bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Pectobacterium Bacteriophage ΦM1 To Escape Two Bifunctional Type III Toxin-Antitoxin and Abortive Infection Systems through Mutations in a Single Viral Gene
Authors: Blower Tim R. , Chai Ray , Przybilski Rita , Chindhy Shahzad , Fang Xinzhe , Kidman Samuel E. , Tan Hui , Luisi Ben F. , Fineran Peter C. , Salmond George P. C. 
Published: February 2017

ABSTRACT

Some bacteria, when infected by their viral parasites (bacteriophages), undergo a suicidal response that also terminates productive viral replication (abortive infection [Abi]). This response can be viewed as an altruistic act protecting the uninfected bacterial clonal population. Abortive infection can occur through the action of type III protein-RNA toxin-antitoxin (TA) systems, such as ToxIN
Pa
from the phytopathogen
Pectobacterium atrosepticum
. Rare spontaneous mutants evolved in the generalized transducing phage ΦM1, which escaped ToxIN
Pa
-mediated abortive infection in
P. atrosepticum
. ΦM1 is a member of the
Podoviridae
and a member of the “KMV-like” viruses, a subset of the T7 supergroup. Genomic sequencing of ΦM1 escape mutants revealed single-base changes which clustered in a single open reading frame. The “escape” gene product, M1-23, was highly toxic to the host bacterium when overexpressed, but mutations in M1-23 that enabled an escape phenotype caused M1-23 to be less toxic. M1-23 is encoded within the DNA metabolism modular section of the phage genome, and when it was overexpressed, it copurified with the host nucleotide excision repair protein UvrA. While the M1-23 protein interacted with UvrA in coimmunoprecipitation assays, a UvrA mutant strain still aborted ΦM1, suggesting that the interaction is not critical for the type III TA Abi activity. Additionally, ΦM1 escaped a heterologous type III TA system (TenpIN
Pl
) from
Photorhabdus luminescens
(reconstituted in
P. atrosepticum
) through mutations in the same protein, M1-23. The mechanistic action of M1-23 is currently unknown, but further analysis of this protein may provide insights into the mode of activation of both systems.

IMPORTANCE
Bacteriophages, the viral predators of bacteria, are the most abundant biological entities and are important factors in driving bacterial evolution. In order to survive infection by these viruses, bacteria have evolved numerous antiphage mechanisms. Many of the studies involved in understanding these interactions have led to the discovery of biotechnological and gene-editing tools, most notably restriction enzymes and more recently the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems. Abortive infection is another such antiphage mechanism that warrants further investigation. It is unique in that activation of the system leads to the premature death of the infected cells. As bacteria infected with the virus are destined to die, undergoing precocious suicide prevents the release of progeny phage and protects the rest of the bacterial population. This altruistic suicide can be caused by type III toxin-antitoxin systems, and understanding the activation mechanisms involved will provide deeper insight into the abortive infection process.
Temperature-Dependent Growth Modeling of Environmental and Clinical Legionella pneumophila Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Genotypes
Authors: Sharaby Yehonatan , Rodríguez-Martínez Sarah , Oks Olga , Pecellin Marina , Mizrahi Hila , Peretz Avi , Brettar Ingrid , Höfle Manfred G. , Halpern Malka 
Published: February 2017

ABSTRACT

Legionella pneumophila
causes waterborne infections resulting in severe pneumonia. High-resolution genotyping of
L. pneumophila
isolates can be achieved by multiple-locus variable-number tandem-repeat analysis (MLVA). Recently, we found that different MLVA genotypes of
L. pneumophila
dominated different sites in a small drinking-water network, with a genotype-related temperature and abundance regime. The present study focuses on understanding the temperature-dependent growth kinetics of the genotypes that dominated the water network. Our aim was to model mathematically the influence of temperature on the growth kinetics of different environmental and clinical
L. pneumophila
genotypes and to compare it with the influence of their ecological niches. Environmental strains showed a distinct temperature preference, with significant differences among the growth kinetics of the three studied genotypes (Gt4, Gt6, and Gt15). Gt4 strains exhibited superior growth at lower temperatures (25 and 30°C), while Gt15 strains appeared to be best adapted to relatively higher temperatures (42 and 45°C). The temperature-dependent growth traits of the environmental genotypes were consistent with their distribution and temperature preferences in the water network. Clinical isolates exhibited significantly higher growth rates and reached higher maximal cell densities at 37°C and 42°C than the environmental strains. Further research on the growth preferences of
L. pneumophila
clinical and environmental genotypes will result in a better understanding of their ecological niches in drinking-water systems as well as in the human body.

IMPORTANCE
Legionella pneumophila
is a waterborne pathogen that threatens humans in developed countries. The bacteria inhabit natural and man-made freshwater environments. Here we demonstrate that different environmental
L. pneumophila
genotypes have different temperature-dependent growth kinetics. Moreover,
Legionella
strains that belong to the same species but were isolated from environmental and clinical sources possess adaptations for growth at different temperatures. These growth preferences may influence the bacterial colonization at specific ecological niches within the drinking-water network. Adaptations for growth at human body temperatures may facilitate the abilities of some
L. pneumophila
strains to infect and cause illness in humans. Our findings may be used as a tool to improve
Legionella
monitoring in drinking-water networks. Risk assessment models for predicting the risk of legionellosis should take into account not only
Legionella
concentrations but also the temperature-dependent growth kinetics of the isolates.
The overlooked human influence in historic and prehistoric floods in the European Alps
Authors: Brisset Elodie , Guiter Frédéric , Miramont Cécile , Troussier Tiané , Sabatier Pierre , Poher Yoann , Cartier Rosine , Arnaud Fabien , Malet Emmanuel , Anthony Edward J. 
Published: February 2017

Abstract
Understanding the role of climate and humans in generating mountain slope instability is crucial because such instability influences downstream fluvial activity and is a major threat to societies. Here, we use the sedimentary archive of Lake Allos (southeastern France), a mountain lake in the European Alps, to characterize mountain flood deposits and vegetation dynamics over the past 7000 yr. Our results support the interpretation of a critical threshold in catchment sensitivity to erosion at 1700 calibrated (cal.) yr B.P. (A.D. 250) probably resulting from long-term, uninterrupted impacts of human activity. The frequency and severity of floods increased dramatically after this date. These results demonstrate that underestimation of human impacts over the Holocene may pose a challenge to a clear understanding of past climate changes because paleoflood records are highly likely to have been affected by geomorphic thresholds. Natural reforestation since the end of the 19th century does not appear to be sufficient to induce a flood regime comparable to that which occurred prior to 1700 cal. yr B.P. This poses the question as to whether forest restoration in high-altitude environments is liable to foster a return to a low-erosion regime over the next decades, or whether the overall severity of soil degradation has been such as to preclude a return to previous conditions.
Aragonitic scleractinian corals in the Cretaceous calcitic sea
Authors: Janiszewska Katarzyna , Mazur Maciej , Escrig Stéphane , Meibom Anders , Stolarski Jarosław 
Published: February 2017

Abstract
Changes in seawater chemistry have affected the evolution of calcifying marine organisms, including their skeletal polymorph (calcite versus aragonite), which is believed to have been strongly influenced by the Mg/Ca ratio at the time these animals first emerged. However, we show that micrabaciids, a scleractinian coral clade that first appeared in the fossil record of the Cretaceous, when the ocean Mg/Ca ratio was near the lowest in the Phanerozoic (thus a priori favoring calcitic mineralogy), formed skeletons composed exclusively of aragonite. Exceptionally preserved aragonitic coralla of Micrabacia from the Late Cretaceous Ripley Formation (southeastern USA) have skeletal microstructures identical to their modern representatives. In addition, skeletons of Micrabacia from Cretaceous chalk deposits of eastern Poland are clearly diagenetically altered in a manner consistent with originally aragonitic mineralogy. These deposits have also preserved fossils of the scleractinian Coelosmilia, the skeleton of which is interpreted as originally calcitic. These findings show that if changes in seawater Mg/Ca ratio influenced the mineralogy of scleractinian corals, the outcome was taxon specific. The aragonitic mineralogy, unique skeletal microstructures and ultrastructures, and low Mg/Ca ratios in both fossil and living micrabaciids indicate that their biomineralization process is strongly controlled and has withstood major fluctuations in seawater chemistry during the past 70 m.y.
Pore fluids in Dead Sea sediment core reveal linear response of lake chemistry to global climate changes
Authors: Levy Elan J. , Stein Mordechai , Lazar Boaz , Gavrieli Ittai , Yechieli Yoseph , Sivan Orit 
Published: February 2017

Abstract
Pore fluids extracted from a 456 m sediment core, recovered within the framework of a multinational and International Continental Scientific Drilling Program (ICDP) co-sponsored effort at the bottom of the terminal Dead Sea, recorded the chemical variations in the deep lake over the past 220 k.y. Mg2+ and Br– were shown to be conservative in the pore fluids, increasing in concentration during interglacial periods, diluting during glacials, and providing excellent proxies for deep lake net water balance changes. Furthermore, the Na/Cl ratio recorded the process of halite precipitation and dissolution induced by these hydrological changes. Mg2+ and Br– records follow a glacial-interglacial pattern, such as observed in atmospheric CO2 concentrations and global sea-surface temperatures, albeit with a phase offset. At the end of the last interglacial (ca. 116 ka), there is a delay in onset of dilution of the deep lake, most likely due to the limnological transition from holomictic to meromictic conditions. The increase in deep lake concentrations at Last Glacial Termination I is delayed as a result of freshwater input into the deep lake during the cooler Younger Dryas period. There is a persistent relationship between precipitation in the watershed and North Atlantic sea-surface temperatures, similar to conditions observed over the past instrumental record. Deviations from the long-term trends occurred during interglacial periods, Marine Isotope Stages MIS 5e and MIS 1, when the deep Dead Sea was significantly diluted, and coincided with Mediterranean sapropel layers S5 and S1.
Prevalence and determinants of undetected dementia in the community: a systematic literature review and a meta-analysis
Authors: Lang Linda , Clifford Angela , Wei Li , Zhang Dongmei , Leung Daryl , Augustine Glenda , Danat Isaac M , Zhou Weiju , Copeland John R , Anstey Kaarin J , Chen Ruoling 
Published: February 2017

ObjectivesDetection of dementia is essential for improving the lives of patients but the extent of underdetection worldwide and its causes are not known. This study aimed to quantify the prevalence of undetected dementia and to examine its correlates.Methods/setting/participantsA systematic search was conducted until October 2016 for studies reporting the proportion of undetected dementia and/or its determinants in either the community or in residential care settings worldwide. Random-effects models calculated the pooled rate of undetected dementia and subgroup analyses were conducted to identify determinants of the variation.Primary and secondary outcome measuresThe outcome measures of interest were the prevalence and determinants of undetected dementia.Results23 studies were eligible for inclusion in this review. The pooled rate of undetected dementia was 61.7% (95% CI 55.0% to 68.0%). The rate of underdetection was higher in China and India (vs Europe and North America), in the community setting (vs residential/nursing care), age of <70 years, male gender and diagnosis by general practitioner. However, it was lower in the studies using Mini-Mental State Examination (MMSE) diagnosis criteria.ConclusionsThe prevalence of undetected dementia is high globally. Wide variations in detecting dementia need to be urgently examined, particularly in populations with low socioeconomic status. Efforts are required to reduce diagnostic inequality and to improve early diagnosis in the community.
Cross-sectional study examining the prevalence, correlates and sequencing of electronic cigarette and tobacco use among 11–16-year olds in schools in Wales
Authors: de Lacy Elen , Fletcher Adam , Hewitt Gillian , Murphy Simon , Moore Graham 
Published: February 2017

ObjectivesTo examine the prevalence and frequency of electronic (e)-cigarette use among young people in Wales, associations with socio-demographic characteristics, smoking and other substances and the sequencing of e-cigarette and tobacco use.DesignA cross-sectional survey of school students in Wales undertaken in 2015.Setting87 secondary schools in Wales.ParticipantsStudents aged 11–16 (n=32 479).ResultsOverall, students were nearly twice as likely to report ever using e-cigarettes (18.5%) as smoking tobacco (10.5%). Use of e-cigarettes at least weekly was 2.7% in the whole sample, rising to 5.7% among those aged 15–16. Almost half (41.8%) of daily smokers reported being regular e-cigarette users. Regular e-cigarette use was more prevalent among current cannabis users (relative risk ratio (RRR)=41.82; 95% CI 33.48 to 52.25)), binge drinkers (RRR=47.88; 95% CI 35.77 to 64.11), users of mephedrone (RRR=32.38; 95% CI 23.05 to 45.52) and laughing gas users (RRR=3.71; 95% CI 3.04 to 4.51). Multivariate analysis combining demographics and smoking status showed that only gender (being male) and tobacco use independently predicted regular use of e-cigarettes (p<0.001). Among weekly smokers who had tried tobacco and e-cigarettes (n=877), the vast majority reported that they tried tobacco before using an e-cigarette (n=727; 82.9%).ConclusionsSince 2013, youth experimentation with e-cigarettes has grown rapidly in Wales and is now almost twice as common as experimentation with tobacco. Regular use has almost doubled, and is increasing among never and non-smokers. These data suggest that e-cigarette use among youth is an emerging public health issue, even though there remains no evidence that it represents a new pathway into smoking. Mixed methods longitudinal research is needed to explore why young people use e-cigarettes, and to develop interventions to prevent further increases in use.
Close look at the experiences of patients enrolled in a clinical trial of acupuncture treatment for atrial fibrillation in Korea: a qualitative study nested within a randomised controlled trial
Authors: Lee Seung Min Kathy , Leem Jungtae , Park Jun Hyeong , Yoon Kang Hyun , Woo Jong Shin , Lee Jung Myung , Kim Jin-Bae , Kim Weon , Lee Sanghoon 
Published: February 2017

ObjectiveTo explore the experiences of patients with atrial fibrillation (AF) in the context of a prospective, two-parallel-armed, participant-blinded and assessor-blinded sham-controlled randomised trial.DesignA nested qualitative study within an ongoing randomised controlled trial to explore acupuncture's antiarrhythmic effects on drug refractory acupuncture in persistent atrial fibrillation (AF) (ACU-AF trial).ParticipantsParticipants were recruited using purposeful sampling and a maximum variation strategy with regard to treatment allocation (treatment or control) and protocol completion (completion or non-completion).SettingThis was a single-centre in-depth interview qualitative study conducted at a tertiary-level university hospital in Seoul, Republic of Korea.ResultsData saturation was reached after 8 participants. Thematic analysis identified that most patients were not aware of their condition until medical check-up; physician referral was the main reason for trial participation, and patients had high expectations regardless of previous acupuncture experiences. Patients tended to depend on their physicians' opinions because they felt helpless of their condition. No one questioned their assigned treatment groups and generally believed acupuncture treatment was different for cardiovascular diseases. A few patients expressed disappointment in the strict and rigid protocols, in which most practitioners refrained from explaining their acupuncture procedures.ConclusionsFor cardiovascular patients their physician's advice was one of the biggest reasons for enrolling in the acupuncture trial therefore relying on standard recruitment methods may not be effective. Fortunately both real and sham acupuncture groups in our sample were receiving treatment as intended, but in the future, designing a more pragmatic trial (better reflecting clinical settings, expanding the inclusion criteria and using more treatment points) will allow researchers to better explore the comprehensive effects of acupuncture. The findings of this study will allow researchers to improve the currently ongoing ACU-AF trial and to further help interpretation of main trial outcomes once the trial is completed.Trial registration number:NCT02110537.
Regional differences in usage of antenatal care and safe delivery services in Indonesia: findings from a nationally representative survey
Authors: Tripathi Vrijesh , Singh Rajvir 
Published: February 2017

BackgroundIndonesia has shown a nominal increase in antenatal care (ANC) coverage from 93% to 96% in the Indonesia Demographic Health Survey (IDHS)—2012. This is high but for a comprehensive assessment of maternal health coverage in Indonesia, safe delivery services need to be assessed in conjunction with ANC coverage.Materials and methodsThe study uses survey data from the IDHS-2012 that was conducted among women aged 15–49 years who gave birth during the past 3 years preceding the survey. Socioeconomic and demographic factors affecting ANC coverage and safe delivery services are analysed by segregating the data into 7 regions of Indonesia.ResultsMultivariate results show that besides wealth and education differentials, regional differences significantly affect the usage of ANC and safe delivery services across the 7 regions. Univariate analyses show that Sulawesi, Maluku and Western New Guinea islands are at a disadvantage in accessing ANC and safe delivery services.ConclusionsThe study recommends that disaggregated regional targets be set in order to further reduce maternal mortality rates in Indonesia.
Longitudinal study of weight, energy intake and physical activity change across two decades in older Scottish women
Authors: Yang Tiffany C , Gryka Anna A , Aucott Lorna S , Duthie Garry G , Macdonald Helen M 
Published: February 2017

BackgroundThe perimenopausal and postmenopausal periods are times of pronounced physiological change in body mass index (BMI), physical activity and energy intake. Understanding these changes in middle age could contribute to formation of potential public health targets.MethodA longitudinal cohort of 5119 perimenopausal women from the Aberdeen Prospective Osteoporosis Screening Study (APOSS) recruited between 1990 and 1994, with follow-up visits at 1997–1999 and 2009–2011. At each visit, participants were weighed, measured and completed socioeconomic and demographic questionnaires. Participants at the first visit were asked to recall body weights at 20, 30 and 40 years of age. We assessed trends in BMI, physical activity and energy intake across and within visits.ResultsOver 2 decades, obesity prevalence doubled from 14% to 28% of the participants, with 69% of participants being categorised as overweight or obese. Greater than 70% of participants gained >5% of their baseline BMI with weight gain occurring across all weight categories. Energy intake and physical activity levels (PALs) did not change during the 2 decades after menopause (p trend=0.06 and 0.11, respectively), but, within the second visit, energy intake increased concomitantly with a decrease in physical activity across increasing quartiles of BMI (p trend <0.001 for all).ConclusionsOverweight and obesity increased by over 50% over the course of 20 years. Weight gain occurred across the adult life course regardless of starting weight. The marked increase in dietary intake and decrease in PALs in middle age suggest a potential critical period for intervention to curb excess weight gain.
The Knarr Field: a new development at the northern edge of the North Sea
Authors: Skarpeid Silje S. , Churchill James M. , Hilton Jamie P. J. , Izatt Chris N. , Poole Matthew T. 
Published: February 2017

Abstract

The Knarr Field is located in the northern Norwegian North Sea, beyond the Brent Group delta fairway. Knarr was discovered in 2008 with the Jordbær well, additional resources were added to the field in 2011 with the successful Jordbær Vest well. The field extends over an area of approximately 20 km
2
. The original oil in place is estimated to be 26 MSm
3
(163 MBBL). The reservoir is the Late Pliensbachian Cook Formation and its current burial depth is approximately −3700 m true vertical depth subsea (TVDSS). In Knarr, the Cook Formation is split into five sandstones that are separated by four shale intervals which can be correlated across the field. The three lower sands (Lower Cook) are interpreted to have been deposited in a tidally-dominated environment, while the upper two sandstones (Upper Cook) were deposited in a wave-dominated shallow-marine setting. The reservoir properties of the Cook Formation in the Knarr area are remarkably good for a reservoir at this depth, with porosities up to 28% and permeabilities in excess of 1 D. The good reservoir properties are the result of grain-coating chlorite, which has inhibited diagenetic quartz development. The field is developed with three oil producers and three water injectors produced via a floating production storage and offloading vessel (FPSO). First oil was achieved in March 2015.