bluuebunny/crossref_metadata_2025_split huggingface dataset:
Active Transport, Physical Activity, and Distance Between Home and School in Children and Adolescents
Authors: Duncan Scott , White Kate , Mavoa Suzanne , Stewart Tom , Hinckson Erica , Schofield Grant 
Published: August 2015

Background:The distance between home and school is the most consistent predictor of active transport in youth: the closer an individual lives to school, the more likely they are to use active transport. While this suggests that it is preferable to live as close to school as possible, the limited physical activity accumulated during short trips may not offer substantial benefits to active transporters.Methods:The current study investigated the predicted physical activity benefits associated with a range of home-school distances in 595 young people aged 5 to 16 years (Years 1 to 11). Physical activity was measured using sealed pedometers over 7 days. Participants’ home addresses and usual transport mode to and from school were collected via a questionnaire completed by parents (Years 1 to 6) and participants (Years 7 to 11).Results:A nonlinear relationship between predicted weekday activity and distance was detected, such that the high probability of active transport at short distances was offset by the low physical activity associated with walking short distances.Conclusions:A distance of approximately 2 km was associated with the best physical activity outcomes related to active transport (9% to 15% increase on weekdays). These findings have potential implications for future interventions and for planning residential developments or facilities.
The Seated Inactivity Trial (SIT): Physical Activity and Dietary Outcomes Associated With 8 Weeks of Imposed Sedentary Time
Authors: Cull Brooke J. , Haub Mark. D. , Rosenkranz Richard R. , Lawler Thomas , Rosenkranz Sara K. 
Published: August 2015

Background:Sedentary time is an independent risk factor for chronic diseases and mortality. It is unknown whether active adults alter their dietary and/or physical activity behaviors in response to imposed sedentary time, possibly modifying risk. The aim of this study was to determine whether imposed sedentary time would alter typical behaviors of active adults.Methods:Sixteen physically active, young adults were randomized to the no-intervention control (CON, n = 8) group or the sedentary-intervention (SIT, n = 8) group. SIT participants attended monitored sedentary sessions (8 wk, 10 h/wk). Assessments including diet and physical activity occurred at baseline, week 4, and week 9.Results:There were no differences (P > .05) between CON and SIT groups for step counts or time spent in sedentary, light, moderate, or vigorous physical activity when comparing a week during imposed sedentary time (week 4) to baseline and week 9. At week 4, caloric intake was not different from baseline (P > .05) in either group. Caloric intake decreased significantly (P > .05) in SIT from baseline to week 9.Conclusions:Active adults did not alter physical activity or dietary behaviors during the imposed sedentary intervention. However, SIT reduced caloric intake from baseline to week 9, indicating a possible compensatory response to imposed sitting in active adults.
Complete Genome Sequence of Phytopathogenic Pectobacterium atrosepticum Bacteriophage Peat1
Authors: Kalischuk Melanie , Hachey John , Kawchuk Lawrence 
Published: August 2015

ABSTRACT

Pectobacterium atrosepticum
is a common phytopathogen causing significant economic losses worldwide. To develop a biocontrol strategy for this blackleg pathogen of solanaceous plants,
P. atrosepticum
bacteriophage Peat1 was isolated and its genome completely sequenced. Interestingly, morphological and sequence analyses of the 45,633-bp genome revealed that phage Peat1 is a member of the family
Podoviridae
and most closely resembles the
Klebsiella pneumoniae
bacteriophage KP34. This is the first published complete genome sequence of a phytopathogenic
P. atrosepticum
bacteriophage, and details provide important information for the development of biocontrol by advancing our understanding of phage-phytopathogen interactions.
Draft Genome Sequences of Ralstonia solanacearum Race 3 Biovar 2 Strains with Different Temperature Adaptations
Authors: Yuan Kat (Xiaoli) , Cullis Jeff , Lévesque C. André , Tambong James , Chen Wen , Lewis Christopher T. , De Boer Solke H. , Li Xiang (Sean) 
Published: August 2015

ABSTRACT

Ralstonia solanacearum
race 3 biovar 2 (R3bv2) causes brown rot of potato in countries with temperate climates. Here, we report two draft genome sequences of
R. solanacearum
R3bv2 NCPPB909 and CFIA906 with different temperature adaptations. Analysis of these genome sequences will provide detailed insight on virulence, functionality, and plant/pest interactions of this widely distributed and regulated pathogen.
Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Clinical Isolate VRE3, with a Sequence Type 16 Pattern and Novel Structural Arrangement of Tn
1546
Authors: Khan Saeed , Sung Kidon , Marasa Bernard , Min Seonggi , Kweon Ohgew , Nawaz Mohamed , Cerniglia Carl 
Published: August 2015

ABSTRACT

Multidrug-resistant
Enterococcus faecium
has emerged as a nosocomial pathogen that may infect the body at various sites, including the gastrointestinal tract, and has serious implications in human health and disease. Here, we present the draft genome sequence of clinical strain VRE3, which exhibited a sequence type 16 (ST16) pattern and carried truncated Tn
1546
, a mobile genetic element encoding a high level of vancomycin resistance.
Complete Genome Sequence of Staphylococcus aureus FCFHV36, a Methicillin-Resistant Strain Heterogeneously Resistant to Vancomycin
Authors: McCulloch John Anthony , Silveira Alessandro Conrado de Oliveira , Lima Moraes Aline da Costa , Pérez-Chaparro Paula Juliana , Ferreira Silva Manoella , Almeida Lara Mendes , d’Azevedo Pedro Alves , Mamizuka Elsa Masae 
Published: August 2015

ABSTRACT

We report here the sequence of the entire chromosome of
Staphylococcus aureus
strain FCFHV36, a methicillin-resistant strain heterogeneously intermediate to vancomycin, bearing a type II staphylococcal chromosome cassette
mec
element (SCC
mec
), belonging to multilocus sequence type (MLST) 105, and isolated from a vertebra of a patient with osteomyelitis.
High-Quality Draft Genome Sequence of Francisella tularensis subsp.
holarctica
Strain OR96-0246
Authors: Atkins L. M. , Holder M. E. , Ajami N. J. , Metcalf G. A. , Weissenberger G. M. , Wang M. , Vee V. , Han Y. , Muzny D. M. , Gibbs R. A. , Petrosino J. F. 
Published: August 2015

ABSTRACT

The bacterial pathogen
Francisella tularensis
was recently renewed as a tier-one select agent.
F. tularensis
subsp.
tularensis
(type A) and
holarctica
(type B) are of clinical relevance. Here, we report the complete genome of a virulent
F. tularensis
type B strain and describe its usefulness in comparative genomics.
Identification of Nocardia Species by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Khot Prasanna D. , Bird Brian A. , Durrant Robert J. , Fisher Mark A. 
Published: August 2015

ABSTRACTMatrix-assisted laser desorption ionization–time of flight mass spectrometry for identification ofNocardiaspecies remains challenging. By identifying 83.1% (64 of 77) and 80% (8 of 10) to the species and complex levels, respectively, and 94.3% (82 of 87) to the genus level, we show that an approach using routine sample preparation, an up-to-date commercial database minimally augmented with custom spectra, and testing at an early stage of growth is promising.
Persistent Infection by a Mycobacterium tuberculosis Strain That Was Theorized To Have Advantageous Properties, as It Was Responsible for a Massive Outbreak
Authors: Pérez-Lago Laura , Navarro Yurena , Montilla Pedro , Comas Iñaki , Herranz Marta , Rodríguez-Gallego Carlos , Ruiz Serrano María Jesús , Bouza Emilio , García de Viedma Darío 
Published: August 2015

ABSTRACT

The strains involved in tuberculosis outbreaks are considered highly virulent and transmissible. We analyzed the case of a patient in Madrid, Spain, who was persistently infected over an 8-year period by the same Beijing
Mycobacterium tuberculosis
strain. The strain was responsible for a severe outbreak on Gran Canaria Island. The case provides us with a unique opportunity to challenge our assumptions about
M. tuberculosis
Beijing strains. No clinical/radiological findings consistent with a virulent strain were documented, and the
in vitro
growth rate of the strain in macrophages was only moderate. No secondary cases stemming from this prolonged active case were detected in the host population. The strain did not acquire resistance mutations, despite constant treatment interruptions, and it remained extremely stable, as demonstrated by the lack of single-nucleotide-polymorphism (SNP)-based differences between the sequential isolates. Our data suggest that the general assumption about
M. tuberculosis
Beijing strains having advantageous properties (in terms of virulence, transmissibility, and the tendency to acquire mutations and resistance) is not always accurate.
Generation of Live Attenuated Influenza Virus by Using Codon Usage Bias
Authors: Fan Rebecca L. Y. , Valkenburg Sophie A. , Wong Chloe K. S. , Li Olive T. W. , Nicholls John M. , Rabadan Raul , Peiris J. S. Malik , Poon Leo L. M. 
Published: August 2015

ABSTRACTSeasonal influenza epidemics and occasional pandemics threaten public health worldwide. New alternative strategies for generating recombinant viruses with vaccine potential are needed. Interestingly, influenza viruses circulating in different hosts have been found to have distinct codon usage patterns, which may reflect host adaptation. We therefore hypothesized that it is possible to make a human seasonal influenza virus that is specifically attenuated in human cells but not in eggs by converting its codon usage so that it is similar to that observed from avian influenza viruses. This approach might help to generate human live attenuated viruses without affecting their yield in eggs. To test this hypothesis, over 300 silent mutations were introduced into the genome of a seasonal H1N1 influenza virus. The resultant mutant was significantly attenuated in mammalian cells and mice, yet it grew well in embryonated eggs. A single dose of intranasal vaccination induced potent innate, humoral, and cellular immune responses, and the mutant could protect mice against homologous and heterologous viral challenges. The attenuated mutant could also be used as a vaccine master donor strain by introducing hemagglutinin and neuraminidase genes derived from other strains. Thus, our approach is a successful strategy to generate attenuated viruses for future application as vaccines.IMPORTANCEVaccination has been one of the best protective measures in combating influenza virus infection. Current licensed influenza vaccines and their production have various limitations. Our virus attenuation strategy makes use of the codon usage biases of human and avian influenza viruses to generate a human-derived influenza virus that is attenuated in mammalian hosts. This method, however, does not affect virus replication in eggs. This makes the resultant mutants highly compatible with existing egg-based vaccine production pipelines. The viral proteins generated from the codon bias mutants are identical to the wild-type viral proteins. In addition, our massive genome-wide mutational approach further minimizes the concern over reverse mutations. The potential use of this kind of codon bias mutant as a master donor strain to generate other live attenuated viruses is also demonstrated. These findings put forward a promising live attenuated influenza vaccine generation strategy to control influenza.
Adenovirus E4-ORF1 Dysregulates Epidermal Growth Factor and Insulin/Insulin-Like Growth Factor Receptors To Mediate Constitutive Myc Expression
Authors: Kong Kathleen , Kumar Manish , Taruishi Midori , Javier Ronald T. 
Published: August 2015

ABSTRACT
The E4-ORF1 protein encoded by human adenovirus stimulates viral replication in human epithelial cells by binding and activating cellular phosphatidylinositol 3-kinase (PI3K) at the plasma membrane and cellular Myc in the nucleus. In this study, we showed that E4-ORF1 hijacks the tyrosine kinase activities of cellular epidermal growth factor receptor (EGFR) and insulin receptor (InsR)/insulin-like growth factor receptor 1 (IGF1R), as well as the lipid kinase activity of PI3K, to mediate constitutive Myc protein expression. We additionally demonstrated that EGFR contributes to constitutive Myc expression through the capacity of E4-ORF1 to induce ligand-independent EGFR activation and stimulation of the Ras/Mek/Erk pathway, the latter activity of which was conserved by human adenoviruses. Results further suggested that EGFR normally forms a complex with the cellular PDZ protein Discs Large 1 (Dlg1), a component of the Dlg1:E4-ORF1:PI3K ternary complex that mediates E4-ORF1-induced PI3K activation, and that E4-ORF1 binds the Dlg1:EGFR complex and promotes the association of EGFR with InsR and IGF1R. In addition to its role in constitutive Myc expression, InsR/IGF1R also negatively regulates EGFR autophosphorylation and EGFR-mediated Ras/Mek/Erk signaling, and data suggested that E4-ORF1 binding to Dlg1 antagonizes these activities. Collectively, our findings suggest that in human epithelial cells, E4-ORF1 targets EGFR, InsR/IGF1R, and PI3K at the plasma membrane to activate cytosolic signaling pathways that sustain Myc protein levels in the nucleus. We postulate that E4-ORF1-induced constitutive Myc expression functions to ensure the formation of nuclear E4-ORF1:Myc complexes, which have been shown to activate Myc and to enhance adenovirus replication.

IMPORTANCE
While human adenoviruses primarily produce self-limited acute infections in humans, these agents are associated with life-threatening diseases in immunocompromised patients and in otherwise healthy individuals infected with certain virulent serotypes. The adenovirus E4-ORF1 protein enhances viral replication by activating the cellular lipid kinase PI3K and the cellular transcription factor Myc. Here we report that E4-ORF1 usurps the functions of the cellular tyrosine kinase receptors EGFR and InsR
/
IGF1R, as well as PI3K, to sustain Myc protein expression in cells. Furthermore, sustained Myc expression depended on E4-ORF1-induced ligand-independent EGFR activation that stimulated Ras/Mek/Erk signaling, a function found to be conserved by human adenoviruses. Given the established roles of PI3K, the Ras/Mek/Erk pathway, and Myc in the adenovirus life cycle, our findings may aid in the development of safer, more effective therapeutic strategies to treat severe adenovirus infections as well as improved adenovirus vectors for use in vaccination and gene and cancer therapy.
A Molecular Staple: D-Loops in the I Domain of Bacteriophage P22 Coat Protein Make Important Intercapsomer Contacts Required for Procapsid Assembly
Authors: D'Lima Nadia G. , Teschke Carolyn M. 
Published: August 2015

ABSTRACT
Bacteriophage P22, a double-stranded DNA (dsDNA) virus, has a nonconserved 124-amino-acid accessory domain inserted into its coat protein, which has the canonical HK97 protein fold. This I domain is involved in virus capsid size determination and stability, as well as protein folding. The nuclear magnetic resonance (NMR) solution structure of the I domain revealed the presence of a D-loop, which was hypothesized to make important intersubunit contacts between coat proteins in adjacent capsomers. Here we show that amino acid substitutions of residues near the tip of the D-loop result in aberrant assembly products, including tubes and broken particles, highlighting the significance of the D-loops in proper procapsid assembly. Using disulfide cross-linking, we showed that the tips of the D-loops are positioned directly across from each other both in the procapsid and the mature virion, suggesting their importance in both states. Our results indicate that D-loop interactions act as “molecular staples” at the icosahedral 2-fold symmetry axis and significantly contribute to stabilizing the P22 capsid for DNA packaging.

IMPORTANCE
Many dsDNA viruses have morphogenic pathways utilizing an intermediate capsid, known as a procapsid. These procapsids are assembled from a coat protein having the HK97 fold in a reaction driven by scaffolding proteins or delta domains. Maturation of the capsid occurs during DNA packaging. Bacteriophage HK97 uniquely stabilizes its capsid during maturation by intercapsomer cross-linking, but most virus capsids are stabilized by alternate means. Here we show that the I domain that is inserted into the coat protein of bacteriophage P22 is important in the process of proper procapsid assembly. Specifically, the I domain allows for stabilizing interactions across the capsid 2-fold axis of symmetry via a D-loop. When amino acid residues at the tip of the D-loop are mutated, aberrant assembly products, including tubes, are formed instead of procapsids, consequently phage production is affected, indicating the importance of stabilizing interactions during the assembly and maturation reactions.
Viral Source-Independent High Susceptibility of Dendritic Cells to Human T-Cell Leukemia Virus Type 1 Infection Compared to That of T Lymphocytes
Authors: Alais Sandrine , Mahieux Renaud , Dutartre Hélène 
Published: August 2015

ABSTRACT

Human T-cell leukemia virus type 1 (HTLV-1)-infected CD4
+
T cells and dendritic cells (DCs) are present in peripheral blood from HTLV-1 carriers. While T-cell infection requires cell-cell contact, DCs might be infected with cell-free virus, at least
in vitro
. However, a thorough comparison of the susceptibilities of the two cell types to HTLV-1 infection using cell-associated and cell-free viral sources has not been performed. We first determined that human primary monocyte-derived dendritic cells (MDDCs) were more susceptible to HTLV-1 infection than their autologous lymphocyte counterparts after contact with chronically infected cells. Next, a comparison of infection efficiency using nonconcentrated or concentrated supernatants from infected cells as well as purified viral biofilm was performed. Integrated provirus was found after exposure of MDDCs or primary lymphocytes to viral biofilm but not to a viral supernatant. Using a large series of primary cell samples (
n
= 21), we demonstrated a higher proviral load in MDDCs exposed to viral biofilm than in lymphocytes. This higher susceptibility is correlated to a higher expression of neuropilin-1 on MDDCs than on autologous activated T lymphocytes. Moreover, we show that MDDCs infected with viral biofilm can transmit the virus to lymphocytes. In conclusion, MDDCs are more susceptible to HTLV-1 infection than autologous lymphocytes
in vitro
, supporting a model in which DC infection might represent an important step during primo-infection
in vivo
.

IMPORTANCE
HTLV-1 is able to infect several cell types, but viral DNA is mainly found in T lymphocytes
in vivo
. This supports a model in which T lymphocytes are the main target of infection. However, during the primo-infection of new individuals, incoming viruses might first encounter dendritic cells (DCs), the specialized immune cells responsible for the antiviral response of the host. HTLV-1 cell-free purified viruses can infect dendritic cells
in vitro
, while T-cell infection is restricted to cell-to-cell transmission. In order to understand the sequence of HTLV-1 dissemination, we undertook a direct comparison of the susceptibilities of the two cell types using cell-associated and cell-free viral sources. We report here that MDDCs are more susceptible to HTLV-1 infection than autologous lymphocytes
in vitro
and are able to efficiently transmit the virus to lymphocytes. Our results suggest that DCs may represent a true viral reservoir, as the first cell type to be infected
in vivo
.
Infectious Diseases at High Altitude
Authors: Basnyat Buddha , Starling Jennifer M. 
Published: August 2015

ABSTRACT
Travel to elevations above 2,500 m is an increasingly common activity undertaken by a diverse population of individuals. These may be trekkers, climbers, miners in high-altitude sites in South America, and more recently, soldiers deployed for high-altitude duty in remote areas of the world. What is also being increasingly recognized is the plight of the millions of pilgrims, many with comorbidities, who annually ascend to high-altitude sacred areas. There are also 400 million people who reside permanently in high mountain ranges, which cover one-fifth of the Earth’s surface. Many of these high-altitude areas are in developing countries, for example, the Himalayan range in South Asia. Although high-altitude areas may not harbor any specific infectious disease agents, it is important to know about the pathogens encountered in the mountains to be better able to help both the ill sojourner and the native high-altitude dweller. Often the same pathogens prevalent in the surrounding lowlands are found at high altitude, but various factors such as immunomodulation, hypoxia, poor physiological adaptation, and harsh environmental stressors at high altitude may enhance susceptibility to these pathogens. Against this background, various gastrointestinal, respiratory, dermatological, neurological, and other infections encountered at high altitude are discussed.
Broad-based molecular autopsy: a potential tool to investigate the involvement of subtle cardiac conditions in sudden unexpected death in infancy and early childhood
Authors: Santori Montserrat , Blanco-Verea Alejandro , Gil Rocio , Cortis Judith , Becker Katrin , Schneider Peter M , Carracedo Angel , Brion Maria 
Published: August 2015

ObjectivesSudden unexplained death in children is a tragic and traumatic event, often worsened when the cause of death cannot be determined. This work aimed to investigate the presence of putative pathogenic genetic variants in a broad spectrum of cardiomyopathy, channelopathy and aortic disease associated genes that may have increased these children's vulnerability to sudden cardiac death.DesignWe performed molecular autopsy of 41 cases of sudden unexplained death in infants and children through massive parallel sequencing of up to 86 sudden cardiac death-related genes. Multiple in silico analyses were conducted together with a thorough review of the literature in order to prioritise the putative pathogenic variants.ResultsA total of 63 variants in 35 cases were validated. The largest proportion of these variants is located within cardiomyopathy genes although this would have been more expected of channelopathy gene variants. Subtle microscopic features of heart tissue may indicate the presence of an early onset cardiomyopathy as a predisposing condition to sudden unexpected death in some individuals.ConclusionsNext-generation sequencing technologies reveal the existence of a wide spectrum of rare and novel genetic variants in sarcomere genes, compared with that of cardiac ion channels, in sudden unexplained death in infants and children. Our findings encourage further investigation of the role of early onset inherited cardiomyopathies and other diseases involving myocardial dysfunction in these deaths. Early detection of variants in these individuals could help to unmask subtle forms of disease within their relatives, who would eventually benefit from better counselling about their genetic history.