bluuebunny/crossref_metadata_2025 huggingface dataset:
Type Synthesis for Remote Center of Motion Mechanisms Based on Coupled Motion of Two Degrees-of-Freedom
Authors: He Yucheng , Zhang Peng , Jin Haiyang , Hu Ying , Zhang Jianwei
Published: July 2016

Robots play an increasingly important role in the development of minimally invasive surgery (MIS). In MIS assistant robot systems, the remote center of motion (RCM) mechanism is a key component, and is the primary choice as end-effector for such systems. In this paper, first, we propose a new type of synthesis method for RCM mechanisms, which is based on the coupled motion of two DOFs to obtain new virtual center of motion (VCM) mechanisms, and then, through different combinations and configurations of VCM mechanisms, a new family of RCM mechanisms is achieved. Second, one of the obtained RCM mechanisms, which is deemed to have potential application prospects in MIS assistant robot, is investigated in detail, and a prototype is designed and fabricated to verify its feasibility. Finally, preliminary experiments are carried out on the prototype; the results show that, compared with existing ones, the new RCM mechanism's volume can be adjusted according to its required workspace, and it will be more compact when the required workspace is small. It will be an applicable option of end-effector for an MIS assistant robot.
Candle soot-based super-amphiphobic coatings resist protein adsorption
Authors: Schmüser Lars , Encinas Noemi , Paven MAXIME , Graham Daniel J. , Castner David G. , Vollmer Doris , Butt Hans Jürgen , Weidner Tobias
Published: July 2016

Super nonfouling surfaces resist protein adhesion and have a broad field of possible applications in implant technology, drug delivery, blood compatible materials, biosensors, and marine coatings. A promising route toward nonfouling surfaces involves liquid repelling architectures. The authors here show that soot-templated super-amphiphobic (SAP) surfaces prepared from fluorinated candle soot structures are super nonfouling. When exposed to bovine serum albumin or blood serum, x-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry analysis showed that less than 2 ng/cm2 of protein was adsorbed onto the SAP surfaces. Since a broad variety of substrate shapes can be coated by soot-templated SAP surfaces, those are a promising route toward biocompatible materials design.
Sound speed as a proxy variable to temperature in Fram Strait
Authors: Dushaw Brian D. , Sagen Hanne , Beszczynska-Möller Agnieszka
Published: July 2016

The application of ocean acoustic tomography in Fram Strait requires a careful assessment of the accuracy to which estimates of sound speed from tomography can be converted to estimates of temperature. The Fram Strait environment is turbulent, with warm, salty, northward-flowing North Atlantic water interacting with cold, fresh, southward-flowing Arctic water. The nature of this environment suggests that salinity could play an important role with respect to sound speed. The properties of sound speed with respect to temperature and salinity in this environment were examined using climatological and in situ glider data. In cold water, a factor of about 4.5 m s−1 °C−1 can be used to scale between sound speed and temperature. In situ data obtained by gliders were used to determine the ambiguities between temperature, salinity, and sound speed. Tomography provides a depth-averaging measurement. While errors in the sound speed-temperature conversion at particular depths may be 0.2 °C or larger, particularly within 50 m of the surface, such errors are suppressed when the depth is averaged. Using a simple scale factor to compute temperature from sound speed introduced an error of about 20 m °C for depth-averaged temperature, a value less than formal uncertainties estimated from acoustic tomography.
Quasi-freestanding epitaxial silicene on Ag(111) by oxygen intercalation
Authors: Du Yi , Zhuang Jincheng , Wang Jiaou , Li Zhi , Liu Hongsheng , Zhao Jijun , Xu Xun , Feng Haifeng , Chen Lan , Wu Kehui , Wang Xiaolin , Dou Shi Xue
Published: July 2016

Quasi-freestanding silicene with massless Dirac fermion characteristics has been successfully obtained by oxygen intercalation.
Targeting macrophage necroptosis for therapeutic and diagnostic interventions in atherosclerosis
Authors: Karunakaran Denuja , Geoffrion Michele , Wei Lihui , Gan Wei , Richards Laura , Shangari Prakriti , DeKemp Ella M. , Beanlands Rachelle A. , Perisic Ljubica , Maegdefessel Lars , Hedin Ulf , Sad Subash , Guo Liang , Kolodgie Frank D. , Virmani Renu , Ruddy Terrence , Rayner Katey J.
Published: July 2016

Necroptosis promotes necrotic core and vulnerable atherosclerosis in humans and mice and is a prospective therapeutic and diagnostic tool.
Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases
Authors: Mazhab-Jafari Mohammad T. , Rubinstein John L.
Published: July 2016

V-ATPases are fascinating molecular machines; cryo-EM is providing unprecedented insight into their structure and dynamics.
Binding of the cytoplasmic domain of CD28 to the plasma membrane inhibits Lck recruitment and signaling
Authors: Dobbins Jessica , Gagnon Etienne , Godec Jernej , Pyrdol Jason , Vignali Dario A. A. , Sharpe Arlene H. , Wucherpfennig Kai W.
Published: July 2016

Ligand binding to the T cell costimulatory receptor CD28 releases its cytoplasmic domain from the plasma membrane to initiate signaling.
RhoA inhibits neural differentiation in murine stem cells through multiple mechanisms
Authors: Yang Junning , Wu Chuanshen , Stefanescu Ioana , Jakobsson Lars , Chervoneva Inna , Horowitz Arie
Published: July 2016

RhoA signaling prevents the neural differentiation of embryonic stem cells by inhibiting both the production and secretion of the BMP antagonist Noggin.
Yersinia ruckeri Isolates Recovered from Diseased Atlantic Salmon (Salmo salar) in Scotland Are More Diverse than Those from Rainbow Trout (Oncorhynchus mykiss) and Represent Distinct Subpopulations
Authors: Ormsby Michael J. , Caws Thomas , Burchmore Richard , Wallis Tim , Verner-Jeffreys David W. , Davies Robert L.
Published: July 2016

Yersinia ruckeri
is the etiological agent of enteric redmouth (ERM) disease of farmed salmonids. Enteric redmouth disease is traditionally associated with rainbow trout (
Oncorhynchus mykiss
, Walbaum), but its incidence in Atlantic salmon (
Salmo salar
) is increasing.
Yersinia ruckeri
isolates recovered from diseased Atlantic salmon have been poorly characterized, and very little is known about the relationship of the isolates associated with these two species. Phenotypic approaches were used to characterize 109
Y. ruckeri
isolates recovered over a 14-year period from infected Atlantic salmon in Scotland; 26 isolates from infected rainbow trout were also characterized. Biotyping, serotyping, and comparison of outer membrane protein profiles identified 19
Y. ruckeri
clones associated with Atlantic salmon but only five associated with rainbow trout; none of the Atlantic salmon clones occurred in rainbow trout and
vice versa
. These findings suggest that distinct subpopulations of
Y. ruckeri
are associated with each species. A new O serotype (designated O8) was identified in 56 biotype 1 Atlantic salmon isolates and was the most common serotype identified from 2006 to 2011 and in 2014, suggesting an increased prevalence during the time period sampled. Rainbow trout isolates were represented almost exclusively by the same biotype 2, serotype O1 clone that has been responsible for the majority of ERM outbreaks in this species within the United Kingdom since the 1980s. However, the identification of two biotype 2, serotype O8 isolates in rainbow trout suggests that vaccines containing serotypes O1 and O8 should be evaluated in both rainbow trout and Atlantic salmon for application in Scotland.

IMPORTANCE
Vaccination plays an important role in protecting Atlantic salmon against the bacterial pathogen
Yersinia ruckeri
, but, in recent years, there has been an increasing incidence of vaccine breakdown in salmon. This is largely because current vaccines are aimed at rainbow trout and are based on serotypes specific for this species. A wider range of serotypes is responsible for infection in Atlantic salmon, but very little is known about the diversity of these strains and their relationships to those recovered from rainbow trout. In the present study, we demonstrate that
Y. ruckeri
isolates recovered from diseased Atlantic salmon in Scotland are more diverse than those from rainbow trout; furthermore, isolates from the two species represent distinct subpopulations. In addition, a new O serotype was identified that is responsible for a significant proportion of the disease in Atlantic salmon. Our findings are likely to have important implications for the development of improved vaccines against
Y. ruckeri
.
Death Becomes Them: Bacterial Community Dynamics and Stilbene Antibiotic Production in Cadavers of Galleria mellonella Killed by Heterorhabditis and Photorhabdus spp
Authors: Wollenberg Amanda C. , Jagdish Tanush , Slough Greg , Hoinville Megan E. , Wollenberg Michael S.
Published: July 2016

Insect larvae killed by entomopathogenic nematodes are thought to contain bacterial communities dominated by a single bacterial genus, that of the nematode's bacterial symbiont. In this study, we used next-generation sequencing to profile bacterial community dynamics in greater wax moth (
Galleria mellonella
) larvae cadavers killed by
Heterorhabditis
nematodes and their
Photorhabdus
symbionts. We found that, although
Photorhabdus
strains did initially displace an
Enterococcus-
dominated community present in uninfected
G. mellonella
insect larvae, the cadaver community was not static. Twelve days postinfection,
Photorhabdus
shared the cadaver with
Stenotrophomonas
species. Consistent with this result,
Stenotrophomonas
strains isolated from infected cadavers were resistant to
Photorhabdus-
mediated toxicity in solid coculture assays. We isolated and characterized a
Photorhabdus-
produced antibiotic from
G. mellonella
cadavers, produced it synthetically, and demonstrated that both the natural and synthetic compounds decreased
G. mellonella-
associated
Enterococcus
growth, but not
Stenotrophomonas
growth,
in vitro
. Finally, we showed that the
Stenotrophomonas
strains described here negatively affected
Photorhabdus
growth
in vitro
. Our results add an important dimension to a broader understanding of
Heterorhabditis
-
Photorhabdus
biology and also demonstrate that interspecific bacterial competition likely characterizes even a theoretically monoxenic environment, such as a
Heterorhabditis
-
Photorhabdus
-parasitized insect cadaver.

IMPORTANCE
Understanding, and eventually manipulating, both human and environmental health depends on a complete accounting of the forces that act on and shape microbial communities. One of these underlying forces is hypothesized to be resource competition. A resource that has received little attention in the general microbiological literature, but likely has ecological and evolutionary importance, is dead/decaying multicellular organisms. Metazoan cadavers, including those of insects, are ephemeral and nutrient-rich environments, where resource competition might shape interspecific macrobiotic and microbiotic interactions. This study is the first to use a next-generation sequencing approach to study the community dynamics of bacteria within a model insect cadaver system: insect larvae parasitized by entomopathogenic nematodes and their bacterial symbionts. By integrating bioinformatic, biochemical, and classic
in vitro
microbiological approaches, we have provided mechanistic insight into how antibiotic-mediated bacterial interactions may shape community dynamics within insect cadavers.
Elucidating and Regulating the Acetoin Production Role of Microbial Functional Groups in Multispecies Acetic Acid Fermentation
Authors: Lu Zhen-Ming , Liu Na , Wang Li-Juan , Wu Lin-Huan , Gong Jin-Song , Yu Yong-Jian , Li Guo-Quan , Shi Jin-Song , Xu Zheng-Hong
Published: July 2016

Acetoin (3-hydroxy-2-butanone) formation in vinegar microbiota is crucial for the flavor quality of Zhenjiang aromatic vinegar, a traditional vinegar produced from cereals. However, the specific microorganisms responsible for acetoin formation in this centuries-long repeated batch fermentation have not yet been clearly identified. Here, the microbial distribution discrepancy in the diacetyl/acetoin metabolic pathway of vinegar microbiota was revealed at the species level by a combination of metagenomic sequencing and clone library analysis. The results showed that
Acetobacter pasteurianus
and 4
Lactobacillus
species (
Lactobacillus buchneri
,
Lactobacillus reuteri
,
Lactobacillus fermentum
, and
Lactobacillus brevis
) might be functional producers of acetoin from 2-acetolactate in vinegar microbiota. Furthermore,
A. pasteurianus
G3-2,
L. brevis
4-22,
L. fermentum
M10-3, and
L. buchneri
F2-5 were isolated from vinegar microbiota by a culture-dependent method. The acetoin concentrations in two cocultures (
L. brevis
4-22 plus
A. pasteurianus
G3-2 and
L. fermentum
M10-3 plus
A. pasteurianus
G3-2) were obviously higher than those in monocultures of lactic acid bacteria (LAB), while
L. buchneri
F2-5 did not produce more acetoin when coinoculated with
A. pasteurianus
G3-2. Last, the acetoin-producing function of vinegar microbiota was regulated
in situ
via augmentation with functional species in vinegar
Pei
. After 72 h of fermentation, augmentation with
A. pasteurianus
G3-2 plus
L. brevis
4-22,
L. fermentum
M10-3, or
L. buchneri
F2-5 significantly increased the acetoin content in vinegar
Pei
compared with the control group. This study provides a perspective on elucidating and manipulating different metabolic roles of microbes during flavor formation in vinegar microbiota.

IMPORTANCE
Acetoin (3-hydroxy-2-butanone) formation in vinegar microbiota is crucial for the flavor quality of Zhenjiang aromatic vinegar, a traditional vinegar produced from cereals. Thus, it is of interest to understand which microbes are driving the formation of acetoin to elucidate the microbial distribution discrepancy in the acetoin metabolic pathway and to regulate the metabolic function of functional microbial groups in vinegar microbiota. Our study provides a perspective on elucidating and manipulating different metabolic roles of microbes during flavor formation in vinegar microbiota.
Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp
Authors: Xu Min , Wang Yemin , Zhao Zhilong , Gao Guixi , Huang Sheng-Xiong , Kang Qianjin , He Xinyi , Lin Shuangjun , Pang Xiuhua , Deng Zixin , Tao Meifeng
Published: July 2016

Genome sequencing projects in the last decade revealed numerous cryptic biosynthetic pathways for unknown secondary metabolites in microbes, revitalizing drug discovery from microbial metabolites by approaches called genome mining. In this work, we developed a heterologous expression and functional screening approach for genome mining from genomic bacterial artificial chromosome (BAC) libraries in
Streptomyces
spp. We demonstrate mining from a strain of
Streptomyces rochei
, which is known to produce streptothricins and borrelidin, by expressing its BAC library in the surrogate host
Streptomyces lividans
SBT5, and screening for antimicrobial activity. In addition to the successful capture of the streptothricin and borrelidin biosynthetic gene clusters, we discovered two novel linear lipopeptides and their corresponding biosynthetic gene cluster, as well as a novel cryptic gene cluster for an unknown antibiotic from
S. rochei
. This high-throughput functional genome mining approach can be easily applied to other streptomycetes, and it is very suitable for the large-scale screening of genomic BAC libraries for bioactive natural products and the corresponding biosynthetic pathways.

IMPORTANCE
Microbial genomes encode numerous cryptic biosynthetic gene clusters for unknown small metabolites with potential biological activities. Several genome mining approaches have been developed to activate and bring these cryptic metabolites to biological tests for future drug discovery. Previous sequence-guided procedures relied on bioinformatic analysis to predict potentially interesting biosynthetic gene clusters. In this study, we describe an efficient approach based on heterologous expression and functional screening of a whole-genome library for the mining of bioactive metabolites from
Streptomyces
. The usefulness of this function-driven approach was demonstrated by the capture of four large biosynthetic gene clusters for metabolites of various chemical types, including streptothricins, borrelidin, two novel lipopeptides, and one unknown antibiotic from
Streptomyces rochei
Sal35. The transfer, expression, and screening of the library were all performed in a high-throughput way, so that this approach is scalable and adaptable to industrial automation for next-generation antibiotic discovery.
Secondary Mineralization of Ferrihydrite Affects Microbial Methanogenesis in Geobacter-Methanosarcina Cocultures
Authors: Tang Jia , Zhuang Li , Ma Jinlian , Tang Ziyang , Yu Zhen , Zhou Shungui
Published: July 2016

The transformation of ferrihydrite to stable iron oxides over time has important consequences for biogeochemical cycling of many metals and nutrients. The response of methanogenic activity to the presence of iron oxides depends on the type of iron mineral, but the effects of changes in iron mineralogy on methanogenesis have not been characterized. To address these issues, we constructed methanogenic cocultures of
Geobacter
and
Methanosarcina
strains with different ferrihydrite mineralization pathways. In this system, secondary mineralization products from ferrihydrite are regulated by the presence or absence of phosphate. In cultures producing magnetite as the secondary mineralization product, the rates of methanogenesis from acetate and ethanol increased by 30.2% and 135.3%, respectively, compared with a control lacking ferrihydrite. Biogenic magnetite was proposed to promote direct interspecies electron transfer between
Geobacter
and
Methanosarcina
in a manner similar to that of
c
-type cytochrome and thus facilitate methanogenesis. Vivianite biomineralization from ferrihydrite in the presence of phosphate did not significantly influence the methanogenesis processes. The correlation between magnetite occurrence and facilitated methanogenesis was supported by increased rates of methane production from acetate and ethanol with magnetite supplementation in the defined cocultures. Our data provide a new perspective on the important role of iron biomineralization in biogeochemical cycling of carbon in diverse anaerobic environments.

IMPORTANCE
It has been found that microbial methanogenesis is affected by the presence of iron minerals, and their influences on methanogenesis are associated with the mineralogical properties of the iron minerals. However, how changes in iron mineralogy affect microbial methanogenesis has not been characterized. To address this issue, we constructed methanogenic cocultures of
Geobacter
and
Methanosarcina
strains with different ferrihydrite mineralization pathways. The experimental results led to two contributions, i.e., (i) the transformation of iron minerals might exert an important influence on methanogenesis under anaerobic conditions and (ii) both biogenic and chemical magnetite can accelerate syntrophic ethanol oxidization between
Geobacter metallireducens
and
Methanosarcina barkeri
. This study sheds new light on the important role of iron biomineralization in the biogeochemical cycling of carbon in diverse anaerobic environments, particularly in iron-rich natural and agricultural wetland soils.
Longitudinal Investigation of Carriage Rates, Counts, and Genotypes of Toxigenic Clostridium difficile in Early Infancy
Authors: Kubota Hiroyuki , Makino Hiroshi , Gawad Agata , Kushiro Akira , Ishikawa Eiji , Sakai Takafumi , Akiyama Takuya , Matsuda Kazunori , Martin Rocio , Knol Jan , Oishi Kenji
Published: July 2016

Asymptomatic infant carriers of toxigenic
Clostridium difficile
are suggested to play a role in the transmission of
C. difficile
infection (CDI) in adults. However, the mode of
C. difficile
carriage in infants remains to be fully elucidated. We investigated longitudinal changes in carriage rates, counts, and strain types of toxigenic
C. difficile
in infants. Stools collected from 111 healthy infants in Belgium periodically from birth until the age of 6 months were examined by quantitative PCR targeting 16S rRNA and toxin genes. Toxigenic
C. difficile
was detected in 18 of 111 infants (16%) in the period up to the age of 6 months. The carriage rate of toxigenic
C. difficile
remained below 5% until the age of 3 months. The carriage rate increased to 13% 1 week after weaning (average age, 143 days) and reached 16% at the age of 6 months. Counts of toxigenic
C. difficile
bacteria ranged from 10
4
to 10
8
cells/g of stool. Notably, two infants retained >10
8
cells/g of stool for at least several weeks. Average counts in the 18 infants hovered around 10
7
cells/g of stool from the age of 3 days until the age of 6 months, showing no age-related trend. Genotyping of toxigenic
C. difficile
isolates from the 18 infants revealed that 11 infants each retained a particular monophyletic strain for at least a month. The genotype most frequently identified was the same as that frequently identified in symptomatic adult CDI patients. Thus, toxigenic
C. difficile
strains—potential causes of CDI in adults—colonized the infants' intestines.

IMPORTANCE
Our study provides longitudinal data on counts and strain types of toxigenic
C. difficile
in infants. We found that considerable numbers of toxigenic
C. difficile
bacteria colonized the infants' intestines. The results of strain typing suggest that toxigenic
C. difficile
carried by healthy infants could be potentially pathogenic to adults. These results and findings are informative not only for ecological studies but also for efforts to prevent or control the spread of CDI in adults.
Consumption of a Bifidobacterium bifidum Strain for 4 Weeks Modulates Dominant Intestinal Bacterial Taxa and Fecal Butyrate in Healthy Adults
Authors: Gargari Giorgio , Taverniti Valentina , Balzaretti Silvia , Ferrario Chiara , Gardana Claudio , Simonetti Paolo , Guglielmetti Simone
Published: July 2016

Modulation of the intestinal microbial ecosystem (IME) is a useful target to establish probiotic efficacy in a healthy population. We conducted a randomized, double-blind, crossover, and placebo-controlled intervention study to determine the impact of
Bifidobacterium bifidum
strain Bb on the IME of adult healthy volunteers of both sexes. High-throughput 16S rRNA gene sequencing was used to characterize the fecal microbiota before and after 4 weeks of daily probiotic cell consumption. The intake of approximately one billion live
B. bifidum
cells affected the relative abundance of dominant taxa in the fecal microbiota and modulated fecal butyrate levels. Specifically,
Prevotellaceae
(
P
= 0.041) and
Prevotella
(
P
= 0.034) were significantly decreased, whereas
Ruminococcaceae
(
P
= 0.039) and
Rikenellaceae
(
P
= 0.010) were significantly increased. We also observed that the probiotic intervention modulated the fecal concentrations of butyrate in a manner dependent on the initial levels of short-chain fatty acids (SCFAs). In conclusion, our study demonstrates that a single daily administration of
Bifidobacterium bifidum
strain Bb can significantly modify the IME in healthy (not diseased) adults. These findings demonstrate the need to reassess the notion that probiotics do not influence the complex and stable IME of a healthy individual.

IMPORTANCE
Foods and supplements claimed to contain health-promoting probiotic microorganisms are everywhere these days and mainly intended for consumption by healthy people. However, it is still debated what actual effects probiotic products may have on the healthy population. In this study, we report the results of an intervention trial aimed at assessing the modifications induced in the intestinal microbial ecosystem of healthy adults from the consumption of a probiotic product. Our results demonstrate that the introduction of a probiotic product in the dietary habits of healthy people may significantly modify dominant taxa of the intestinal microbiota, resulting in the modulation of short-chain fatty acid concentrations in the gut. The overall changes witnessed in the probiotic intervention indicate a mechanism of microbiota modulation that could have potential effects on human health.
The Riemerella anatipestifer
AS87_01735
Gene Encodes Nicotinamidase PncA, an Important Virulence Factor
Authors: Wang Xiaolan , Liu Beibei , Dou Yafeng , Fan Hongjie , Wang Shaohui , Li Tao , Ding Chan , Yu Shengqing
Published: July 2016

Riemerella anatipestifer
is a major bacterial pathogen that causes septicemic and exudative diseases in domestic ducks. In our previous study, we found that deletion of the
AS87_01735
gene significantly decreased the bacterial virulence of
R. anatipestifer
strain Yb2 (mutant RA625). The
AS87_01735
gene was predicted to encode a nicotinamidase (PncA), a key enzyme that catalyzes the conversion of nicotinamide to nicotinic acid, which is an important reaction in the NAD
+
salvage pathway. In this study, the
AS87_01735
gene was expressed and identified as the PncA-encoding gene, using an enzymatic assay. Western blot analysis demonstrated that
R. anatipestifer
PncA was localized to the cytoplasm. The mutant strain RA625 (named Yb2Δ
pncA
in this study) showed a similar growth rate but decreased NAD
+
quantities in both the exponential and stationary phases in tryptic soy broth culture, compared with the wild-type strain Yb2. In addition, Yb2Δ
pncA
-infected ducks showed much lower bacterial loads in their blood, and no visible histological changes were observed in the heart, liver, and spleen. Furthermore, Yb2Δ
pncA
immunization of ducks conferred effective protection against challenge with the virulent wild-type strain Yb2. Our results suggest that the
R. anatipestifer
AS87_01735
gene encodes PncA, which is an important virulence factor, and that the Yb2Δ
pncA
mutant can be used as a novel live vaccine candidate.

IMPORTANCE
Riemerella anatipestifer
is reported worldwide as a cause of septicemic and exudative diseases of domestic ducks. The
pncA
gene encodes a nicotinamidase (PncA), a key enzyme that catalyzes the conversion of nicotinamide to nicotinic acid, which is an important reaction in the NAD
+
salvage pathway. In this study, we identified and characterized the
pncA
-homologous gene
AS87_01735
in
R. anatipestifer
strain Yb2.
R. anatipestifer
PncA is a cytoplasmic protein that possesses similar PncA activity, compared with other organisms. Generation of the
pncA
mutant Yb2Δ
pncA
led to a decrease in the NAD
+
content, which was associated with decreased capacity for invasion and attenuated virulence in ducks. Furthermore, Yb2Δ
pncA
immunization of ducks conferred effective protection against challenge with the virulent wild-type strain Yb2. Altogether, these results suggest that PncA contributes to the virulence of
R. anatipestifer
and that the Yb2Δ
pncA
mutant can be used as a novel live vaccine candidate.
Silicate weathering and North Atlantic silica burial during the Paleocene-Eocene Thermal Maximum
Authors: Penman Donald E.
Published: July 2016

During the Paleocene-Eocene Thermal Maximum (PETM, ca. 56 Ma), thousands of gigatons of carbon were released into the ocean and atmosphere over several thousand years, offering the opportunity to study the response of ocean biogeochemistry to a carbon cycle perturbation of a similar magnitude to projected anthropogenic CO2 release. PETM scenarios typically invoke accelerated chemical weathering of terrestrial silicate rocks as a significant negative feedback driving the recovery and termination of the event. However, the implications of this mechanism for the geochemical cycling of silica during the PETM have received little attention. I use “back-of-the-envelope” calculations and a simple two-box geochemical model of the marine silica cycle to demonstrate that the sequestration of thousands of gigatons of carbon by enhanced silicate weathering during the PETM would have dramatically increased the riverine supply of dissolved silica (H4SiO4) to the oceans. This would have elevated seawater [H4SiO4], encouraging both increased opal (SiO2) production by siliceous organisms and enhanced preservation of SiO2 in the water column and sediments. Both of these factors would have promoted a prompt (due to the relatively short oceanic residence time of silica) increase in sedimentary opal burial, thus balancing the marine silica budget. Several recently recovered deep-sea sedimentary records from the central North Atlantic demonstrate elevated SiO2 content across the Paleocene-Eocene boundary, which I argue is the result of enhanced production and/or preservation of SiO2 in response to elevated [H4SiO4] in the North Atlantic, representing the ultimate fate of excess Si weathered from the continents during the PETM.
A matter of minutes: Breccia dike paleomagnetism provides evidence for rapid crater modification
Authors: Fairchild Luke M. , Swanson-Hysell Nicholas L. , Tikoo Sonia M.
Published: July 2016

During an impact event, a crater’s transient structure adjusts gravitationally. Within medium-sized complex craters, a central uplift rises and collapses resulting in large-scale rotations of the target rock. Estimated crater modification rates from numerical models indicate that complex impact craters modify to a structurally stable state within tens of seconds to several minutes after excavation. However, there is little direct geologic evidence constraining these rates. We show how paleomagnetic measurements of lithic breccia dikes emplaced during crater excavation can be used to constrain the rate of crater modification within the central uplift of the ∼34-km-diameter Slate Islands impact structure, Ontario, Canada. The uniformity and linearity of paleomagnetic directions among the clasts and matrix of breccia dikes throughout the impact structure indicate that breccia dikes were frictionally heated above the magnetite Curie temperature (580 °C) during their emplacement and subsequently cooled in situ through magnetic blocking temperatures. The tight grouping of these paleomagnetic directions implies that these breccia dikes cooled and locked in magnetic remanence over a time interval in which the impact structure was not experiencing structural rotations and had already reached a stable state. Conductive cooling of the thinnest sampled breccia dike would have led to the recording of magnetic remanence approximately six minutes after emplacement. This constraint necessitates a stable crater structure only minutes after impact and presents a rare case in which a geological process can be resolved on such a short time scale.
Fault zone characteristics and basin complexity in the southern Salton Trough, California
Authors: Persaud Patricia , Ma Yiran , Stock Joann M. , Hole John A. , Fuis Gary S. , Han Liang
Published: July 2016

Ongoing oblique slip at the Pacific–North America plate boundary in the Salton Trough produced the Imperial Valley (California, USA), a seismically active area with deformation distributed across a complex network of exposed and buried faults. To better understand the shallow crustal structure in this region and the connectivity of faults and seismicity lineaments, we used data primarily from the Salton Seismic Imaging Project to construct a three-dimensional P-wave velocity model down to 8 km depth and a velocity profile to 15 km depth, both at 1 km grid spacing. A VP = 5.65–5.85 km/s layer of possibly metamorphosed sediments within, and crystalline basement outside, the valley is locally as thick as 5 km, but is thickest and deepest in fault zones and near seismicity lineaments, suggesting a causative relationship between the low velocities and faulting. Both seismicity lineaments and surface faults control the structural architecture of the western part of the larger wedge-shaped basin, where two deep subbasins are located. We estimate basement depths, and show that high velocities at shallow depths and possible basement highs characterize the geothermal areas.
Evidence for a reducing Archean ambient mantle and its effects on the carbon cycle
Authors: Aulbach Sonja , Stagno Vincenzo
Published: July 2016

Chemical reduction-oxidation mechanisms within mantle rocks link to the terrestrial carbon cycle by influencing the depth at which magmas can form, their composition, and ultimately the chemistry of gases released into the atmosphere. The oxidation state of the uppermost mantle has been widely accepted to be unchanged over the past 3800 m.y., based on the abundance of redox-sensitive elements in greenstone belt–associated samples of different ages. However, the redox signal in those rocks may have been obscured by their complex origins and emplacement on continental margins. In contrast, the source and processes occurring during decompression melting at spreading ridges are relatively well constrained. We retrieve primary redox conditions from metamorphosed mid-oceanic ridge basalts (MORBs) and picrites of various ages (ca. 3000–550 Ma), using V/Sc as a broad redox proxy. Average V/Sc values for Proterozoic suites (7.0 ± 1.4, 2σ, n = 6) are similar to those of modern MORB (6.8 ± 1.6), whereas Archean suites have lower V/Sc (5.2 ± 0.4, n = 5). The lower Archean V/Sc is interpreted to reflect both deeper melt extraction from the uppermost mantle, which becomes more reduced with depth, and an intrinsically lower redox state. The pressure-corrected oxygen fugacity (expressed relative to the fayalite-magnetite-quartz buffer, ΔFMQ, at 1 GPa) of Archean sample suites (ΔFMQ –1.19 ± 0.33, 2σ) is significantly lower than that of post-Archean sample suites, including MORB (ΔFMQ –0.26 ± 0.44). Our results imply that the reducing Archean atmosphere was in equilibrium with Earth’s mantle, and further suggest that magmatic gases crossed the threshold that allowed a build-up in atmospheric O2 levels ca. 3000 Ma, accompanied by the first “whiffs” of oxygen in sediments of that age.
Three-dimensional textural and quantitative analyses of orogenic gold at the nanoscale
Authors: Sayab M. , Suuronen J.-P. , Molnár F. , Villanova J. , Kallonen A. , O’Brien H. , Lahtinen R. , Lehtonen M.
Published: July 2016

Ore textures provide direct clues for tracking ore-forming processes. In this regard, most of our knowledge is generally based on two-dimensional (2-D) image analyses, leaving a considerable gap in comprehending three-dimensional (3-D) in-situ textural settings. Recent advances in lab-based and synchrotron radiation–based X-ray computed microtomography and nanotomography have made it possible to visualize and quantify rock volumes in a 3-D space. In this study, we first analyzed microscale textures in oriented drill cores from the world-class Suurikuusikko orogenic gold deposit of northern Finland using lab-based X-ray computed microtomography. The technique revealed a kinematic history and a number of in-situ 3-D quantitative aspects including size, shape, spatial distribution, and geometrical orientation of arsenopyrite and pyrite in a highly altered host-rock matrix. For 3-D nanotomography, the experimental procedure known as holotomography was adopted. Individual arsenopyrite crystals were separated and scanned with voxel sizes ranging from 50 nm to 150 nm using the X-ray nanoprobe beamline (ID16B) at the European Synchrotron Radiation Facility, France. This ultrahigh-resolution technique illustrated the 3-D distribution of micron- to nanoscale gold inclusions, mostly associated with primary rutile or along secondary microfractures inside arsenopyrite. The workflow, from micro- to nanotomography, outlined in this study offers an indispensable new technique in quantifying and characterizing 3-D textural settings of ores, which is otherwise impossible with conventional 2-D imaging devices. The method can also be highly useful in evaluating the amenability of ores to treatment with different processing options.
Meroblastic cleavage identifies some Ediacaran Doushantuo (China) embryo-like fossils as metazoans
Authors: Yin Zongjun , Zhu Maoyan , Bottjer David J. , Zhao Fangchen , Tafforeau Paul
Published: July 2016

Ediacaran Doushantuo (Formation) embryo-like fossils (EDEFs, ca. 600 Ma) from South China display cellular and sub-cellular structures and provide a unique window on the early evolution of multicellular eukaryotes. But there have been widely disparate interpretations of these fossils. Here we report new fossil embryo-like forms from the Doushantuo phosphorite that exhibit a meroblastic cleavage pattern. Our results from high-resolution propagation phase contrast–synchrotron radiation X-ray microtomography (PPC-SRµCT) demonstrate that these fossils preserve features directly comparable to those of modern meroblastic animal embryos that utilize discoidal cleavage. Given that discoidal-type meroblastic cleavage occurs only in metazoans, the phylogenetic positions of these fossils probably fall into the animal branch of the holozoan tree. Meroblastic as well as holoblastic cleavage forms were thus present by ca. 600 Ma, substantiating the conclusion derived from molecular clock estimates that a variety of metazoan lineages had evolved by the mid-Ediacaran after the termination of the Marinoan glaciation, if not earlier.
Selecting children for head CT following head injury
Authors: Kemp A , Nickerson E , Trefan L , Houston R , Hyde P , Pearson G , Edwards R , Parslow RC , Maconochie I
Published: July 2016

Objective

Indicators for head CT scan defined by the 2007 National Institute for Health and Care Excellence (NICE) guidelines were analysed to identify CT uptake, influential variables and yield.

Design

Cross-sectional study.

Setting

Hospital inpatient units: England, Wales, Northern Ireland and the Channel Islands.

Patients

Children (<15 years) admitted to hospital for more than 4 h following a head injury (September 2009 to February 2010).

Interventions

CT scan.

Main outcome measures

Number of children who had CT, extent to which NICE guidelines were followed and diagnostic yield.

Results

Data on 5700 children were returned by 90% of eligible hospitals, 84% of whom were admitted to a general hospital. CT scans were performed on 30.4% of children (1734), with a higher diagnostic yield in infants (56.5% (144/255)) than children aged 1 to 14 years (26.5% (391/1476)). Overall, only 40.4% (984 of 2437 children) fulfilling at least one of the four NICE criteria for CT actually underwent one. These children were much less likely to receive CT if admitted to a general hospital than to a specialist centre (OR 0.52 (95% CI 0.45 to 0.59)); there was considerable variation between healthcare regions. When indicated, children >3 years were much more likely to have CT than those <3 years (OR 2.35 (95% CI 2.08 to 2.65)).

Conclusion

Compliance with guidelines and diagnostic yield was variable across age groups, the type of hospital and region where children were admitted. With this pattern of clinical practice the risks of both missing intracranial injury and overuse of CT are considerable.
Accumulated workloads and the acute:chronic workload ratio relate to injury risk in elite youth football players
Authors: Bowen Laura , Gross Aleksander Stefan , Gimpel Mo , Li François-Xavier
Published: July 2016

Aim

The purpose of this study was to investigate the relationship between physical workload and injury risk in elite youth football players.

Methods

The workload data and injury incidence of 32 players were monitored throughout 2 seasons. Multiple regression was used to compare cumulative (1, 2, 3 and 4-weekly) loads and acute:chronic (A:C) workload ratios (acute workload divided by chronic workload) between injured and non-injured players for specific GPS and accelerometer-derived variables:total distance (TD), high-speed distance (HSD), accelerations (ACC) and total load. Workloads were classified into discrete ranges by z-scores and the relative risk was determined.

Results

A very high number of ACC (≥9254) over 3 weeks was associated with the highest significant overall (relative risk (RR)=3.84) and non-contact injury risk (RR=5.11). Non-contact injury risk was significantly increased when a high acute HSD was combined with low chronic HSD (RR=2.55), but not with high chronic HSD (RR=0.47). Contact injury risk was greatest when A:C TD and ACC ratios were very high (1.76 and 1.77, respectively) (RR=4.98).

Conclusions

In general, higher accumulated and acute workloads were associated with a greater injury risk. However, progressive increases in chronic workload may develop the players' physical tolerance to higher acute loads and resilience to injury risk.
Prevalence of overweight and obesity and some associated factors among adult residents of northeast China: a cross-sectional study
Authors: Wang Rui , Zhang Peng , Gao Chunshi , Li Zhijun , Lv Xin , Song Yuanyuan , Yu Yaqin , Li Bo
Published: July 2016

Objectives

This study aims to estimate the prevalence of overweight and obesity and determine potential influencing factors among adults in northeast China.

Methods

A cross-sectional survey was conducted in Jilin Province, northeast China, in 2012. A total of 9873 men and 10 966 women aged 18–79 years from the general population were included using a multistage stratified random cluster sampling design. Data were obtained from face-to-face interview and physical examination. After being weighted according to a complex sampling scheme, the sample was used to estimate the prevalence of overweight (body mass index (BMI) 24–27.9 kg/m2) and obesity (BMI >28 kg/m2) in Jilin Province, and analyse influencing factors through corresponding statistical methods based on complex sampling design behaviours.

Results

The overall prevalence of overweight was 32.3% (male 34.3%; female 30.2%), and the prevalence of obesity was 14.6% (male 16.3%; female 12.8%) in Jilin Province. The prevalence of both overweight and obesity were higher in men than women (p<0.001). Influencing factors included sex, age, marriage status, occupation, smoking, drinking, diet and hours of sleep (p<0.05).

Conclusions

This study estimated that the prevalence of overweight and obesity among adult residents of Jilin Province, northeast China, were high. The results of this study will be submitted to the Health Department of Jilin Province and other relevant departments as a reference, which should inform policy makers in developing education and publicity to prevent and control the occurrence of overweight and obesity.
Assessing health disparities in children using a modified housing-related socioeconomic status measure: a cross-sectional study
Authors: Ryu Euijung , Wi Chung-Il , Crow Sheri S , Armasu Sebastian M , Wheeler Philip H , Sloan Jeff A , Yawn Barbara P , Beebe Timothy J , Williams Arthur R , Juhn Young J
Published: July 2016

Objectives

Socioeconomic status (SES) is a well-established risk factor for many health outcomes. Recently, we developed an SES measure based on 4 housing-related characteristics (termed HOUSES) and demonstrated its ability to assess health disparities. In this study, we aimed to evaluate whether fewer housing-related characteristics could be used to provide a similar representation of SES.

Study setting and participants

We performed a cross-sectional study using parents/guardians of children aged 1–17 years from 2 US Midwestern counties (n=728 in Olmsted County, Minnesota, and n=701 in Jackson County, Missouri).

Primary and secondary outcome measures

For each participant, housing-related characteristics used in the formulation of HOUSES (assessed housing value, square footage, number of bedrooms and number of bathrooms) were obtained from the local government assessor's offices, and additional SES measures and health outcomes with known associations to SES (obesity, low birth weight and smoking exposure) were collected from a telephone survey. Housing characteristics with the greatest contribution for predicting the health outcomes were added to formulate a modified HOUSES index.

Results

Among the 4 housing characteristics used in the original HOUSES, the strongest contributions for predicting health outcomes were observed from assessed housing value and square footage (combined contribution ranged between 89% and 96%). Based on this observation, these 2 were used to calculate a modified HOUSES index. Correlation between modified HOUSES and other SES measures was comparable to the original HOUSES for both locations. Consistent with the original HOUSES formula, the strongest association with modified HOUSES was observed with smoking exposure (OR=0.24 with 95% CI 0.11 to 0.49 for comparing participants in highest HOUSES vs lowest group; overall p<0.001).

Conclusions

The modified HOUSES requires only 2 readily available housing characteristics thereby improving the feasibility of using this index as a proxy for SES in multiple communities, especially in the US Midwestern region.
Referrals to integrative medicine in a tertiary hospital: findings from electronic health record data and qualitative interviews
Authors: Griffin Kristen H , Nate Kent C , Rivard Rachael L , Christianson Jon B , Dusek Jeffery A
Published: July 2016

Objective

To examine patterns of, and decision-making processes, informing referrals for inpatient access to integrative medicine (IM) services at a large, acute care hospital.

Design

Retrospective electronic health record review and structured qualitative interviews.

Setting

A 630-bed tertiary care hospital with an IM service available to inpatients.

Participants

IM referrals of all inpatients aged ≥18 years between July 2012 and December 2014 were identified using the hospital's electronic health record. Fifteen physicians, 15 nurses and 7 administrators were interviewed to better understand roles and perspectives in referring patients for IM services.

Results

In the study hospital, primary sources of referrals for IM services were the orthopaedic and neuroscience/spine service lines. While the largest absolute number of IM referrals was made for patients with lengths of stay of 3 days or fewer, a disproportionate number of total IM referrals was made for patients with long lengths of stay (≥10 days), compared with a smaller percentage of patients in the hospital with lengths of stay ≥10 days. Physicians and nurses were more likely to refer patients who displayed strong symptoms (eg, pain and anxiety) and/or did not respond to conventional therapies. IM referrals were predominantly nurse-initiated. A built-in delay in the time from referral initiation to service delivery discouraged referrals of some patients.

Conclusions

Conventional providers refer patients for IM services when these services are available in a tertiary hospital. Referral patterns are influenced by patient characteristics, operational features and provider perspectives. Nurses play a key role in the referral process. Overcoming cultural and knowledge differences between conventional and IM providers is likely to be a continuing challenge to providing IM in inpatient settings.