds. The ponds studied had zones where
E. coli
concentrations were mostly higher than average and zones where the concentrations were mostly lower than average over the entire observation period, covering the season when water was used for irrigation. Accounting for the existence of such zones will improve the design and implementation of microbial water quality monitoring.
Differential RNA Sequencing Implicates Sulfide as the Master Regulator of S
0
Metabolism in Chlorobaculum tepidum and Other Green Sulfur Bacteria
Authors: Hilzinger Jacob M. , Raman Vidhyavathi , Shuman Kevin E. , Eddie Brian J. , Hanson Thomas E.
Published: November 2017

The green sulfur bacteria (
Chlorobiaceae
) are anaerobes that use electrons from reduced sulfur compounds (sulfide, S
0
, and thiosulfate) as electron donors for photoautotrophic growth.
Chlorobaculum tepidum
, the model system for the
Chlorobiaceae
, both produces and consumes extracellular S
0
globules depending on the availability of sulfide in the environment. These physiological changes imply significant changes in gene regulation, which has been observed when sulfide is added to
Cba. tepidum
growing on thiosulfate. However, the underlying mechanisms driving these gene expression changes, i.e., the specific regulators and promoter elements involved, have not yet been defined. Here, differential RNA sequencing (dRNA-seq) was used to globally identify transcript start sites (TSS) that were present during growth on sulfide, biogenic S
0
, and thiosulfate as sole electron donors. TSS positions were used in combination with RNA-seq data from cultures growing on these same electron donors to identify both basal promoter elements and motifs associated with electron donor-dependent transcriptional regulation. These motifs were conserved across homologous
Chlorobiaceae
promoters. Two lines of evidence suggest that sulfide-mediated repression is the dominant regulatory mode in
Cba. tepidum
. First, motifs associated with genes regulated by sulfide overlap key basal promoter elements. Second, deletion of the
Cba. tepidum
1277
(
CT1277
) gene, encoding a putative regulatory protein, leads to constitutive overexpression of the sulfide:quinone oxidoreductase CT1087 in the absence of sulfide. The results suggest that sulfide is the master regulator of sulfur metabolism in
Cba. tepidum
and the
Chlorobiaceae
. Finally, the identification of basal promoter elements with differing strengths will further the development of synthetic biology in
Cba. tepidum
and perhaps other
Chlorobiaceae
.

IMPORTANCE
Elemental sulfur is a key intermediate in biogeochemical sulfur cycling. The photoautotrophic green sulfur bacterium
Chlorobaculum tepidum
either produces or consumes elemental sulfur depending on the availability of sulfide in the environment. Our results reveal transcriptional dynamics of
Chlorobaculum tepidum
on elemental sulfur and increase our understanding of the mechanisms of transcriptional regulation governing growth on different reduced sulfur compounds. This report identifies genes and sequence motifs that likely play significant roles in the production and consumption of elemental sulfur. Beyond this focused impact, this report paves the way for the development of synthetic biology in
Chlorobaculum tepidum
and other
Chlorobiaceae
by providing a comprehensive identification of promoter elements for control of gene expression, a key element of strain engineering.
Cry64Ba and Cry64Ca, Two ETX/MTX2-Type Bacillus thuringiensis Insecticidal Proteins Active against Hemipteran Pests
Authors: Liu Yonglei , Wang Yinglong , Shu Changlong , Lin Kejian , Song Fuping , Bravo Alejandra , Soberón Mario , Zhang Jie
Published: November 2017

Genetically modified crops that express insecticidal
Bacillus thuringiensis
(Bt) proteins have become a primary approach for control of lepidopteran (moth) and coleopteran (beetle) pests that feed by chewing the plants. However, the sap-sucking insects (Hemiptera) are not particularly susceptible to Bt toxins. In this study, we describe two Cry toxins (Cry64Ba and Cry64Ca) from Bt strain 1012 that showed toxicity against two important hemipteran rice pests,
Laodelphax striatellus
and
Sogatella furcifera
. Both of these proteins contain an ETX/MTX2 domain and share common sequence features with the β-pore-forming toxins. Coexpression of
cry64Ba
and
cry64Ca
genes in the acrystalliferous Bt strain HD73
−
resulted in high insecticidal activity against both hemipteran pests. No toxicity was observed on other pests such as
Ostrinia furnacalis
,
Plutella xylostella
, or
Colaphellus bowringi
. Also, no hemolytic activity or toxicity against cancer cells was detected. Binding assays showed specific binding of the Cry64Ba/Cry64Ca toxin complex to brush border membrane vesicles isolated from
L. striatellus
. Cry64Ba and Cry64Ca are Bt Cry toxins highly effective against hemipteran pests and could provide a novel strategy for the environmentally friendly biological control of rice planthoppers in transgenic plants.

IMPORTANCE
In Asia, rice is an important staple food, whose production is threatened by rice planthoppers. To date, no effective
Bacillus thuringiensis
(Bt) protein has been shown to have activity against rice planthoppers. We cloned two Bt toxin genes from Bt strain 1012 that showed toxicity against small brown planthoppers (
Laodelphax striatellus
) and white-backed planthoppers (
Sogatella furcifera
). To our knowledge, the proteins encoded by the
cry64Ba
and
cry64Ca
genes are the most efficient insecticidal Bt Cry proteins with activity against hemipteran insects reported so far. Cry64Ba and Cry64Ca showed no toxicity against some lepidopteran or coleopteran pests. These two proteins should be able to be used for integrated hemipteran pest management.
Diversity of Three-Dimensional Structures and Catalytic Mechanisms of Alginate Lyases
Authors: Xu Fei , Wang Peng , Zhang Yu-Zhong , Chen Xiu-Lan
Published: November 2017

Alginate is a linear polysaccharide produced mainly by brown algae in marine environments. Alginate consists of a linear block copolymer made up of two monomeric units, β-
d
-mannuronate (M) and its C-5 epimer α-
l
-guluronate (G). Alginate lyases are polysaccharide lyases (PL) that degrade alginate via a β-elimination reaction. These enzymes play an important role in marine carbon recycling and also have widespread industrial applications. So far, more than 1,774 alginate lyase sequences have been identified and are distributed into 7 PL families. In this review, the folds, conformational changes during catalysis, and catalytic mechanisms of alginate lyases are described. Thus far, structures for 15 alginate lyases have been solved and are divided into 3 fold classes: the β-jelly roll class (PL7, -14, and -18), the (α/α)n toroid class (PL5, -15, and -17), and the β-helix fold (PL6). These enzymes adopt two different mechanisms for catalysis, and three kinds of conformational changes occur during this process. Moreover, common features in the structures, conformational changes, and catalytic mechanisms are summarized, providing a comprehensive understanding on alginate lyases.
High Prevalence and Genetic Diversity of Large phiCD211 (phiCDIF1296T)-Like Prophages in Clostridioides difficile
Authors: Garneau Julian R. , Sekulovic Ognjen , Dupuy Bruno , Soutourina Olga , Monot Marc , Fortier Louis-Charles
Published: November 2017

Clostridioides difficile
(formerly
Clostridium difficile
) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified in
C. difficile
so far, with a genome of 131 kbp. It shares morphological and genomic similarity with other large siphophages, like phage 949, infecting
Lactococcus lactis
, and phage c-st, infecting
Clostridium botulinum
. A PhageTerm analysis indicated the presence of 378-bp direct terminal repeats at the phiCD211 genome termini. Among striking features of phiCD211, the presence of several transposase and integrase genes suggests past recombination events with other mobile genetic elements. Several gene products potentially influence the bacterial lifestyle and fitness, including a putative AcrB/AcrD/AcrF multidrug resistance protein, an EzrA septation ring formation regulator, and a spore protease. We also identified a CRISPR locus and a
cas3
gene. We screened 2,584
C. difficile
genomes available and detected 149 prophages sharing ≥80% nucleotide identity with phiCD211 (5% prevalence). Overall, phiCD211-like phages were detected in
C. difficile
strains corresponding to 21 different multilocus sequence type groups, showing their high prevalence. Comparative genomic analyses revealed the existence of several clusters of highly similar phiCD211-like phages. Of note, large chromosome inversions were observed in some members, as well as multiple gene insertions and module exchanges. This highlights the great plasticity and gene coding potential of the phiCD211/phiCDIF1296T genome. Our analyses also suggest active evolution involving recombination with other mobile genetic elements.

IMPORTANCE
Clostridioides difficile
is a clinically important pathogen representing a serious threat to human health. Our hypothesis is that genetic differences between strains caused by the presence of integrated prophages could explain the apparent differences observed in the virulence of different
C. difficile
strains. In this study, we provide a full characterization of phiCD211, also known as phiCDIF1296T, the largest phage known to infect
C. difficile
so far. Screening 2,584
C. difficile
genomes revealed the presence of highly similar phiCD211-like phages in 5% of the strains analyzed, showing their high prevalence. Multiple-genome comparisons suggest that evolution of the phiCD211-like phage community is dynamic, and some members have acquired genes that could influence bacterial biology and fitness. Our study further supports the relevance of studying phages in
C. difficile
to better understand the epidemiology of this clinically important human pathogen.
Loop of Streptomyces Feruloyl Esterase Plays an Important Role in the Enzyme's Catalyzing the Release of Ferulic Acid from Biomass
Authors: Uraji Misugi , Tamura Haruka , Mizohata Eiichi , Arima Jiro , Wan Kun , Ogawa Ken'ichi , Inoue Tsuyoshi , Hatanaka Tadashi
Published: November 2017

Feruloyl esterases (FAEs) are key enzymes required for the production of ferulic acid from agricultural biomass. Previously, we identified and characterized R18, an FAE from
Streptomyces cinnamoneus
NBRC 12852, which showed no sequence similarity to the known FAEs. To determine the region involved in its catalytic activity, we constructed chimeric enzymes using R18 and its homolog (TH2-18) from
S. cinnamoneus
strain TH-2. Although R18 and TH2-18 showed 74% identity in their primary sequences, the recombinant proteins of these two FAEs (recombinant R18 [rR18] and rTH2-18) showed very different specific activities toward ethyl ferulate. By comparing the catalytic activities of the chimeras, a domain comprised of residues 140 to 154 was found to be crucial for the catalytic activity of R18. Furthermore, we analyzed the crystal structure of rR18 at a resolution of 1.5 Å to elucidate the relationship between its activity and its structure. rR18 possessed a typical catalytic triad, consisting of Ser-191, Asp-214, and His-268, which was characteristic of the serine esterase family. By structural analysis, the above-described domain was found to be present in a loop-like structure (the R18 loop), which possessed a disulfide bond conserved in the genus
Streptomyces
. Moreover, compared to rTH2-18 of its parental strain, the TH2-18 mutant, in which Pro and Gly residues were inserted into the domain responsible for forming the R18 loop, showed markedly high
k
cat
values using artificial substrates. We also showed that the FAE activity of TH2-18 toward corn bran, a natural substrate, was improved by the insertion of the Gly and Pro residues.

IMPORTANCE
Streptomyces
species are widely distributed bacteria that are predominantly present in soil and function as decomposers in natural environments. They produce various enzymes, such as carbohydrate hydrolases, esterases, and peptidases, which decompose agricultural biomass. In this study, based on the genetic information on two
Streptomyces cinnamoneus
strains, we identified novel feruloyl esterases (FAEs) capable of producing ferulic acid from biomass. These two FAEs shared high similarity in their amino acid sequences but did not resemblance any known FAEs. By comparing chimeric proteins and performing crystal structure analysis, we confirmed that a flexible loop was important for the catalytic activity of
Streptomyces
FAEs. Furthermore, we determined that the catalytic activity of one FAE was improved drastically by inserting only 2 amino acids into its loop-forming domain. Thus, differences in the amino acid sequence of the loop resulted in different catalytic activities. In conclusion, our findings provide a foundation for the development of novel enzymes for industrial use.
Draft Whole-Genome Sequences of 18
Flavobacterium
spp
Authors: Stine Cynthia B. , Li Cong , Crosby Tina C. , Hasbrouck Nicholas R. , Lam Claudia , Tadesse Daniel A.
Published: November 2017

We report here the draft whole-genome sequences for 18
Flavobacterium
species type strains that have historically been associated with fish gill disease.
Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages
Authors: Esplin Ian N. D. , Berg Jordan A. , Sharma Ruchira , Allen Robert C. , Arens Daniel K. , Ashcroft Cody R. , Bairett Shannon R. , Beatty Nolan J. , Bickmore Madeline , Bloomfield Travis J. , Brady T. Scott , Bybee Rachel N. , Carter John L. , Choi Minsey C. , Duncan Steven , Fajardo Christopher P. , Foy Brayden B. , Fuhriman David A. , Gibby Paul D. , Grossarth Savannah E. , Harbaugh Kala , Harris Natalie , Hilton Jared A. , Hurst Emily , Hyde Jonathan R. , Ingersoll Kayleigh , Jacobson Caitlin M. , James Brady D. , Jarvis Todd M. , Jaen-Anieves Daniella , Jensen Garrett L. , Knabe Bradley K. , Kruger Jared L. , Merrill Bryan D. , Pape Jenny A. , Payne Anderson Ashley M. , Payne David E. , Peck Malia D. , Pollock Samuel V. , Putnam Micah J. , Ransom Ethan K. , Ririe Devin B. , Robinson David M. , Rogers Spencer L. , Russell Kerri A. , Schoenhals Jonathan E. , Shurtleff Christopher A. , Simister Austin R. , Smith Hunter G. , Stephenson Michael B. , Staley Lyndsay A. , Stettler Jason M. , Stratton Mallorie L. , Tateoka Olivia B. , Tatlow P. J. , Taylor Alexander S. , Thompson Suzanne E. , Townsend Michelle H. , Thurgood Trever L. , Usher Brittian K. , Whitley Kiara V. , Ward Andrew T. , Ward Megan E. H. , Webb Charles J. , Wienclaw Trevor M. , Williamson Taryn L. , Wells Michael J. , Wright Cole K. , Breakwell Donald P. , Hope Sandra , Grose Julianne H.
Published: November 2017

Erwinia amylovora
is the causal agent of fire blight, a devastating disease affecting some plants of the
Rosaceae
family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of
E. amylovora
bacteriophages.
Complete Genome Sequence of a Psychrotolerant Denitrifying Bacterium,
Janthinobacterium svalbardensis
PAMC 27463
Authors: Cho Yong-Joon , Jung You-Jung , Hong Soon Gyu , Kim Ok-Sun
Published: November 2017

We report here the complete genome sequence of
Janthinobacterium svalbardensis
PAMC 27463 isolated from a freshwater lake on Barton Peninsula on King George Island, Antarctica. The genome consists of a chromosome with 6,274,078 bp which contains 5,585 genes, including 121 RNA genes.
Draft Genome Sequence and Annotation of the Apicomplexan Parasite
Besnoitia besnoiti
Authors: Schares Gereon , Venepally Pratap , Lorenzi Hernán A.
Published: November 2017

The apicomplexan parasite
Besnoitia besnoiti
is the causative agent of bovine besnoitiosis that affects livestock, particularly cattle. The definitive host of
B. besnoiti
is unknown and its transmission only partially understood. Here, we report the first draft genome sequence, assembly, and annotation of this parasite.
Draft Genome Sequence of Agrobacterium tumefaciens Biovar 1 Strain 186, Isolated from Walnut
Authors: Poret-Peterson Amisha T. , Bhatnagar Srijak , McClean Ali E. , Kluepfel Daniel A.
Published: November 2017

Agrobacterium tumefaciens
biovar 1 strain 186 was isolated from a walnut tree expressing crown gall symptoms. The draft genome sequence of this strain harbored genes for crown gall formation and will be useful for understanding its virulence on Paradox, the predominant hybrid rootstock used for the cultivation of English walnut in California.
Complete Genome Sequence of Xanthomonas campestris pv.
viticola
Strain CCRMXCV 80 from Brazil
Authors: Lima Nelson B. , Gama Marco A. S. , Mariano Rosa L. R. , Silva Wilson J. , Farias Antônio R. G. , Falcão Raul M. , Sousa-Paula Lucas C. , Benko-Iseppon Ana M. , Paiva Sérgio S. L. , Balbino Valdir Q. , Souza Elineide B.
Published: November 2017

Here, we report the complete 5.3-Mb genome sequence of
Xanthomonas campestris
pv.
viticola
(CCRMXCV 80), which causes grapevine (
Vitis vinifera
L.) bacterial canker. Genome data will improve our understanding of the strain’s comparative genomics and epidemiology, and help to further define plant protection and quarantine procedures.
Draft Genome Sequence of
Saccharomycopsis fodiens
CBS 8332, a Necrotrophic Mycoparasite with Biocontrol Potential
Authors: Junker Klara , Hesselbart Ana , Wendland Jürgen
Published: November 2017

Saccharomycopsis fodiens
is an ascomycetous necrotrophic mycoparasite. Predator-prey interaction leads to killing of the host cell by a penetration peg and utilization of cell content by the predator. Here, we report the 14.9-Mb
S. fodiens
draft genome sequence assembled into 9 large scaffolds and 13 minor scaffolds (<20 kb).
Whole-Genome Sequence of
Pantoea americana
Strain VS1, an Extended-Spectrum β-Lactamase-Producing Epibiont Isolated from
Magnolia grandiflora
Authors: Lata Pushpa , Govindarajan Subramaniam S. , Qi Feng , Li Jian-Liang , Maurya Santosh K. , Sahoo Malaya K.
Published: November 2017

Pantoea americana
strain VS1, an extended-spectrum β-lactamase-producing epibiont, was isolated from
Magnolia grandiflora
in central Florida, USA. Here, we report the
de novo
whole-genome sequence of this strain, which consists of a total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and comprising 4,836 predicted coding sequences.
Draft Genome Sequence of the Mucoid Pseudomonas aeruginosa Clinical Isolate PA34
Authors: Harrison Lucas B. , Hanson Nancy D.
Published: November 2017

Pseudomonas aeruginosa
is a serious threat to patients suffering from cystic fibrosis. These organisms are exposed to a unique set of selective pressures within the lung. Here, we report the draft genome sequence of a mucoid
P. aeruginosa
clinical isolate obtained from a cystic fibrosis patient colonized with
P. aeruginosa
.
Kinesthetically Exploring Chromosomes from Cell Division and Meiosis to Mendelian Genetics
Authors: Heineman Richard H.
Published: November 2017

Physical models are widely used to help students understand what happens to chromosomes during mitosis and meiosis. They can also be used to explicate the genotype-phenotype map. This laboratory exercise combines both these subjects at a level appropriate for a college-level genetics class. Students first trace the steps of mitosis and oogenesis, with special attention to ploidy and chromosome count. They then use the alleles arrived at by this process to build marshmallow creatures. Finally, they are introduced to more complicated modes of inheritance such as sex-linked traits, incomplete dominance, multiple alleles, and polygenic traits. Evidence of positive student attitudes and learning outcomes is presented.
Using a Nurse’s Graphic Medicine Memoir to Help Students Learn about HIV/AIDSReview of:
Taking Turns: Stories from HIV/AIDS Care Unit 371
; MK Czerwiec; (2017). The Pennsylvania State University Press, University Park, PA. 224 pages.
Authors: Wessner David R.
Published: November 2017

Review of: Taking Turns: Stories from HIV/AIDS Care Unit 371; MK Czerwiec; (2017). The Pennsylvania State University Press, University Park, PA. 224 pages.
Interventions to improve adherence to reporting guidelines in health research: a scoping review protocol
Authors: Blanco David , Kirkham Jamie J , Altman Douglas G , Moher David , Boutron Isabelle , Cobo Erik
Published: November 2017

Introduction

There is evidence that the use of some reporting guidelines, such as the Consolidated Standards for Reporting Trials, is associated with improved completeness of reporting in health research. However, the current levels of adherence to reporting guidelines are suboptimal. Over the last few years, several actions aiming to improve compliance with reporting guidelines have been taken and proposed. We will conduct a scoping review of interventions to improve adherence to reporting guidelines in health research that have been evaluated or suggested, in order to inform future interventions.

Methods and analysis

Our review will follow the Joanna Briggs Institute scoping review methods manual. We will search for relevant studies in MEDLINE, EMBASE and Cochrane Library databases. Moreover, we will carry out lateral searches from the reference lists of the included studies, as well as from the lists of articles citing the included ones. One reviewer will screen the full list, which will be randomly split into two halves and independently screened by the other two reviewers. Two reviewers will perform data extraction independently. Discrepancies will be solved through discussion. In addition, this search strategy will be supplemented by a grey literature search. The interventions found will be classified as assessed or suggested, as well as according to different criteria, in relation to their target (journal policies, journal editors, authors, reviewers, funders, ethical boards or others) or the research stage at which they are performed (design, conducting, reporting or peer review). Descriptive statistical analysis will be performed.

Ethics and dissemination

A paper summarising the findings from this review will be published in a peer-reviewed journal. This scoping review will contribute to a better understanding and a broader perspective on how the problem of adhering better to reporting guidelines has been tackled so far. This could be a major first step towards developing future strategies to improve compliance with reporting guidelines in health research.
Prevalence and recognition of obesity and its associated comorbidities: cross-sectional analysis of electronic health record data from a large US integrated health system
Authors: Pantalone Kevin M , Hobbs Todd M , Chagin Kevin M , Kong Sheldon X , Wells Brian J , Kattan Michael W , Bouchard Jonathan , Sakurada Brian , Milinovich Alex , Weng Wayne , Bauman Janine , Misra-Hebert Anita D , Zimmerman Robert S , Burguera Bartolome
Published: November 2017

Objective

To determine the prevalence of obesity and its related comorbidities among patients being actively managed at a US academic medical centre, and to examine the frequency of a formal diagnosis of obesity, via International Classification of Diseases, Ninth Revision (ICD-9) documentation among patients with body mass index (BMI) ≥30 kg/m2.

Design

The electronic health record system at Cleveland Clinic was used to create a cross-sectional summary of actively managed patients meeting minimum primary care physician visit frequency requirements. Eligible patients were stratified by BMI categories, based on most recent weight and median of all recorded heights obtained on or before the index date of 1July 2015. Relationships between patient characteristics and BMI categories were tested.

Setting

A large US integrated health system.

Results

A total of 324 199 active patients with a recorded BMI were identified. There were 121 287 (37.4%) patients found to be overweight (BMI ≥25 and <29.9), 75 199 (23.2%) had BMI 30–34.9, 34 152 (10.5%) had BMI 35–39.9 and 25 137 (7.8%) had BMI ≥40. There was a higher prevalence of type 2 diabetes, pre-diabetes, hypertension and cardiovascular disease (P value<0.0001) within higher BMI compared with lower BMI categories. In patients with a BMI >30 (n=134 488), only 48% (64 056) had documentation of an obesity ICD-9 code. In those patients with a BMI >40, only 75% had an obesity ICD-9 code.

Conclusions

This cross-sectional summary from a large US integrated health system found that three out of every four patients had overweight or obesity based on BMI. Patients within higher BMI categories had a higher prevalence of comorbidities. Less than half of patients who were identified as having obesity according to BMI received a formal diagnosis via ICD-9 documentation. The disease of obesity is very prevalent yet underdiagnosed in our clinics. The under diagnosing of obesity may serve as an important barrier to treatment initiation.
Frequency of 6-week follow-up appointment scheduling after intrauterine device insertion
Authors: Bernard Abigail , Satterwhite Catherine L , Reddy Madhuri
Published: November 2017

Introduction

Long-acting reversible contraception (LARC) is widely recommended to reduce unintended pregnancy in the USA. As intrauterine device (IUD) use increases, evaluating the role of post-insertion follow-up is important.

Methods

A retrospective patient record review was conducted to assess the follow-up experience of women who had an IUD placed at the University of Kansas Medical Center from 1 January to 30 June 2015. Data were collected on patient demographics, IUD placement, follow-up visit attendance, and outcomes in the 12 months following placement. The primary outcome of interest was the proportion of patients who attended a 6-week follow-up visit. Secondary outcomes included adverse events detected at the 6-week visit and IUD removal within a year of placement.

Results

Among 380 women who had an IUD inserted, physician documentation of a recommended 6-week follow-up visit was present in 91.3% of patient medical records. Two-thirds (66.6%) of patients receiving a recommendation returned for a follow-up visit. Of the 380 women who had an IUD placed, 66 (17.4%) had their IUD removed within 1 year of placement. Of those, 50 women attended the 6-week follow-up visit and 16 did not (19.8% vs 12.6%, p=0.08). Of the IUD removals, 14 occurred at the 6-week visit. After excluding IUD removals which occurred at the 6-week visit, attending a 6-week follow-up visit was not associated with IUD removal or retention (p=0.52).

Conclusion

Despite recommendations to forgo the 6-week follow-up visit, visits were still common, with no demonstrated value added.
Optimising the performance and interpretation of small bowel capsule endoscopy
Authors: Beg Sabina , Parra-Blanco Adolfo , Ragunath Krish
Published: November 2017

Small bowel capsule endoscopy has become a commonly used tool in the investigation of gastrointestinal symptoms and is now widely available in clinical practice. In contrast to conventional endoscopy, there is a lack of clear consensus on when competency is achieved or the way in which capsule endoscopy should be performed in order to maintain quality and clinical accuracy. Here we explore the evidence on the key factors that influence the quality of small bowel capsule endoscopy services.
Gut roundtable meeting paper: selected recent advances in hepatocellular carcinoma
Authors: Gerbes Alexander , Zoulim Fabien , Tilg Herbert , Dufour Jean-François , Bruix Jordi , Paradis Valérie , Salem Riad , Peck-Radosavljevic Markus , Galle Peter R , Greten Tim F , Nault Jean-Charles , Avila Matias A
Published: November 2017

Hepatocellular carcinoma (HCC) ranks number three among the most frequent causes of death from solid tumors worldwide. With obesity and fatty liver diseases as risk factors on the rise, HCC represents an ever increasing challenge. While there is still no curative treatment for most patients numerous novel drugs have been proposed, but most ultimately failed in phase III trials. This manuscript targets therapeutic advances and most burning issues. Expert key point summaries and urgent research agenda are provided regarding risk factors, including microbiota, need for prognostic and predictive biomarkers and the equivocal role of liver biopsy. Therapeutic topics highlighted are locoregional techniques, combination therapies and the potential of immunotherapy. Finally the manuscript provides a critical evaluation of novel targets and strategies for personalized treatment of HCC.
Nocturnal serum melatonin levels in sulfur mustard exposed patients with sleep disorders
Authors: Mousavi Seyyedeh Soghra , Vahedi E , Shohrati M , Panahi Y , Parvin S
Published: November 2017

Background

Sulfur mustard (SM) exposure causes respiratory disorders, progressive deterioration in lung function and mortality in injured victims and poor sleep quality is one of the most common problems among SM-exposed patients. Since melatonin has a critical role in regulation of sleep and awareness, this study aimed to evaluate the serum melatonin levels in SM-injured subjects.

Methods

A total of 30 SM-exposed male patients and 10 controls was evaluated. Sleep quality was evaluated by the Pittsburgh Sleep Quality Index (PSQI); daytime sleepiness was measured by the Epworth Sleepiness Scale (ESS), and the risk of obstructive sleep apnoea was determined by the STOP-Bang questionnaire. Polysomnography (PSG) and pulmonary function tests (PFTs) were also available. Nocturnal serum melatonin levels were measured using an ELISA kit.

Results

The mean of PSQI, ESS and STOP-Bang scores in patients (11.76±3.56, 12.6±3.03 and 5.03±1.09, respectively) were significantly (p<0.01) higher than those in the controls (2.78±0.83, 4.69±1.15 and 1.18±0.82, respectively). PFTs also showed declined respiratory quality in SM-patients. There was a significant difference regarding the PSG results between patients and controls (p<0.01). The mean of nocturnal serum melatonin levels in patients (29.78±19.31 pg/mL) was significantly (p=0.005) lower than that in the controls (78.53±34.41 pg/mL).

Conclusions

Reduced nocturnal serum melatonin and respiratory disorders can be the reasons for poor sleep quality among these patients.

Trial registration number

IRCT2015092924267N1, Pre-results.
Ethics, health policy, and Zika: From emergency to global epidemic?
Authors: Jamrozik Euzebiusz , Selgelid Michael J
Published: November 2017

Zika virus was recognised in 2016 as an important vector-borne cause of congenital malformations and Guillain-Barré syndrome, during a major epidemic in Latin America, centred in Northeastern Brazil. The WHO and Pan American Health Organisation (PAHO), with partner agencies, initiated a coordinated global response including public health intervention and urgent scientific research, as well as ethical analysis as a vital element of policy design. In this paper, we summarise the major ethical issues raised during the Zika epidemic, highlighting the PAHO ethics guidance and the role of ethics in emergency responses, before turning to ethical issues that are yet to be resolved. Zika raises traditional bioethical issues related to reproduction, prenatal diagnosis of serious malformations and unjust disparities in health outcomes. But the epidemic has also highlighted important issues of growing interest in public health ethics, such as the international spread of infectious disease; the central importance of reproductive healthcare in preventing maternal and neonatal morbidity and mortality; diagnostic and reporting biases; vector control and the links between vectors, climate change, and disparities in the global burden of disease. Finally, there are controversies regarding Zika vaccine research and eventual deployment. Zika virus was a neglected disease for over 50 years before the outbreak in Brazil. As it continues to spread, public health agencies should promote gender equity and disease control efforts in Latin America, while preparing for the possibility of a global epidemic.
Stent-assisted coiling of cerebral aneurysms: a single-center clinical and angiographic analysis
Authors: Wang Jun , Vargas Jan , Spiotta Alejandro , Chaudry Imran , Turner Raymond D , Lena Jonathan , Turk Aquilla
Published: November 2017

Objective

This study retrospectively compared the clinical and angiographic outcomes of treating cerebral aneurysms with Neuroform (NEU), Enterprise (EP), and Low-profile Visualized Intraluminal Support (LVIS/LVIS Jr) stents.

Materials and methods

We conducted a retrospective analysis of a procedural database. All aneurysm procedures using any of the three types of self-expanding nitinol stents (NEU, EP and LVIS/LVIS Jr) were included. Intra-procedure complications, post-procedure complications, and angiographic results (Raymond–Roy grade scale, RRGS) were analyzed retrospectively. A multivariate logistic regression analysis was conducted to identify predictors of intra-procedure and post-procedure complications.

Results

Two hundred and forty-three aneurysms in 229 patients treated with stent-assisted coiling were included (NEU group: 109 aneurysms; EP group: 61 aneurysms; LVIS/LVIS Jr: 73 aneurysms). The LVIS/LVIS Jr group was associated with the lowest rate of initial complete occlusion (RRGS I: 47.9%; 35/73). Follow-up showed the proportion of RRGS I increased for all stent groups but was greatest in the LVIS/LVIS Jr group. Overall, 17 intra-procedural complications were seen in 229 patients (7.4%) and 15 post-procedural complications were found in 198 patients at follow-up (7.6%), with no differences between stent groups. Thrombotic events were the most common complications and occurred in 13 patients (13/229, 5.7%).

Conclusions

All three types of stents used to treat cerebral aneurysms with unfavorable neck were safe and effective, providing suitable support for the coil mass. LVIS/LVIS Jr promotes better progressive aneurysm complete occlusion than the other two stents but seems to cause more common intra-procedural stent-related thrombotic events and fewer post-procedural complications.
Is bridging therapy still required in stroke due to carotid artery terminus occlusions?
Authors: Bourcier Romain , Alexandre Pierre-Louis , Eugène François , Delasalle-Guyomarch Béatrice , Guillon Benoit , Kerleroux Basile , Saleme Suzana , Marnat Gaultier , Boucebci Samy , Mirza Mahmood , Ferré Jean-Christophe , Papagiannaki Chrysanthi , Desal Hubert
Published: November 2017

Introduction

Studies comparing endovascular stroke treatment using mechanical thrombectomy (MT) with or without prior IV tissue plasminogen activator (tPa) have included only 30% of internal carotid artery terminus occlusions (ICA-O), a known predictor of recanalization failure with IV tPa.

Objective

To carry out a retrospective multicenter analysis of prospectively collected data of consecutive patients to investigate the impact of intravenous thrombolysis on ICA-O by comparing patients treated with MT alone or bridging therapy (BT).

Material and methods

Patients with ICA-O treated with MT alone or BT were retrospectively examined and compared. Demographic data, vascular risk factors, treatment modalities, complications, technical and clinical outcomes were recorded. A propensity score (PS) analysis was used to compare modified Rankin Scale (mRS) score at 3 months and intracerebral hemorrhage (ICH) between groups.

Results

141 consecutive patients (60% BT/40% MT) were included between January 2014 and June 2016. Baseline characteristics did not differ between the groups. There was no significant difference in the rate of Thrombolysis in Cerebral Infarction 2b/3, distal emboli, and median number of passes between the groups. There was a significant difference between BT and MT groups in the median time between imaging and groin puncture (median 97 min vs 75, p=0.007), the rate of ICH (44% vs 27%, p=0.05), but not for symptomatic ICH (18% vs 13%, p=0.49). With PS, there was a trend towards a higher rate of ICH (OR=2.3, 95% CI 0.9 to 5.9, p=0.09) in the BT group compared with the MT alone group, with no difference in mRS score ≤2 at 3 months (OR=1.6, 95% CI 0.7 to 3.7, p=0.29).

Conclusion

There was no significant difference in clinical outcomes between patients receiving bridging therapy versus direct thrombectomy. Bridging therapy delayed time to groin puncture and increased ICH rate.
Psychometric validation of the needs assessment tool: progressive disease in interstitial lung disease
Authors: Johnson Miriam J , Jamali Armita , Ross Joy , Fairhurst Caroline , Boland Jason , Reigada Carla , Hart Simon Paul , Grande Gunn , Currow David C , Wells Athol U , Bajwah Sabrina , Papadopoulos Thanos , Bland J Martin , Yorke Janelle
Published: November 2017

The inter-rater/test–retest reliability and construct validity of a palliative care needs assessment tool in interstitial lung disease (NAT:PD-ILD) were tested using NAT:PD-ILD-guided video-recorded consultations, and NAT:PD-ILD-guided consultations, and patient and carer-report outcomes (St George’s Respiratory Questionnaire (SGRQ)-ILD, Carer Strain Index (CSI)/Carer Support Needs Assessment Tool (CSNAT)). 11/16 items reached at least fair inter-rater agreement; 5 items reached at least moderate test–retest agreement. 4/6 patient constructs demonstrated agreement with SGRQ-I scores (Kendall’s tau-b, 0.24–20.36; P<0.05). 4/7 carer constructs agreed with the CSI/CSNAT items (kappa, 0.23–20.53). The NAT:PD-ILD is reliable and valid. Clinical effectiveness and implementation are to be evaluated.
End of veterinary school as we know it
Authors: Maccabe Andrew T.
Published: November 2017

Disruptive innovation will transform veterinary education in the next 10 years, predicts Andrew Maccabe
Constraints on the equation of state of neutron star matter based on observations
Authors: Ngo Quang Thin , Shinmura Shoji
Published: November 2017

Many calculations of the neutron star (NS) equation of state (EOS) have been performed over the years. Recent observations of NSs have begun to play an important role in finding the realistic EOS. In this paper, we compare mass–radius relations derived from various EOSs with observational data of NSs. In addition, we adjust EOSs to be consistent with observational data from NSs and employ Bayesian statistical analyses to obtain constraints on the EOS. Our results show that the EOS needs to be softened in the medium density region ([Formula: see text]–[Formula: see text], where [Formula: see text] is the saturation density) and to have a rapid change of stiffness around an energy density of [Formula: see text] 650 MeV/fm3.
Dynamics of gene expression with positive feedback to histone modifications at bivalent domains
Authors: Huang Rongsheng , Lei Jinzhi
Published: November 2017

Experiments have shown that in embryonic stem cells, the promoters of many lineage-control genes contain “bivalent domains”, within which the nucleosomes possess both active (H3K4me3) and repressive (H3K27me3) marks. Such bivalent modifications play important roles in maintaining pluripotency in embryonic stem cells. Here, to investigate gene expression dynamics when there are regulations in bivalent histone modifications and random partition in cell divisions, we study how positive feedback to histone methylation/demethylation controls the transition dynamics of the histone modification patterns along with cell cycles. We constructed a computational model that includes dynamics of histone marks, three-stage chromatin state transitions, transcription and translation, feedbacks from protein product to enzymes to regulate the addition and removal of histone marks, and the inheritance of nucleosome state between cell cycles. The model reveals how dynamics of both nucleosome state transition and gene expression are dependent on the enzyme activities and feedback regulations. Results show that the combination of stochastic histone modification at each cell division and the deterministic feedback regulation work together to adjust the dynamics of chromatin state transition in stem cell regenerations.