bluuebunny/crossref_metadata_2025 huggingface dataset:
Patterns of Fetal Growth Based on Ultrasound Measurement and its Relationship with Small for Gestational Age at Birth in Rural Vietnam
Authors: Nguyen Phuong Hong , Addo O. Yaw , Young Melissa , Gonzalez‐Casanova Ines , Pham Hoa , Truong Truong V. , Nguyen Son , Martorell Reynaldo , Ramakrishnan Usha
Published: February 2016

Background

Small for gestational age (SGA) is a global health problem. Identifying the timing of fetal growth faltering is critical for developing preventive interventions. We aim to describe patterns of fetal growth and to predict SGA at birth using fetal ultrasound measurements.

Methods

We studied 1412 pregnant women enrolled in a randomised‐controlled trial evaluating maternal micronutrient supplementation in Thai Nguyen province, Vietnam. Ultrasound examinations included biparietal diameter (BPD), head circumference (HC) and abdominal circumference (AC), and femur length (FL). Measures were assessed using the new international fetal growth standards (INTERGROWTH‐21st Project). Generalised linear mixed logit regression models were used to examine the association between ultrasound measures and SGA at birth.

Results

Overall fetal growth restriction began in early pregnancy and continued through delivery, but the timing of growth faltering varied by measure: it began by 20 weeks for HC, BPD and AC, earlier as compared to FL growth that started >30 weeks. SGA infants had significantly lower mean fetal growth parameters as early as 14 weeks. Ultrasound measures below the 10th percentile were associated with a two to four times higher risk of SGA at birth compared to fetuses greater than the 50th percentile, with the largest odds ratios for AC (OR 3.9, 95% confidence interval (CI) 2.7, 5.7).

Conclusions

Fetal growth faltering by ultrasound begins in early gestation among rural Vietnamese populations; these patterns clearly identified those to be born SGA. Efforts to prevent fetal growth faltering must begin early in pregnancy and perhaps even before pregnancy.
Maternal Dietary Patterns are Associated with Lower Levels of Cardiometabolic Markers during Pregnancy
Authors: Martin Chantel L. , Siega‐Riz Anna Maria , Sotres‐Alvarez Daniela , Robinson Whitney R. , Daniels Julie L. , Perrin Eliana M. , Stuebe Alison M.
Published: February 2016

Background

Elevated levels of cardiometabolic markers are characteristic of normal pregnancy, however, insulin resistance and increased glucose, triglyceride, and cholesterol levels can adversely influence maternal and child health. Diet is a modifiable behaviour that could have significant impact on maternal cardiometabolic levels during pregnancy. We investigated the association between dietary patterns and cardiometabolic markers (glucose, insulin, insulin resistance (HOMA‐IR), triglycerides, and cholesterol) during pregnancy.

Methods

Data from the Pregnancy, Infection, and Nutrition prospective cohort study (2000–05) was used (n = 513). Diet was assessed using a food frequency questionnaire. Dietary patterns were derived using latent class analysis (LCA) and the Dietary Approaches to Stop Hypertension (DASH) diet. Linear regression was used to examine the dietary patterns–cardiometabolic markers association during pregnancy.

Results

Three dietary patterns evolved from the LCA characterised by high intakes of: (1) hamburgers, hot dogs, bacon, French fries, fried chicken, white bread, and soft drinks; (2) some vegetables, fruit juice, refined grains, mixed dishes, processed meat, and empty calorie foods; and (3) fruits, vegetables, whole grains, low‐fat dairy, breakfast bars, and water. After adjustment for potential confounders including prepregnancy body mass index, a diet consistent with Latent Class 3 was negatively associated with maternal insulin (μU/mL: β = −0.12; 95% CI −0.23, −0.01) and HOMA‐IR (β = −0.13; 95% CI −0.25, −0.00). Additionally, DASH scores within Tertile 3 (higher dietary quality) were also negatively associated with maternal triglycerides (mg/dL).

Conclusions

The study findings suggest an association between maternal dietary patterns and several cardiometabolic markers during pregnancy.
Ectopic expression of SlAGO7 alters leaf pattern and inflorescence architecture and increases fruit yield in tomato
Authors: Lin Dongbo , Xiang Ya , Xian Zhiqiang , Li Zhengguo
Published: February 2016

ARGONAUTE7 (AGO7), a key regulator of the trans‐acting small interfering RNAs (ta‐siRNA) pathway, plays a conserved role in controlling leaf pattern among species. However, little is known about the ta‐siRNA pathway in regulating inflorescence architecture and fruit yield. In this study, we characterized the expression pattern, subcellular localization and developmental functions of SlAGO7 in tomato (Solanum lycopersicum). Overexpressing SlAGO7 in tomato exhibited pleiotropic phenotypes, including improved axillary bud formation, altered leaf morphology and inflorescence architecture, and increased fruit yield. Cross‐sectioning of leaves showed that the number of vascular bundles was significantly increased in 35:SlAGO7 lines. Overexpression of SlAGO7 increased the production of ta‐siRNA, and repressed the expression ta‐siRNA‐targeted genes (SlARF2a, SlARF2b, SlARF3 and SlARF4). Further analysis showed that overexpression of SlAGO7 alters the expression of key genes implicated in leaf morphology, inflorescence architecture, auxin transport and signaling. In addition, the altered auxin response of 35:SlAGO7 lines were also investigated. These results suggested that SlAGO7 plays a positive role in determining inflorescence architecture and fruit yield though the ta‐siRNA pathway. Therefore, SlAGO7 represents a useful gene that can be incorporated in tomato breeding programs for developing cultivars with yield potential.
Renewable Resources, Pollution and Trade
Authors: Rus Horatiu A.
Published: February 2016

Detrimental spillovers from industrial activity onto resource‐based productive sectors are very common, yet their effects remain understudied. While international trade often creates conditions for the over‐exploitation of open‐access renewable resources, it also provides opportunities for separating different productive sectors spatially. The existing literature suggests that a diversified exporter of the renewable resource good tends to lose from trade in both welfare and conservation terms as a result of over‐depletion, while the exporter of the non‐resource good gains. However, the resource stock externality of harvesting and the inter‐industry pollution externality often coexist in reality. In a small open economy framework, this paper shows that acknowledging their interaction changes the nature of the autarkic equilibrium and enriches the set of resource conservation and welfare outcomes from trade. Depending on the relative damage inflicted by the two industries on the environment, which in turn are functions of the pollution intensity and bioeconomic parameters, it is possible that the inter‐sectoral pollution externality persists and specialization in manufacturing is not optimal from a welfare perspective.
Asymptotic Properties of the Empirical Spatial Extremogram
Authors: Cho Yong Bum , Davis Richard A. , Ghosh Souvik
Published: February 2016

The extremogram is a useful tool for measuring extremal dependence and checking model adequacy in a time series. We define the extremogram in the spatial domain when the data is observed on a lattice or at locations distributed as a Poisson point process in d‐dimensional space. We establish a central limit theorem for the empirical spatial extremogram. We show these conditions are applicable for max‐moving average processes and Brown–Resnick processes and illustrate the empirical extremogram's performance via simulation. We also demonstrate its practical use with a data set related to rainfall in a region in Florida and ground‐level ozone in the eastern United States.
Developmental trajectories of cerebrovascular reactivity in healthy children and young adults assessed with magnetic resonance imaging
Authors: Leung Jackie , Kosinski Przemyslaw D. , Croal Paula L. , Kassner Andrea
Published: February 2016

Key points

Cerebrovascular reactivity (CVR) reflects the vasodilatory reserve of cerebral resistance vessels.

Normal development in children is associated with significant changes in blood pressure, cerebral blood flow (CBF) and cerebral oxygen metabolism. Therefore, it stands to reason that CVR will also undergo changes during this period.

The study acquired magnetic resonance imaging measures of CVR and CBF in healthy children and young adults to trace their changes with age.

We found that CVR changes in two phases, increasing with age until the mid‐teens, followed by a decrease. Baseline CBF declined steadily with age.

We conclude that CVR varies with age during childhood, which prompts future CVR studies involving children to take into account the effect of development.

Cerebrovascular reactivity (CVR) reflects the vasculature's ability to accommodate changes in blood flow demand thereby serving as a critical imaging tool for mapping vascular reserve. Normal development is associated with extensive physiological changes in blood pressure, cerebral blood flow and cerebral metabolic rate of oxygen, all of which can affect CVR. Moreover, the evolution of these physiological parameters is most prominent during childhood. Therefore, the aim of this study was to use non‐invasive magnetic resonance imaging (MRI) to characterize the developmental trajectories of CVR in healthy children and young adults, and relate them to changes in cerebral blood flow (CBF). Thirty‐four healthy subjects (17 males, 17 females; age 9–30 years) underwent CVR assessment using blood oxygen level‐dependent MRI in combination with a computer controlled CO2 stimulus. In addition, baseline CBF was measured with a pulsed arterial spin labelling sequence. CVR exhibited a gradual increase with age in both grey and white matter up to 14.7 years. After this break point, a negative correlation with age was detected. Baseline CBF maintained a consistent negative linear correlation across the entire age range. The significant age‐dependent changes in CVR and CBF demonstrate the evolution of cerebral haemodynamics in children and should be taken into consideration. The shift in developmental trajectory of CVR from increasing to decreasing suggests that physiological factors beyond baseline CBF also influence CVR.
Notch regulation of gastrointestinal stem cells
Authors: Demitrack Elise S. , Samuelson Linda C.
Published: February 2016

The gastrointestinal (GI) tract epithelium is continuously replenished by actively cycling stem and progenitor cells. These cell compartments are regulated to balance proliferation and stem cell renewal with differentiation into the various mature cell types to maintain tissue homeostasis. In this topical review we focus on the role of the Notch signalling pathway to regulate GI stem cell function in adult small intestine and stomach. We first present the current view of stem and progenitor cell populations in these tissues and then summarize the studies that have established the Notch pathway as a key regulator of gastric and intestinal stem cell function. Notch signalling has been shown to be a niche factor required for maintenance of GI stem cells in both tissues. In addition, Notch has been described to regulate epithelial cell differentiation. Recent studies have revealed key similarities and differences in how Notch regulates stem cell function in the stomach compared to intestine. We summarize the literature regarding Notch regulation of GI stem cell proliferation and differentiation, highlighting tissue‐specific functions to compare and contrast Notch in the stomach and intestine.

image
Second Law Analysis of Magnetorheological Rotational Flow With Viscous Dissipation
Authors: Hazbavi Abbas
Published: February 2016

In this study, the influences of the applied magnetic field and fluid elasticity were investigated for a nonlinear viscoelastic fluid obeying the Carreau equation between concentric annulus where the inner cylinder rotates at a constant angular velocity and the outer cylinder is stationary. The governing motion and energy balance equations are coupled while viscous dissipation is taken into account, adding complexity to the already highly correlated set of differential equations. The numerical solution is obtained for the narrow gap limit and steady-state base flow. Magnetic field effect on local entropy generation due to steady two-dimensional laminar forced convection flow was investigated. This study was focused on the entropy generation characteristics and its dependency on various dimensionless parameters. The effects of the Hartmann number, the Brinkman number, the Deborah number, and the fluid elasticity on the stability of the flow were investigated. The application of the magnetic field induces a resistive force acting in the opposite direction of the flow, thus causing its deceleration. Moreover, the study shows that the presence of magnetic field tends to slowdown the fluid motion and thus increases the fluid temperature. However, the total entropy generation number decreases as the Hartmann number and fluid elasticity increase and it increases with increasing Brinkman number.
Turbine Blade Tip Cooling With Blade Rotation—Part II: Shroud Coolant Injection
Authors: Tamunobere Onieluan , Acharya Sumanta
Published: February 2016

In this paper, blade tip cooling is investigated with coolant injection from the shroud alone and a combination of shroud coolant injection and tip cooling. With a nominal rotation speed of 1200 rpm, each blade consists of a cut back squealer tip with a tip clearance of 1.7% of the blade span. The blades also consist of tip holes and pressure side (PS) shaped holes, while the shroud has an array of angled holes and a circumferential slot upstream of the rotor section. Different combinations of the three cooling configurations (tip and PS holes, shroud angled holes, and shroud circumferential slot) are utilized to study the effectiveness of coolant injected from the shroud as a complementary method of cooling the blade tip. The measurements are done using liquid crystal thermography. Blowing ratios of 0.5, 1.0, 2.0, 3.0, and 4.0 are studied for shroud slot cooling, and blowing ratios of 1.0, 2.0, 3.0, 4.0, and 5.0 are studied for shroud hole cooling. For cases with coolant injection from the blade tip, the blowing ratios used are 1.0, 2.0, 3.0, and 4.0. The results show an increase in film cooling effectiveness with increasing blowing ratio for shroud hole coolant injection. The increased effectiveness from shroud hole coolant is concentrated mainly in the tip region below the shroud holes and toward the blade suction side and the suction side squealer rim. Slot coolant injection results in increased effectiveness on the blade tip near the blade leading edge up to a maximum blowing ratio, after which the cooling effectiveness decreases with increasing blowing ratio. The combination of the different cooling methods results in better overall cooling coverage of the blade tip with the shroud hole and blade tip coolant combination being the most effective. The level of coolant protection is strongly dependent on the blowing ratio and combination of blowing ratios.
Controlling Corner Stall Separation With Plasma Actuators in a Compressor Cascade
Authors: Akcayoz Eray , Duc Vo Huu , Mahallati Ali
Published: February 2016

This paper presents a numerical and experimental assessment of a plasma actuation concept for controlling corner stall separation in a highly loaded compressor cascade. CFD simulations were first carried out to assess actuator effectiveness and determine the best actuation parameters. Subsequently, experiments were performed to demonstrate the concept and confirmed the CFD tool validity at a Reynolds number of 1.5 × 105. Finally, the validated CFD tool was used to simulate the concept at higher velocities, beyond the experimental capability of existing plasma actuators. These results were used to obtain a preliminary scaling law that would allow approximation of the plasma actuation requirements at realistic operating conditions. Several configurations were examined, but the most effective setup was found to be when plasma actuators were mounted upstream of the separation point on both the suction surface and the endwall. Most of the improvement in total pressure loss stemmed from the suction surface actuator. Comparison with experimental data showed that the CFD simulations could capture the flow features and the effect of plasma actuation reasonably well. Simulations at higher flow velocities indicated that the required plasma actuator strength scales approximately with the square of the Reynolds number.
Solid phase epitaxial regrowth of (001) anatase titanium dioxide
Authors: Barlaz David Eitan , Seebauer Edmund G.
Published: February 2016

The growing interest in metal oxide based semiconductor technologies has driven the need to produce high quality epitaxial films of one metal oxide upon another. Largely unrecognized in synthetic efforts is that some metal oxides offer strongly polar surfaces and interfaces that require electrostatic stabilization to avoid a physically implausible divergence in the potential. The present work examines these issues for epitaxial growth of anatase TiO2 on strontium titanate (001). Solid phase epitaxial regrowth yields only the (001) facet, while direct crystalline growth by atomic layer deposition yields both the (112) and (001). The presence of amorphous TiO2 during regrowth may provide preferential stabilization for formation of the (001) facet.
The race for a Zika vaccine is on
Authors: Cohen Jon
Published: February 2016

Researchers see many approaches—but a vaccine likely will take years.
Nematicity in stripe-ordered cuprates probed via resonant x-ray scattering
Authors: Achkar A. J. , Zwiebler M. , McMahon Christopher , He F. , Sutarto R. , Djianto Isaiah , Hao Zhihao , Gingras Michel J. P. , Hücker M. , Gu G. D. , Revcolevschi A. , Zhang H. , Kim Y.-J. , Geck J. , Hawthorn D. G.
Published: February 2016

Disentangling intertwined orders

In copper oxide superconductors, several types of order compete for supremacy. In addition to superconductivity, researchers have found periodic patterns in charge density (CDW order), as well as an asymmetry in the electronic density within the unit cell of some cuprates (nematicity). CDW order has been detected in the underdoped regime of all major cuprate families, but the ubiquity of nematicity is less clear. Achkar
et al.
used resonant x-ray scattering to find that, in the copper oxide planes of three lanthanum-based cuprates, nematicity has a temperature dependence distinct from that of a related structural distortion. This implies that there are additional, electronic mechanisms for nematicity

Science
, this issue p.
576
Hair follicle aging is driven by transepidermal elimination of stem cells via COL17A1 proteolysis
Authors: Matsumura Hiroyuki , Mohri Yasuaki , Binh Nguyen Thanh , Morinaga Hironobu , Fukuda Makoto , Ito Mayumi , Kurata Sotaro , Hoeijmakers Jan , Nishimura Emi K.
Published: February 2016

Quiescent and aging hair follicle stem cells

Stem cells enable normal cell homeostasis, but they also exist in a quiescent state, ready to proliferate and differentiate after tissue damage. Now, two studies reveal features of stem cells in the hair follicle, an epithelial mini-organ of the skin that is responsible for hair growth and recycling (see the Perspective by Chuong and Lei). Wang
et al.
found that the Foxc1 transcription factor is induced in activated hair follicle stem cells, which in turn promote Nfatc1 and BMP signaling, to reinforce quiescence. Matsumura
et al.
analyzed hair follicle stem cells during aging. They identified type XVII collagen (COL17A1) as key to hair thinning. DNA damage-induced depletion of COL17A1 triggered cell differentiation resulting in the shedding of epidermal keratinocytes from the skin surface. These changes then caused hair follicle shrinkage and hair loss.

Science
, this issue p.
559
, p.
613
; see also p.
10.1126/science.aad4395
Foxc1 reinforces quiescence in self-renewing hair follicle stem cells
Authors: Wang Li , Siegenthaler Julie A. , Dowell Robin D. , Yi Rui
Published: February 2016

Quiescent and aging hair follicle stem cells

Stem cells enable normal cell homeostasis, but they also exist in a quiescent state, ready to proliferate and differentiate after tissue damage. Now, two studies reveal features of stem cells in the hair follicle, an epithelial mini-organ of the skin that is responsible for hair growth and recycling (see the Perspective by Chuong and Lei). Wang
et al.
found that the Foxc1 transcription factor is induced in activated hair follicle stem cells, which in turn promote Nfatc1 and BMP signaling, to reinforce quiescence. Matsumura
et al.
analyzed hair follicle stem cells during aging. They identified type XVII collagen (COL17A1) as key to hair thinning. DNA damage-induced depletion of COL17A1 triggered cell differentiation resulting in the shedding of epidermal keratinocytes from the skin surface. These changes then caused hair follicle shrinkage and hair loss.

Science
, this issue p.
559
, p.
613
; see also p.
10.1126/science.aad4395
Nuclear magnetic resonance detection and spectroscopy of single proteins using quantum logic
Authors: Lovchinsky I. , Sushkov A. O. , Urbach E. , de Leon N. P. , Choi S. , De Greve K. , Evans R. , Gertner R. , Bersin E. , Müller C. , McGuinness L. , Jelezko F. , Walsworth R. L. , Park H. , Lukin M. D.
Published: February 2016

Sensing single proteins with diamonds

Nuclear magnetic resonance is a powerful technique for medical imaging and the structural analysis of materials, but is usually associated with large-volume samples. Lovchinsky
et al.
exploited the magnetic properties of a single spin associated with a defect in diamond and manipulated it with a quantum-logic protocol. They demonstrated the magnetic resonance detection and spectroscopy of multiple nuclear species within individual ubiquitin proteins attached to a specially treated diamond surface at room temperature.

Science
, this issue p.
836
Ice sheet in peril
Authors: Hvidberg Christine S.
Published: February 2016

Radar data reveal how sensitive the Greenland Ice Sheet is to long-term climatic changes

[Also see Report by

MacGregor
et al.

]
Throttling back the heart's molecular motor
Authors: Warshaw David M.
Published: February 2016

A small molecule inhibits mutated forms of myosin that cause cardiac hypertrophy

[Also see Report by

Green
et al.

]
Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut
Authors: Howitt Michael R. , Lavoie Sydney , Michaud Monia , Blum Arthur M. , Tran Sara V. , Weinstock Joel V. , Gallini Carey Ann , Redding Kevin , Margolskee Robert F. , Osborne Lisa C. , Artis David , Garrett Wendy S.
Published: February 2016

Tuft cells help contain parasites

Trillions of microbes inhabit our guts, including worms and other parasites. Epithelial cells that line the gut orchestrate parasite-targeted immune responses. Howitt
et al.
now identify a key cellular player in immunity to parasites: tuft cells (see the Perspective by Harris). Tuft cells make up a small fraction of gut epithelial cells but expand when parasites colonize or infect the gut. Parasites cause tuft cells to secrete large amounts of interleukin-25, a key cytokine for parasite clearance that also indirectly feeds back on tuft cells to expand their numbers. Tuft cells express chemosensory signaling machinery: disrupting this blocked parasite-triggered tuft cell expansion and weakened the ability of mice to control a parasitic infection.

Science
, this issue p.
1329
; see also p.
1264
Genome Sequence of Mycobacteriophage Cabrinians
Authors: Chudoff Dylan , Conboy Andrew , Conboy Danielle , Atoulelou Mireille , Hasan Sakina , Martinez Alexandria , Mastrando Jessica , Roy Renoy , Schmidt Robert , Sheed Kabreeze , Smith Jewel , Sperratore Morgan , Struga Rexhina , Starr Katelyn , Suppi Regina , Uguru Ugo , Terry Katrina , Villafuerte Rosendo , Yuan Vanessa , Dunbar David
Published: February 2016

Mycobacteriophage Cabrinians is a newly isolated phage capable of infecting both
Mycobacterium phlei
and
Mycobacterium smegmatis
and was recovered from a soil sample in New York City, NY. Cabrinians has a genome length of 56,669 bp, encodes 101 predicted proteins, and is a member of mycobacteriophages in cluster F.
Draft Genome Sequence of Lactococcus lactis subsp.
lactis
bv. diacetylactis CRL264, a Citrate-Fermenting Strain
Authors: Zuljan Federico , Espariz Martín , Blancato Victor S. , Esteban Luis , Alarcón Sergio , Magni Christian
Published: February 2016

We report the draft genome sequence of
Lactococcus lactis
subsp.
lactis
bv
.
diacetylactis CRL264, a natural strain isolated from artisanal cheese from northwest Argentina.
L. lactis
subsp.
lactis
bv
.
diacetylactis is one of the most important microorganisms used as starter culture around the world. The CRL264 strain constitutes a model microorganism in the studies on the generation of aroma compounds (diacetyl, acetoin, and 2,3-butanediol) by lactic acid bacteria. Our genome analysis shows similar genetic organization to other available genomes of
L. lactis
bv. diacetylactis strains.
Draft Genome Sequences of Four Enterococcus faecium Strains Isolated from Argentine Cheese
Authors: Martino Gabriela P. , Quintana Ingrid M. , Espariz Martín , Blancato Victor S. , Gallina Nizo Gabriel , Esteban Luis , Magni Christian
Published: February 2016

We report the draft genome sequences of four
Enterococcus faecium
strains isolated from Argentine regional cheeses. These strains were selected based on their technological properties, i.e., their ability to produce aroma compounds (diacetyl, acetoin, and 2,3-butanediol) from citrate. The goal of our study is to provide further genetic evidence for the rational selection of enterococci strains based on their pheno- and genotype in order to be used in cheese production.
Draft Genome of Debaryomyces fabryi CBS 789
T
, Isolated from a Human Interdigital Mycotic Lesion
Authors: Tafer Hakim , Sterflinger Katja , Lopandic Ksenija
Published: February 2016

The yeast genus
Debaryomyces
comprises species isolated from various natural habitats, man-made environments, and clinical materials. Here, the draft genome of
D. fabryi
CBS 789
T
, isolated from a human interdigital mycotic lesion, is presented.
Draft Genome Sequence of Altererythrobacter marensis DSM 21428
T
, Isolated from Seawater
Authors: Cheng Hong , Wu Yue-Hong , Huo Ying-Yi , Wang Chun-Sheng , Xu Xue-Wei
Published: February 2016

Altererythrobacter marensis
DSM 21428
T
was isolated from seawater collected around Mara Island, South Korea. The genomic characteristics of this strain support its potential for alkane-related compound degradation.
A. marensis
DSM 21428
T
has potential applications in bioremediation projects concerning offshore petroleum spill prevention and response.
A Spontaneous Deletion of the
US1.67/US2
Genomic Region on the Bovine Herpesvirus 1 Strain Cooper
Authors: Campos F. S. , Paim W. P. , Silva A. G. , Santos R. N. , Firpo R. M. , Scheffer C. M. , Finoketti F. , Franco A. C. , Roehe P. M.
Published: February 2016

Bovine herpesvirus 1 (BoHV-1) is an alphaherpesvirus with a genome of 135 kb. Some BoHV-1 genes are nonessential and may be deleted from the viral genome. Here, a spontaneous gene deletion was identified in the BoHV-1 strain Cooper. Genes of the
US1.67/US2
region were absent, as determined by next-generation sequencing.
Draft Genome Sequence of Bacillus cecembensis PN5
T
(DSM 21993), a Psychrotolerant Bacterium Isolated from Soil Samples near the Pindari Glacier
Authors: Wang Jie-ping , Liu Bo , Liu Guo-hong , Ge Ci-bin , Chen Qian-qian , Che Jian-mei , Chen De-ju
Published: February 2016

Bacillus cecembensis
PN5
T
is a Gram-positive, aerobic, and spore-forming bacterium with very high intrinsic heat resistance. Here, we report the 4.72-Mb draft genome sequence of
B. cecembensis
PN5
T
, the first genome sequence of this species, which will promote its fundamental research.
Draft Genome Sequence of Bacillus shackletonii LMG 18435
T
, Isolated from Volcanic Mossy Soil
Authors: Wang Jie-ping , Liu Bo , Liu Guo-hong , Ge Ci-bin , Xiao Rong-feng , Zheng Xue-fang , Shi Huai
Published: February 2016

Bacillus shackletonii
LMG 18435
T
is a Gram-positive, aerobic, and spore-forming bacterium. Here, we report the 5.30-Mb draft genome sequence of
B. shackletonii
LMG 18435
T
, which will promote its fundamental research and provide useful information for genomic taxonomy and phylogenomics of
Bacillus
-like bacteria.
Draft Genome Sequence of Bacillus plakortidis P203
T
(DSM 19153), an Alkali- and Salt-Tolerant Marine Bacterium
Authors: Wang Jie-ping , Liu Bo , Liu Guo-hong , Ge Ci-bin , Xiao Rong-feng , Zheng Xue-fang , Shi Huai
Published: February 2016

Bacillus plakortidis
P203
T
is a Gram-positive, spore-forming, and alkali- and salt-tolerant marine bacterium. Here, we report the 3.97-Mb draft genome sequence of
B. plakortidis
P203
T
, which will promote its fundamental research and provide useful information for genomic taxonomy and phylogenomics of
Bacillus
-like bacteria.
Complete Genome Sequence of a Genotype XVII Newcastle Disease Virus, Isolated from an Apparently Healthy Domestic Duck in Nigeria
Authors: Shittu Ismaila , Sharma Poonam , Joannis Tony M. , Volkening Jeremy D. , Odaibo Georgina N. , Olaleye David O. , Williams-Coplin Dawn , Solomon Ponman , Abolnik Celia , Miller Patti J. , Dimitrov Kiril M. , Afonso Claudio L.
Published: February 2016

The first complete genome sequence of a strain of Newcastle disease virus (NDV) of genotype XVII is described here. A velogenic strain (duck/Nigeria/903/KUDU-113/1992) was isolated from an apparently healthy free-roaming domestic duck sampled in Kuru, Nigeria, in 1992. Phylogenetic analysis of the fusion protein gene and complete genome classified the isolate as a member of NDV class II, genotype XVII.
A Toxoplasma gondii Ortholog of
Plasmodium
GAMA Contributes to Parasite Attachment and Cell Invasion
Authors: Huynh My-Hang , Carruthers Vern B.
Published: February 2016

Toxoplasma gondii
is a successful human pathogen in the same phylum as malaria-causing
Plasmodium
parasites. Invasion of a host cell is an essential process that begins with secretion of adhesive proteins onto the parasite surface for attachment and subsequent penetration of the host cell. Conserved invasion proteins likely play roles that were maintained through the divergence of these parasites. Here, we identify a new conserved invasion protein called glycosylphosphatidylinositol-anchored micronemal antigen (GAMA). Tachyzoites lacking TgGAMA were partially impaired in parasite attachment and invasion of host cells, yielding the first genetic evidence of a specific role in parasite entry into host cells. These findings widen our appreciation of the repertoire of conserved proteins that apicomplexan parasites employ for cell invasion.
Epidemic Keratoconjunctivitis-Causing Adenoviruses Induce MUC16 Ectodomain Release To Infect Ocular Surface Epithelial Cells
Authors: Menon Balaraj B. , Zhou Xiaohong , Spurr-Michaud Sandra , Rajaiya Jaya , Chodosh James , Gipson Ilene K.
Published: February 2016

Human adenoviruses (HAdVs) are double-stranded DNA viruses that cause infections across all mucosal tissues in the body. At the ocular surface, HAdVs cause keratoconjunctivitis (E. Ford, K. E. Nelson, and D. Warren, Epidemiol Rev 9:244–261, 1987, and C. M. Robinson, D. Seto, M. S. Jones, D. W. Dyer, and J. Chodosh, Infect Genet Evol 11:1208–1217, 2011, doi:10.1016/j.meegid.2011.04.031)—a highly contagious infection that accounts for nearly 60% of conjunctivitis cases in the United States (R. P. Sambursky, N. Fram, and E. J. Cohen, Optometry 78:236–239, 2007, doi:10.1016/j.optm.2006.11.012, and A. M. Pihos, J Optom 6:69–74, 2013, doi:10.1016/j.optom.2012.08.003). The infection begins with HAdV entry within ocular surface epithelial cells; however, the mechanisms used by HAdVs to transit the otherwise protective mucosal barrier of ocular surface epithelial cells prior to entry remain unknown. Here, we report that the highly virulent keratoconjunctivitis-causing HAdV-D37 induces release of the extracellular domain (ectodomain) of MUC16, a major component of the mucosal barrier of ocular surface epithelial cells, prior to infecting underlying cells. Currently, there is no specific treatment for controlling this infection. Understanding the early steps involved in the pathogenesis of keratoconjunctivitis and using this information to intercept adenoviral entry within cells may guide the development of novel strategies for controlling the infection.
Open-Source Sequence Clustering Methods Improve the State Of the Art
Authors: Kopylova Evguenia , Navas-Molina Jose A. , Mercier Céline , Xu Zhenjiang Zech , Mahé Frédéric , He Yan , Zhou Hong-Wei , Rognes Torbjørn , Caporaso J. Gregory , Knight Rob
Published: February 2016

Massive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate that recent clustering algorithms can significantly improve accuracy and preserve estimated diversity without the application of aggressive filtering. Moreover, these tools are all open source, apply multiple levels of multithreading, and scale to the demands of modern next-generation sequencing data, which is essential for the analysis of massive multidisciplinary studies such as the Earth Microbiome Project (EMP) (J. A. Gilbert, J. K. Jansson, and R. Knight, BMC Biol 12:69, 2014,
http://dx.doi.org/10.1186/s12915-014-0069-1
).
A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli
Authors: Balasubramanian Divya , Ragunathan Preethi T. , Fei Jingyi , Vanderpool Carin K.
Published: February 2016

sRNAs are ubiquitous and versatile regulators of bacterial gene expression. A number of well-characterized examples in
E. coli
are highly conserved and present in the
E. coli
core genome. In contrast, the sRNA DicF (identified over 20 years ago but remaining poorly characterized) is encoded by a gene carried on a defective prophage element in many
E. coli
genomes. Here, we characterize DicF in order to better understand how horizontally acquired sRNA regulators impact bacterial gene expression and physiology. Our data confirm the long-hypothesized DicF-mediated regulation of
ftsZ
, encoding the bacterial tubulin homolog required for cell division. We further uncover DicF-mediated posttranscriptional control of metabolic gene expression. Ectopic production of DicF is highly toxic to
E. coli
cells, but the toxicity is not attributable to DicF regulation of
ftsZ.
Further work is needed to reveal the biological roles of and benefits for the host conferred by DicF and other products encoded by defective prophages.
‘Too much of a coincidence’: identical twins with exertional heatstroke in the same race
Authors: Smith R , Jones N , Martin D , Kipps C
Published: February 2016

This report discusses a unique case of monozygotic male twins who both collapsed with exertional heat stroke (EHS) during the same marathon in relatively cool conditions. The twins were official race pacers in a popular city marathon held in the early spring in the UK. Both recovered uneventfully due to the prompt recognition of EHS and use of aggressive cooling measures, which prevented life-threatening complications. The case illustrates that EHS is a complex illness with a possible genetic predisposition, which can occur among runners even in cooler conditions. This link is explored together with the influence of their role as race pacers and the additional backpack worn in the development of EHS.
Postnuclear disaster evacuation and chronic health in adults in Fukushima, Japan: a long-term retrospective analysis
Authors: Nomura Shuhei , Blangiardo Marta , Tsubokura Masaharu , Ozaki Akihiko , Morita Tomohiro , Hodgson Susan
Published: February 2016

Objective

Japan's 2011 Fukushima Daiichi Nuclear Power Plant incident required the evacuation of over a million people, creating a large displaced population with potentially increased vulnerability in terms of chronic health conditions. We assessed the long-term impact of evacuation on diabetes, hyperlipidaemia and hypertension.

Participants

We considered participants in annual public health check-ups from 2008 to 2014, administrated by Minamisoma City and Soma City, located about 10–50 km from the Fukushima nuclear plant.

Methods

Disease risks, measured in terms of pre-incident and post-incident relative risks, were examined and compared between evacuees and non-evacuees/temporary-evacuees. We also constructed logistic regression models to assess the impact of evacuation on the disease risks adjusted for covariates.

Results

Data from a total of 6406 individuals aged 40–74 years who participated in the check-ups both at baseline (2008–2010) and in one or more post-incident years were analysed. Regardless of evacuation, significant post-incident increases in risk were observed for diabetes and hyperlipidaemia (relative risk: 1.27–1.60 and 1.12–1.30, respectively, depending on evacuation status and post-incident year). After adjustment for covariates, the increase in hyperlipidaemia was significantly greater among evacuees than among non-evacuees/temporary-evacuees (OR 1.18, 95% CI 1.06 to 1.32, p<0.01).

Conclusions

The singularity of this study is that evacuation following the Fukushima disaster was found to be associated with a small increase in long-term hyperlipidaemia risk in adults. Our findings help identify discussion points on disaster planning, including preparedness, response and recovery measures, applicable to future disasters requiring mass evacuation.
Systematic review finds major deficiencies in sample size methodology and reporting for stepped-wedge cluster randomised trials
Authors: Martin James , Taljaard Monica , Girling Alan , Hemming Karla
Published: February 2016

Background

Stepped-wedge cluster randomised trials (SW-CRT) are increasingly being used in health policy and services research, but unless they are conducted and reported to the highest methodological standards, they are unlikely to be useful to decision-makers. Sample size calculations for these designs require allowance for clustering, time effects and repeated measures.

Methods

We carried out a methodological review of SW-CRTs up to October 2014. We assessed adherence to reporting each of the 9 sample size calculation items recommended in the 2012 extension of the CONSORT statement to cluster trials.

Results

We identified 32 completed trials and 28 independent protocols published between 1987 and 2014. Of these, 45 (75%) reported a sample size calculation, with a median of 5.0 (IQR 2.5–6.0) of the 9 CONSORT items reported. Of those that reported a sample size calculation, the majority, 33 (73%), allowed for clustering, but just 15 (33%) allowed for time effects. There was a small increase in the proportions reporting a sample size calculation (from 64% before to 84% after publication of the CONSORT extension, p=0.07). The type of design (cohort or cross-sectional) was not reported clearly in the majority of studies, but cohort designs seemed to be most prevalent. Sample size calculations in cohort designs were particularly poor with only 3 out of 24 (13%) of these studies allowing for repeated measures.

Discussion

The quality of reporting of sample size items in stepped-wedge trials is suboptimal. There is an urgent need for dissemination of the appropriate guidelines for reporting and methodological development to match the proliferation of the use of this design in practice. Time effects and repeated measures should be considered in all SW-CRT power calculations, and there should be clarity in reporting trials as cohort or cross-sectional designs.
How might health services capture patient-reported safety concerns in a hospital setting? An exploratory pilot study of three mechanisms
Authors: O'Hara Jane Kathryn , Armitage Gerry , Reynolds Caroline , Coulson Claire , Thorp Liz , Din Ikhlaq , Watt Ian , Wright John
Published: February 2016

Introduction

Emergent evidence suggests that patients can identify and report safety issues while in hospital. However, little is known about the best method for collecting information from patients about safety concerns. This study presents an exploratory pilot of three mechanisms for collecting data on safety concerns from patients during their hospital stay.

Method

Three mechanisms for capturing safety concerns were coproduced with healthcare professionals and patients, before being tested in an exploratory trial using cluster randomisation at the ward level. Nine wards participated, with each mechanism being tested over a 3-month study period. Patients were asked to feed back safety concerns via the mechanism on their ward (interviewing at their bedside, paper-based form or patient safety ‘hotline’). Safety concerns were subjected to a two-stage review process to identify those that would meet the definition of a patient safety incident. Differences between mechanisms on a range of outcomes were analysed using inferential statistics. Safety concerns were thematically analysed to develop reporting categories.

Results

178 patients were recruited. Patients in the face-to-face interviewing condition provided significantly more safety concerns per patient (1.91) compared with the paper-based form (0.92) and the patient safety hotline (0.43). They were also significantly more likely to report one or more concerns, with 64% reporting via the face-to-face mechanism, compared with 41% via the paper-based form and 19% via the patient safety hotline. No mechanism differed significantly in the number of classified patient safety incidents or physician-rated preventability and severity.

Discussion

Interviewing at the patient's bedside is likely to be the most effective means of gathering safety concerns from inpatients, potentially providing an opportunity for health services to gather patient feedback about safety from their perspective.
DEPA classification: a proposal for standardising PRP use and a retrospective application of available devices
Authors: Magalon J , Chateau A L , Bertrand B , Louis M L , Silvestre A , Giraudo L , Veran J , Sabatier F
Published: February 2016

Background/aim

Significant biological differences in platelet-rich plasma (PRP) preparations have been highlighted and could explain the large variability in the clinical benefit of PRP reported in the literature. The scientific community now recommends the use of classification for PRP injection; however, these classifications are focused on platelet and leucocyte concentrations. This presents the disadvantages of (1) not taking into account the final volume of the preparation; (2) omitting the presence of red blood cells in PRP and (3) not assessing the efficiency of production.

Methods

On the basis of standards classically used in the Cell Therapy field, we propose the DEPA (Dose of injected platelets, Efficiency of production, Purity of the PRP, Activation of the PRP) classification to extend the characterisation of the injected PRP preparation. We retrospectively applied this classification on 20 PRP preparations for which biological characteristics were available in the literature.

Results

Dose of injected platelets varies from 0.21 to 5.43 billion, corresponding to a 25-fold increase. Only a Magellan device was able to obtain an A score for this parameter. Assessments of the efficiency of production reveal that no device is able to recover more than 90% of platelets from the blood. Purity of the preparation reveals that a majority of the preparations are contaminated by red blood cells as only three devices reach an A score for this parameter, corresponding to a percentage of platelets compared with red blood cells and leucocytes over 90%.

Conclusions

These findings should provide significant help to clinicians in selecting a system that meets their specific needs for a given indication.
The death of patients with terminal cancer: the distress experienced by their children and medical professionals who provide the children with support care
Authors: Otani Hiroyuki , Ozawa Miwa , Morita Tatsuya , Kawami Ayako , Sharma Sahana , Shiraishi Keiko , Oshima Akira
Published: February 2016

Background

Few studies have been conducted on the experiences of children of terminally ill patients or hospital-based medical professionals supporting such children.

Aim

This study explored distress among individuals whose parents died of cancer in childhood and among hospital-based medical professionals supporting such children.

Design

A qualitative study.

Setting/participants

The sample was 12 adults whose parents had died of cancer in childhood and 20 hospital-based medical professionals supporting children of patients’ with terminal cancer. In-depth interviews were conducted, focusing on the distress experienced by the participants. The data were analysed thematically.

Results

Among adults whose parents died of cancer in childhood, we identified themes related to the period before death (eg, concealing the parent's illness), the time of death (eg, alienation due to isolation from the parent), soon after death (eg, fear and shock evoked by the bizarre circumstances, regrets regarding the relationship with the deceased parent before death), several years thereafter (ie, distinctive reflection during adolescence, prompted by the parent's absence) and the present time (ie, unresolved feelings regarding losing the parent). We identified seven themes among the medical professionals (eg, lack of knowledge/experience with children, the family's attempts to shield the child from the reality of death, estrangement from the family once they leave the hospital).

Conclusions

An important finding of the study is that the participants’ grief reaction to their parents’ deaths during childhood was prolonged. Moreover, hospital medical professionals may find it difficult to directly support affected children. Comprehensive support involving organisations (eg, local communities) may be necessary for children who have lost a parent.