bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Epidemic of Extended-Spectrum-β-Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone,
H
30-Rx
Authors: Price Lance B. , Johnson James R. , Aziz Maliha , Clabots Connie , Johnston Brian , Tchesnokova Veronika , Nordstrom Lora , Billig Maria , Chattopadhyay Sujay , Stegger Marc , Andersen Paal S. , Pearson Talima , Riddell Kim , Rogers Peggy , Scholes Delia , Kahl Barbara , Keim Paul , Sokurenko Evgeni V. 
Published: December 2013

ABSTRACT

The
Escherichia coli
sequence type 131 (ST131) clone is notorious for extraintestinal infections, fluoroquinolone resistance, and extended-spectrum beta-lactamase (ESBL) production, attributable to a CTX-M-15-encoding mobile element. Here, we applied pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing to reconstruct the evolutionary history of the ST131 clone. PFGE-based cluster analyses suggested that both fluoroquinolone resistance and ESBL production had been acquired by multiple ST131 sublineages through independent genetic events. In contrast, the more robust whole-genome-sequence-based phylogenomic analysis revealed that fluoroquinolone resistance was confined almost entirely to a single, rapidly expanding ST131 subclone, designated
H
30-R. Strikingly, 91% of the CTX-M-15-producing isolates also belonged to a single, well-defined clade nested within
H
30-R, which was named
H
30-Rx due to its more extensive resistance. Despite its tight clonal relationship with
H
30Rx, the CTX-M-15 mobile element was inserted variably in plasmid and chromosomal locations within the
H
30-Rx genome. Screening of a large collection of recent clinical
E. coli
isolates both confirmed the global clonal expansion of
H
30-Rx and revealed its disproportionate association with sepsis (relative risk, 7.5;
P
< 0.001). Together, these results suggest that the high prevalence of CTX-M-15 production among ST131 isolates is due primarily to the expansion of a single, highly virulent subclone,
H
30-Rx.

IMPORTANCE
We applied an advanced genomic approach to study the recent evolutionary history of one of the most important
Escherichia coli
strains in circulation today. This strain, called sequence type 131 (ST131), causes multidrug-resistant bladder, kidney, and bloodstream infections around the world. The rising prevalence of antibiotic resistance in
E. coli
is making these infections more difficult to treat and is leading to increased mortality. Past studies suggested that many different ST131 strains gained resistance to extended-spectrum cephalosporins independently. In contrast, our research indicates that most extended-spectrum-cephalosporin-resistant ST131 strains belong to a single highly pathogenic subclone, called
H
30-Rx. The clonal nature of
H
30-Rx may provide opportunities for vaccine or transmission prevention-based control strategies, which could gain importance as
H
30-Rx and other extraintestinal pathogenic
E. coli
subclones become resistant to our best antibiotics.
Emergence of the Epidemic Methicillin-Resistant Staphylococcus aureus Strain USA300 Coincides with Horizontal Transfer of the Arginine Catabolic Mobile Element and
speG
-mediated Adaptations for Survival on Skin
Authors: Planet Paul J. , LaRussa Samuel J. , Dana Ali , Smith Hannah , Xu Amy , Ryan Chanelle , Uhlemann Anne-Catrin , Boundy Sam , Goldberg Julia , Narechania Apurva , Kulkarni Ritwij , Ratner Adam J. , Geoghegan Joan A. , Kolokotronis Sergios-Orestis , Prince Alice 
Published: December 2013

ABSTRACT

The arginine catabolic mobile element (ACME) is the largest genomic region distinguishing epidemic USA300 strains of methicillin-resistant
Staphylococcus aureus
(MRSA) from other
S. aureus
strains. However, the functional relevance of ACME to infection and disease has remained unclear. Using phylogenetic analysis, we have shown that the modular segments of ACME were assembled into a single genetic locus in
Staphylococcus epidermidis
and then horizontally transferred to the common ancestor of USA300 strains in an extremely recent event. Acquisition of one ACME gene,
speG
, allowed USA300 strains to withstand levels of polyamines (e.g., spermidine) produced in skin that are toxic to other closely related
S. aureus
strains.
speG
-mediated polyamine tolerance also enhanced biofilm formation, adherence to fibrinogen/fibronectin, and resistance to antibiotic and keratinocyte-mediated killing. We suggest that these properties gave USA300 a major selective advantage during skin infection and colonization, contributing to the extraordinary evolutionary success of this clone.

IMPORTANCE
Over the past 15 years, methicillin-resistant
Staphylococcus aureus
(MRSA) has become a major public health problem. It is likely that adaptations in specific MRSA lineages (e.g., USA300) drove the spread of MRSA across the United States and allowed it to replace other, less-virulent
S. aureus
strains. We suggest that one major factor in the evolutionary success of MRSA may have been the acquisition of a gene (
speG
) that allows
S. aureus
to evade the toxicity of polyamines (e.g., spermidine and spermine) that are produced in human skin. Polyamine tolerance likely gave MRSA multiple fitness advantages, including the formation of more-robust biofilms, increased adherence to host tissues, and resistance to antibiotics and killing by human skin cells.
Oral antibiotics at discharge for children with acute osteomyelitis: a rapid cycle improvement project
Authors: Brady Patrick W , Brinkman William B , Simmons Jeffrey M , Yau Connie , White Christine M , Kirkendall Eric S , Schaffzin Joshua K , Conway Patrick H , Vossmeyer Michael T 
Published: December 2013

BackgroundSubstantial evidence demonstrates comparable cure rates for oral versus intravenous therapy for routine osteomyelitis. Evidence adoption is often slow and in our centre virtually all patients with osteomyelitis were discharged on intravenous therapy.ObjectiveFor patients with acute osteomyelitis admitted to the hospital medicine service, we aimed to increase the proportion of cases discharged on oral antibiotics to at least 70%.MethodsThe setting for our observational time series study was a large academic children's hospital. The model for improvement and plan-do-study-act cycles were used to test, refine and implement interventions identified through our key driver diagram. Our multifaceted intervention included a shared decision-making tool, an order set in our electronic health record, and education to faculty and trainees. We also included an identify and mitigate intervention to target providers caring for children with osteomyelitis in near-real time and reinforce the evidence-based recommendations. Data were analysed on an annotated g-chart of osteomyelitis cases between patients discharged on intravenous antibiotics. Structured chart review was used to identify treatment failures as well as length of stay and hospital charges in preintervention and postintervention groups.ResultsThe osteomyelitis cases between patients discharged on intravenous antibiotics increased from a median of 0 preintervention to a maximum of 9 cases following our identify and mitigate intervention. The direction and magnitude of successive improvements observed satisfied criteria for special cause variation. Improvement has been sustained for 1 year. Treatment failure and complications were uncommon in preintervention and postintervention phases. No significant differences in length of stay or charges were detected.ConclusionsEven for uncommon conditions, rapid and sustained evidence adoption is possible using quality improvement methods.
Ordovician to Silurian magmatism on the Utsira High, North Sea: implications for correlations between the onshore and offshore Caledonides
Authors: Lundmark A. M. , Sæther T. , Sørlie R. 
Published: December 2013

Abstract

The age and tectonic significance of two basement granitoids cored on the Utsira High, Viking Graben, North Sea, are constrained by zircon LA-ICPMS data. Syenite in well 25/10-2R is dated to 482±2 Ma, with εHf
(482)
values from −4.4 to −5.8, and granite in well 16/1-12 yields an age of 436±3 Ma with εHf
(436)
values from +3.7 to −0.5. The evolved Hf-signature of the syenite demonstrates 482 Ma reworking of Palaeoproterozoic–Archaean crust, interpreted to reflect Taconian–Grampian orogenesis. New and recently published data from the offshore Caledonides allow a first-order correlation of the Utsira High basement with the surrounding on- and offshore Caledonides. The Utsira High occupies a similar position with respect to Dalradian rocks as the Scottish Midland Valley terrane. Geophysical data indicate a volcanic arc beneath the East Shetland Basin, forming a northwards continuation of the Utsira High basement. We propose that the offshore volcanic arc segments represent the northeastern continuation of the Scottish Grampian orogen across the Mesozoic North Sea rift. A north-striking terrane boundary fault is proposed to separate the volcanic arc from the East Shetland Platform and merge northwards with the offshore extension of the Great Glen Fault–Møre Trøndelag Fault Complex.

Supplementary material:

U–Pb and Lu–Hf isotopic data are available at
http://www.geolsoc.org.uk/SUP18705
.
II.
On the Rhizopoda, and their Importance in various Geological Forms
Authors: Campbell Henry J. 
Published: December 2013

In the first place he referred to their place in the scale of creation, then mentioned their characteristic features both in a zoological and geological point of view.
If, while sauntering along the sea-beach, you lift a handful of drift sand, and examine it carefully with a magnifying glass, you will discover a number of minute beautifully formed shells; these are the skeletons of the Polythalamia, or Foraminiferæ, which belong to the Rhizopoda.
For a considerable time after their discovery, they were ranked by naturalists in the class Cephalopoda of the Mollusca, and it was not until the researches of Dujardin, in 1833, proved beyond doubt that the creatures to which these minute, variously formed shells owed their existence were intimately related to the Amœba. The Foraminiferæ are procured in the sand from the Adriatic, Red, and Mediterranean Seas, also along nearly all the coasts in the world.

Dallas remarks ‶that the Foraminiferæ occur in such great numbers, that the fine calcareous sand which constitutes the sea-shore in many places consists
almost entirely
of their microscopic coats. At former periods of the earth’s history they existed in even greater profusion than at present; and their fragile shells form the principal constitutents of several very important geological forms.″

The stone which is universally employed in Paris for building is almost entirely composed of the fossil shells of an animal belonging to this order, the Miliola. It is also probable that the animals, whose fossil shells termed Nummulites, which are found in great quantities in the chalk and lower tertiary strata, are also to be regarded as members of this class. Whole mountains in the neighbourhood of the Mediterranean consist almost entirely of their shells; and the Pyramids of Egypt, which have been reckoned amongst the wonders of the world, are chiefly built with a limestone which is composed for the most part of nummulites.
In conclusion, attention was directed to the various works of Hogg, Lyell, Dukes, &c., on the Foraminiferæ.
The geology of Chishanya, Buhera District, Southern Rhodesia
Authors: Swift William H. 
Published: December 2013

The area described consists of Pre-Cambrian granite, overlain unconformably in the south-east by sediments of the Umkondo System. An alkaline complex, consisting of syenites, nepheline-syenite, ijolites and carbonatites, occurs in the granite, and both granite and Umkondo sediments are cut by dykes of alkaline rocks, nepheline-basalts, nepheline-basanites and phonolites.
Evidence is presented indicating that the alkaline dykes are magmatic in origin and that the carbonatite is an intrusive rock which is not derived from limestone of the Umkondo System. The syenite is regarded as fenitised granite and it appears possible that the ijolite may also be a fenitised rock. The origin of the nepheline-syenite is discussed.
Some comparisons are made with the alkaline ring-complexes at Shawa and Dorowa (Southern Rhodesia) and the opinion is expressed that the carbonate cores of these are also magmatic carbonatites.
Mineralogy of basalts from the western Kilpatrick Hills and its bearing on the petrogenesis of Scottish Carboniferous olivine-basalts
Authors: Hamilton John 
Published: December 2013

Some of the results of an investigation of olivine-basalts of Calciferous Sandstone age from the western part of the Kilpatrick Hills are recorded. In particular, aspects of the mineralogy of the three essential minerals—pyroxene, feldspar and olivine—are described and discussed.
The pyroxene phenocrysts in some types of basalt are believed to have been corroded and regrown in an environment slightly different from that in which they originally grew. The groundmass pyroxene in all the basalts appears to be augite, not pigeonite as in some other petrographic provinces.
Evidence suggesting that some feldspar phenocrysts have had a complicated history is presented and the composition-zoning of olivine phenocrysts is described.
The part played by pre-existing gabbroic material in the genesis and evolution of the different basalt types is discussed. It is suggested that the Scottish Calciferous Sandstone olivine-basalts may have resulted from the differential fusion of gabbro in a manner which allowed volatiles and feldspathic material to advance slightly ahead of the more pyroxenic fractions.
Relations of movement and metamorphism in the Dalradians of Banffshire
Authors: Johnson M.R.W. 
Published: December 2013

The Dalradian rocks of Banffshire have been affected by at least four periods of folding. The earliest period resulted in the formation of isoclinal folds which are presumed to be related to large-scale recumbent folds, such as the recumbent anticline of Banffshire and Aberdeenshire postulated mainly on stratigraphical grounds by Professor H. H. Read. The Boyndie Syncline, first described by Sutton and Watson and the only major fold recognised in the Banffshire coast section, belongs to the third fold period.
Textural evidence is given for polymetamorphism in the Banffshire Dalradian. The movements responsible for the primary recumbent folds were probably accompanied by only a low-grade metamorphism. The main phases of constructive metamorphism occurred before, during and after the second fold movements. The metamorphic climax, during which both Buchan and Barrovian types of metamorphic mineral assemblages developed, is shown to have occurred after the second fold movements. The andalusite-cordierite-staurolite assemblages (Buchan type) apparently formed at a higher structural level than the garnet-staurolite-(kyanite) (Barrovian type of assemblages). During the third and fourth fold movements lower grade metamorphic conditions prevailed; local retrograde metamorphism occurred.
By reference to the work of Rast, Sturt and Harris a comparison is made between the available time-scales of structural and metamorphic events in Banffshire and Perthshire. Many points of similarity are revealed; in particular it is found that the climax of metamorphism (indicated by the Buchan metamorphism in Banffshire and the main Barrovian type metamorphism in Perthshire) is co-eval in the two regions, which represent different structural levels.
On an upheaval of land near Novai Zembla
Authors: Brown Robert 
Published: December 2013

During the past summer the Norwegians, among other explorations in the Arctic Sea, had discovered to the north of Novai Zembla a group of low islands, which, on account of the presence of tropical fruits washed on them by the Gulf Stream, had been named the ‶Gulf Stream Islands.″ The two largest of them had been named the Hellwalds and Brown’s Islands. But the most curious fact above them was, that less than 300 years ago the Dutch took soundings in 100 feet on this very spot, so that within that period these low sandy islands, scattered with boulders, had been raised above the sea, showing an elevation of land since the year 1592 of more than a 100 feet. It was said that the sea around Spitzbergen was shoaling, and that on that account the Right whale of commerce (
Balæna mysticetus
) was no longer a member of the Spitzbergen fauna, though at one time killed in enormous numbers in every bay. In the course of some verbal remarks on the subject of the rise and fall of northern lands, Dr Brown took occasion to doubt that north of lat. 72° the west coast of Greenland was sinking. He considered that there was every proof that the whole coast, from Cape Farewell to Smith’s Sound, was gradually being depressed. In reference to some remarks made at a former meeting of the Society, he might mention that, if we were not yet perfectly acquainted with the nature of the glacial remains in Britain from a study of the great Greenland ice, it was not because geologists were not intimately enough acquainted with the nature of the ‶ice cap″ in that country. During the last few years no fewer than four parties of naturalists—Swedish, Danish, and English—had visited Greenland, and given the result of their observations to the world; and one of the most eminent of Danish geologists—Dr Rink—had resided no less than twenty-one years in the country. If, therefore, we are not yet fully able to explain the nature of the glacial remains in Britain from the analogies of Greenland ice, it was not for want either of knowledge or perseverance. All that could be learned had been learned, as the Greenland residents had already borne witness to.

Mr W. T. Black exhibited a number of beautiful photographs of Mount Vesuvius as it appeared during the eruption in 1872.
The following Gentlemen were elected Fellows of the Society:

R
obert
E
theridge
, junior, F.G.S., of the Geological Survey of Scotland, Edinburgh.

W. T. B
lack
, 2 George Square.
Diffusion-Weighted Image and Fluid-Attenuated Inversion Recovery Image Mismatch
Authors: Kim Bum Joon , Kim Hye-Jin , Lee Deok Hee , Kwon Sun U. , Kim Sang Joon , Kim Jong S. , Kang Dong-Wha 
Published: December 2013

Background and Purpose—
Mismatch in lesion visibility between diffusion-weighted image and fluid-attenuated inversion recovery image (DWI–FLAIR mismatch) has been proposed as a biomarker for the estimation of ischemic lesion age. The actual onset in some patients with unclear-onset stroke (UnCOS) may be close to the first-found abnormal time. We hypothesized that patients with UnCOS within a particular time window might have a similar DWI–FLAIR mismatch profile with patients with clear-onset stroke (COS).

Methods—
Patients who underwent MRI within 6 hours from first-found abnormal time were recruited retrospectively. Clinical characteristics and the proportion of DWI–FLAIR and perfusion-weighted image–DWI mismatch in each time window were compared between UnCOS and COS.

Results—

The final analysis included 259 patients (114 with UnCOS and 145 with COS). Patients with UnCOS were older and had more severe stroke at baseline. Risk factors, stroke subtypes, and perfusion-weighted image–DWI mismatch did not differ between the 2 groups. The proportion of patients with DWI–FLAIR mismatch in UnCOS did not differ from COS within 2 hours of first-found abnormal time (50.0% versus 51.5%;
P
=0.92), but it was significantly lower in UnCOS than in COS at 2 to 3 hours (16.1% versus 44.4%;
P
=0.02), 3 to 4 hours (13.8% versus 36.4%;
P
=0.04), and 4 to 5 hours (5.6% versus 29.6%;
P
=0.05).

Conclusions—
The proportion of DWI–FLAIR mismatch in UnCOS within the first 2 hours from first-found abnormal time was similar with COS, but it sharply decreased beyond 2 hours. These data suggest that patients with UnCOS within 2 hours of symptom detection may be good candidates for multimodal imaging-based thrombolysis.
Boundary Layer Updrafts Driven by Airflow over Heated Terrain
Authors: Kirshbaum Daniel J. , Wang Chun-Chih 
Published: December 2013

Abstract
This study presents linear and nonlinear scalings for boundary layer ascent forced by airflow over heated terrain and compares them to results from corresponding high-resolution numerical simulations. Close agreement between theory and simulation is found over most of the parameter space considered, including variations in background winds, boundary layer stability, mountain height, and diabatic heating rate. As expected, the linear and nonlinear scalings perform best for linear and nonlinear flows, respectively. For a convective boundary layer, the scalings accurately predict vertical motion for all flows considered, including those that extend well into the nonlinear regime. Thus, these scalings may ultimately help to improve the parameterization of subgrid orographic ascent in large-scale models. The vertical velocity scalings are less accurate for mechanically blocked flows in stable boundary layers, for which a simple vertical displacement scaling is superior. Although the scalings do not treat interactions between mechanical and thermal flow responses, these interactions are generally weak except in blocked flows with strong surface heating. Numerical simulations of such cases suggest that a hydrostatically induced pressure decrease in the lee associated with the diabatic surface heating drives stronger flow reversal within the wake and leeside convergence downwind of it, both of which produce strong surface-based updrafts. Thus, nonlinear interactions between mechanical and thermal flow responses may significantly enhance the likelihood of convection initiation over heated mountains.
Measuring Cognition in Teams
Authors: Wildman Jessica L. , Salas Eduardo , Scott Charles P. R. 
Published: December 2013

Objective: The purpose of this article is twofold: to provide a critical cross-domain evaluation of team cognition measurement options and to provide novice researchers with practical guidance when selecting a measurement method. Background: A vast selection of measurement approaches exist for measuring team cognition constructs including team mental models, transactive memory systems, team situation awareness, strategic consensus, and cognitive processes. Methods: Empirical studies and theoretical articles were reviewed to identify all of the existing approaches for measuring team cognition. These approaches were evaluated based on theoretical perspective assumed, constructs studied, resources required, level of obtrusiveness, internal consistency reliability, and predictive validity. Results: The evaluations suggest that all existing methods are viable options from the point of view of reliability and validity, and that there are potential opportunities for cross-domain use. For example, methods traditionally used only to measure mental models may be useful for examining transactive memory and situation awareness. The selection of team cognition measures requires researchers to answer several key questions regarding the theoretical nature of team cognition and the practical feasibility of each method. Conclusions: We provide novice researchers with guidance regarding how to begin the search for a team cognition measure and suggest several new ideas regarding future measurement research. Applications: We provide (1) a broad overview and evaluation of existing team cognition measurement methods, (2) suggestions for new uses of those methods across research domains, and (3) critical guidance for novice researchers looking to measure team cognition.