bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple origins and chromosomal novelty in the allotetraploid Tragopogon castellanus (Asteraceae)
Authors: Mavrodiev Evgeny V. , Chester Michael , Suárez‐Santiago Víctor N. , Visger Clayton J. , Rodriguez Roseana , Susanna Alfonso , Baldini Riccardo M. , Soltis Pamela S. , Soltis Douglas E. 
Published: January 2015

Summary

Tragopogon includes two classic examples of recently formed allopolyploid species in North America: T. mirus and T. miscellus. Older Tragopogon allotetraploids from Eurasia offer ideal taxa for comparing the longer term outcomes of allopolyploidy.

To help resolve the ancestry of one of these older polyploids, phylogenetic analyses of multiple populations of the allotetraploid T. castellanus (2n = 24) and its putative diploid parents, T. crocifolius and T. lamottei, were conducted using sequences from nuclear (internal transcribed spacer, ITS; and alcohol dehydrogenase 1A, Adh) and plastid (trnT‐trnL spacer, trnL intron, trnL‐trnF spacer and rpl16 intron) loci. Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used to investigate the chromosomal constitution of T. castellanus.

Our data confirm that the widely distributed T. crocifolius and the Iberian endemic, T. lamottei, are the diploid parents of T. castellanus, and that this polyploid formed at least three times.

One group of populations of T. castellanus is distinct in exhibiting two pairs of rearranged chromosomes. These data suggest that some of the chromosomal variants that originate in young polyploids (here, an intergenomic translocation) may become fixed in populations, contributing to novelty in older polyploid lineages. The geographical distributions of the allopolyploids and parents are also complex, with allotetraploid populations being disjunct from one or both of the most closely related diploid parental populations.
Findings of a Naloxone Database and its Utilization to Improve Safety and Education in a Tertiary Care Medical Center
Authors: Rosenfeld David M. , Betcher Jeffrey A. , Shah Ruby A. , Chang Yu‐Hui H. , Cheng Meng‐Ru , Cubillo Efrain I. , Griffin Julia M. , Trentman Terrence L. 
Published: January 2015

AbstractIntroductionAnalyzing hospital naloxone use may assist in identification of areas for quality and safety improvement. Our primary objective is to quantitate the incidence of hospital naloxone use and to assess certain patient populations at risk.MethodsDuring the years 2008 to 2011, each clinical scenario where naloxone was administered on an in‐patient care ward was reviewed. The events were assessed to separate situations where naloxone rescue was effective in reversing opioid‐induced intoxication vs. others. Further analysis was conducted to stratify patient populations at greatest risk.ResultsNaloxone was administered for well‐defined opioid‐induced respiratory depression and oversedation 61% of the time, the remainder used for patient deterioration of other etiology. Surgical populations are at risk with an incidence of 3.8/1,000 hospitalized patients, and this is the greatest within 24 hours of surgery. General surgical patients represent the highest surgical patient risk at 5.5/1,000. Medical patients represent lower risk at 2.0/1,000. Patients with patient‐controlled analgesia and epidural opioid infusion are high risk at 12.1 and 13.1/1,000 patients, respectively. Many quality and safety interventions were gradually implemented in response to this data and are summarized. These include nursing and provider education, electronic medical record modification, and more stringent patient monitoring practices.ConclusionExamination of naloxone use can assist in the identification and stratification of patients at risk for opioid‐induced respiratory depression and oversedation and can serve as a driver for improvements in hospital patient safety. This information can also guide other institutions interested in similar improvements.
Downstream lightening and upward heavying: Experiments with sediments differing in density
Authors: Viparelli Enrica , Solari Luca , Hill K. M. 
Published: January 2015

AbstractSorting and selective transport of particles by material density is important for understanding a wide range of processes, including the formation of mineral placers, deposition of mine tailings and routing of tracers and contaminants. This article describes an experimental study of the transport of mixtures of particles of differing density in a sediment‐feed flume. During the runs, a downstream prograding wedge‐shaped deposit was formed. Results show two sorting processes: (i) longitudinal sorting characterized by preferential deposition of heavy particles in the upstream part of the deposit – downstream lightening; and (ii) vertical sorting with less dense particles preferentially deposited in the lowermost portion of the migrating front – upward heavying. Downstream lightening is the analogue of the well‐known downstream fining observed in the more studied case of mixtures of heterogeneous size with the same density. In both cases, the lighter particles are carried further downstream than the heavier particles. Upward heavying is unexpected when compared with deposits of heterogeneous size and same‐density particles, where the heaviest (i.e. coarsest) particles are deposited in the lowermost part of the front. The physical mechanism underlying this upward heavying might be related to the physics of gravity‐driven granular flows; the front of the deposit acts like a dense granular flow down an inclined plane. In this case, the denser particles settle away from the free surface and at the top of the heap, while the lighter particles flow to the bottom. As the front of the deposit advances, this progressively gives rise to an upward heavying pattern. The application of classical surface‐based fractional bedload transport models suggests that equal mobility is not approached in the case of mixtures of particles with uniform size and different densities. This study hypothesizes that other mechanics related to the physics of the segregation processes in these systems contribute to these results.
A mitral annulus tracking approach for navigation of off‐pump beating heart mitral valve repair
Authors: Li Feng P. , Rajchl Martin , Moore John , Peters Terry M. 
Published: January 2015

Purpose:To develop and validate a real‐time mitral valve annulus (MVA) tracking approach based on biplane transesophageal echocardiogram (TEE) data and magnetic tracking systems (MTS) to be used in minimally invasive off‐pump beating heart mitral valve repair (MVR).Methods:The authors’ guidance system consists of three major components: TEE, magnetic tracking system, and an image guidance software platform. TEE provides real‐time intraoperative images to show the cardiac motion and intracardiac surgical tools. The magnetic tracking system tracks the TEE probe and the surgical tools. The software platform integrates the TEE image planes and the virtual model of the tools and the MVA model on the screen. The authors’ MVA tracking approach, which aims to update the MVA model in near real‐time, comprises of three steps: image based gating, predictive reinitialization, and registration based MVA tracking. The image based gating step uses a small patch centered at each MVA point in the TEE images to identify images at optimal cardiac phases for updating the position of the MVA. The predictive reinitialization step uses the position and orientation of the TEE probe provided by the magnetic tracking system to predict the position of the MVA points in the TEE images and uses them for the initialization of the registration component. The registration based MVA tracking step aims to locate the MVA points in the images selected by the image based gating component by performing image based registration.Results:The validation of the MVA tracking approach was performed in a phantom study and a retrospective study on porcine data. In the phantom study, controlled translations were applied to the phantom and the tracked MVA was compared to its “true” position estimated based on a magnetic sensor attached to the phantom. The MVA tracking accuracy was 1.29 ± 0.58 mm when the translation distance is about 1 cm, and increased to 2.85 ± 1.19 mm when the translation distance is about 3 cm. In the study on porcine data, the authors compared the tracked MVA to a manually segmented MVA. The overall accuracy is 2.37 ± 1.67 mm for single plane images and 2.35 ± 1.55 mm for biplane images. The interoperator variation in manual segmentation was 2.32 ± 1.24 mm for single plane images and 1.73 ± 1.18 mm for biplane images. The computational efficiency of the algorithm on a desktop computer with an Intel® Xeon® CPU @3.47 GHz and an NVIDIA GeForce 690 graphic card is such that the time required for registering four MVA points was about 60 ms.Conclusions:The authors developed a rapid MVA tracking algorithm for use in the guidance of off‐pump beating heart transapical mitral valve repair. This approach uses 2D biplane TEE images and was tested on a dynamic heart phantom and interventional porcine image data. Results regarding the accuracy and efficiency of the authors’ MVA tracking algorithm are promising, and fulfill the requirements for surgical navigation.
Low Physical Activity Levels and Associated Factors in Brazilian Adolescents From Public High Schools
Authors: dos Santos Silva Roberto Jerônimo , Santos Silva Diego Augusto , Oliveira Antônio C. 
Published: January 2015

Background:Several studies have shown that physical activity levels have declined in many countries, even with the regular practice of physical education in schools. The purpose of this study was to identify the prevalence of low physical activity levels and associated factors in adolescents enrolled in public high schools in Northeastern Brazil.Methods:The sample was composed of 2259 adolescents (62.3% female) aged 16.26 ± 1.1 years. A questionnaire was applied to collect data on physical activity levels, sociodemographic information, tobacco use and alcohol consumption, nutritional status and sedentary behavior. Descriptive statistics and Poisson regression hierarchized model with Prevalence Rate (PR) and P ≤ .05 were used.Results:Higher prevalence of low physical activity level (89.1%) was observed. It was observed that 19.6% of individuals did not attend physical education classes regularly. Association was identified between low physical activity level and older girls (P = .02) and not attending physical education classes (P < .01). In males, the group most likely to have that low physical activity level was those whose parents studied until three years (P = .04).Conclusions:Low physical activity level was present in most adolescents, more evident in girls. Lifestyle changes are needed, with substitution of sedentary activities for physical and sport activities in schools.
Physical Activity Matters: Associations Among Body Mass Index, Physical Activity, and Health-Related Quality of Life Trajectories Over 10 Years
Authors: Feeny David , Garner Rochelle , Bernier Julie , Thompson Amanda , McFarland Bentson H. , Huguet Nathalie , Kaplan Mark S. , Ross Nancy A. , Blanchard Chris M. 
Published: January 2015

Background:The objective of this study was to assess the associations among body mass index (BMI), leisure time physical activity (LTPA) and health-related quality of life (HRQL) trajectories among adults.Methods:Self-reported data were drawn from the Canadian National Population Health Survey, with respondents being interviewed every 2 years between 1996–97 and 2006–07. Using growth curve modeling, HRQL trajectories for individuals aged 18 and over were associated with measures of BMI and LTPA. Growth models were constructed separately for males and females.Results:Findings suggested that, for males, BMI categories had little impact on baseline HRQL, and no impact on the rate of change in HRQL. Among women, higher BMI categories were associated with significantly lower baseline HRQL. However, BMI had no impact on the rate of change of HRQL. Conversely, for both men and women and regardless of BMI category, LTPA had significant impacts on baseline HRQL, as well as the rate of change in HRQL. Individuals who were inactive or sedentary had much steeper declines in HRQL as they aged, as compared with individuals who were active in their leisure time.Conclusions:The results underscore the importance of LTPA in shaping trajectories of HRQL.
Incorporating Physical Activity Measures Into Environmental Monitoring of National Parks: An Example From Yosemite
Authors: Walden-Schreiner Chelsey , Leung Yu-Fai , Floyd Myron F. 
Published: January 2015

Background:To address increasing prevalence of obesity and associated chronic disease, recent national initiatives have called upon federal agencies to promote healthy lifestyles and provide opportunities for physical activity. In response, the U.S. National Park Service has developed strategies promoting health through physical activity in addition to its well-established biodiversity and landscape conservation mission. Incorporating physical activity measures with routine environmental monitoring would help identify areas where parks can promote active pursuits with minimal environmental impact. This study provides one example of how protocols developed for visitor and environmental monitoring can generate data to evaluate physical activity.Methods:Researchers implemented an observational study in high-use meadows of Yosemite National Park during the summer of 2011. Variables measured include the spatial location of visitors and activity type. Metabolic equivalents (METs) were assigned to activity categories and analyzed for average energy expenditure.Results:Mean METs values indicated sedentary to light physical activity across the meadows, with greater means in areas with boardwalks or paved pathways.Conclusions:Data leveraged in this study provide park managers an example of adapting existing monitoring programs to incorporate indicators relevant to physical activity evaluation and how physical activity may impact resource conditions in national parks.
Cadence, Peak Vertical Acceleration, and Peak Loading Rate During Ambulatory Activities: Implications for Activity Prescription for Bone Health
Authors: Rowlands Alex V. , Schuna John M. , Stiles Victoria H. , Tudor-Locke Catrine 
Published: January 2015

Background:Previous research has reported peak vertical acceleration and peak loading rate thresholds beneficial to bone mineral density (BMD). Such thresholds are difficult to translate into meaningful recommendations for physical activity. Cadence (steps/min) is a more readily interpretable measure of ambulatory activity.Objective:To examine relationships between cadence, peak vertical acceleration and peak loading rate during ambulation and identify the cadence associated with previously reported bone-beneficial thresholds for peak vertical acceleration (4.9 g) and peak loading rate (43 BW/s).Methods:Ten participants completed 8 trials each of: slow walking, brisk walking, slow running, and fast running. Acceleration data were captured using a GT3×+ accelerometer worn at the hip. Peak loading rate was collected via a force plate.Results:Strong relationships were identified between cadence and peak vertical acceleration (r = .96, P < .05) and peak loading rate (r = .98, P < .05). Regression analyses indicated cadences of 157 ± 12 steps/min (2.6 ± 0.2 steps/s) and 122 ± 10 steps/min (2.0 ± 0.2 steps/s) corresponded with the 4.9 g peak vertical acceleration and 43 BW/s peak loading rate thresholds, respectively.Conclusions:Cadences ≥ 2.0 to 2.6 steps/s equate to acceleration and loading rate thresholds related to bone health. Further research is needed to investigate whether the frequency of daily occurrences of this cadence is associated with BMD.
Alginate Lyases from Alginate-Degrading Vibrio splendidus 12B01 Are Endolytic
Authors: Badur Ahmet H. , Jagtap Sujit Sadashiv , Yalamanchili Geethika , Lee Jung-Kul , Zhao Huimin , Rao Christopher V. 
Published: January 2015

ABSTRACT

Alginate lyases are enzymes that degrade alginate through β-elimination of the glycosidic bond into smaller oligomers. We investigated the alginate lyases from
Vibrio splendidus
12B01, a marine bacterioplankton species that can grow on alginate as its sole carbon source. We identified, purified, and characterized four polysaccharide lyase family 7 alginates lyases, AlyA, AlyB, AlyD, and AlyE, from
V. splendidus
12B01. The four lyases were found to have optimal activity between pH 7.5 and 8.5 and at 20 to 25°C, consistent with their use in a marine environment. AlyA, AlyB, AlyD, and AlyE were found to exhibit a turnover number (
k
cat
) for alginate of 0.60 ± 0.02 s
−1
, 3.7 ± 0.3 s
−1
, 4.5 ± 0.5 s
−1
, and 7.1 ± 0.2 s
−1
, respectively. The

K
m

values of AlyA, AlyB, AlyD, and AlyE toward alginate were 36 ± 7 μM, 22 ± 5 μM, 60 ± 2 μM, and 123 ± 6 μM, respectively. AlyA and AlyB were found principally to cleave the β-1,4 bonds between β-
d
-mannuronate and α-
l
-guluronate and subunits; AlyD and AlyE were found to principally cleave the α-1,4 bonds involving α-
l
-guluronate subunits. The four alginate lyases degrade alginate into longer chains of oligomers.
Acid-Adapted Strains of Escherichia coli K-12 Obtained by Experimental Evolution
Authors: Harden Mark M. , He Amanda , Creamer Kaitlin , Clark Michelle W. , Hamdallah Issam , Martinez Keith A. , Kresslein Robert L. , Bush Sean P. , Slonczewski Joan L. 
Published: January 2015

ABSTRACT

Enteric bacteria encounter a wide range of pHs throughout the human intestinal tract. We conducted experimental evolution of
Escherichia coli
K-12 to isolate clones with increased fitness during growth under acidic conditions (pH 4.5 to 4.8). Twenty-four independent populations of
E. coli
K-12 W3110 were evolved in LBK medium (10 g/liter tryptone, 5 g/liter yeast extract, 7.45 g/liter KCl) buffered with homopiperazine-
N
,
N
′-bis-2-(ethanosulfonic acid) and malate at pH 4.8. At generation 730, the pH was decreased to 4.6 with HCl. By 2,000 generations, all populations had achieved higher endpoint growth than the ancestor at pH 4.6 but not at pH 7.0. All evolving populations showed a progressive loss of activity of lysine decarboxylase (CadA), a major acid stress enzyme. This finding suggests a surprising association between acid adaptation and moderation of an acid stress response. At generation 2,000, eight clones were isolated from four populations, and their genomes were sequenced. Each clone showed between three and eight missense mutations, including one in a subunit of the RNA polymerase holoenzyme (
rpoB
,
rpoC
, or
rpoD
). Missense mutations were found in
adiY
, the activator of the acid-inducible arginine decarboxylase (
adiA
), and in
gcvP
(glycine decarboxylase), a possible acid stress component. For tests of fitness relative to that of the ancestor,
lacZ
::
kan
was transduced into each strain. All acid-evolved clones showed a high fitness advantage at pH 4.6. With the cytoplasmic pH depressed by benzoate (at external pH 6.5), acid-evolved clones showed decreased fitness; thus, there was no adaptation to cytoplasmic pH depression. At pH 9.0, acid-evolved clones showed no fitness advantage. Thus, our acid-evolved clones showed a fitness increase specific to low external pH.
Environmental Surveillance of Poliovirus in Sewage Water around the Introduction Period for Inactivated Polio Vaccine in Japan
Authors: Nakamura Tomofumi , Hamasaki Mitsuhiro , Yoshitomi Hideaki , Ishibashi Tetsuya , Yoshiyama Chiharu , Maeda Eriko , Sera Nobuyuki , Yoshida Hiromu 
Published: January 2015

ABSTRACTEnvironmental virus surveillance was conducted at two independent sewage plants from urban and rural areas in the northern prefecture of the Kyushu district, Japan, to trace polioviruses (PVs) within communities. Consequently, 83 PVs were isolated over a 34-month period from April 2010 to January 2013. The frequency of PV isolation at the urban plant was 1.5 times higher than that at the rural plant. Molecular sequence analysis of the viral VP1 gene identified all three serotypes among the PV isolates, with the most prevalent serotype being type 2 (46%). Nearly all poliovirus isolates exhibited more than one nucleotide mutation from the Sabin vaccine strains. During this study, inactivated poliovirus vaccine (IPV) was introduced for routine immunization on 1 September 2012, replacing the live oral poliovirus vaccine (OPV). Interestingly, the frequency of PV isolation from sewage waters declined before OPV cessation at both sites. Our study highlights the importance of environmental surveillance for the detection of the excretion of PVs from an OPV-immunized population in a highly sensitive manner, during the OPV-to-IPV transition period.
Isolation and Screening of Thermophilic Bacilli from Compost for Electrotransformation and Fermentation: Characterization of Bacillus smithii ET 138 as a New Biocatalyst
Authors: Bosma Elleke F. , van de Weijer Antonius H. P. , Daas Martinus J. A. , van der Oost John , de Vos Willem M. , van Kranenburg Richard 
Published: January 2015

ABSTRACT

Thermophilic bacteria are regarded as attractive production organisms for cost-efficient conversion of renewable resources to green chemicals, but their genetic accessibility is a major bottleneck in developing them into versatile platform organisms. In this study, we aimed to isolate thermophilic, facultatively anaerobic bacilli that are genetically accessible and have potential as platform organisms. From compost, we isolated 267 strains that produced acids from C
5
and C
6
sugars at temperatures of 55°C or 65°C. Subsequently, 44 strains that showed the highest production of acids were screened for genetic accessibility by electroporation. Two
Geobacillus thermodenitrificans
isolates and one
Bacillus smithii
isolate were found to be transformable with plasmid pNW33n. Of these,
B. smithii
ET 138 was the best-performing strain in laboratory-scale fermentations and was capable of producing organic acids from glucose as well as from xylose. It is an acidotolerant strain able to produce organic acids until a lower limit of approximately pH 4.5. As genetic accessibility of
B. smithii
had not been described previously, six other
B. smithii
strains from the DSMZ culture collection were tested for electroporation efficiencies, and we found the type strain DSM 4216
T
and strain DSM 460 to be transformable. The transformation protocol for
B. smithii
isolate ET 138 was optimized to obtain approximately 5 × 10
3
colonies per μg plasmid pNW33n. Genetic accessibility combined with robust acid production capacities on C
5
and C
6
sugars at a relatively broad pH range make
B. smithii
ET 138 an attractive biocatalyst for the production of lactic acid and potentially other green chemicals.
Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase
Authors: Du Ying , Yuan Bo , Zeng Yonghui , Meng Jianyu , Li Heng , Wang Ruigang , Li Guojing , Feng Fuying 
Published: January 2015

ABSTRACT
Clavibacter sp. strain CF11, which was isolated from soil at a tomato-planting greenhouse in Inner Mongolia, North China, has a high capability for producing cold-active cellulase at low temperatures. Here, we report the draft genome sequence of strain CF11, which comprises 2,437 protein-coding sequences and 49 RNA-coding sequences.