bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic Affiliation of New Genomes Should Be Verified Using Average Nucleotide Identity and Multilocus Phylogenetic Analysis
Authors: Figueras María José , Beaz-Hidalgo Roxana , Hossain Mohammad J. , Liles Mark R. 
Published: December 2014

ABSTRACT
The average nucleotide identity (ANI) determines if two genomes belong to the same species. Using ANI, we detected mislabeled genomes and recommend verifying with ANI and multilocus phylogenetic analysis the species affiliations of the announced genomes. The slightly different results obtained with different ANI calculation software can potentially mislead taxonomic inferences.
A Novel Itera-Like Densovirus Isolated by Viral Metagenomics from the Sea Barley
Hordeum marinum
Authors: François S. , Bernardo P. , Filloux D. , Roumagnac P. , Yaverkovski N. , Froissart R. , Ogliastro M. 
Published: December 2014

ABSTRACT

Densoviruses (DVs) infect arthropods and belong to the
Parvoviridae
family. Here, we report the complete coding sequence of a novel DV isolated from the plant
Hordeum marinum
(
Poaceae
) by viral metagenomics, and we confirmed reamplification by PCR. Phylogenetic analyses showed that this novel DV is related to the genus
Iteradensovirus
.
Draft Genome Sequence of Marine Flavobacterium Jejuia pallidilutea Strain 11shimoA1 and Pigmentation Mutants
Authors: Takatani Naoki , Nakanishi Masato , Meirelles Pedro , Mino Sayaka , Suda Wataru , Oshima Kenshiro , Hattori Masahira , Ohkuma Moriya , Hosokawa Masashi , Miyashita Kazuo , Thompson Fabiano L. , Niwa Ako , Sawabe Toko , Sawabe Tomoo 
Published: December 2014

ABSTRACT

Here, we present the draft genome sequence of a novel carotenoid 2′-isopentenylsaproxanthin producer,
Jejuia pallidilutea
strain 11shimoA1, isolated from the surface of seaweed in Japan, and the ethyl methanesulfonate-induced pigmentation mutants. This genomic information will help to not only elucidate the 2′-isopentenylsaproxanthin biosynthetic pathway but also understand the evolution of flavobacteria.
Draft Genome Sequence of a Metabolically Diverse Antarctic Supraglacial Stream Organism,
Polaromonas
sp. Strain CG9_12, Determined Using Pacific Biosciences Single-Molecule Real-Time Sequencing Technology
Authors: Smith Heidi J. , Foreman Christine M. , Ramaraj Thiruvarangan 
Published: December 2014

ABSTRACT

Polaromonas
species are found in a diversity of environments and are particularly common in icy ecosystems.
Polaromonas
sp. strain CG9_12 is an aerobic, Gram-negative, catalase-positive, white-pigmented bacterium of the
Proteobacteria
phylum. Here, we present the draft genome sequence of
Polaromonas
sp. strain CG9_12, isolated from an Antarctic supraglacial stream.
Complete Genome Sequence of Listeria monocytogenes Lm60, a Strain with an Enhanced Cold Adaptation Capacity
Authors: Tasara Taurai , Weinmaier Thomas , Klumpp Jochen , Rattei Thomas , Stephan Roger 
Published: December 2014

ABSTRACT

The complete genome sequence of
Listeria monocytogenes
Lm60, a fast cold-adapting serotype 1/2a human isolate, is presented.
Draft Genome Sequence of the Nicotinate-Metabolizing Soil Bacterium Bacillus niacini DSM 2923
Authors: Harvey Zachary H. , Snider Mark J. 
Published: December 2014

ABSTRACT

Bacillus niacini
is a member of a small yet diverse group of bacteria able to catabolize nicotinic acid. We report here the availability of a draft genome for
B. niacini
, which we will use to understand the evolution of its namesake phenotype, which appears to be unique among the species in its phylogenetic neighborhood.
Draft Genome Sequence of
Sphingopyxis
sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium
Authors: Kim Jonghyun , Kim Soo Jung , Kim Seon Hee , Kim Seung Il , Moon Yoon-Jung , Park Sung-Joon , Kahng Hyung-Yeel , Chung Young-Ho 
Published: December 2014

ABSTRACT

Sphingopyxis
sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene, was isolated from crude oil–contaminated seashore in Tae-an, South Korea. Here, we report the draft genome sequence of this strain, which comprises 3,118,428 bp with a G+C content of 62.85 mol%.
Draft Genome Sequence of C:P1.5-1,10-8:F3-6:ST-11 Meningococcal Clinical Isolate Associated with a Cluster on a Cruise Ship
Authors: Neri A. , Fazio C. , Ciammaruconi A. , Anselmo A. , Fortunato A. , Palozzi A. , Vacca P. , Fillo S. , Lista F. , Stefanelli P. 
Published: December 2014

ABSTRACT

Meningococcal serogroup C strains, in particular those belonging to the ST-11 clonal complex, are known to cause invasive diseases worldwide. We report the genome sequence of a
Neisseria meningitidis
strain linked to a cluster of cases of invasive meningococcal disease on a cruise ship that was described in 2012.
Potential economic impacts from improving breastfeeding rates in the UK
Authors: Pokhrel S , Quigley M A , Fox-Rushby J , McCormick F , Williams A , Trueman P , Dodds R , Renfrew M J 
Published: December 2014

RationaleStudies suggest that increased breastfeeding rates can provide substantial financial savings, but the scale of such savings in the UK is not known.ObjectiveTo calculate potential cost savings attributable to increases in breastfeeding rates from the National Health Service perspective.Design and settingsCost savings focussed on where evidence of health benefit is strongest: reductions in gastrointestinal and lower respiratory tract infections, acute otitis media in infants, necrotising enterocolitis in preterm babies and breast cancer (BC) in women. Savings were estimated using a seven-step framework in which an incidence-based disease model determined the number of cases that could have been avoided if breastfeeding rates were increased. Point estimates of cost savings were subject to a deterministic sensitivity analysis.ResultsTreating the four acute diseases in children costs the UK at least £89 million annually. The 2009–2010 value of lifetime costs of treating maternal BC is estimated at £959 million. Supporting mothers who are exclusively breast feeding at 1 week to continue breast feeding until 4 months can be expected to reduce the incidence of three childhood infectious diseases and save at least £11 million annually. Doubling the proportion of mothers currently breast feeding for 7–18 months in their lifetime is likely to reduce the incidence of maternal BC and save at least £31 million at 2009–2010 value.ConclusionsThe economic impact of low breastfeeding rates is substantial. Investing in services that support women who want to breast feed for longer is potentially cost saving.
Extended insulin boluses cannot control postprandial glycemia as well as a standard bolus in children and adults using insulin pump therapy
Authors: Lopez Prudence , Smart Carmel , Morbey Claire , McElduff Patrick , Paterson Megan , King Bruce R 
Published: December 2014

IntroductionInsulin pumps are able to deliver bolus insulin as a standard, extended or combination bolus. There is minimal research to determine which bolus is preferable in different settings. Anecdotally, many patients utilizes only the standard bolus (SB) due to uncertainty regarding when and how to program the different bolus types. We compared postprandial glycemia when five different extended boluses (EBs) and an SB were used following a test meal. We sought to determine the impact of varying rates of insulin delivery from an EB on early postprandial glycemia.MethodsWe conducted a randomized, repeated measures trial of 20 children and adults comparing postprandial glycemic excursions following EBs given at five different rates with SB as a control. All EBs were delivered over 2 h. Rates of EBs were chosen to reflect EBs used in clinical practice: EB1HR=100% of insulin:carbohydrate ratio (ICR) per hour (200% ICR total dose); EB2HR=50% of ICR per hour; EB3HR=33% of ICR per hour; EB4HR=25% of ICR per hour; EB6HR=16% ICR per hour. A standardized breakfast was given and activity was standardized. Continuous glucose monitoring was used to assess glycemia for 2 h after the meal.ResultsThe mean postprandial glycemic excursions were lower at 30, 60, and 90 min (p<0.05) for SB compared with all EBs. The mean peak postprandial glycemic excursion and the area under the curve was lower for SB compared with all EBs (p<0.05).DiscussionEBs resulted in higher postprandial glycemic excursions than SB for 2 h after the meal. For a moderate glycemic index meal EBs are unable to control glycemia for 2 h after a meal as well as SB. Further studies with different meal types are required to determine the impact of differential delivery of the EB on postprandial glycemia.Trial registration numberACTRN12612000609853.
Synovial plicae of the knee joint: the role of advanced MRI
Authors: Vassiou Katerina , Vlychou Marianna , Zibis Aristidis , Nikolopoulou Athina , Fezoulidis Ioannis , Arvanitis Dimitrios 
Published: December 2014

ABSTRACTSynovial plicae are normal anatomical structures of the knee that may become symptomatic. MRI is an established technique for evaluating the anatomy of the knee, and it is a valuable tool for detecting plicae because of its high resolution resulting in increased tissue characterisation. At MRI, knee plicae appear as low-signal-intensity structures of variable size and thickness, and they are better visualised at fluid-sensitive sequences with or without fat suppression. The combined use of clinical examination and MRI may also facilitate the diagnosis of fibrotic or inflamed plicae that may be symptomatic. Arthroscopy remains the gold standard for recognition and repair of knee plicae in cases of knee dysfunction.
Fundamental controls on fluid flow in carbonates: current workflows to emerging technologies
Authors: Agar Susan M. , Geiger Sebastian 
Published: December 2014

Abstract
The introduction reviews topics relevant to the fundamental controls on fluid flow in carbonate reservoirs and to the prediction of reservoir performance. The review provides research and industry contexts for papers in this volume only. A discussion of global context and frameworks emphasizes the value yet to be captured from compare and contrast studies. Multidisciplinary efforts highlight the importance of greater integration of sedimentology, diagenesis and structural geology. Developments in analytical and experimental methods, stimulated by advances in the materials sciences, support new insights into fundamental (pore-scale) processes in carbonate rocks. Subsurface imaging methods relevant to the delineation of heterogeneities in carbonates highlight techniques that serve to decrease the gap between seismically resolvable features and well-scale measurements. Methods to fuse geological information across scales are advancing through multiscale integration and proxies. A surge in computational power over the last two decades has been accompanied by developments in computational methods and algorithms. Developments related to visualization and data interaction support stronger geoscience–engineering collaborations. High-resolution and real-time monitoring of the subsurface are driving novel sensing capabilities and growing interest in data mining and analytics. Together, these offer an exciting opportunity to learn more about the fundamental fluid-flow processes in carbonate reservoirs at the interwell scale.
Enhanced Tumorigenic Potential of Colorectal Cancer Cells by Extracellular Sulfatases
Authors: Vicente Carolina M. , Lima Marcelo A. , Yates Edwin A. , Nader Helena B. , Toma Leny 
Published: December 2014

Abstract
Heparan sulfate endosulfatase-1 and -2 (SULF1 and SULF2) are two important extracellular 6-O-endosulfatases that remove 6-O sulfate groups of N-glucosamine along heparan sulfate (HS) proteoglycan chains often found in the extracellular matrix. The HS sulfation pattern influences signaling events at the cell surface, which are critical for interactions with growth factors and their receptors. SULFs are overexpressed in several types of human tumors, but their role in cancer is still unclear because their molecular mechanism has not been fully explored and understood. To further investigate the functions of these sulfatases in tumorigenesis, stable overexpression models of these genes were generated in the colorectal cancer cells, Caco-2 and HCT-116. Importantly, mimicking overexpression of these sulfatases resulted in increased viability and proliferation, and augmented cell migration. These effects were reverted by shRNA-mediated knockdown of SULF1 or SULF2 and by the addition of unfractionated heparin. Detailed structural analysis of HS from cells overexpressing SULFs showed reduction in the trisulfated disaccharide UA(2S)-GlcNS(6S) and corresponding increase in UA(2S)-GlcNS disaccharide, as well as an unexpected rise in less common disaccharides containing GlcNAc(6S) residues. Moreover, cancer cells transfected with SULFs demonstrated increased Wnt signaling. In summary, SULF1 or SULF2 overexpression contributes to colorectal cancer cell proliferation, migration, and invasion.
Implications: This study reveals that sulfatases have oncogenic effects in colon cancer cells, suggesting an important role for these enzymes in cancer progression. Mol Cancer Res; 13(3); 510–23. ©2014 AACR.
Prevalence of Nonatheromatous Lesions in Peripheral Arterial Disease
Authors: O’Neill W. Charles , Han Kum Hyun , Schneider Thomas M. , Hennigar Randolph A. 
Published: December 2014

Objective—
The histopathology of peripheral arterial disease and the accompanying calcification are poorly defined, and it is not known whether this varies according to different risk factors.

Approach and Results—
Sections from 176 upper and lower leg arteries were examined histologically in specimens from amputations of 60 patients with peripheral arterial disease, of whom 58% had diabetes mellitus, 35% had end-stage renal disease, and 48% had a history of smoking. The most common findings were calcification of the media (72% of arteries) and intimal thickening without lipid (68% of arteries), with the presence of atheromas in only 23% of arteries. Intimal calcification occurred in 43% and was generally much less extensive than medial calcification. Nonatheromatous intimal thickening was frequently severe, resulting in complete occlusion in some vessels. The absence of lipid and macrophages was confirmed by staining with oil red O and staining for CD68. Other than a greater prevalence and severity of medial calcification in end-stage renal disease, the findings did not differ between diabetics, patients with end-stage renal disease, or smokers.

Conclusions—
The results indicate that the majority of arteries in patients with peripheral arterial disease have a vascular lesion that is distinct from atherosclerosis, suggesting a different pathogenesis. This pattern does not differ substantially between patients with different risk factors for peripheral arterial disease. The bulk of vascular calcification in the lower extremities is medial rather than intimal.
Genome-Wide Meta-Analyses of Plasma Renin Activity and Concentration Reveal Association With the Kininogen 1 and Prekallikrein Genes
Authors: Lieb Wolfgang , Chen Ming-Huei , Teumer Alexander , de Boer Rudolf A. , Lin Honghuang , Fox Ervin R. , Musani Solomon K. , Wilson James G. , Wang Thomas J. , Völzke Henry , Petersen Ann-Kristin , Meisinger Christine , Nauck Matthias , Schlesinger Sabrina , Li Yong , Menard Jöel , Hercberg Serge , Wichmann H.-Erich , Völker Uwe , Rawal Rajesh , Bidlingmaier Martin , Hannemann Anke , Dörr Marcus , Rettig Rainer , van Gilst Wiek H. , van Veldhuisen Dirk J. , Bakker Stephan J.L. , Navis Gerjan , Wallaschofski Henri , Meneton Pierre , van der Harst Pim , Reincke Martin , Vasan Ramachandran S. 
Published: December 2014

Background—
The renin–angiotensin–aldosterone system (RAAS) is critical for regulation of blood pressure and fluid balance and influences cardiovascular remodeling. Dysregulation of the RAAS contributes to cardiovascular and renal morbidity. The genetic architecture of circulating RAAS components is incompletely understood.

Methods and Results—

We meta-analyzed genome-wide association data for plasma renin activity (n=5275), plasma renin concentrations (n=8014), and circulating aldosterone (n=13289) from ≤4 population-based cohorts of European and European-American ancestry, and assessed replication of the top results in an independent sample (n=6487). Single-nucleotide polymorphisms (SNPs) in 2 independent loci displayed associations with plasma renin activity at genome-wide significance (
P
<5×10
−8
). A third locus was close to this threshold (rs4253311 in
kallikrein
B
[KLKB1],
P
=5.5×10
−8
). Two of these loci replicated in an independent sample for both plasma renin and aldosterone concentrations (SNP rs5030062 in
kininogen 1
[KNG1]:
P
=0.001 for plasma renin,
P
=0.024 for plasma aldosterone concentration; and rs4253311 with
P
<0.001 for both plasma renin and aldosterone concentration). SNPs in the
NEBL
gene reached genome-wide significance for plasma renin concentration in the discovery sample (top SNP rs3915911;
P
=8.81×10
−9
), but did not replicate (
P
=0.81). No locus reached genome-wide significance for aldosterone. SNPs rs5030062 and rs4253311 were not related to blood pressure or renal traits; in a companion study, variants in the
kallikrein B locus
were associated with B-type natriuretic peptide concentrations in blacks.

Conclusions—

We identified 2 genetic loci (
kininogen 1
and
kallikrein B
) influencing key components of the RAAS, consistent with the close interrelation between the kallikrein–kinin system and the RAAS.
Symptomatic Carotid Atherosclerotic Disease
Authors: Howard Dominic P.J. , van Lammeren Guus W. , Rothwell Peter M. , Redgrave Jessica N. , Moll Frans L. , de Vries Jean-Paul P.M. , de Kleijn Dominique P.V. , den Ruijter Hester M. , de Borst Gert Jan , Pasterkamp Gerard 
Published: December 2014

Background and Purpose—
For symptomatic patients with carotid artery stenosis, the risk benefit for surgical intervention may vary among patient groups. Various modalities of plaque imaging have been promoted as potential tools for additional risk stratification, particularly in patients with moderate stenosis. However, it remains uncertain to what extent carotid plaque components predict risk of future ipsilateral ischemic stroke.

Methods—
In 2 large atherosclerotic carotid plaque biobank studies, we related histological characteristics of 1640 carotid plaques with a validated risk model for the prediction of individual 1- and 5-year stroke risk.

Results—

No significant heterogeneity between the studies was found. Predicted 5-year stroke risk (top versus bottom quartile) was related to plaque thrombus (odds ratio, 1.42; 95% confidence interval, 1.11–1.89;
P
=0.02), fibrous content (0.65; 0.49–0.87;
P
=0.004), macrophage infiltration (1.41; 1.05–1.90;
P
=0.02), high microvessel density (1.49; 1.05–2.11;
P
=0.03), and overall plaque instability (1.40; 1.05–1.87;
P
=0.02). This association was not observed for cap thickness, calcification, intraplaque hemorrhage, or lymphocyte infiltration. Plaques removed within 30 days of most recent symptomatic event were most strongly correlated with predicted stroke risk.

Conclusions—
Features of the vulnerable carotid plaque, including plaque thrombus, low fibrous content, macrophage infiltration, and microvessel density, correlate with predicted stroke risk. This study provides a basis for plaque imaging studies focused on stroke risk stratification.
Two-Layered Susceptibility Vessel Sign on 3-Tesla T2*-Weighted Imaging Is a Predictive Biomarker of Stroke Subtype
Authors: Yamamoto Nobuaki , Satomi Junichiro , Tada Yoshiteru , Harada Masafumi , Izumi Yuishin , Nagahiro Shinji , Kaji Ryuji 
Published: December 2014

Background and Purpose—
A susceptibility vessel sign (SVS) on 1.5-tesla (T)-T2*-weighted images may predict cardioembolism. It has also been detected in patients with large artery atherosclerosis. In patients with major vessel occlusion, the SVS was comprised 2 layers on 3T-T2*-weighted images. We assessed the efficacy of 2-layered SVS on 3T-T2*-weighted imaging scans for predicting cardioembolism.

Methods—
Our study included 132 patients who had ischemic stroke within the preceding 24 hours and presented with internal carotid artery or middle cerebral artery occlusion because of cardioembolism or large artery atherosclerosis. We compared 2-layered SVS and SVS on 3T-T2*-weighted imaging scans for their sensitivity, specificity, and diagnostic odds ratio for predicting cardioembolism.

Results—

We enrolled 132 patients (72 men; mean age, 74.5 years); of these, 63 (47.7%) were presented with cardioembolism. Although the sensitivity of SVS and 2-layered SVS for cardioembolism and large artery atherosclerosis was not statistically different (74.6% and 58.0%, respectively), the sensitivity of 2-layered SVS was significantly higher in patients with cardioembolism (42.9%) than those with large artery atherosclerosis (2.9%;
P
<0.001). The specificity and diagnostic odds ratio for 2-layered SVS for cardioembolism were 97.1% and 25.1; for SVS they were 42.0% and 2.1, respectively.

Conclusion—
The specificity of 2-layered SVS for cardioembolism was high. It may be useful for predicting cardioembolism and for the management of patients with acute ischemic stroke.
The genus Leucophenga (Diptera, Drosophilidae), part IV: the ornata species group from the East Asia, with morphological and molecular evidence (II)
Authors: Huang Jia , Li Tong , Chen Hongwei 
Published: December 2014

Twenty-one species of the Leucophenga ornata species group are surveyed (including 12 new species): L. atrinervis Okada, 1968; L. digmasoma Lin & Wheeler, 1972; L. multipunctata Chen & Aotsuka, 2003; L. nigrinervis Duda, 1924; L. pectinata Okada, 1968; L. pentapunctata Panigrahy & Gupta, 1982; L. quadripunctata (de Meijere, 1908); L. regina Malloch, 1935; L. trivittata Okada, 1990; L. acutifoliacea sp. nov.; L. albiterga sp. nov.; L. angustifoliacea sp. nov.; L. baculifoliacea sp. nov.; L. cornuta sp. nov.; L. hirticeps sp. nov.; L. latifascia sp. nov.; L. pinguifoliacea sp. nov.; L. retihirta sp. nov. L. securis sp. nov.; L. sinupenis sp. nov.; L. villosa sp. nov.; these species (except for L. baculifoliacea sp. nov.) having pubescence on the distal portion of aedeagus. A key to all the examined species of the ornata group in this study is provided. We try to improve our species delimitation by integrating the DNA sequences data with morphological information. The intra- and interspecific pairwise K-2P (Kimura’s two-parameter) distances are summarized.
Predicting Critical Transitions in ENSO Models. Part I: Methodology and Simple Models with Memory
Authors: Mukhin Dmitry , Loskutov Evgeny , Mukhina Anna , Feigin Alexander , Zaliapin Ilia , Ghil Michael 
Published: December 2014

Abstract
A new empirical approach is proposed for predicting critical transitions in the climate system based on a time series alone. This approach relies on nonlinear stochastic modeling of the system’s time-dependent evolution operator by the analysis of observed behavior. Empirical models that take the form of a discrete random dynamical system are constructed using artificial neural networks; these models include state-dependent stochastic components. To demonstrate the usefulness of such models in predicting critical climate transitions, they are applied here to time series generated by a number of delay-differential equation (DDE) models of sea surface temperature anomalies. These DDE models take into account the main conceptual elements responsible for the El Niño–Southern Oscillation phenomenon. The DDE models used here have been modified to include slow trends in the control parameters in such a way that critical transitions occur beyond the learning interval in the time series. Numerical results suggest that the empirical models proposed herein are able to forecast sequences of critical transitions that manifest themselves in future abrupt changes of the climate system’s statistics.