bluuebunny/crossref_metadata_2025_split huggingface dataset:
Results From Brazil’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Nardo Nelson , Silva Diego Augusto Santos , de Moraes Ferrari Gerson Luis , Petroski Edio Luiz , Pacheco Ricardo Lucas , Martins Priscila Custódio , Oliveira Luis Carlos , Araújo Timóteo Leandro , Mendes Anselmo Alexandre , Lazarin Samara Pereira Brito , dos Santos Tamires Leal Cordeiro , Matsudo Victor 
Published: November 2016

Background:Very few studies have comprehensively analyzed the physical activity of children and adolescents in Brazil. The purpose of this article is to show the methodology and summarize findings from the first Brazilian Report Card on Physical Activity for Children and Youth.Methods:Three Brazilian research institutions coordinated the activities to develop the Brazilian 2016 Report Card. The data available were collected independently and then synthesized by the Research Work Group using the grade system developed for the First Global Matrix released in 2014, which included 9 indicators of physical activity. Where possible, grades were assigned based on the percentage of children and youth meeting each indicator: A is 81% to 100%; B is 61% to 80%; C is 41% to 60%; D is 21% to 40%; F is 0% to 20%; INC is incomplete data.Results:Among the 9 indicators, only 5 had sufficient data for grading. Overall Physical Activity received a C- grade, Active Transportation received a C+ grade, Sedentary Behavior received a D+ grade, and Government Strategies and Investments received a D grade.Conclusions:The low grades observed highlight the need for continued efforts aimed at improving physical activity in Brazilian children.
Results From South Korea’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Song Yoonkyung , Yang Hyuk In , Lee Eun-Young , Yu Mi-Seong , Kang Min Jae , Kang Hyun Joo , Song Wook , Kim YeonSoo , Park Hyon , Lee Han Joo , Suh Sang-hoon , Spence John C. , Jeon Justin Y. 
Published: November 2016

Background:South Korea’s 2016 Report Card on Physical Activity for Children and Youth is the first assessment of physical activity according to the indicators set by Active Healthy Kids Global Alliance.Methods:National surveys were used as preferred sources of data. This was then supported by peer-reviewed papers and government reports identified by a systematic search of the literature written in English or Korean. A Research Working Group then graded indicators based on the collected evidence.Results:Each indicator was graded as follows: Overall Physical Activity, D-; Organized Sport and Physical Activity Participation, C-; Active Transport, C+; Sedentary Behavior, F; School, D; Government and Investment, C; Active Play, Physical Literacy, Family and Peers, and Community and Built Environment were graded INC (incomplete) due to lack of available evidence.Conclusions:Though the final grades of key indicators for South Korean children and youth are not satisfactory, increasing interests and investments have been demonstrated at a national level. More evidence is required for comprehensive assessment on all indicators to better inform policy and practice. This should be accompanied by the use of consistent criteria to contribute to global efforts for active healthy kids.
Patient-Specific
Bacteroides
Genome Variants in Pouchitis
Authors: Vineis Joseph H. , Ringus Daina L. , Morrison Hilary G. , Delmont Tom O. , Dalal Sushila , Raffals Laura H. , Antonopoulos Dionysios A. , Rubin David T. , Eren A. Murat , Chang Eugene B. , Sogin Mitchell L. 
Published: November 2016

ABSTRACT

A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of
Bacteroides
during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified
Bacteroides
populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of
Bacteroides
isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of
Bacteroides fragilis
from the mucosa versus lumen. Each patient harbored
Bacteroides
spp. that are closely related to commonly occurring clinical isolates, including
Bacteroides ovatus
,
B. thetaiotaomicron
,
B. vulgatus
, and
B. fragilis
, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique
Bacteroides
capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch.

IMPORTANCE
This longitudinal study provides an opportunity to describe shifts in the microbiomes of individual patients who suffer from ulcerative colitis (UC) prior to and following inflammation. Pouchitis serves as a model for UC with a predictable incidence of disease onset and enables prospective longitudinal investigations of UC etiology prior to inflammation. Because of insufficient criteria for predicting which patients will develop UC or pouchitis, the interpretation of cross-sectional study designs suffers from lack of information about the microbiome structure and host gene expression patterns that directly correlate with the onset of disease. Our unique longitudinal study design allows each patient to serve as their own control, providing information about the state of the microbiome and host prior to and during the course of disease. Of significance to the broader community, this study identifies microbial strains that may have genetic elements that trigger the onset of disease in susceptible hosts.
The Paralogous Histone Deacetylases Rpd3 and Rpd31 Play Opposing Roles in Regulating the White-Opaque Switch in the Fungal Pathogen Candida albicans
Authors: Xie Jing , Jenull Sabrina , Tscherner Michael , Kuchler Karl 
Published: November 2016

ABSTRACT

Chromatin modifications affect gene regulation in response to environmental stimuli in numerous biological processes. For example,
N
-acetyl-glucosamine and CO
2
induce a morphogenetic conversion between white (W) and opaque (O) cells in
MTL
(mating-type locus) homozygous and heterozygous (
a
/α) strains of the human fungal pathogen
Candida albicans
. Here, we identify 8 histone-modifying enzymes playing distinct roles in the regulation of W/O switching in
MTL
homozygous and heterozygous strains. Most strikingly, genetic removal of the paralogous genes
RPD3
and
RPD31
, both of which encode almost identical orthologues of the yeast histone deacetylase (HDAC) Rpd3, reveals opposing roles in W/O switching of
MTL
a
/α strains. We show that Rpd3 and Rpd31 functions depend on
MTL
genotypes. Strikingly, we demonstrate that Rpd3 and Rpd31, which are almost identical except for a divergent C-terminal extension present in Rpd31, exert their functions in distinct regulatory complexes referred to as CaRpd3L and CaRpd31S complexes. Moreover, we identify the
Candida
orf19.7185 product Ume1, the orthologue of yeast Ume1, as a shared core subunit of CaRpd3L and CaRpd31S. Mechanistically, we show that the opposing roles of Rpd3 and Rpd31 require their deacetylase activities. Importantly, CaRpd3L interacts with the heterodimeric transcriptional repressor
a
1/α2, thus controlling expression of
WOR1
encoding the master regulator of W/O switching. Thus, our work provides novel insight about regulation mechanisms of W/O switching in
MTL
a
/α strains. This is the first example of two highly conserved HDACs exerting opposing regulatory functions in the same process in a eukaryotic cell.

IMPORTANCE
RPD3
-like histone deacetylases (also called class I HDACs) are conserved from unicellular eukaryotes to mammals. Specifically, the genome of the human fungal pathogen
Candida albicans
, the most frequent cause of invasive fungal infections of high morbidity and mortality, harbors two almost identical paralogous HDACs, Rpd3 and Rpd31. We show here for the first time that Rpd3 and Rpd31 acquired functional divergence related to a distinct C-terminal domain. Rpd3 and Rpd31 associate with different complexes in the control regions of the master regulator gene
WOR1
, which is required for white-opaque (W/O) morphogenesis, respectively. The ability to switch is important for fungal pathogenesis, since it enables distinct host niche colonization. This work is to the best of our knowledge the first description of two paralogous HDACs playing opposing functional roles in the same developmental process. Our work adds a new angle concerning the molecular understanding of HDACs in the regulation of cell fate decisions.
Capsular Polysaccharide Expression in CommensalStreptococcusSpecies: Genetic and Antigenic Similarities to Streptococcus pneumoniae
Authors: Skov Sørensen Uffe B. , Yao Kaihu , Yang Yonghong , Tettelin Hervé , Kilian Mogens 
Published: November 2016

ABSTRACTExpression of a capsular polysaccharide is considered a hallmark of most invasive species of bacteria, includingStreptococcus pneumoniae, in which the capsule is among the principal virulence factors and is the basis for successful vaccines. Consequently, it was previously assumed that capsule production distinguishesS. pneumoniaefrom closely related commensals of the mitis group streptococci. Based on antigenic and genetic analyses of 187 mitis group streptococci, including 90 recognized serotypes ofS. pneumoniae, we demonstrated capsule production by the Wzy/Wzx pathway in 74% of 66S. mitisstrains and in virtually all tested strains ofS. oralis(subspeciesoralis,dentisani, andtigurinus) andS. infantis. Additional analyses of genomes ofS. cristatus,S. parasanguinis,S. australis,S. sanguinis,S. gordonii,S. anginosus,S. intermedius, andS. constellatusrevealed complete capsular biosynthesis (cps) loci in all strains tested. Truncatedcpsloci were detected in three strains ofS. pseudopneumoniae, in 26% ofS. mitisstrains, and in a singleS. oralisstrain. The level of sequence identities ofcpslocus genes confirmed that the structural polymorphism of capsular polysaccharides inS. pneumoniaeevolved by import ofcpsfragments from commensalStreptococcusspecies, resulting in a mosaic of genes of different origins. The demonstrated antigenic identity of at least eight of the numerous capsular polysaccharide structures expressed by commensal streptococci with recognized serotypes ofS. pneumoniaeraises concerns about potential misidentifications in addition to important questions concerning the consequences for vaccination and host-parasite relationships both for the commensals and for the pathogen.IMPORTANCEExpression of a capsular polysaccharide is among the principal virulence factors ofStreptococcus pneumoniaeand is the basis for successful vaccines against infections caused by this important pathogen. Contrasting with previous assumptions, this study showed that expression of capsular polysaccharides by the same genetic mechanisms is a general property of closely related species of streptococci that form a significant part of our commensal microbiota. The demonstrated antigenic identity of many capsular polysaccharides expressed by commensal streptococci andS. pneumoniaeraises important questions concerning the consequences for vaccination and host-parasite relationships both for the commensals and the pathogen.
A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli
Authors: Oron-Gottesman Adi , Sauert Martina , Moll Isabella , Engelberg-Kulka Hanna 
Published: November 2016

ABSTRACT

Escherichia coli
mazEF
is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM), composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF)-like element in ribosomal protein bS1 (bacterial S1), apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA.

IMPORTANCE
The genetic code is a universal characteristic of all living organisms. It defines the set of rules by which nucleotide triplets specify which amino acid will be incorporated into a protein. Our results represent the first existing report on a stress-induced bias in the reading of the genetic code. We found that in
E. coli
, under stress, the amino acid threonine is encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. This is because under stress, MazF generates a stress-induced translation machinery (STM) in which MazF cleaves in-frame ACA sites of the processed mRNAs.
Oncolytic reovirus as a combined antiviral and anti-tumour agent for the treatment of liver cancer
Authors: Samson Adel , Bentham Matthew J , Scott Karen , Nuovo Gerard , Bloy Abigail , Appleton Elizabeth , Adair Robert A , Dave Rajiv , Peckham-Cooper Adam , Toogood Giles , Nagamori Seishi , Coffey Matthew , Vile Richard , Harrington Kevin , Selby Peter , Errington-Mais Fiona , Melcher Alan , Griffin Stephen 
Published: November 2016

ObjectiveOncolytic viruses (OVs) represent promising, proinflammatory cancer treatments. Here, we explored whether OV-induced innate immune responses could simultaneously inhibit HCV while suppressing hepatocellular carcinoma (HCC). Furthermore, we extended this exemplar to other models of virus-associated cancer.Design and resultsClinical grade oncolytic orthoreovirus (Reo) elicited innate immune activation within primary human liver tissue in the absence of cytotoxicity and independently of viral genome replication. As well as achieving therapy in preclinical models of HCC through the activation of innate degranulating immune cells, Reo-induced cytokine responses efficiently suppressed HCV replication both in vitro and in vivo. Furthermore, Reo-induced innate responses were also effective against models of HBV-associated HCC, as well as an alternative endogenous model of Epstein–Barr virus-associated lymphoma. Interestingly, Reo appeared superior to the majority of OVs in its ability to elicit innate inflammatory responses from primary liver tissue.ConclusionsWe propose that Reo and other select proinflammatory OV may be used in the treatment of multiple cancers associated with oncogenic virus infections, simultaneously reducing both virus-associated oncogenic drive and tumour burden. In the case of HCV-associated HCC (HCV-HCC), Reo should be considered as an alternative agent to supplement and support current HCV-HCC therapies, particularly in those countries where access to new HCV antiviral treatments may be limited.
Dynamical study of Debye temperature and combined density of states of TiO2
Authors: Srivastava U. C. 
Published: November 2016

In present paper, it is focused on theoretical study of TiO2 with particular emphasis on vibrational phonon properties by means of van der Waals three-body force shell model (VTBFSM). Present model includes van der Waals interactions (VWI) and three-body interactions (TBI) in the framework of both ion polarizable rigid shell model (RSM) with short-range interactions effective up to the second neighbor. The Coulombic ion–ion interaction contribution to the dynamical matrix is calculated by the Kellerman.1 Therefore, it may be inferred that the present model is the most realistic model for complete harmonic dynamical behavior of the crystals. The lattice dynamical study of phonon properties of transition metal titanium dioxide (TiO2) has been presented by means of VTBFS model. Titanium is an extremely light semiconducting material, exhibiting stable bcc structure in a certain temperature range 0–300 K normal pressures Debye temperature variation and combined density of states (CDS) of TiO2 has been studied in this work. At high temperature, strength and oxidation resistance of Ti alloys has improved. The model predictions are found to be in reasonable agreement with experimental data.2
Fracture Mechanical Analysis of Open Cell Ceramic Foams Under Thermal Shock Loading
Authors: Settgast C. , Abendroth M. , Kuna M. 
Published: November 2016

Ceramic foams made by replica techniques containing sharp-edged cavities, which are potential crack initiators and therefore have to be analyzed using fracture mechanical methods. The ceramic foams made of novel carbon bonded alumina are used as filters in metal melt filtration applications, where the filters are exposed to a thermal shock. During the casting process the filters experience a complex thermo-mechanical loading, which is difficult to measure. Modern numerical methods allow the simulation of such complex processes. As a simplified foam structure an open Kelvin cell is used as a representative volume element. A three-dimensional finite element model containing realistic sharp-edged cavities and three-dimensional sub-models along these sharp edges are used to compute the transient temperature, stress and strain fields at the Kelvin foam. The sharp edges are evaluated using fracture mechanical methods like the [Formula: see text]-integral technique. The results of this study describe the influence of the pore size, relative density of the ceramic foam, the heat transfer and selected material parameters on the fracture mechanical behaviour.
Controversies in the history of geology and their educational importance for facilitating understanding of the nature of science
Authors: Clary Renee M. 
Published: November 2016

Abstract
Controversies in the history of geology are inherently interesting to students, and offer an effective method for conveying the scientific process and the cultural and social influences under which science progresses. Historical controversies can also address the basic understandings of the nature of science (NOS), which students need in order to develop an authentic understanding of the scientific process. Four controversial vignettes in the history of geology are overviewed: Agassiz's Glacial Theory, Darwin's theory on reef formation, the Cope–Marsh dinosaur wars and Byrd's flight over the North Pole. The controversies are analysed using the NOS matrix to demonstrate their effectiveness for teaching the nature of science via historical episodes in geology. Surveys of practising teachers also provide further documentation for the importance of historical controversies in the science classroom, as well as student interest in them.
Selective Reversible Inhibition of Autophagy in Hypoxic Breast Cancer Cells Promotes Pulmonary Metastasis
Authors: Dower Christopher M. , Bhat Neema , Wang Edward W. , Wang Hong-Gang 
Published: November 2016

AbstractAutophagy influences how cancer cells respond to nutrient deprivation and hypoxic stress, two hallmarks of the tumor microenvironment (TME). In this study, we explored the impact of autophagy on the pathophysiology of breast cancer cells using a novel hypoxia-dependent, reversible dominant-negative strategy to regulate autophagy at the cellular level within the TME. Suppression of autophagy via hypoxia-induced expression of the kinase-dead unc-51-like autophagy-activating kinase (ULK1) mutant K46N increased lung metastases in MDA-MB-231 xenograft mouse models. Consistent with this effect, expressing a dominant-negative mutant of ULK1 or ATG4b or a ULK1-targeting shRNA facilitated cell migration in vitro. Functional proteomic and transcriptome analysis revealed that loss of hypoxia-regulated autophagy promotes metastasis via induction of the fibronectin integrin signaling axis. Indeed, loss of ULK1 function increased fibronectin deposition in the hypoxic TME. Together, our results indicated that hypoxia-regulated autophagy suppresses metastasis in breast cancer by preventing tumor fibrosis. These results also suggest cautions in the development of autophagy-based strategies for cancer treatment. Cancer Res; 77(3); 646–57. ©2016 AACR.
Label-Free Raman Spectroscopy Detects Stromal Adaptations in Premetastatic Lungs Primed by Breast Cancer
Authors: Paidi Santosh Kumar , Rizwan Asif , Zheng Chao , Cheng Menglin , Glunde Kristine , Barman Ishan 
Published: November 2016

Abstract
Recent advances in animal modeling, imaging technology, and functional genomics have permitted precise molecular observations of the metastatic process. However, a comprehensive understanding of the premetastatic niche remains elusive, owing to the limited tools that can map subtle differences in molecular mediators in organ-specific microenvironments. Here, we report the ability to detect premetastatic changes in the lung microenvironment, in response to primary breast tumors, using a combination of metastatic mouse models, Raman spectroscopy, and multivariate analysis of consistent patterns in molecular expression. We used tdTomato fluorescent protein expressing MDA-MB-231 and MCF-7 cells of high and low metastatic potential, respectively, to grow orthotopic xenografts in athymic nude mice and allow spontaneous dissemination from the primary mammary fat pad tumor. Label-free Raman spectroscopic mapping was used to record the molecular content of premetastatic lungs. These measurements show reliable distinctions in vibrational features, characteristic of the collageneous stroma and its cross-linkers as well as proteoglycans, which uniquely identify the metastatic potential of the primary tumor by recapitulating the compositional changes in the lungs. Consistent with histological assessment and gene expression analysis, our study suggests that remodeling of the extracellular matrix components may present promising markers for objective recognition of the premetastatic niche, independent of conventional clinical information. Cancer Res; 77(2); 247–56. ©2016 AACR.
Mouse Models of Pediatric Supratentorial High-grade Glioma Reveal How Cell-of-Origin Influences Tumor Development and Phenotype
Authors: Sreedharan Smitha , Maturi Naga Prathyusha , Xie Yuan , Sundström Anders , Jarvius Malin , Libard Sylwia , Alafuzoff Irina , Weishaupt Holger , Fryknäs Mårten , Larsson Rolf , Swartling Fredrik J. , Uhrbom Lene 
Published: November 2016

Abstract
High-grade glioma (HGG) is a group of primary malignant brain tumors with dismal prognosis. Whereas adult HGG has been studied extensively, childhood HGG, a relatively rare disease, is less well-characterized. Here, we present two novel platelet-derived growth factor (PDGF)-driven mouse models of pediatric supratentorial HGG. Tumors developed from two different cells of origin reminiscent of neural stem cells (NSC) or oligodendrocyte precursor cells (OPC). Cross-species transcriptomics showed that both models are closely related to human pediatric HGG as compared with adult HGG. Furthermore, an NSC-like cell-of-origin enhanced tumor incidence, malignancy, and the ability of mouse glioma cells (GC) to be cultured under stem cell conditions as compared with an OPC-like cell. Functional analyses of cultured GC from these tumors showed that cells of NSC-like origin were more tumorigenic, had a higher rate of self-renewal and proliferation, and were more sensitive to a panel of cancer drugs compared with GC of a more differentiated origin. These two mouse models relevant to human pediatric supratentorial HGG propose an important role of the cell-of-origin for clinicopathologic features of this disease. Cancer Res; 77(3); 802–12. ©2016 AACR.