bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal dynamics of circadian phase shifting response to consecutive night shifts in healthcare workers: role of light–dark exposure
Authors: Stone Julia E. , Sletten Tracey L. , Magee Michelle , Ganesan Saranea , Mulhall Megan D. , Collins Allison , Howard Mark , Lockley Steven W. , Rajaratnam Shantha M. W. 
Published: March 2018

Key points
Shift work is highly prevalent and is associated with significant adverse health impacts.
There is substantial inter‐individual variability in the way the circadian clock responds to changing shift cycles. The mechanisms underlying this variability are not well understood.
We tested the hypothesis that light–dark exposure is a significant contributor to this variability; when combined with diurnal preference, the relative timing of light exposure accounted for 71% of individual variability in circadian phase response to night shift work.
These results will drive development of personalised approaches to manage circadian disruption among shift workers and other vulnerable populations to potentially reduce the increased risk of disease in these populations.
AbstractNight shift workers show highly variable rates of circadian adaptation. This study examined the relationship between light exposure patterns and the magnitude of circadian phase resetting in response to night shift work. In 21 participants (nursing and medical staff in an intensive care unit) circadian phase was measured using 6‐sulphatoxymelatonin at baseline (day/evening shifts or days off) and after 3–4 consecutive night shifts. Daily light exposure was examined relative to individual circadian phase to quantify light intensity in the phase delay and phase advance portions of the light phase response curve (PRC). There was substantial inter‐individual variability in the direction and magnitude of phase shift after three or four consecutive night shifts (mean phase delay −1:08 ± 1:31 h; range −3:43 h delay to +3:07 h phase advance). The relative difference in the distribution of light relative to the PRC combined with diurnal preference accounted for 71% of the variability in phase shift. Regression analysis incorporating these factors estimated phase shift to within ±60 min in 85% of participants. No participants met criteria for partial adaptation to night work after three or four consecutive night shifts. Our findings provide evidence that the phase resetting that does occur is based on individual light exposure patterns relative to an individual's baseline circadian phase. Thus, a ‘one size fits all’ approach to promoting adaptation to shift work using light therapy, implemented without knowledge of circadian phase, may not be efficacious for all individuals.
Integrase-Mediated Recombination of the
bel-1
Gene Cassette Encoding the Extended-Spectrum β-Lactamase BEL-1
Authors: Bouheraoua Nacim , Poirel Laurent , Bourreau Baptiste , Bonnin Rémy , Laroche Laurent , Naas Thierry , Nordmann Patrice 
Published: March 2018

ABSTRACT

Integrons are genetic elements that can acquire and rearrange gene cassettes. The
bla
BEL-1
gene encodes an extended-spectrum β-lactamase, BEL-1, that is present at the second position of the variable region of class 1 integrons identified in
Pseudomonas aeruginosa
. The mobility of the
bel-1
gene cassette was analyzed under physiological conditions and with the integrase gene being overexpressed. Cassette mobility in
Escherichia coli
was detected by excision/integration into the recipient integron In
3
on the conjugative plasmid R388 with the overproduced integrase. Despite several antibiotic pressures, the
bel-1
cassette remained at the second position in the integron, highlighting its stability in
P. aeruginosa
. Overexpression of the integrase gene in
E. coli
induced
bel-1
cassette recombination. However, cassettes containing two genes (
bla
BEL-1
and
smr2
or
bla
BEL-1
and
aacA4
) were excised, suggesting that the
bel-1
cassette
attC
site was defective. We show that
bel-1
is a stable gene cassette under physiological growth conditions, irrespective of the selective antibiotic pressure, that may be mobilized upon overexpression of the integrase gene.
Evaluation of the
In Vitro
Activity of Eravacycline against a Broad Spectrum of Recent Clinical Anaerobic Isolates
Authors: Snydman David R. , McDermott Laura A. , Jacobus Nilda V. , Kerstein Kathryn , Grossman Trudy H. , Sutcliffe Joyce A. 
Published: March 2018

ABSTRACT

The novel fluorocycline antibiotic eravacycline is in development for use in the treatment of serious infections caused by susceptible and multidrug-resistant (MDR) aerobic and anaerobic Gram-negative and Gram-positive pathogens. Eravacycline and 11 comparator antibiotics were tested against recent anaerobic clinical isolates, including MDR
Bacteroides
spp. and
Clostridium difficile
. Eravacycline was potent
in vitro
against all the isolates tested, including strains with tetracycline-specific resistance determinants and MDR anaerobic pathogens resistant to carbapenems and/or β-lactam–β-lactamase inhibitor combinations.
On the Enigma of Glutathione-Dependent Styrene Degradation in Gordonia rubripertincta CWB2
Authors: Heine Thomas , Zimmerling Juliane , Ballmann Anne , Kleeberg Sebastian Bruno , Rückert Christian , Busche Tobias , Winkler Anika , Kalinowski Jörn , Poetsch Ansgar , Scholtissek Anika , Oelschlägel Michel , Schmidt Gert , Tischler Dirk 
Published: March 2018

ABSTRACTAmong bacteria, only a single styrene-specific degradation pathway has been reported so far. It comprises the activity of styrene monooxygenase, styrene oxide isomerase, and phenylacetaldehyde dehydrogenase, yielding phenylacetic acid as the central metabolite. The alternative route comprises ring-hydroxylating enzymes and yields vinyl catechol as central metabolite, which undergoesmeta-cleavage. This was reported to be unspecific and also allows the degradation of benzene derivatives. However, some bacteria had been described to degrade styrene but do not employ one of those routes or only parts of them. Here, we describe a novel “hybrid” degradation pathway for styrene located on a plasmid of foreign origin. As putatively also unspecific, it allows metabolizing chemically analogous compounds (e.g., halogenated and/or alkylated styrene derivatives).Gordonia rubripertinctaCWB2 was isolated with styrene as the sole source of carbon and energy. It employs an assembled route of the styrene side-chain degradation and isoprene degradation pathways that also funnels into phenylacetic acid as the central metabolite. Metabolites, enzyme activity, genome, transcriptome, and proteome data reinforce this observation and allow us to understand this biotechnologically relevant pathway, which can be used for the production of ibuprofen.IMPORTANCEThe degradation of xenobiotics by bacteria is not only important for bioremediation but also because the involved enzymes are potential catalysts in biotechnological applications. This study reveals a novel degradation pathway for the hazardous organic compound styrene inGordonia rubripertinctaCWB2. This study provides an impressive illustration of horizontal gene transfer, which enables novel metabolic capabilities. This study presents glutathione-dependent styrene metabolization in an (actino-)bacterium. Further, the genomic background of the ability of strain CWB2 to produce ibuprofen is demonstrated.
Draft Genome Sequence of the First New Delhi Metallo-β-Lactamase (NDM-1)-Producing Escherichia coli Strain Isolated in Peru
Authors: Tamariz Jesus , Llanos Carlos , Seas Carlos , Montenegro Paola , Lagos Jose , Fernandes Miriam R. , Cerdeira Louise , Lincopan Nilton 
Published: March 2018

ABSTRACT

We present here the draft genome sequence of the first New Delhi metallo-β-lactamase (NDM-1)-producing
Escherichia coli
strain, belonging to sequence type 155 (ST155), isolated in Peru. Assembly of this draft genome resulted in 5,061,184 bp, revealing a clinically significant resistome for β-lactams, aminoglycosides, tetracyclines, phenicols, sulfonamides, trimethoprim, and fluoroquinolones.
Genome Sequence of the Amphotericin B-Resistant Candida duobushaemulonii Strain B09383
Authors: Chow Nancy A. , Gade Lalitha , Batra Dhwani , Rowe Lori A. , Juieng Phalasy , Loparev Vladimir N. , Litvintseva Anastasia P. 
Published: March 2018

ABSTRACT

Candida duobushaemulonii
is a drug-resistant yeast that can cause invasive candidiasis. Here, we report the first genome sequence of
C. duobushaemulonii
, isolate B09383, generated using PacBio sequencing technology. The estimated genome size was 12.5 Mb with a GC content of 46.84%.
Escherichia coli H-Genotyping PCR: a Complete and Practical Platform for Molecular H Typing
Authors: Banjo Masaya , Iguchi Atsushi , Seto Kazuko , Kikuchi Taisei , Harada Tetsuya , Scheutz Flemming , Iyoda Sunao , Matsumoto Masakado , Unno Yuri , Nakajima Hiroshi , Kariya Hideaki , Hozumi Nodoka , Kameyama Yoshihiko , Noda Makiko , Kadokura Yukiko , Obara Atsumi , Harada Seiya , Hama Natsuki , Nomoto Ryohei , Kurazono Takayuki , Tsunomori Yoshie , Hoshi Toshinobu , Kitahashi Tomoko , Kimata Keiko , Isobe Junko Junko , Ojima Hiroko , Takaki Yumika , Aoki Junko , Yamamoto Kazunari , Taoka Yukihiro , Nagata Akihiro , Iwasaki Satomi , Tsuru Nami , Yoshino Shuji , Ohtsuka Hitoshi , Kameyama Mitsuhiro , Obane Noriko , Ogawa Atsuko , Matsumoto Yuko 
Published: March 2018

ABSTRACT

In
Escherichia coli
, more than 180 O groups and 53 H types have been recognized. The O:H serotyping of
E. coli
strains is an effective method for identifying strains with pathogenic potential and classifying them into clonal groups. In particular, the serotyping of Shiga toxin-producing
E. coli
(STEC) strains provides valuable information to evaluate the routes, sources, and prevalence of agents in outbreak investigations and surveillance. Here, we present a complete and practical PCR-based H-typing system,
E. coli
H-genotyping PCR, consisting of 10 multiplex PCR kits with 51 single PCR primer pairs. Primers were designed based on a detailed comparative analysis of sequences from all H-antigen (flagellin)-encoding genes,
fliC
and its homologs. The specificity of this system was confirmed by using all H type reference strains. Additionally, 362 serotyped wild strains were also used to evaluate its practicality. All 277 H-type-identified isolates gave PCR products that corresponded to the results of serological H typing. Moreover, 76 nonmotile and nine untypeable strains could be successfully subtyped into any H type by the PCR system. The
E. coli
H-genotyping PCR developed here allows broader, rapid, and low-cost subtyping of H types and will assist epidemiological studies as well as surveillance of pathogenic
E. coli
.
Control of HIV-1 Pathogenesis in Viremic Nonprogressors Is Independent of Gag-Specific Cytotoxic T Lymphocyte Responses
Authors: Salgado Maria , Garcia-Minambres Albert , Dalmau Judith , Jiménez-Moyano Esther , Viciana Pompeyo , Alejos Belén , Clotet Bonaventura , Prado Julia G. , Martinez-Picado Javier 
Published: March 2018

ABSTRACT

Viremic nonprogressors (VNPs) constitute a very scarce group of untreated human immunodeficiency virus type 1 (HIV-1)-infected individuals who maintain stable CD4
+
T cell counts despite high levels of HIV-1 replication. The specific factors associated with this atypical control of the HIV infection have been poorly described. Since specific T cell responses seem to be one of the main causes of HIV-1 control in elite controllers, we studied whether HIV-1 Gag-specific cytotoxic T lymphocyte (CTL) responses could also modulate disease control in VNPs. We characterized the immune responses from four VNPs compared to those of five standard progressors (SPs) during the first years of HIV-1 infection. We observed no differences in the breadth and frequency of Gag-specific cellular responses. Furthermore, we obtained 217 HIV-1
Gag
clonal sequences in which the viral variability of Gag increased over 3 years of infection for synonymous and nonsynonymous mutations in both VNPs and SPs. VNPs evolution rates in
gag
were comparable to SPs. This observation is in line with a similar accumulation of CTL putative escape mutations in Gag epitopes targeted by CTL responses. Altogether, the absence of viral pathogenesis in VNP individuals seems to be independent of HIV-Gag-specific CTL responses. This novel information guides to the study of alternative mechanism of HIV-1 pathogenesis control.

IMPORTANCE
Control of HIV infection has been widely studied in elite controllers or long-term nonprogressor models. However, there is a less-known group of individuals, termed viremic nonprogressors (VNPs), who maintain stable CD4
+
T cell counts despite high plasma viremia. The mechanisms involved in this remarkable control of HIV-1 pathogenesis clearly have implications for the development of new drugs and vaccines. We show here for the first time that VNPs have immune responses and HIV-gag evolution similar to those of standard progressors. Remarkably, we demonstrate that the mechanism of pathogenesis control in these individuals differs from some elite controllers that are reported to have improved immune control. This is noteworthy since it opens the door to new, as-yet-unknown mechanisms for HIV control. Our novel results advance the understanding of mechanisms involved in viremic nonprogression and suggest that there are alternative mechanisms to the adaptive immune responses for an effective control of viral pathogenesis.
GCAT|Genomes for life: a prospective cohort study of the genomes of Catalonia
Authors: Obón-Santacana Mireia , Vilardell Mireia , Carreras Anna , Duran Xavier , Velasco Juan , Galván-Femenía Iván , Alonso Teresa , Puig Lluís , Sumoy Lauro , Duell Eric J , Perucho Manuel , Moreno Victor , de Cid Rafael 
Published: March 2018

PurposeThe prevalence of chronic non-communicable diseases (NCDs) is increasing worldwide. NCDs are the leading cause of both morbidity and mortality, and it is estimated that by 2030, they will be responsible for 80% of deaths across the world. The Genomes for Life (GCAT) project is a long-term prospective cohort study that was designed to integrate and assess the role of epidemiological, genomic and epigenomic factors in the development of major chronic diseases in Catalonia, a north-east region of Spain.ParticipantsAt the end of 2017, the GCAT Study will have recruited 20 000 participants aged 40–65 years. Participants who agreed to take part in the study completed a self-administered computer-driven questionnaire, and underwent blood pressure, cardiac frequency and anthropometry measurements. For each participant, blood plasma, blood serum and white blood cells are collected at baseline. The GCAT Study has access to the electronic health records of the Catalan Public Healthcare System. Participants will be followed biannually at least 20 years after recruitment.Findings to dateAmong all GCAT participants, 59.2% are women and 83.3% of the cohort identified themselves as Caucasian/white. More than half of the participants have higher education levels, 72.2% are current workers and 42.1% are classified as overweight (body mass index ≥25 and <30 kg/m2). We have genotyped 5459 participants, of which 5000 have metabolome data. Further, the whole genome of 808 participants will be sequenced by the end of 2017.Future plansThe first follow-up study started in December 2017 and will end by March 2018. Residences of all subjects will be geocoded during the following year. Several genomic analyses are ongoing, and metabolomic and genomic integrations will be performed to identify underlying genetic variants, as well as environmental factors that influence metabolites.
Electroacupuncture plus standard of care for managing refractory functional dyspepsia: protocol of a pragmatic trial with economic evaluation
Authors: Chung Vincent C H , Wong Charlene H L , Ching Jessica Y L , Sun Wai Zhu , Ju Yan Li , Hung Sheung Sheung , Lin Wai Ling , Leung Ka Chun , Wong Samuel Y S , Wu Justin C Y 
Published: March 2018

IntroductionThis trial proposes to compare the effectiveness and cost-effectiveness of electroacupuncture (EA) plus on-demand gastrocaine with waiting list for EA plus on-demand gastrocaine in providing symptom relief and quality-of-life improvement among patients with functional dyspepsia (FD).Methods and analysisThis is a single-centre, pragmatic, randomised parallel-group, superiority trial comparing the outcomes of (1) EA plus on-demand gastrocaine group and (2) waiting list to EA plus on-demand gastrocaine group. 132 (66/arm) endoscopically confirmed,Helicobacter pylori-negative patients with FD will be recruited. Enrolled patients will respectively be receiving (1) 20 sessions of EA over 10 weeks plus on-demand gastrocaine; or (2) on-demand gastrocaine and being nominated on to a waiting list for EA, which entitles them 20 sessions of EA over 10 weeks after 12 weeks of waiting. The primary outcome will be the between-group difference in proportion of patients achieving adequate relief of symptoms over 12 weeks. The secondary outcomes will include patient-reported change in global symptoms and individual symptoms, Nepean Dyspepsia Index, Nutrient Drink Test, 9-item Patient Health Questionnaire (PHQ9), and 7-item Generalised Anxiety Disorder Scale (GAD7). Adverse events will be assessed formally. Results on direct medical costs and on the EuroQol (EQ-5D) questionnaire will also be used to assess cost-effectiveness. Analysis will follow the intention-to-treat principle using appropriate univariate and multivariate methods. A mixed model analysis taking into account missing data of these outcomes will be performed. Cost-effectiveness analysis will be performed using established approach.Ethics and disseminationThe study is supported by the Health and Medical Research Fund, Government of the Hong Kong Special Administrative Region of China. It has been approved by the Joint Chinese University of Hong Kong – New Territories East Cluster Clinical Research Ethics Committee. Results will be published in peer-reviewed journals and be disseminated in international conference.Trial registration numberChiCTR-IPC-15007109; Pre-result.
Recruitment for exercise or physical activity interventions: a protocol for systematic review
Authors: Hoover Jeffrey C , Alenazi Aqeel M , Alothman Shaima , Alshehri Mohammed M , Rucker Jason , Kluding Patricia 
Published: March 2018

IntroductionRecruiting participants into research trials is essential for the advancement of scientific knowledge that depends on clinical research studies. For the field of exercise and physical activity, there is an added difficulty in recruiting participants because participants must be willing to participate in an intervention that requires a significant commitment of both time and physical effort. Therefore, we have planned a systematic review to analyse how methodological factors, intervention characteristics and participant demographics impact recruitment rates in specific populations. This information will help researchers improve the design and recruitment approach in future studies.Methods and analysisA mixed methods systematic review will be performed on studies that implement physical activity interventions and present data on participant recruitment. We plan on searching the Pubmed, Cumulative Index to Nursing and Allied Health Literature and Online Resource for Recruitment research in Clinical Trials databases for potentially eligible articles from database inception through 10 February 2017. A standardised approach will be used to identify studies through a review of titles, abstracts and reference lists. The process for each eligible study is to determine their eligibility, extract data from eligible studies and rate each eligible study’s methodological quality. Exploratory multivariate regression models will be used to determine the effects of methodological factors, intervention characteristics and participant demographics on the recruitment variables of interest.Ethics and disseminationBecause all of the data used in this systematic review has been published, this review does not require ethical approval. The results of this review will be disseminated through peer-reviewed publication as well as through conference presentations.PROSPERO registration numberCRD42017057284.
Self-reported body silhouette trajectories across the lifespan and excessive daytime sleepiness in adulthood: a retrospective analysis. The Paris Prospective Study III
Authors: Lisan Quentin , Tafflet Muriel , Charles Marie-Aline , Thomas Frédérique , Boutouyrie Pierre , Guibout Catherine , Haba-Rubio José , Périer Marie Cécile , Pannier Bruno , Marques-Vidal Pedro , Jouven Xavier , Empana Jean-Philippe 
Published: March 2018

ObjectivesExcessive daytime sleepiness (EDS) is a common sleep complaint in the population and is increasingly recognised as deleterious for health. Simple and sensitive tools allowing identifying individuals at greater risk of EDS would be of public health importance. Hence, we determined trajectories of body silhouette from early childhood to adulthood and evaluated their association with EDS in adulthood.DesignA retrospective analysis in a prospective community-based study.Participants6820 men and women self-reported their silhouette at ages 8, 15, 25, 35 and 45 using the body silhouettes proposed by Stunkardet al. EDS was defined by an Epworth Sleepiness Scale score ≥11.Main outcome measurePresence of EDS in adulthood.ResultsThe study population comprised 6820 participants (mean age 59.8 years, 61.1% men). Five distinct body silhouettes trajectories over the lifespan were identified: 31.9% ‘lean stable’, 11.1% ‘lean increase’, 16.1% ‘lean-marked increase’, 32.5% ‘moderate stable’ and 8.4% ‘heavy stable’. Subjects with a ‘heavy-stable’ trajectory (OR 1.24, 95% CI 0.94 to 1.62) and those with a ‘lean-marked increase’ trajectory (OR 1.46, 95% CI 1.18 to 1.81) were more likely to have EDS when compared with the ‘lean-stable’ group after adjusting for confounding. Further adjustment for birth weight strengthened the magnitude of the ORs.ConclusionIncreasing body silhouette and to a lesser extent constantly high body silhouette trajectory from childhood to adulthood are associated with increased likelihood of EDS, independently of major confounding variables.Trial registration numberNCT00741728; Pre-results.