bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tricin‐lignins: occurrence and quantitation of tricin in relation to phylogeny
Authors: Lan Wu , Rencoret Jorge , Lu Fachuang , Karlen Steven D. , Smith Bronwen G. , Harris Philip J. , del Río José Carlos , Ralph John 
Published: August 2016

SummaryTricin [5,7‐dihydroxy‐2‐(4‐hydroxy‐3,5‐dimethoxyphenyl)‐4H‐chromen‐4‐one], a flavone, was recently established as an authentic monomer in grass lignification that likely functions as a nucleation site. It is linked onto lignin as an aryl alkyl ether by radical coupling with monolignols or their acylated analogs. However, the level of tricin that incorporates into lignin remains unclear. Herein, three lignin characterization methods: acidolysis; thioacidolysis; and derivatization followed by reductive cleavage; were applied to quantitatively assess the amount of lignin‐integrated tricin. Their efficiencies at cleaving the tricin‐(4′–O–β)‐ether bonds and the degradation of tricin under the corresponding reaction conditions were evaluated. A hexadeuterated tricin analog was synthesized as an internal standard for accurate quantitation purposes. Thioacidolysis proved to be the most efficient method, liberating more than 91% of the tricin with little degradation. A survey of different seed‐plant species for the occurrence and content of tricin showed that it is widely distributed in the lignin from species in the family Poaceae (order Poales). Tricin occurs at low levels in some commelinid monocotyledon families outside the Poaceae, such as the Arecaceae (the palms, order Arecales) and Bromeliaceae (Poales), and the non‐commelinid monocotyledon family Orchidaceae (Orchidales). One eudicotyledon was found to have tricin (Medicago sativa, Fabaceae). The content of lignin‐integrated tricin is much higher than the extractable tricin level in all cases. Lignins, including waste lignin streams from biomass processing, could therefore provide a large and alternative source of this valuable flavone, reducing the costs, and encouraging studies into its application beyond its current roles.
The journey toward safer and optimized blood service in China: national strategy and progress
Authors: Wang Ya , Wu Yanyun , Chen Yongjun , Li Changqing , Lu Li , AuBuchon James P. , Liu Zhong 
Published: August 2016

BACKGROUNDThe objective was to analyze and evaluate the effects of strategic measures the Chinese government attempted and undertook throughout the fast‐changing and difficult transition periods of the blood service system.STUDY DESIGN AND METHODSWe systematically reviewed data and information regarding policy, blood collection, service system, and clinical transfusion practice, which were the most representative indicators on a national level from 1978 to 2015.RESULTSBlood donation in China has successfully transitioned from paid donation, then compulsory (but nonremunerated) donation, to voluntary nonremunerated donation. The volume of blood collection has steadily increased from 4,000,000 red blood cell (RBC; 200 mL/unit) units in 1998 to 22,000,000 RBC units in 2014. The percentage of human immunodeficiency virus (HIV) transfusion‐transmitted infections in newly diagnosed HIV/AIDS has reduced from 29.6% in 2005 to less than 0.15% in 2013. The use of component therapy has increased from 18% in 1989 to 99% in 2014.CONCLUSIONSInvolvement of the government through enforcement of new statutes and regulations helped improve blood safety and clinical transfusion practice.
Eliminating Nox2 reactive oxygen species production protects dystrophic skeletal muscle from pathological calcium influx assessed in vivo by manganese‐enhanced magnetic resonance imaging
Authors: Loehr James A. , Stinnett Gary R. , Hernández‐Rivera Mayra , Roten Wesley T. , Wilson Lon J. , Pautler Robia G. , Rodney George G. 
Published: August 2016

Key points
Inhibiting Nox2 reactive oxygen species (ROS) production reduced in vivo calcium influx in dystrophic muscle.
The lack of Nox2 ROS production protected against decreased in vivo muscle function in dystrophic mice.
Manganese‐enhanced magnetic resonance imaging (MEMRI) was able to detect alterations in basal calcium levels in skeletal muscle and differentiate disease status.
Administration of Mn2+ did not affect muscle function or the health of the animal, and Mn2+ was cleared from skeletal muscle rapidly.
We conclude that MEMRI may be a viable, non‐invasive technique to monitor molecular alterations in disease progression and evaluate the effectiveness of potential therapies for Duchenne muscular dystrophy.
AbstractDuchenne muscular dystrophy (DMD) is an X‐linked progressive degenerative disease resulting from a mutation in the gene that encodes dystrophin, leading to decreased muscle mechanical stability and force production. Increased Nox2 reactive oxygen species (ROS) production and sarcolemmal Ca2+ influx are early indicators of disease pathology, and eliminating Nox2 ROS production reduces aberrant Ca2+ influx in young mdx mice, a model of DMD. Various imaging modalities have been used to study dystrophic muscle in vivo; however, they are based upon alterations in muscle morphology or inflammation. Manganese has been used for indirect monitoring of calcium influx across the sarcolemma and may allow detection of molecular alterations in disease progression in vivo using manganese‐enhanced magnetic resonance imaging (MEMRI). Therefore, we hypothesized that eliminating Nox2 ROS production would decrease calcium influx in adult mdx mice and that MEMRI would be able to monitor and differentiate disease status in dystrophic muscle. Both in vitro and in vivo data demonstrate that eliminating Nox2 ROS protected against aberrant Ca2+ influx and improved muscle function in dystrophic muscle. MEMRI was able to differentiate between different pathological states in vivo, with no long‐term effects on animal health or muscle function. We conclude that MEMRI is a viable, non‐invasive technique to differentiate disease status and might provide a means to monitor and evaluate the effectiveness of potential therapies in dystrophic muscle.
The Individual, Social, and Environmental Correlates of Physical Activity and Screen Time in Irish Children: Growing Up in Ireland Study
Authors: Garcia Jeanette M. , Healy Sean , Rice David 
Published: August 2016

Background:The aim of this study was to use a social-ecological approach to examine the influence of individual, social, and environmental factors on moderate-to-vigorous physical activity (MVPA) and screen-time in a sample of 9-year-old children in Ireland.Methods:The sample was 1509 boys and girls from the Growing Up in Ireland (GUI) national study. MVPA, screen time, and individual, social, and environmental variables were assessed via questionnaires completed by children, their parents, and their teachers. Multiple regression was used to identify factors that correlated with children’s MVPA and screen-time levels.Results:For boys, factors such as activity with friends (P < .0001) and popularity (P < .01) were associated with MVPA, while factors such as BMI (P < .01) and MVPA (P < .01) were associated with screen time. Similarly for girls, factors such as activity with friends (P < .0001) and sociability were associated with MVPA, however factors such as BMI (P < .05), and access to play space (P < .05) were more closely associated with screen time.Conclusion:Social factors were more closely associated with MVPA, while individual factors were significantly correlated with screen time for both boys and girls. Correlates differed for boys and girls, suggesting that interventions should consider both the target population as well as the activity behavior.
Physical Activity–Related Obesity Risk Classification Model and All-Cause Mortality
Authors: Loprinzi Paul D. , Addoh Ovuokerie 
Published: August 2016

Background:This study evaluated a physical activity–related obesity model on mortality.Methods:Data from the 1999–2006 NHANES were used (N = 16,077), with follow-up through 2011. Physical activity (PA) was subjectively assessed, with body mass index (BMI) and waist circumference (WC) objectively measured. From these, 12 mutually exclusive groups (G) were evaluated, including: G1: Normal BMI, Normal WC and Active; G2: Normal BMI, Normal WC and Inactive; G3: Normal BMI, High WC and Active; G4: Normal BMI, High WC and Inactive; G5: Overweight BMI, Normal WC and Active; G6: Overweight BMI, Normal WC and Inactive; G7: Overweight BMI, High WC and Active; G8: Overweight BMI, High WC and Inactive; G9: Obese BMI, Normal WC and Active; G10: Obese BMI, Normal WC and Inactive; G11: Obese BMI, High WC and Active; and G12: Obese BMI, High WC and Inactive.Results:Compared with G2, the following had a reduced mortality risk: G1, G3, G5, G6, G7, G8, G9, and G11. Compared with G12, the following had a reduced mortality risk: G1, G3, G5, G7, G9, and G11. In each respective group for BMI and WC, the active group had a reduced mortality risk.Conclusions:Across all BMI and WC combinations, PA improved mortality risk identification.
A Physical Activity Intervention for Brazilian Students From Low Human Development Index Areas: A Cluster-Randomized Controlled Trial
Authors: Filho Valter C. Barbosa , da Silva Kelly Samara , Mota Jorge , Beck Carmem , da Silva Lopes Adair 
Published: August 2016

Background:Promoting physical activity (PA) in low- and middle-income countries is an important public health topic as well as a challenge for practice. This study aimed to assess the effect of a school-based intervention on different PA-related variables among students.Methods:This cluster-randomized-controlled trial included 548 students in the intervention group and 537 in the control group (11–18 years-old) from 6 schools in neighborhoods with low Human Development Index (0.170–0.491) in Fortaleza, Brazil. The intervention included strategies focused on training teachers, opportunities for PA in the school environment and health education. Variables measured at baseline and again at the 4-months follow-up included the weekly time in different types of moderate-to-vigorous PA (MVPA), preference for PA during leisure-time, PA behavioral change stage and active commuting to school. Generalized linear models and binary logistic regressions were used.Results:An intervention effect was found by increasing the weekly time in MVPA (effect size = 0.17), popular games (effect size = 0.35), and the amount of PA per week (effect size = 0.27) among students (all P < .05).Conclusions:The intervention was effective in promoting improvements in some PA outcomes, but the changes were not sufficient to increase the proportion of those meeting PA recommendations.
What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B
Authors: Connor Thomas R. , Owen Sian V. , Langridge Gemma , Connell Steve , Nair Satheesh , Reuter Sandra , Dallman Timothy J. , Corander Jukka , Tabing Kristine C. , Le Hello Simon , Fookes Maria , Doublet Benoît , Zhou Zhemin , Feltwell Theresa , Ellington Matthew J. , Herrera Silvia , Gilmour Matthew , Cloeckaert Axel , Achtman Mark , Parkhill Julian , Wain John , De Pinna Elizabeth , Weill François-Xavier , Peters Tansy , Thomson Nick 
Published: August 2016

ABSTRACT

For 100 years, it has been obvious that
Salmonella enterica
strains sharing the serotype with the formula 1,4,[5],12:b:1,2—now known as Paratyphi B—can cause diseases ranging from serious systemic infections to self-limiting gastroenteritis. Despite considerable predicted diversity between strains carrying the common Paratyphi B serotype, there remain few methods that subdivide the group into groups that are congruent with their disease phenotypes. Paratyphi B therefore represents one of the canonical examples in
Salmonella
where serotyping combined with classical microbiological tests fails to provide clinically informative information. Here, we use genomics to provide the first high-resolution view of this serotype, placing it into a wider genomic context of the
Salmonella enterica
species. These analyses reveal why it has been impossible to subdivide this serotype based upon phenotypic and limited molecular approaches. By examining the genomic data in detail, we are able to identify common features that correlate with strains of clinical importance. The results presented here provide new diagnostic targets, as well as posing important new questions about the basis for the invasive disease phenotype observed in a subset of strains.

IMPORTANCE
Salmonella enterica
strains carrying the serotype Paratyphi B have long been known to possess Jekyll and Hyde characteristics; some cause gastroenteritis, while others cause serious invasive disease. Understanding what makes up the population of strains carrying this serotype, as well as the source of their invasive disease, is a 100-year-old puzzle that we address here using genomics. Our analysis provides the first high-resolution view of this serotype, placing strains carrying serotype Paratyphi B into the wider genomic context of the
Salmonella enterica
species. This work reveals a history of disease dating back to the middle ages, caused by a group of distinct lineages with various abilities to cause invasive disease. By quantifying the key genomic differences between the invasive and noninvasive populations, we are able to identify key virulence-related targets that can form the basis of simple, rapid, point-of-care tests.
The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility
Authors: Kable Mary E. , Srisengfa Yanin , Laird Miles , Zaragoza Jose , McLeod Jeremy , Heidenreich Jessie , Marco Maria L. 
Published: August 2016

ABSTRACT

Currently, the bacterial composition of raw milk in tanker trucks and the outcomes of transfer and storage of that milk at commercial processing facilities are not well understood. We set out to identify the bacteria in raw milk collected for large-scale dairy product manufacturing. Raw bovine milk samples from 899 tanker trucks arriving at two dairy processors in San Joaquin Valley of California during three seasons (spring, summer, and fall) were analyzed by community 16S rRNA gene sequencing. This analysis revealed highly diverse bacterial populations, which exhibited seasonal differences. Raw milk collected in the spring contained the most diverse bacterial communities, with the highest total cell numbers and highest proportions being those of
Actinobacteria
. Even with this complexity, a core microbiota was present, consisting of 29 taxonomic groups and high proportions of
Streptococcus
and
Staphylococcus
and unidentified members of
Clostridiales
. Milk samples were also collected from five large-volume silos and from 13 to 25 tankers whose contents were unloaded into each of them during 2 days in the summer. Transfer of the milk to storage silos resulted in two community types. One group of silos contained a high proportion of
Streptococcus
spp. and was similar in that respect to the tankers that filled them. The community found in the other group of silos was distinct and dominated by
Acinetobacter
. Overall, despite highly diverse tanker milk community structures, distinct milk bacterial communities were selected within the processing facility environment. This knowledge can inform the development of new sanitation procedures and process controls to ensure the consistent production of safe and high-quality dairy products on a global scale.

IMPORTANCE
Raw milk harbors diverse bacteria that are crucial determinants of the quality and safety of fluid milk and (fermented) dairy products. These bacteria enter farm milk during transport, storage, and processing. Although pathogens are destroyed by pasteurization, not all bacteria and their associated enzymes are eliminated. Our comprehensive analyses of the bacterial composition of raw milk upon arrival and shortly after storage at major dairy processors showed that the communities of milk microbiota are highly diverse. Even with these differences, there was a core microbiota that exhibited distinct seasonal trends. Remarkably, the effects of the processing facility outweighed those of the raw milk microbiome and the microbial composition changed distinctly within some but not all silos within a short time after transfer. This knowledge can be used to inform cleaning and sanitation procedures as well as to enable predictions of the microbial communities in raw milk that result in either high-quality or defective products.
Bacteroidales
Secreted Antimicrobial Proteins Target Surface Molecules Necessary for Gut Colonization and Mediate Competition
In Vivo
Authors: Roelofs Kevin G. , Coyne Michael J. , Gentyala Rahul R. , Chatzidaki-Livanis Maria , Comstock Laurie E. 
Published: August 2016

ABSTRACT

We recently showed that human gut
Bacteroidales
species secrete antimicrobial proteins (BSAPs), and we characterized
in vitro
the first such BSAP produced by
Bacteroides fragilis
. In this study, we identified a second potent BSAP produced by the ubiquitous and abundant human gut species
Bacteroides uniformis
. The two BSAPs contain a membrane attack complex/perforin (MACPF) domain but share very little sequence similarity. We identified the target molecules of BSAP-sensitive cells and showed that each BSAP targets a different class of surface molecule: BSAP-1 targets an outer membrane protein of sensitive
B. fragilis
strains, and BSAP-2 targets the O-antigen glycan of lipopolysaccharide (LPS) of sensitive
B. uniformis
strains. Species-wide genomic and phenotypic analyses of
B. fragilis
and
B. uniformis
showed that BSAP-producing strains circumvent killing by synthesizing an orthologous nontargeted surface molecule. The BSAP genes are adjacent to the gene(s) encoding their target replacements, suggesting coacquisition. Using a gnotobiotic mouse competitive-colonization model, we found that the BSAP surface targets are important for colonization of the mammalian gut, thereby explaining why they are maintained in sensitive strains and why they were replaced rather than deleted in BSAP-producing strains. Using isogenic BSAP-producing, -sensitive, and -resistant strains, we show that a BSAP-producing strain outcompetes a sensitive strain but not a resistant strain in the mammalian gut. Human gut metagenomic datasets reveal that BSAP-1-sensitive strains do not cooccur with BSAP-1-producing strains in human gut microbiotas, further supporting the idea that BSAPs are important competitive factors with relevance to the strain-level composition of the human gut microbiota.

IMPORTANCE
We know relatively little about the ecology of the human intestinal microbiota and the combination of factors that dictate which strains and species occupy an individual’s gut microbial community. Interference competition, mediated by bacterial factors that directly harm other members, is beginning to be appreciated as important in contributing to species- and strain-level dynamics of abundant gut bacteria. Here, we show that gut
Bacteroidales
secrete antimicrobial proteins (BSAPs) that antagonize strains of the same species. We show that BSAPs target molecules of sensitive cells that are important for gut colonization and therefore are maintained in sensitive cells. In an experimental animal model of gut colonization, a BSAP-1-producing strain antagonized and outcompeted an isogenic sensitive strain. Furthermore, metagenomic analyses showed that BSAP-1-producing and -sensitive strains are not found together in human gut microbiotas. These data suggest that BSAPs are strong ecological drivers shaping the strain-level composition of gut communities.
Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis
Authors: Hiras Jennifer , Wu Yu-Wei , Deng Kai , Nicora Carrie D. , Aldrich Joshua T. , Frey Dario , Kolinko Sebastian , Robinson Errol W. , Jacobs Jon M. , Adams Paul D. , Northen Trent R. , Simmons Blake A. , Singer Steven W. 
Published: August 2016

ABSTRACT

Glycoside hydrolases (GHs) are key enzymes in the depolymerization of plant-derived cellulose, a process central to the global carbon cycle and the conversion of plant biomass to fuels and chemicals. A limited number of GH families hydrolyze crystalline cellulose, often by a processive mechanism along the cellulose chain. During cultivation of thermophilic cellulolytic microbial communities, substantial differences were observed in the crystalline cellulose saccharification activities of supernatants recovered from divergent lineages. Comparative community proteomics identified a set of cellulases from a population closely related to actinobacterium
Thermobispora bispora
that were highly abundant in the most active consortium. Among the cellulases from
T. bispora
, the abundance of a GH family 12 (GH12) protein correlated most closely with the changes in crystalline cellulose hydrolysis activity. This result was surprising since GH12 proteins have been predominantly characterized as enzymes active on soluble polysaccharide substrates. Heterologous expression and biochemical characterization of the suite of
T. bispora
hydrolytic cellulases confirmed that the GH12 protein possessed the highest activity on multiple crystalline cellulose substrates and demonstrated that it hydrolyzes cellulose chains by a predominantly random mechanism. This work suggests that the role of GH12 proteins in crystalline cellulose hydrolysis by cellulolytic microbes should be reconsidered.

IMPORTANCE
Cellulose is the most abundant organic polymer on earth, and its enzymatic hydrolysis is a key reaction in the global carbon cycle and the conversion of plant biomass to biofuels. The glycoside hydrolases that depolymerize crystalline cellulose have been primarily characterized from isolates. In this study, we demonstrate that adapting microbial consortia from compost to grow on crystalline cellulose generated communities whose soluble enzymes exhibit differential abilities to hydrolyze crystalline cellulose. Comparative proteomics of these communities identified a protein of glycoside hydrolase family 12 (GH12), a family of proteins previously observed to primarily hydrolyze soluble substrates, as a candidate that accounted for some of the differences in hydrolytic activities. Heterologous expression confirmed that the GH12 protein identified by proteomics was active on crystalline cellulose and hydrolyzed cellulose by a random mechanism, in contrast to most cellulases that act on the crystalline polymer in a processive mechanism.