bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of Influenza Rapid Diagnostic Tests to H5N1 and 2009 Pandemic H1N1 Viruses
Authors: Sakai-Tagawa Yuko , Ozawa Makoto , Tamura Daisuke , Le Mai thi Quynh , Nidom Chairul A. , Sugaya Norio , Kawaoka Yoshihiro 
Published: June 2010

ABSTRACTSimple and rapid diagnosis of influenza is useful for making treatment decisions in the clinical setting. Although many influenza rapid diagnostic tests (IRDTs) are available for the detection of seasonal influenza virus infections, their sensitivity for other viruses, such as H5N1 viruses and the recently emerged swine origin pandemic (H1N1) 2009 virus, remains largely unknown. Here, we examined the sensitivity of 20 IRDTs to various influenza virus strains, including H5N1 and 2009 pandemic H1N1 viruses. Our results indicate that the detection sensitivity to swine origin H1N1 viruses varies widely among IRDTs, with some tests lacking sufficient sensitivity to detect the early stages of infection when the virus load is low.
Clinical and Molecular Characteristics of Infections with CO
2
-Dependent Small-Colony Variants of
Staphylococcus aureus
Authors: Gómez-González Carmen , Acosta Joshi , Villa Jennifer , Barrado Laura , Sanz Francisca , Orellana M. Ángeles , Otero Joaquín R. , Chaves Fernando 
Published: June 2010

ABSTRACT

Most
Staphylococcus aureus
small-colony variants (SCVs) are auxotrophs for menadione, hemin, or thymidine but rarely for CO
2
. We conducted a prospective investigation of all clinical cases of CO
2
-dependent
S. aureus
during a 3-year period. We found 14 CO
2
-dependent isolates of
S. aureus
from 14 patients that fulfilled all requirements to be considered SCVs, 9 of which were methicillin resistant. The clinical presentations included four cases of catheter-related bacteremia, one complicated by endocarditis; two deep infections (mediastinitis and spondylodiscitis); four wound infections; two respiratory infections; and two cases of nasal colonization. Pulsed-field gel electrophoresis typing showed that the 14 isolates were distributed into 4 types corresponding to sequence types ST125-
agr
group II (
agr
II), ST30-
agr
III, ST34-
agr
III, and ST45-
agr
I. An array hybridization technique performed on the 14 CO
2
-dependent isolates and 20
S. aureus
isolates with normal phenotype and representing the same sequence types showed that all possessed the enterotoxin gene cluster
egc
, as well as the genes for α-hemolysin and δ-hemolysin; biofilm genes
icaA
,
icaC
, and
icaD
; several microbial surface components recognizing adhesive matrix molecules (MSCRAMM) genes (
clfA
,
clfB
,
ebh
,
eno
,
fib
,
ebpS
,
sdrC
, and
vw
); and the
isaB
gene. Our study confirms the importance of CO
2
-dependent SCVs of
S. aureus
as significant pathogens. Clinical microbiologists should be aware of this kind of auxotrophy because recovery and identification are challenging and not routine. Further studies are necessary to determine the incidence of CO
2
auxotrophs of
S. aureus
, the factors that select these strains in the host, and the genetic basis of this type of auxotrophy.
Diagnostic Accuracy and Analytical Sensitivity of IDEIA Norovirus Assay for Routine Screening of Human Norovirus
Authors: Costantini Verónica , Grenz LaDonna , Fritzinger Angela , Lewis David , Biggs Christianne , Hale Antony , Vinjé Jan 
Published: June 2010

ABSTRACT

Noroviruses (NoVs) are recognized as the leading cause of epidemic and sporadic acute gastroenteritis. Early detection of NoV is crucial to control the spread of the disease. In this study, we evaluated the diagnostic accuracy, analytical sensitivity, and analytical reactivity of the IDEIA Norovirus assay (an enzyme immunoassay [EIA]) in a prospective and retrospective study design. A total of 557 prospectively collected fecal samples and a panel of 97 archived fecal samples, including 21 different GI and GII genotypes, were tested by conventional reverse transcription-PCR (RT-PCR)/bidirectional sequencing, real-time RT-PCR, and electron microscopy. The sensitivity and specificity of the EIA were 57.6% and 91.9%, respectively. The sensitivity for detecting NoV in fecal samples from outbreaks improved from 44.1% when three samples were tested to 76.9% when five samples per outbreak were tested. The EIA was able to detect strains from 7 GI and 11 GII genotypes. The analytical sensitivity of the EIA was 3.1 × 10
6
and 1.6 × 10
7
virus particles g
−1
of fecal sample for NoV GI and GII strains, respectively. Most GII samples positive by EIA had a threshold cycle (

C
T

) of <26.5, and 50% of the GII samples negative by EIA had a

C
T

of >25.6, suggesting that, although strains from genotypes GI.8, GII.10, and GII.16 were not detected, the low sensitivity of the EIA is primarily caused by low virus concentration. In conclusion, the current EIA may be of use as a rapid screening test during a norovirus outbreak investigation when multiple fecal samples are available; however, sporadic samples should be tested by molecular methods.
Caught in the Act:
In Vivo
Development of Macrolide Resistance to
Campylobacter jejuni
Infection
Authors: Lindow J. C. , Poly F. , Tribble D. R. , Guerry P. , Carmolli M. P. , Baqar S. , Porter C. K. , Pierce K. K. , Darsley M. J. , Sadigh K. S. , Dill E. A. , Kirkpatrick B. D. 
Published: June 2010

ABSTRACT

We report the first instance of macrolide resistance developing
in vivo
following appropriate antibiotic use in a healthy volunteer as a part of a controlled human infection with
Campylobacter jejuni. In vivo
development of macrolide resistance may be an important contributor to antibiotic resistance in
C. jejuni
.
Modifications to the Hemagglutinin Cleavage Site Control the Virulence of a Neurotropic H1N1 Influenza Virus
Authors: Sun Xiangjie , Tse Longping V. , Ferguson A Damon , Whittaker Gary R. 
Published: June 2010

ABSTRACT

A key determinant of influenza virus pathogenesis is mutation in the proteolytic cleavage site of the hemagglutinin (HA). Typically, low-pathogenicity forms of influenza virus are cleaved by trypsin-like proteases, whereas highly pathogenic forms are cleaved by different proteases (e.g., furin). Influenza virus A/WSN/33 (WSN) is a well-studied H1N1 strain that is trypsin independent
in vitro
and has the ability to replicate in mouse brain. Previous studies have indicated that mutations in the neuraminidase (NA) gene allow the recruitment of an alternate protease (plasminogen/plasmin) for HA activation. In this study we have identified an additional mutation in the P2 position of the WSN HA cleavage site (S328Y) that appears to control virus spread in a plasmin-dependent manner. We reconstructed recombinant WSN viruses containing tyrosine (Y), phenylalanine (F), or serine (S) in the P2 position of the cleavage site. The Y328 and F328 viruses allowed plaque formation in the absence of trypsin, whereas the S328 virus was unable to form plaques under these conditions. In mice, Y328 and F328 viruses were able to efficiently spread following intracranial inoculation; in contrast, the S328 virus showed only limited infection of mouse brain. Following intranasal inoculation, all viruses could replicate efficiently, but with Y328 and F328 viruses showing a limited growth defect. We also show that wild-type HA (Y328) was more efficiently cleaved by plasmin than S328 HA. Our studies form the foundation for a more complete understanding of the molecular determinants of influenza virus pathogenesis and the role of the plasminogen/plasmin system in activating HA.
RELATIVE VON NEUMANN ENTROPY FOR EVALUATING AMINO ACID CONSERVATION
Authors: JOHANSSON FREDRIK , TOH HIROYUKI 
Published: June 2010

The Shannon entropy is a common way of measuring conservation of sites in multiple sequence alignments, and has also been extended with the relative Shannon entropy to account for background frequencies. The von Neumann entropy is another extension of the Shannon entropy, adapted from quantum mechanics in order to account for amino acid similarities. However, there is yet no relative von Neumann entropy defined for sequence analysis. We introduce a new definition of the von Neumann entropy for use in sequence analysis, which we found to perform better than the previous definition. We also introduce the relative von Neumann entropy and a way of parametrizing this in order to obtain the Shannon entropy, the relative Shannon entropy and the von Neumann entropy at special parameter values. We performed an exhaustive search of this parameter space and found better predictions of catalytic sites compared to any of the previously used entropies.
Size Dependence of Quick Cavity Filling Behavior in Ultraviolet Nanoimprint Lithography Using Pentafluoropropane Gas
Authors: Youn Sung-Won , Hiroshima Hiroshi , Takahashi Masaharu , Maeda Ryutaro 
Published: June 2010

Rapid bubble elimination using pentafuoropropane (CFH2CH2CF3, HFC-245fa, CAS No. 460-3-1) condensing gas is one of the most promising methods to realize ultrahigh-speed ultraviolet nanoimprint lithography (UV-NIL). In this study, we investigated the shrinkage behaviors and elimination time of bubbles for different cavity sizes and resist thicknesses by employing a UV-NIL stepper with a real-time monitoring system. As predicted, a smaller cavity size resulted in a faster filling. Unlike the prediction from an analysis model based on Stefan's equation, a nonlinear decrease in bubble elimination time was observed in accordance with the decrease in cavity size (area). Instead, a linear relationship between bubble elimination time and cavity width was found for a certain range of cavity widths (W). In the cavity width, range from 25 to 340 µm, bubble elimination time was almost proportional to cavity width and could be defined as 0.00145×W(s). When the cavity width was 25 µm, the complete filling time was less than 0.033 s, indicating the potential to realize a ultrahigh-throughput nanopatterning process. Regarding the effect of initial resist thickness on a bubble shrinkage behavior, bubble elimination time tended to increase with the decrease in resist thickness.
The Moine Supergroup of NW Scotland: insights into the analysis of polyorogenic supracrustal sequences
Authors: Strachan R. A. , Holdsworth R. E. , Krabbendam M. , Alsop G. I. 
Published: June 2010

Abstract

The Moine Supergroup of NW Scotland is a thick sequence of early Neoproterozoic sedimentary rocks, with minor igneous intrusions, that display evidence for multiple phases of regional deformation and metamorphism. The descriptions and interpretations of the ‘Moine Schists’ provided by the 1907 memoir (

Peach
et al.
1907

) have been proved to be essentially correct and have laid the groundwork for a century of distinguished and influential research that has reached far beyond the confines of NW Scotland. The Survey workers recognized the sedimentary protoliths of these rocks, realized that they had been deposited unconformably on inliers of reworked basement gneisses that now occupy the cores of major folds, and understood the likely complexity of folding and the kinematic significance of mineral lineations. Further advances in understanding of the Moine rocks were mainly achieved through two techniques that were not available to the Survey workers of 100 years ago – geochronology and palaeomagnetism. Isotopic studies have confirmed the view of the Survey workers that the Moine rocks are of Precambrian age, and furthermore have demonstrated a complex, polyorogenic history.
Deformation partitioning, foliation successions and their significance for orogenesis: hiding lengthy deformation histories in mylonites
Authors: Bell T. H. 
Published: June 2010

Abstract

Although orogenesis commonly lasts 100 million years, a maximum of three foliations are usually preserved within any outcrop. They record little of the total history due to the effects of preferential partitioning of progressive shearing along S
0
. Such reactivation eventually destroys or rotates multiple successive foliations into parallelism with any layering that is present. Plate motion subjects a collisional orogen to spatially partitioned, episodic, but non-stop deformation. The bulk forces operating are horizontal and intermittently vertical (associated with gravitational load due to crustal thickening) forming sub-vertical and sub-horizontal foliations. These orientations are preserved in the strain shadows of anything competent that hinders reactivation of the compositional layering. Deformation partitioning results in portions of rock remaining unaffected for many events. Gravitational collapse of over-thickened orogen cores leads to significant extrusion in orogen rims and a dominance of sub-horizontal foliations in the latter and episodically continues throughout orogenesis. Reactivation causes decrenulation and/or rotation of foliations into parallelism with S
0
, destroying evidence that multiple sub-vertical and sub-horizontal foliations have developed except where preserved as inclusion trails in porphyroblasts and multiply truncated foliations in mylonites. However, the same processes operate in both the cores of orogens and ductile portions of their margins.
Toward a solution of the 3D balancing problem in curved segments of orogens
Authors: Hatcher Robert D. , Geiser Peter 
Published: June 2010

Abstract
Sections in strongly to moderately curved foreland fold-thrust belts may be restorable, but retrodeformation of two-dimensional (2D) serial sections produces overlap of their hinterland ends, making the incompatibility problem obvious. Outward-radiating displacement vectors predict along-strike stretching that increases toward the outer portions of arcuate foreland fold-thrust belts. Balancing of curved foreland fold-thrust belts becomes a three-dimensional (3D) material balance problem, involving non-plane strain. We propose a technique that will solve the 3D balancing problem if: (1) boundary pin lines, consisting of strike-boundary and normal-boundary lines, are present and identifiable; (2) a set of constant-length lines can be defined; (3) a set of section lines is constructed normal to tectonic strike; and (4) a set of boundary and internal constant-area regions is defined. This technique recognizes as false the unstated assumption that the deformed and undeformed state coordinate frames are identical. Accordingly, the displacement vector field of curved orogens does not parallel the deformed state strike normals. Instead, physically possible displacement vector fields require body rotations about a set of vertical axes during deformation, indicating that, during deformation, out-of-plane motions occur normal to the deformed-state strike normals relative to the external deformed-state coordinate frame. The final position of the plane strain surfaces parallels the deformed-state position of the strike normals, because they rotate into this position.
Mylonites: lessons from Eriboll
Authors: White S. H. 
Published: June 2010

Abstract
Eriboll has been an important area in understanding the geology and structure of the NW Highlands of Scotland. It came to prominence during the Highland Controversy between Nicol and Murchison in the 1850s. Nicol recognized a major regional, or grand, dislocation (the Moine Thrust Zone) at Eriboll whereas Murchison denied its existence. An important element in the resolution of the controversy was the repeated observation of a distinctive schistose rock that often marked Nicol's dislocation. Lapworth named it a ‘mylonite’ and related its development to mechanical metamorphism resulting from tectonic (milling) movements along the dislocation. Peach, Horne and co-workers, whose contributions to early mylonite studies are often overlooked, described the effects of increasing strain on mylonite development, recorded the prominent lineation within mylonites and identified its kinematic significance via thrust geometries and a first use of shear sense indicators. In this contribution those elements of the Highland Controversy that led to the identification of mylonites will be reviewed, concentrating on the contributions of Lapworth and of Peach, Horne and co-workers. It will include an examination and discussion of the mylonites from Lapworth's locality and of the mylonitized Moine schists at Eriboll. It will conclude with comments on mylonite classification and nomenclature.
Moine Thrust zone mylonites at the Stack of Glencoul: II - results of vorticity analyses and their tectonic significance
Authors: Law R. D. 
Published: June 2010

Abstract

This paper presents quantitative data from the Stack of Glencoul on flow vorticities associated with mylonite generation in the hanging wall and footwall of the Moine Thrust, using samples collected in a vertical traverse from 80 m above the thrust plane to 8.5 m beneath the thrust. Estimated vorticity numbers (Wm) in Moine pelites and psammites above the thrust range from 0.775–0.725 (
c
. 43–47% pure shear component) increasing downwards to 0.83–0.75 (35–45% pure shear) at 10 cm above the thrust. Wm values in dynamically recrystallized Cambrian quartzites at 0.5–14.5 cm beneath the thrust range from 0.99–0.90 (10–30% pure shear). At 3.0–8.5 m beneath the thrust estimated Wm values are less than 0.75 in the quartzites, although there is some thin section-scale partitioning with Wm values of 0.75–0.65 (45–55% pure shear) in domains of dynamically recrystallized quartz and Wm values <0.65 (>55% pure shear) in domains of relict detrital quartz grains. Integration of strain and vorticity analyses indicates a vertical shortening of 50–75% in these gently dipping mylonites located at the base of the Moine Nappe. The tectonic implications of vertical shortening (thinning) and transport-parallel stretching at the base of the Moine Nappe are discussed.
Strain within the ultrahigh-pressure Western Gneiss region of Norway recorded by quartz CPOs
Authors: Barth Nicolas C. , Hacker Bradley R. , Seward Gareth G. E. , Walsh Emily O. , Young David , Johnston Scott 
Published: June 2010

Abstract
Electron back-scatter diffraction (EBSD) was used to measure the crystal preferred orientations (CPOs) from 101 samples across the ultrahigh-pressure Western Gneiss region of Norway to assess slip systems, sense of shear, CPO strength, and strain geometry. The CPOs suggest a dominance of prism 〈a〉 slip, with lesser amounts of prism [c] slip and basal 〈a〉 slip; there are few Type I and Type II girdles. The major structural feature in the study area – the high-strain, top-W, normal-sense Nordfjord–Sogn Detachment Zone – is characterized by asymmetric and strong CPOs; an eastern domain with strong asymmetric CPOs shows top-E shear. Strain throughout the study area was characterized by a mix of plane strain and constriction with no evidence of flattening. Adjacent gneiss and quartzite/vein samples have similar CPOs.
Basement-influenced rifting and basin development: a reappraisal of post-Caledonian faulting patterns from the North Coast Transfer Zone, Scotland
Authors: Wilson R. W. , Holdsworth R. E. , Wild L. E. , McCaffrey K. J. W. , England R. W. , Imber J. , Strachan R. A. 
Published: June 2010

Abstract
The post-Caledonian development of the West Orkney Basin is regularly cited as a classic example of basement-influenced rifting. This paper presents the first detailed multidisciplinary analysis of the three-dimensional (3D) geometries and distribution of post-Caledonian faults in onshore northernmost Scotland, examining their relationships to basement fabrics and comparing them to rift-related structures developed offshore in the West Orkney Basin. Two phases of rift-related faulting are distinguished: 1) Devonian ENE–WSW extension localized in the east of the basin and related to regional sinistral transtension along the Great Glen Fault; and 2) Permo-Triassic NW–SE extension focused to the west of the basin and probably contemporaneous with movements along the Minch Fault. A complex North Coast Transfer Zone is developed along the northern Scottish coast linking Mesozoic rifts that reactivated Caledonian structures in the West Orkney Basin (Naver Thrust) to those bounding the North Minch Basin (Outer Hebrides Fault Zone). Polymodal faulting patterns are widespread in onshore exposures. Fault patterns vary due to changes in the obliquity between regional rifting vectors and variably orientated pre-existing structures in each basement terrane. The geometric complexity and spatial variations in fault patterns onshore can be correlated with changes in basement structures, despite limited direct reactivation of pre-existing fabrics.
Lithospheric-scale extension during Grampian orogenesis in Scotland
Authors: Viete Daniel R. , Richards Simon W. , Lister Gordon S. , Oliver Grahame J. H. , Banks Graham J. 
Published: June 2010

Abstract
This contribution presents a new model for the Grampian-age tectonothermal development of the Buchan Block and Barrovian-type regions to its west, in the Grampian Terrane, Scotland. The model has drawn on evidence gathered from field mapping, microstructural analysis, metamorphic petrology and mafic magma geochemistry to propose that emplacement of the Grampian gabbros and regional metamorphic heating associated with production of Barrovian- and Buchan-type units occurred during syn-orogenic (Grampian-age), lithospheric-scale extension. Extension followed lithospheric thickening associated with the initiation of Grampian orogenesis and was followed by renewed lithospheric thickening and termination of the extensional heating. Mantle melting to produce the Grampian gabbros of the Grampian Terrane was achieved by extensional thinning of the lithosphere and decompression melting of the asthenosphere at depths of less than 70 km. Advection of heat from the mantle with emplacement of the Grampian gabbros augmented elevated heat budgets associated with attenuation of isotherms during extension. Deposition of the uppermost Dalradian (the Whitehills and Boyndie Bay Groups and the Macduff Slates) occurred during Grampian-age lithospheric extension. A gently-dipping, mid-crustal detachment focused metamorphic heat sources and accommodated significant lithospheric-scale strain, allowing independent thermal evolution of units in its hanging wall (the Buchan Block) and footwall (Barrovian-type units).
Depositional properties and geochemistry of Holocene perched springline tufa deposits and associated spring waters: a case study from the Denizli Province, Western Turkey
Authors: Özkul Mehmet , Gökgöz Alİ , HorvatinčIć Nada 
Published: June 2010

Abstract

The Güney waterfall area is a perched springline tufa site developed on the southeast slope of the Büyük Menderes River near Güney town, in the Denizli province, Western Turkey. The site is 12 km away from Güney and 72 km from the city centre of Denizli. The spring waters emerge from the boundary between Palaeozoic marble and micaschist and precipitated tufa deposits downslope at the altitudes ranging from 220 to 400 metres. The tufa deposits cover an area of about 20 hectares. Flat upper surfaces of the deposits are indicative of mature stage. The waters are of the Ca–HCO
3
type and supersaturated with respect to CaCO
3
. The stable isotope values of the spring waters are −49.94 for δ
2
H and −7.15 for δ
18
O. The δ
13
C and δ
18
O values of active and passive tufa samples are in the range from −9.13 to −6.0‰, and from −8.44 to −7.40‰, respectively. These isotopic values are typical for fresh water tufa. The passive tufas give the
14
C age in the range from 2000 to 5800 yr BP. According to the
14
C age data, passive tufas are not older than Holocene. The stable isotope composition is similar south European examples.