bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing Teachers’ Competencies to Read and Interpret Graphs from Learning Progress Assessment: Results from Tests and Interviews
Authors: Zeuch Nina , Förster Natalie , Souvignier Elmar
Published: January 2017

Learning progress assessment (LPA) provides formative information about effectiveness of instructional decisions. Learning curves are usually presented as graphical illustrations. However, little is known about teachers understanding and interpreting of graphically presented information. An instrument to measure competencies in reading graphs from learning progress assessment (LPA‐test) was developed. One‐hundred and twenty‐four student teachers and 36 teachers completed the LPA‐test and a second test that assessed reading graphical information from diagrams. In addition, interviews from 10 teachers provided information about thinking processes while dealing with graphs on learning progress information. Technical adequacy of the LPA‐test proved to be satisfactory. Results in the LPA‐test underline the capacity that most teachers generally have when learning graphing. Interviews reveal that teachers skip a thorough description of the graphical illustration, concentrate on marginal details, and tend to immediately transmit students’ achievement into school grades without structuring information.
Democracy, Law, Compliance
Authors: Herzog Don
Published: January 2017

Professors Schauer and McAdams both seek a more or less sweepingly general theory of why we obey the law. But we should split, not lump. There are different reasons different actors in different social settings obey different laws–not only, but not least, out of regard for democratic decision making.
EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes
Authors: Panda Arijit , Sen Diya , Ghosh Arup , Gupta Akash , C. Mathu Malar , Prakash Mishra Gyan , Singh Deeksha , Ye Wenwu , Tyler Brett M. , Tripathy Sucheta
Published: January 2017

We have developed EumicrobeDBLite—a lightweight comprehensive genome resource and sequence analysis platform for oomycete organisms. EumicrobeDBLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). In this version, GUS has been greatly simplified with the removal of many obsolete modules and the redesign of others to incorporate contemporary data. Several dependences, such as perl object layers used for data loading in VMD, have been replaced with independent lightweight scripts. EumicrobeDBLite now runs on a powerful annotation engine developed at our laboratory, called ‘Genome Annotator Lite’. Currently, this database has 26 publicly available genomes and 10 expressed sequence tag (EST) datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non‐coding data, tRNA genes, repeats and EST alignments. In addition, we have defined 44 777 core conserved proteins from 12 oomycete organisms which form 2974 clusters. Synteny viewing is enabled by the incorporation of the Genome Synteny Viewer (GSV) tool. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. The browser has been upgraded to enable user upload of GFF files for quick view of genome annotation comparisons. The toolkit page integrates the EMBOSS package and has a gene prediction tool. Annotations for the organisms are updated once every 6 months to ensure quality. The database resource is available at www.eumicrobedb.org.
The transcriptional regulatory network mediated by banana (Musa acuminata) dehydration‐responsive element binding (MaDREB) transcription factors in fruit ripening
Authors: Kuang Jian‐Fei , Chen Jian‐Ye , Liu Xun‐Cheng , Han Yan‐Chao , Xiao Yun‐Yi , Shan Wei , Tang Yang , Wu Ke‐Qiang , He Jun‐Xian , Lu Wang‐Jin
Published: January 2017

Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established significance of dehydration‐responsive element binding (DREB) TFs in plant abiotic stress responses, the involvement of DREBs in fruit ripening is yet to be determined.

Here, we identified four genes encoding ripening‐regulated DREB TFs in banana (Musa acuminata), MaDREB1, MaDREB2, MaDREB3, and MaDREB4, and demonstrated that they play regulatory roles in fruit ripening.

We showed that MaDREB1–MaDREB4 are nucleus‐localized, induced by ethylene and encompass transcriptional activation activities. We performed a genome‐wide chromatin immunoprecipitation and high‐throughput sequencing (ChIP‐Seq) experiment for MaDREB2 and identified 697 genomic regions as potential targets of MaDREB2. MaDREB2 binds to hundreds of loci with diverse functions and its binding sites are distributed in the promoter regions proximal to the transcriptional start site (TSS). Most of the MaDREB2‐binding targets contain the conserved (A/G)CC(G/C)AC motif and MaDREB2 appears to directly regulate the expression of a number of genes involved in fruit ripening. In combination with transcriptome profiling (RNA sequencing) data, our results indicate that MaDREB2 may serve as both transcriptional activator and repressor during banana fruit ripening.

In conclusion, our study suggests a hierarchical regulatory model of fruit ripening in banana and that the MaDREB TFs may act as transcriptional regulators in the regulatory network.
Production, amplification and systemic propagation of redox messengers in plants? The phloem can do it all!
Authors: Gaupels Frank , Durner Jörg , Kogel Karl‐Heinz
Published: January 2017

Rapid long‐distance signalling is an emerging topic in plant research, and is particularly associated with responses to biotic and abiotic stress. Systemic acquired resistance (SAR) to pathogen attack is dependent on nitric oxide (NO) and reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). By comparison, systemic wound responses (SWRs) and systemic acquired acclimation (SAA) to abiotic stress encounters are triggered by rapid waves of H2O2, calcium and electrical signalling. Efforts have been made to decipher the relationship between redox messengers, calcium and other known systemic defence signals. Less is known about possible routes of signal transduction throughout the entire plant. Previously, the phloem has been suggested to be a transport conduit for mobile signals inducing SAR, SWR and SAA. This review highlights the role of the phloem in systemic redox signalling by NO and ROS. A not yet identified calcium‐dependent NO source and S‐nitrosoglutathione reductase are candidate regulators of NO homeostasis in the phloem, whereas ROS concentrations are controlled by NADPH oxidases and the H2O2‐scavenging enzyme ascorbate peroxidase. Possible amplification mechanisms in phloem‐mediated systemic redox signalling are discussed.
Allelic variations and differential expressions detected at quantitative trait loci for salt stress tolerance in wheat
Authors: Oyiga Benedict C. , Sharma Ram C. , Baum Michael , Ogbonnaya Francis C. , Léon Jens , Ballvora Agim
Published: January 2017

The increasing salinization of agricultural lands is a threat to global wheat production. Understanding of the mechanistic basis of salt tolerance (ST) is essential for developing breeding and selection strategies that would allow for increased wheat production under saline conditions to meet the increasing global demand. We used a set that consists of 150 internationally derived winter and facultative wheat cultivars genotyped with a 90K SNP chip and phenotyped for ST across three growth stages and for ionic (leaf K+ and Na+ contents) traits to dissect the genetic architecture regulating ST in wheat. Genome‐wide association mapping revealed 187 Single Nucleotide Polymorphism (SNPs) (R2 = 3.00–30.67%), representing 37 quantitative trait loci (QTL), significantly associated with the ST traits. Of these, four QTL on 1BS, 2AL, 2BS and 3AL were associated with ST across the three growth stages and with the ionic traits. Novel QTL were also detected on 1BS and 1DL. Candidate genes linked to these polymorphisms were uncovered, and expression analyses were performed and validated on them under saline and non‐saline conditions using transcriptomics and qRT‐PCR data. Expressed sequence comparisons in contrasting ST wheat genotypes identified several non‐synonymous/missense mutation sites that are contributory to the ST trait variations, indicating the biological relevance of these polymorphisms that can be exploited in breeding for ST in wheat.
Mechanistic studies of sesquiterpene cyclases based on their carbon isotope ratios at natural abundance
Authors: Tan Wenhua , Bartram Stefan , Boland Wilhelm
Published: January 2017

During the process of terpene biosynthesis, C–C bond breaking and forming steps are subjected to kinetic carbon isotope effects, leading to distinct carbon isotopic signatures of the products. Accordingly, carbon isotopic signatures could be used to reveal the ‘biosynthetic history’ of the produced terpenoids. Five known sesquiterpene cyclases, regulating three different pathways, representing simple to complex biosynthetic sequences, were heterologously expressed and used for in vitro assays with farnesyl diphosphate as substrate. Compound specific isotope ratio mass spectrometry measurements of the enzyme substrate farnesyl diphosphate (FDP) and the products of all the five cyclases were performed. The calculated δ13C value for FDP, based on δ13C values and relative amounts of the products, was identical with its measured δ13C value, confirming the reliability of the approach and the precision of measurements. The different carbon isotope ratios of the products reflect the complexity of their structure and are correlated with the frequency of carbon–carbon bond forming and breaking steps on their individual biosynthetic pathways. Thus, the analysis of carbon isotopic signatures of terpenes at natural abundance can be used as a powerful tool in elucidation of associated biosynthetic mechanisms of terpene synthases and in future in vivo studies even without ‘touching’ the plant.
Combined effect of virus infection and water stress on water flow and water economy in grapevines
Authors: El Aou‐ouad Hanan , Pou Alicia , Tomás Magdalena , Montero Rafael , Ribas‐Carbo Miquel , Medrano Hipólito , Bota Josefina
Published: January 2017

Water limitation is one of the major threats affecting grapevine production. Thus, improving water‐use efficiency (WUE) is crucial for a sustainable viticulture industry in Mediterranean regions. Under field conditions, water stress (WS) is often combined with viral infections as those are present in major grape‐growing areas worldwide. Grapevine leafroll‐associated virus 3 (GLRaV‐3) is one of the most important viruses affecting grapevines. Indeed, the optimization of water use in a real context of virus infection is an important topic that needs to be understood. In this work, we have focused our attention on determining the interaction of biotic and abiotic stresses on WUE and hydraulic conductance (Kh) parameters in two white grapevine cultivars (Malvasia de Banyalbufar and Giró Ros). Under well‐watered (WW) conditions, virus infection provokes a strong reduction (P < 0.001) in Kpetiole in both cultivars; however, Kleaf was only reduced in Malvasia de Banyalbufar. Moreover, the presence of virus also reduced whole‐plant hydraulic conductance (Khplant) in 2013 and 2014 for Malvasia de Banyalbufar and in 2014 for Giró Ros. Thus, the effect of virus infection on water flow might explain the imposed stomatal limitation. Under WS conditions, the virus effect on Kplant was negligible, because of the bigger effect of WS than virus infection. Whole‐plant WUE (WUEWP) was not affected by the presence of virus neither under WW nor under WS conditions, indicating that plants may adjust their physiology to counteract the virus infection by maintaining a tight stomatal control and by sustaining a balanced carbon change.
A Systematic Review of Mass Media Campaigns for Suicide Prevention: Understanding Their Efficacy and the Mechanisms Needed for Successful Behavioral and Literacy Change
Authors: Torok Michelle , Calear Alison , Shand Fiona , Christensen Helen
Published: January 2017

Mass media campaigns are increasingly seen as an important part of suicide prevention; however, despite their popularity, their efficacy is not well understood. The current review aimed to address key knowledge gaps regarding how mass media campaigns can be optimized to prevent suicide, by looking at their global efficacy, and mechanisms related to successful outcomes. A systematic review of the international literature examined studies which evaluated mass media campaigns targeted at suicide prevention, where suicide behaviors (mortality, attempts) or suicide literacy (knowledge, attitudes, help‐seeking) was identified as a primary outcome. Thirteen articles describing 12 unique campaigns met eligibility criteria. For behavioral outcomes, mass media campaigns appear to be most effective when delivered as part of a multicomponent suicide prevention strategy, while “standalone campaigns” were modestly useful for increasing suicide literacy. Level of exposure, repeat exposure, and community engagement appeared to be fundamental to the success of these campaigns; however, these constructs were poorly adhered to in the development and implementation of campaigns. Overall, the mixed quality of the included studies highlights a need for increased quantity, consistency, and quality of evaluations to advance the evidence base.
Cataracts in the Norwegian Buhund—current prevalence and characteristics
Authors: Kristiansen Elin , Revold Tobias , Lingaas Frode , Narfström Kristina , Pedersen Pia Bjerre , Kielland Camilla , Dahl Stein , Ropstad Ernst‐Otto
Published: January 2017

Objective

To evaluate prevalence and characteristics of cataracts in the Norwegian Buhund breed 20 years after high reported prevalence of especially pulverulent nuclear cataracts (PNCs).

Animals studied

Two hundred and fifty Norwegian Buhund dogs in Norway, Sweden, and Denmark (117 males and 133 females) with previously unknown eye health status were included. Forty‐five dogs had multiple examinations (two to six times over a 6‐year period). Median age was 4.4 years [0.2–15.2] at first examination and 5.3 years [0.2–15.2] at last examination.

Procedures

All dogs underwent regular screening for inherited eye diseases.

Results

At the last observation of each dog, 52.4% were affected by PNC, categorized as minimal (33 of 250 dogs; 13.2%), mild (31 dogs; 12.4%), moderate (38 dogs; 15.2%), or pronounced (29 dogs; 11.6%). Moderate or pronounced changes were only seen in older dogs, and progressive changes were identified in some of the re‐examined dogs. Some dogs, free of lenticular changes at early examinations, were affected by PNC at re‐examinations. The odds for finding PNC increased with dog's age up to approximately 8 years. Presumably inherited cataracts other than PNC were found in 53 dogs (21.2%) with cortical (17.6%) and posterior polar (6.4%) locations as the most common ones.

Conclusions

The high prevalence of PNC in the breed reported 20 years ago persists. PNCs are not always visible in young dogs, and the rate of progression varies. The prevalence of other types of cataract is also high, but cataracts rarely cause loss of vision in this breed.
Effects of hypercapnia on the lung
Authors: Shigemura Masahiko , Lecuona Emilia , Sznajder Jacob I.
Published: January 2017

Gases are sensed by lung cells and can activate specific intracellular signalling pathways, and thus have physiological and pathophysiological effects. Carbon dioxide (CO2), a primary product of oxidative metabolism, can be sensed by eukaryotic cells eliciting specific responses via recently identified signalling pathways. However, the physiological and pathophysiological effects of high CO2 (hypercapnia) on the lungs and specific lung cells, which are the primary site of CO2 elimination, are incompletely understood. In this review, we provide a physiological and mechanistic perspective on the effects of hypercapnia on the lungs and discuss the recent understanding of CO2 modulation of the alveolar epithelial function (lung oedema clearance), epithelial cell repair, innate immunity and airway function.

image
Flux projection beamforming for monochromatic source localization in enclosed space
Authors: Li Xiaolei , Yu Gaokun , Wang Ning , Gao Dazhi , Wang Haozhong
Published: January 2017

Monochromatic sound source localization becomes difficult in enclosed space. According to the reciprocity theorem, a self-consistent method of source localization in enclosed space, referred to as the flux projection beamforming, is proposed, only using the measurement of the sound pressure and normal velocity on the closed boundary at a single frequency. Its validity is examined both by experiment and simulation.
Resonant mode characterisation of a cylindrical Helmholtz cavity excited by a shear layer
Authors: Bennett Gareth J. , Stephens David B. , Rodriguez Verdugo Francisco
Published: January 2017

This paper investigates the interaction between the shear-layer over a circular cavity with a relatively small opening and the flow-excited acoustic response of the volume within to shear-layer instability modes. Within the fluid-resonant category of cavity oscillation, most research has been conducted on rectangular geometries: generally restricted to longitudinal standing waves, or when cylindrical: to Helmholtz resonance. In practical situations, however, where the cavity is subject to a range of flow speeds, many different resonant mode types may be excited. The current work presents a cylindrical cavity design where Helmholtz oscillation, longitudinal resonance, and azimuthal acoustic modes may all be excited upon varying the flow speed. Experiments performed show how lock-on between each of the three fluid-resonances and shear-layer instability modes can be generated. A circumferential array of microphones flush-mounted with the internal surface of the cavity wall was used to decompose the acoustic pressure field into acoustic modes and has verified the excitation of higher order azimuthal modes by the shear-layer. For azimuthal modes especially, the location of the cavity opening affects the pressure response. A numerical solution is validated and provides additional insight and will be applied to more complex aeronautical and automotive geometries in the future.
The tyrosine kinase Src promotes phosphorylation of the kinase TBK1 to facilitate type I interferon production after viral infection
Authors: Li Xuelian , Yang Mingjin , Yu Zhou , Tang Songqing , Wang Lei , Cao Xuetao , Chen Taoyong
Published: January 2017

The tyrosine kinase Src couples activation of multiple pattern recognition receptors to the production of type I interferon.
RETRACTED: The receptor tyrosine kinase AXL mediates nuclear translocation of the epidermal growth factor receptor
Authors: Brand Toni M. , Iida Mari , Corrigan Kelsey L. , Braverman Cara M. , Coan John P. , Flanigan Bailey G. , Stein Andrew P. , Salgia Ravi , Rolff Jana , Kimple Randall J. , Wheeler Deric L.
Published: January 2017

The kinase AXL promotes cetuximab resistance by promoting the nuclear accumulation of EGFR.
2016: Signaling Breakthroughs of the Year
Authors: Adler Elizabeth M.
Published: January 2017

Signaling research advances in neuroscience, immunology, and cellular metabolism provide insight into both basic biology and human disease.
NIK sends mitochondria to the periphery
Authors: VanHook Annalisa M.
Published: January 2017

The kinase NIK promotes tumor cell invasion by stimulating the translocation of mitochondria to the cell periphery.
Papers of note in
Science
354
(6319)
Authors: VanHook Annalisa M.
Published: January 2017

This week’s articles highlight the development of hair and sweat glands in human skin, how calcium signals affect the sensitivity of a mouse’s whiskers, peptide hormone processing in plants, and conformational changes that enable bacteriorhodopsin to harvest energy from light.
Papers of note in
Science Translational Medicine
8
(370)
Authors: Ferrarelli Leslie K.
Published: January 2017

This week’s articles highlight advances in treating spinobulbar muscular dystrophy by activating adenylyl cyclase and autoimmune disease by inhibiting protein interactions that mediate T cell signaling.
Papers of note in
Nature
540
(7634)
Authors: Gough Nancy R.
Published: January 2017

This week’s articles highlight a way to enhance crop yield by manipulating sugar signaling, how blood flow patterns affect mechanical signaling in endothelial cells, how an innate immune sensor blocks PI3K signaling in the gut, and structural insights into cannabinoid receptors.
Placing the nuclear pore in the metformin mechanism of action
Authors: Gough Nancy R.
Published: January 2017

Metformin reduces cellular ATP and restricts passive transport through the nuclear pore to limit nuclear activation of a protein that activates mTORC1.
Draft Genome Sequences of 40 Pseudomonas aeruginosa Clinical Strains Isolated from the Sputum of a Single Cystic Fibrosis Patient Over an 8-Year Period
Authors: Bianconi Irene , D'Arcangelo Silvia , Benedet Mattia , Bailey Kate E. , Esposito Alfonso , Piffer Elena , Mariotto Alex , Baldo Ermanno , Dinnella Grazia , Gualdi Paola , Schinella Michele , Donati Claudio , Jousson Olivier
Published: January 2017

We report draft genome sequences of 40
Pseudomonas aeruginosa
strains, isolated from the sputum of a single cystic fibrosis patient over eight years. Analyses indicated a correlation between multidrug-resistant phenotypes and population structure. Our data provide new insights into the mechanisms leading to acquisition of antibiotic resistance in
P. aeruginosa
.
Draft Genome Sequences of Itaconate-Producing
Ustilaginaceae
Authors: Geiser Elena , Ludwig Florian , Zambanini Thiemo , Wierckx Nick , Blank Lars M.
Published: January 2017

Some smut fungi of the family
Ustilaginaceae
produce itaconate from glucose.
De novo
genome sequencing of nine itaconate-producing
Ustilaginaceae
revealed genome sizes between 19 and 25 Mbp. Comparison to the itaconate cluster of
U. maydis
MB215 revealed all essential genes for itaconate production contributing to metabolic engineering for improving itaconate production.
Complete Genome Sequences of Curli-Negative and Curli-Positive Isolates of Foodborne Escherichia coli O157:H7 Strain 86-24
Authors: Sharma Vijay K. , Bayles Darrell O. , Alt David P. , Looft Torey
Published: January 2017

Escherichia coli
O157:H7 strain 86-24 does not produce curli fimbriae, but gives rise to curli-positive isolates at a variable frequency. Here, we report the complete genome sequences of curli-negative and curli-positive isolates of strain 86-24.
Complete Genome Sequence of Type Strain Campylobacter fetus subsp.
fetus
ATCC 27374
Authors: Oliveira Luciana M. , Resende Daniela M. , Dorneles Elaine M. S. , Horácio Elvira C. A. , Alves Fernanda L. , Gonçalves Leilane O. , Tavares Grace S. , Stynen Ana Paula R. , Lage Andrey P. , Ruiz Jeronimo C.
Published: January 2017

Campylobacter fetus
subsp.
fetus
is a zoonotic bacterium important for animal and public health. The complete sequencing and annotation of the genome of the type strain
C. fetus
subsp.
fetus
ATCC 27374 are reported here.
Draft Genome Sequence of Bacillus subtilis Ia1a, a New Strain for Poly-γ-Glutamic Acid and Exopolysaccharide Production
Authors: Ibrahim Mohammad H. A. , Cress Brady F. , Linhardt Robert J. , Koffas Mattheos A. G. , Gross Richard A.
Published: January 2017

We report here the 4.092-Mb high-quality draft genome assembly of a newly isolated poly-γ-glutamic acid–producing strain,
Bacillus subtilis
Ia1a. The genome sequence is considered a critical tool to facilitate the engineering of improved production strains. Exopolysaccharides and many industrially important enzymes can be produced by this new strain utilizing different carbon sources.
Draft Genome Sequence of Pediococcus parvulus 2.6, a Probiotic β-Glucan Producer Strain
Authors: Pérez-Ramos Adrián , Mohedano M. Luz , Puertas Ana , Lamontanara Antonella , Orru Luigi , Spano Giuseppe , Capozzi Vittorio , Dueñas M. Teresa , López Paloma
Published: January 2017

We report here the draft genome sequence of the probiotic
Pediococcus parvulus
2.6, a lactic acid bacterial strain isolated from ropy cider. The bacterium produces a prebiotic and immunomodulatory exopolysaccharide, and this is the first strain of the
P. parvulus
species whose genome has been characterized.
Draft Genome Sequence of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strain CCUG 62462, Isolated from a Urine Sample
Authors: Johnning Anna , Jakobsson Hedvig E. , Boulund Fredrik , Salvà-Serra Francisco , Moore Edward R. B. , Åhrén Christina , Karami Nahid , Kristiansson Erik
Published: January 2017

The draft genome sequence has been determined for an extended-spectrum-β-lactamase (ESBL)-producing (
bla
CTX-M-15
)
Escherichia coli
strain (CCUG 62462), composed of 119 contigs and a total size of 5.27 Mb. This
E. coli
is serotype O25b and sequence type 131, a pandemic clonal group, causing worldwide antimicrobial-resistant infections.
Draft Genome Sequence of Blautia faecis Strain Marseille-P328, Isolated from the Human Ascending Colon
Authors: Ricaboni Davide , Mailhe Morgane , Labas Noémie , Vitton Véronique , Raoult Didier , Million Matthieu
Published: January 2017

Blautia faecis
strain Marseille P328 was isolated from the ascending colon of a French patient. We sequenced the 4.45-Mb genome of the strain and compared it with that of other species of the
Blautia
genus.
Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3
Authors: De Vries Dana R. , Martin Alexandra L. , Ganz Holly H. , Eisen Jonathan A. , Coil David A.
Published: January 2017

Here, we present the draft genome sequence of
Enterococcus faecalis
strain UCD-PD3. The assembly contains 2,861,314 bp in 73 contigs. This strain was isolated from a feral domestic cat (
Felis catus
) anal sac secretion sample, as part of a project on isolating and characterizing the microbes present in feline anal sacs.
Genome Sequence of
Rheinheimera salexigens
sp. nov. Isolated from a Fishing Hook off O‘ahu, Hawai‘i
Authors: Wan Xuehua , Hou Shaobin , Hayashi Kazukuni , Anderson James , Donachie Stuart P.
Published: January 2017

Rheinheimera salexigens
KH87
T
is an obligately halophilic gammaproteobacterium. The strain's draft genome sequence, generated by the Roche 454 GS FLX+ platform, comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding sequences and 58 tRNA coding regions. The G+C content is 42 mol%.
High-Quality Draft Genome Sequence of the Actinobacterium Nocardia terpenica IFM 0406, Producer of the Immunosuppressant Brasilicardins, Using Illumina and PacBio Technologies
Authors: Buchmann Anina , Eitel Michael , Koch Pierre , Schwarz Paul N. , Stegmann Evi , Wohlleben Wolfgang , Wolański Marcin , Krawiec Michał , Zakrzewska-Czerwińska Jolanta , Méndez Carmen , Botas Alma , Núñez Luz Elena , Morís Francisco , Cortés Jesus , Gross Harald
Published: January 2017

The bacterium
Nocardia terpenica
IFM 0406 is known as the producer of the immunosuppressant brasilicardin A. Here, we report the completely sequenced genome of strain IFM 0406, which facilitates the heterologous expression of the brasilicardin biosynthetic gene cluster but also unveils the intriguing biosynthetic capacity of the strain to produce secondary metabolites.
Complete Genome Sequence of Delftia tsuruhatensis CM13 Isolated from Murine Proximal Colonic Tissue
Authors: Saffarian Azadeh , Mulet Céline , Tournebize Régis , Naito Tomoaki , Sansonetti Philippe J. , Pédron Thierry
Published: January 2017

We report here the complete genome sequence of
Delftia tsuruhatensis
CM13, isolated from murine proximal colonic tissue. The genome assembly using PacBio single-molecule real-time sequencing resulted in a single scaffold of 7.19 Mb.
Genome Sequence of the Poly-3-Hydroxybutyrate Producer Clostridium acetireducens DSM 10703
Authors: Flüchter Sebastian , Poehlein Anja , Schiel-Bengelsdorf Bettina , Daniel Rolf , Dürre Peter
Published: January 2017

Here, we report the genome sequence of
Clostridium acetireducens
(DSM 10703
T
), a strictly anaerobic bacterium capable of fermenting acetate and leucine to butyrate, isovalerate, and poly-3-hydroxybutyrate. The draft genome consists of a circular chromosome with a size of 2.4 Mb and harbors 2,239 predicted protein-encoding genes.
Genome Sequences of Multidrug-Resistant Salmonella enterica subsp.
enterica
Serovar Infantis Strains from Broiler Chicks in Hungary
Authors: Wilk Tímea , Szabó Móni , Szmolka Ama , Kiss János , Barta Endre , Nagy Tibor , Olasz Ferenc , Nagy Béla
Published: January 2017

Three strains of
Salmonella enterica
serovar Infantis isolated from healthy broiler chickens from 2012 to 2013 have been sequenced. Comparison of these and previously published
S
. Infantis genome sequences of broiler origin in 1996 and 2004 will provide new insight into the genome evolution and recent spread of
S
. Infantis in poultry.
Complete Genome Sequence of Community-Acquired Klebsiella pneumoniae KP36, a Strain Isolated from a Patient with an Upper Urinary Tract Infection
Authors: Lin Wei-Hung , Zheng Po-Xing , Liu Tsunglin , Tseng Chin-Chung , Chen Wei-Chu , Wang Ming-Cheng , Wu Jiunn-Jong
Published: January 2017

Here, we announce the complete genome sequence of
Klebsiella pneumoniae
KP36, a strain isolated from a patient with a severe community-acquired urinary tract infection. This genome provides insights into the pathogenesis of a pandemic
K. pneumoniae
strain from a community-acquired urinary tract infection.
Complete Genome Sequence of
Rhodococcus
sp. Strain WMMA185, a Marine Sponge-Associated Bacterium
Authors: Adnani Navid , Braun Doug R. , McDonald Bradon R. , Chevrette Marc G. , Currie Cameron R. , Bugni Tim S.
Published: January 2017

The
Rhodococcus
strain WMMA185 was isolated from the marine sponge
Chondrilla nucula
as part of ongoing drug discovery efforts. Analysis of the 4.44-Mb genome provides information regarding interspecies interactions as pertains to regulation of secondary metabolism and natural product biosynthetic potentials.
Genome Sequence of “
Anthococcus
,” a Novel Genus of the Family
Streptococcaceae
Isolated from Flowers
Authors: Chuah Li-Oon , Yap Kien-Pong , Thong Kwai Lin , Liong Min Tze , Ahmad Rosma , Shamila-Syuhada Ahamed Kamal , Rusul Gulam
Published: January 2017

Here, we report the draft whole-genome sequence of “
Anthococcus
,” a novel genus of the family
Streptococcaceae
isolated from fresh flowers of a durian (
Durio zibethinus
) tree. The draft genome of
Anthococcus
sp. strain DF1 contains 2,157,756 bp, with a G+C content of 33.0%.
Genome Sequences of Multidrug-Resistant, Colistin-Susceptible and -Resistant Klebsiella pneumoniae Clinical Isolates from Pakistan
Authors: Crawford Matthew A. , Timme Ruth , Lomonaco Sara , Lascols Christine , Fisher Debra J. , Sharma Shashi K. , Strain Errol , Allard Marc W. , Brown Eric W. , McFarland Melinda A. , Croley Tim , Hammack Thomas S. , Weigel Linda M. , Anderson Kevin , Hodge David R. , Pillai Segaran P. , Morse Stephen A. , Khan Erum , Hughes Molly A.
Published: January 2017

The emergence and spread of colistin resistance among multidrug-resistant (MDR)
Klebsiella pneumoniae
represent a critical threat to global health. Here, we report the complete genome sequences of 10 MDR, colistin-susceptible and -resistant
K. pneumoniae
clinical isolates obtained in Pakistan between 2010 and 2013.
Draft Genome Sequences of Type Strains Bacillus drentensis DSM 15600
T
and Bacillus novalis DSM 15603
T
Authors: Liu Bo , Liu Guo-Hong , Zhu Yu-jing , Wang Jie-Ping , Che Jian-Mei , Chen Qian-Qian , Chen Zheng
Published: January 2017

Here, we report the draft genome sequences of
Bacillus drentensis
DSM 15600
T
and
Bacillus novalis
DSM 15603
T
with 5,305,306 bp and 5,667,584 bp, respectively, which will provide useful information for the functional gene mining and application of these two species. The average DNA G+C contents were 38.91% and 40.01%, respectively.
Racecadotril for the treatment of severe acute watery diarrhoea in children admitted to a tertiary hospital in Kenya
Authors: Gharial Jaspreet , Laving Ahmed , Were Fred
Published: January 2017

Background

Diarrhoea is the second most common cause of death in children under 5 years of age in Kenya. It is usually treated with oral rehydration, zinc and continued feeding. Racecadotril has been in use for over 2 decades; however, there is a paucity of data regarding its efficacy from Africa.

Objectives

The objectives of this study were: to compare the number of stools in the first 48 hours in children with severe gastroenteritis requiring admission and treated with either racecadotril or placebo, to study the impact of racecadotril on duration of inpatient stay as well as duration of diarrhoea and to describe the side effect profile of racecadotril.

Methods

This was a randomised, double-blinded, placebo-controlled trial. It enrolled children between the age of 3 and 60 months who were admitted with severe acute gastroenteritis. They received either racecadotril or placebo in addition to oral rehydration solution (ORS) and zinc and were followed up daily.

Results

120 children were enrolled into the study. There were no differences in the demographics or outcomes between the 2 groups. Stools at 48 hours: median (IQR) of 5 (3–7) and 5 (2.5–7.5), respectively; p=0.63. The duration of inpatient stay: median (IQR): 4 days (1.5–6.5) and 4.5 (1.8–6.3); p=0.71. The duration of illness: 3 days (2–4) and 2 days (1–3); p=0.77. The relative risk of a severe adverse event was 3-fold higher in the drug group but was not statistically significant (95% CI 0.63 to 14.7); p=0.16.

Conclusions

Racecadotril has no impact on the number of stools at 48 hours, the duration of hospital stay or the duration of diarrhoea in children admitted with severe gastroenteritis and managed with ORS and zinc.

Trial registration number

PACTR201403000694398; Pre-results.
PPH Butterfly: a novel device to treat postpartum haemorrhage through uterine compression
Authors: Cunningham Caroline , Watt Peter , Aflaifel Nasreen , Collins Simon , Lambert Dot , Porter John , Lavender Tina , Fisher Tony , Weeks Andrew
Published: January 2017

Objective

Postpartum haemorrhage (PPH) is a significant cause of maternal morbidity and mortality. The most common cause is an inability of the uterus to contract adequately after childbirth. In bimanual compression (BMC), one hand is placed within the vagina and the other hand is on the abdominal wall to compress the uterus. It is effective, but very uncomfortable for the woman. We designed a device that could replicate BMC without inserting a hand vaginally, therefore being less invasive. It could also help in diagnosing the source of the bleeding.

Design

Mixed methods, combining an iterative design process with input from clinicians in simulations, and focus groups of clinicians and consumers.

Setting

Department of Women's and Children's Health and Department of Medical Physics and Clinical Engineering, University of Liverpool, UK.

Methods

A multidisciplinary team developed the design, using an obstetric manikin. Clinician and consumer groups also gave input on the concept and design. A healthcare product company and prototype manufacturer provided input into strategy, design and manufacture.

Results

The PPH Butterfly is a single piece, plastic medical device that replicates BMC. It is designed to be easy to use and low-cost and allows for smooth insertion and removal. It is acceptable to clinicians and consumers and performs well in tests.

Conclusions

This is the first device designed to replicate BMC while being less invasive. It could potentially be an effective form of PPH management, while also diagnosing the source of the bleeding. The device will now be tested in humans.
Could low Safety Attitudes Questionnaire scores be indicative of an environment where it may be difficult to get new training practices established?
Authors: Channing Sarah , Ryan Neil , Barnes Sophie , Collins Kate , van der Nelson Helen , Mears Jane , Siassakos Dimitrios
Published: January 2017

Introduction

Simulation-based, multiprofessional team training (SBMPTT) is used widely in healthcare, with evidence that it can improve clinical outcomes and be associated with a positive safety culture. Our aim was to explore the impact of introducing this type of training to a gynaecological team.

Methods

In this interrupted time-series study, ‘Safety Attitudes Questionnaire’ (SAQ) data was collected both before and after SBMPTT was introduced to a gynaecological team.

Results

Low baseline SAQ scores coincided with difficulty in establishing the training, meaning that at the end of our study period only a small proportion of staff had actually attended a training session. Despite trends towards improvement in scores for safety climate, teamwork climate and job satisfaction, no statistically significant difference was observed. There was however an improved perception of the level of collaboration between nursing staff and doctors after the introduction of training.

Conclusions and Discussion

In this paper we explore a hypothesis that low baseline SAQ scores may highlight that the multiprofessional teams most in need of training work in environments where it is more challenging to implement. There is evidence from other specialties that multiprofessional team training works, now we need to understand how to address the barriers to getting it started. In this paper we suggest how the SAQ could be used as a directive tool for improvement; using the detailed analysis of the local safety culture it provides to both inform future training design and also provide management with an objective marker of progress.
Using simulation to address care of the transgender patient in nursing curricula
Authors: Díaz Desiree A , Maruca Annette , Gonzalez Laura , Stockmann Cherrill , Hoyt Erica
Published: January 2017

This descriptive study explored the use of simulation as a means to increase cognitive and reflective practice as well as determining if simulation can alter perceptions and attitudes related to the lesbian, gay, bisexual and transgender (LGBT) community. This manuscript describes how student nurses perceive their role when providing care to and, more specifically, the care of transgender patients. The research question asks: How does a transgender simulation impact the attitudes and beliefs of nursing students related to the LGBT community? One-hundred and fifty-nine students, with a subset of 120 students attending a school in central Florida and 50 students attending a Connecticut programme, participated in the completion of the instruments. The Gender Affirmative Practice (GAP) scale was used to evaluate their attitudes and practice concerning LGBT issues. Findings suggest that the majority of the students rarely or never discuss pertinent sexual orientation issues. Students are not comfortable creating a climate that allows for self-identification by gay/ lesbians, despite admitting to being open and accepting the LGBT community with their faculty. Limitations were based on multisite location and the use of the GAP. It is important for nursing students, and healthcare providers, to acknowledge and recognise the unique vulnerabilities of transgender persons who are seeking healthcare. The exposure to transgender individuals in a clinical setting may be limited; therefore, the use of simulation will offer the opportunity to examine their beliefs and reflect on their attitudes towards this population. Simulation incorporating mental health issues is a newer training technique in which psychosocial aspects of healthcare are addressed.
Clot friction variation with fibrin content; implications for resistance to thrombectomy
Authors: Gunning Gillian M , McArdle Kevin , Mirza Mahmood , Duffy Sharon , Gilvarry Michael , Brouwer Patrick A
Published: January 2017

Background

Despite significant advancements in the procedural efficacy of mechanical thrombectomy in patients with ischemic stroke in recent years, there still remains a portion of the population that does not achieve good recanalization. The reasons for this may be varied. We hypothesized that static friction between the clot and the vessel, or catheter wall might contribute to the difficulty in removing the clot.

Objective

To determine if there is a relationship between clot composition and the resistance to sliding (friction) which might contribute to resistance to clot removal.

Methods

As clot composition can vary significantly, we investigated five different types of clot in order to measure their respective frictional properties. To do this, a custom-made testing apparatus was created, consisting of various replaceable low-friction surfaces on which the clots could be placed. The surface was then gradually tilted until the clots began to slide; the angle at which this occurred is related to the coefficient of friction of the clots. The experiment was repeated on a bovine aortic surface in order to confirm the results.

Results

We found that fibrin-rich clots (<20% red blood cell content) have a significantly higher coefficient of friction than clots with a red blood cell content >20%. This result was confirmed by repeating the experiment on a bovine aortic surface as a representation of the interaction between clots and the arterial wall.

Conclusions

The friction properties of clots were found to be related to the content ratio of fibrin to red blood cells. Future imaging techniques that could show fibrin and red blood cell content might help us to predict the ‘stickiness’ of a clot.
Associations between physical activity, screen time, and fitness among 6- to 10-year-old children living in Edmonton, Canada
Authors: Potter Morgan , Spence John C. , Boulé Normand G. , Stearns Jodie A. , Carson Valerie
Published: January 2017

The objectives of this study were to describe fitness levels; examine associations between physical activity (PA), screen time (ST), and fitness; and examine sex-moderating effects in a sample of children. Participants were 649 children (age, 7.8 ± 0.6 years; 52.4% female) from Edmonton, Canada. Hours/week of PA and ST were parent-reported. PA was also objectively measured with pedometers and expressed in increments of 1000 steps/day. Fitness components (i.e., vertical jump, sit-and-reach, waist circumference, grip strength, predicted maximal oxygen consumption, push-ups, partial curl-ups, overall fitness) were measured according to the Canadian Physical Activity, Fitness, and Lifestyle Approach protocols and expressed as z scores or low/high fitness. Positive associations were observed between PA and overall fitness for both the complete (subjective: β = 0.009, 95% confidence interval (CI): 0.001−0.017) and partial (≥3 available fitness measures; subjective: β = 0.006, 95% CI: 0.000−0.011; objective: β = 0.025, 95% CI: 0.007−0.042) fitness scores. Subjective (β = 0.011, 95% CI: 0.000−0.022) and objective (β = 0.043, 95% CI: 0.008−0.078) PAs were positively associated with vertical jump. Children with higher objective PA were more likely to be in the high push-ups group (odds ratio = 1.156, 95% CI: 1.054−1.267). PA was positively associated with predicted maximal oxygen uptake (subjective: β = 0.040, 95% CI: 0.018−0.063; objective: β = 0.084, 95% CI: 0.012−0.157) and grip strength (subjective: β = 0.025, 95% CI: 0.011−0.040) in boys only. ST was negatively associated with grip strength (β = –0.016, 95% CI: –0.028 to –0.004) in boys. PA was associated with several components of fitness, especially in boys. However, few associations were observed between ST and fitness. Promoting regular PA in young children may address declining fitness levels.
Efficacy of a randomized trial examining commercial weight loss programs and exercise on metabolic syndrome in overweight and obese women
Authors: Baetge Claire , Earnest Conrad P. , Lockard Brittanie , Coletta Adriana M. , Galvan Elfego , Rasmussen Christopher , Levers Kyle , Simbo Sunday Y. , Jung Y. Peter , Koozehchian Majid , Oliver Jonathan , Dalton Ryan , Sanchez Brittany , Byrd Michael J. , Khanna Deepesh , Jagim Andrew , Kresta Julie , Greenwood Mike , Kreider Richard B.
Published: January 2017

While commercial dietary weight-loss programs typically advise exercise, few provide actual programing. The goal of this study was to compare the Curves Complete 90-day Challenge (CC, n = 29), which incorporates exercising and diet, to programs advocating exercise (Weight Watchers Points Plus (WW, n = 29), Jenny Craig At Home (JC, n = 27), and Nutrisystem Advance Select (NS, n = 28)) or control (n = 20) on metabolic syndrome (MetS) and weight loss. We randomized 133 sedentary, overweight women (age, 47 ± 11 years; body mass, 86 ± 14 kg; body mass index, 35 ± 6 kg/m2) into respective treatment groups for 12 weeks. Data were analyzed using chi square and general linear models adjusted for age and respective baseline measures. Data are means ± SD or mean change ± 95% confidence intervals (CIs). We observed a significant trend for a reduction in energy intake for all treatment groups and significant weight loss for all groups except control: CC (−4.32 kg; 95% CI, −5.75, −2.88), WW (−4.31 kg; 95% CI, −5.82, −2.96), JC (−5.34 kg; 95% CI, −6.86, −3.90), NS (−5.03 kg; 95% CI, −6.49, −3.56), and control (0.16 kg, 95% CI, −1.56, 1.89). Reduced MetS prevalence was observed at follow-up for CC (35% vs. 14%, adjusted standardized residuals (adjres.) = 3.1), but not WW (31% vs. 28% adjres. = 0.5), JC (37% vs. 42%, adjres. = −0.7), NS (39% vs. 50% adjres. = −1.5), or control (45% vs. 55% adjres. = −1.7). While all groups improved relative fitness (mL·kg−1·min−1) because of weight loss, only the CC group improved absolute fitness (L/min). In conclusion, commercial programs offering concurrent diet and exercise programming appear to offer greater improvements in MetS prevalence and cardiovascular function after 12 weeks of intervention.
Analysis of codon usage patterns inMorus notabilisbased on genome and transcriptome data
Authors: Wen Yan , Zou Ziliang , Li Hongshun , Xiang Zhonghuai , He Ningjia
Published: January 2017

Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tree), and analyze genome-wide codon usage in 12 other species within the order Rosales. The codon usage of M. notabilis was affected by nucleotide composition, mutation pressure, nature selection, and gene expression level. Translational selection optimal codons were identified and highly expressed genes of M. notabilis tended to use the optimal codons. Genes with higher expression levels have shorter coding region and lower amino acid complexity. Housekeeping genes showed stronger translational selection, which, notably, was not caused by the large differences between the expression level of housekeeping genes and other genes.
Terahertz Response of Tightly Concatenated Two Dimensional InGaAs Field-Effect Transistors Integrated on a Single Chip
Authors: Yermolayev D. M. , Polushkin E. A. , Koval’chuk A. V. , Shapoval S. Yu. , Marem’yanin K. V. , Gavrilenko V. I. , Maleev N. A. , Ustinov V. M. , Zemlyakov V. E. , Yegorkin V. I. , Bespalov V. A. , Popov V. V. , Khmyrova I.
Published: January 2017

THz response of AlGaAs/InGaAs/GaAs HEMT structure has been investigated. The structure consists of the serpentine chain of series connected HEMTs. The source of one is the drain for the subsequent transistor. Experiments have been showed THz response peculiarities of such structures and enhanced noise equivalent power.