bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility of Pyrosequencing in Identifying Bacteria Directly from Positive Blood Culture Bottles
Authors: Jordan J. A. , Jones-Laughner J. , Durso M. B. 
Published: December 2008

ABSTRACT

Growth in liquid media is the gold standard for detecting microorganisms associated with bloodstream infections. The Gram stain provides the first clue as to the etiology of infection, with phenotypic identification completed 1 or 2 days later. Providing more detailed information than the Gram stain can impart, and in less time than subculturing, would allow the use of more directed empirical therapy and, thus, reduce the patient's exposure to unnecessary or ineffective antibiotics sooner. The study had two objectives, as follows: (i) to identify new targets to improve our ability to differentiate among certain enteric gram-negative rods or among certain
Streptococcus
species and (ii) to determine whether real-time PCR and pyrosequencing could as accurately identify organisms directly from positive blood culture bottles as culture-based methods. Two hundred and fifty-five consecutive positive blood culture bottles were included. The results showed a high level of agreement between the two approaches; of the 270 bacteria isolated from the 255 blood culture bottles, results for pyrosequencing and culture-based identifications were concordant for 264/270 (97.8%) bacteria with three failed sequences, and three sequences without match. Additionally, compared to the universal 16S rRNA gene target, the new 23S rRNA gene targets greatly improved our ability to differentiate among certain enteric gram-negative rods or among certain
Streptococcus
species. In conclusion, combining real-time PCR and pyrosequencing provided valuable information beyond that derived from the initial Gram stain and in less time than phenotypic culture-based identification. This strategy, if implemented, could result in a more directed empirical therapy in patients and would promote responsible antibiotic stewardship.
Transmission Networks and Population Turnover of Echovirus 30
Authors: Leitch E. C. McWilliam , Bendig J. , Cabrerizo M. , Cardosa J. , Hyypiä T. , Ivanova O. E. , Kelly A. , Kroes A. C. M. , Lukashev A. , MacAdam A. , McMinn P. , Roivainen M. , Trallero G. , Evans D. J. , Simmonds P. 
Published: December 2008

ABSTRACTGlobally, echovirus 30 (E30) is one of the most frequently identified enteroviruses and a major cause of meningitis. Despite its wide distribution, little is known about its transmission networks or the dynamics of its recombination and geographical spread. To address this, we have conducted an extensive molecular epidemiology and evolutionary study of E30 isolates collected over 8 years from a geographically wide sample base (11 European countries, Asia, and Australia). 3Dpol sequences fell into several distinct phylogenetic groups, interspersed with other species B serotypes, enabling E30 isolates to be classified into 38 recombinant forms (RFs). Substitutions in VP1 and 3Dpol regions occurred predominantly at synonymous sites (ratio of nonsynonymous to synonymous substitutions, 0.05) with VP1 showing a rapid substitution rate of 8.3 × 10−3substitutions per site per year. Recombination frequency was tightly correlated with VP1 divergence; viruses differing by evolutionary distances of >0.1 (or 6 years divergent evolution) almost invariably (>97%) had different 3Dpol groups. Frequencies of shared 3Dpol groups additionally correlated with geographical distances, with Europe and South Asia showing turnover of entirely distinct virus populations. Population turnover of E30 was characterized by repeated cycles of emergence, dominance, and disappearance of individual RFs over periods of 3 to 5 years, although the existence and nature of evolutionary selection underlying these population replacements remain unclear. The occurrence of frequent “sporadic” recombinants embedded within VP1 groupings of other RFs and the much greater number of 3Dpol groups than separately identifiable VP1 lineages suggest frequent recombination with an external diverse reservoir of non-E30 viruses.
Level of Herpes Simplex Virus Type 1 Latency Correlates with Severity of Corneal Scarring and Exhaustion of CD8+T Cells in Trigeminal Ganglia of Latently Infected Mice
Authors: Mott Kevin R. , Bresee Catherine J. , Allen Sariah J. , BenMohamed Lbachir , Wechsler Steven L. , Ghiasi Homayon 
Published: December 2008

ABSTRACTA hallmark of infection with herpes simplex virus type 1 (HSV-1) is the establishment of latency in ganglia of the infected individual. During the life of the latently infected individual, the virus can occasionally reactivate, travel back to the eye, and cause recurrent disease. Indeed, a major cause of corneal scarring (CS) is the scarring induced by HSV-1 following reactivation from latency. In this study, we evaluated the relationship between the amount of CS and the level of the HSV-1 latency-associated transcript (LAT) in trigeminal ganglia (TG) of latently infected mice. Our results suggested that the amount of CS was not related to the amount of virus replication following primary ocular HSV-1 infection, since replication in the eyes was similar in mice that did not develop CS, mice that developed CS in just one eye, and mice that developed CS in both eyes. In contrast, mice with no CS had significantly less LAT, and thus presumably less latency, in their TG than mice that had CS in both eyes. Higher CS also correlated with higher levels of mRNAs for PD-1, CD4, CD8, F4/80, interleukin-4, gamma interferon, granzyme A, and granzyme B in both cornea and TG. These results suggest that (i) the immunopathology induced by HSV-1 infection does not correlate with primary virus replication in the eye; (ii) increased CS appears to correlate with increased latency in the TG, although the possible cause-and-effect relationship is not known; and (iii) increased latency in mouse TG correlates with higher levels of PD-1 mRNA, suggesting exhaustion of CD8+T cells.
Basin architecture and syndepositional fault activity during deposition of the Neoproterozoic Mackenzie Mountains supergroup, Northwest Territories, CanadaNorthwest Territories Geoscience Office Contribution 0040.
Authors: Turner Elizabeth C. , Long Darrel G.F. 
Published: December 2008

The early Neoproterozoic Mackenzie Mountains supergroup (MMSG; ∼4 km thick, <1083 Ma, >779 Ma) was deposited in a large but poorly understood basin. Analysis of new and existing stratigraphic data reveals unexpected, abrupt changes in thickness and lithofacies patterns in formation scale and smaller units over short distances parallel and perpendicular to depositional strike. These isopach and lithofacies patterns depict irregularly subsiding syndepositional sub-basins. These basins may have developed during basin extension in a lower-plate segment of an evolving passive margin, as the result of episodic, excessive subsidence along growth faults parallel to the basin margin, and crustal-scale (transfer) faults at a high angle to the margin. The extent of the lower-plate area is inferred to correspond to the distribution of the MMSG (∼500 km strike length); upper-plate segments are inferred to flank the MMSG embayment to the northwest and southeast. A lower-plate model for the arcuate MMSG embayment has important implications for the Mackenzie Mountains zinc district. The present-day regional distribution of known carbonate-hosted base-metal showings suggests that the configuration of the thinned, faulted Neoproterozoic lower-plate segment, together with later reactivation of basement-rooted transfer faults during Neoproterozoic–Paleozoic rifting or Laramide compression, may have been important in focussing metalliferous fluids into overlying units.
Removal of the lichen mat by reindeer enhances tree growth in a northern Scots pine forest
Authors: Macias Fauria Marc , Helle Timo , Niva Aarno , Posio Heikki , Timonen Mauri 
Published: December 2008

Reindeer ( Rangifer tarandus L.) lichen grazing enhanced Scots pine ( Pinus sylvestris L.) growth in a northeastern Fennoscandian forest. Lichen mat removal by grazing in a previously ungrazed area increased soil versus air temperature coupling. This caused faster soil spring warming and higher soil temperatures during late spring and summer, which are related to an earlier start of and better growth conditions during the trees’ growing season. Tree growth was related to spring and summer climate during the study period, 1896–2001. Snowmelt date, and ultimately soil warming and start of the growing season, may have caused the relationships between tree growth and spring climate. A drop in July temperature and an increase in the spring signals were found and attributed to the “divergence problem,” a widespread weakening in the relationships between tree growth and summer temperature in northern latitudes observed in the late 20th century. Differences in the relationships between tree growth and climate were found between trees growing in grazed and ungrazed parts of the stand. Tree growth differences were detected ∼10 years after the removal of the lichen mat. The fertilizing effect of reindeers on tree growth was considered minimal in this study, but its influence cannot be completely ruled out. Grazing intensity may thus be an important component of boreal forest carbon uptake.
Landscape-level variation in forest response to hurricane disturbance across a storm track
Authors: Busby Posy E. , Motzkin Glenn , Boose Emery R. 
Published: December 2008

Hurricane wind speeds at a given site are related to the intensity of the storm and the distance and direction from the storm center. As a result, forest damage is expected to vary predictably with respect to location relative to the storm track. To determine whether patterns of forest response along the track of a major hurricane in coastal New England were consistent with the expected patterns of wind damage, we investigated tree growth responses to the storm in several study sites that are similar with respect to site conditions, vegetation, and disturbance history. Growth responses to a severe hurricane in 1944 varied predictably among study sites with respect to distance from the storm track. Sites closest to the storm track experienced lesser wind damage and exhibited minimal growth responses, whereas sites farther east of the storm track and closer to the area of maximum estimated wind speed were characterized by greater wind damage and growth changes. Variation in estimated wind speed among our study sites (5–10 m/s) is not much greater than anticipated increases in hurricane intensity predicted under future climate scenarios (3–7 m/s). Thus, our results suggest that the magnitude of anticipated increases in wind speeds associated with Atlantic hurricanes may be sufficient to cause changes in forest response.
Standardized approaches in effectiveness monitoring programs and regional relevance: lessons from the Bowron River Watershed Riparian Evaluation Project
Authors: Nordin L. J. , Rex J. F. , Maloney D. A. , Tschaplinski P. J. 
Published: December 2008

Streams and riparian areas in the Bowron River watershed were assessed using the riparian management routine effectiveness evaluation, a protocol developed for postharvest operational monitoring in British Columbia. Located in the British Columbia interior, the study watershed has had several decades to recover since a period of intensive salvage logging from 1977 to 1987 in response to a spruce beetle ( Dendroctonus rufipennis ) outbreak. Correlations were found with site-specific watershed characteristics and attributes that are used to answer the protocol indicator questions. Channel width was the strongest covariate, exhibiting the most significant relationships with the stream and riparian attributes. Suggestions on how to adjust standard protocols for stream size and landscape heterogeneity are discussed and include the use of appropriate reference sites for baseline data. We used correlations with watershed characteristics and multiple regressions based on regional reference sites to predict upper and lower threshold values by which attribute measurements could be compared. Sites that were assessed above or below threshold values for an attribute were considered to be outside the range of natural variation and were given a failing score. Attributes with the most failures 20–30 years postharvest were disturbed ground, bare soil, undercut banks, and shade.
Recruitment patterns following a severe drought: long-term compositional shifts in Patagonian forests
Authors: Suarez María L. , Kitzberger Thomas 
Published: December 2008

Severe droughts have the potential of inducing transient shifts in forest canopy composition by altering species-specific adult tree mortality patterns. However, permanent vegetation change will occur only if tree recruitment patterns are also affected. Here, we analyze how a massive mortality event triggered by the 1998–1999 drought affected adult and sapling mortality and recruitment in a mixed Nothofagus dombeyi (Mirb.) Blume – Austrocedrus chilensis (D. Don) Flor. et Boult. forests of northern Patagonia. Comparing drought-induced and tree-fall gaps, we assessed changes in forest composition, microenvironments, and seedling density and survival of both species. Drought-kill disturbance shifted species composition of both canopy and sapling cohorts in favour of A. chilensis. Drought gaps were characterized by a shadier and more xeric environment, affecting the recruitment pattern of N. dombeyi seedlings. The seedling cohort was composed mostly of A. chilensis, and its survival was always higher than that of N. dombeyi. Additionally, A. chilensis seedlings showed higher plasticity than N. dombeyi seedlings, increasing its root to shoot ratios in drought gaps. The results suggest that extreme drought itself is a strong driving force in forest dynamics, with important imprints on forest landscapes. Future climate-change scenarios, projecting an increased in frequency and severity of droughts, alert us about expected long-term compositional shifts in many forest ecosystems.
Belowground competition influences growth of natural regeneration in thinned Douglas-fir stands
Authors: Devine Warren D. , Harrington Timothy B. 
Published: December 2008

Using a factorial combination of understory removal and trenching treatments, we examined the influences of belowground competition from understory and overstory vegetation on growth of naturally established Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco var. menziesii) saplings in thinned stands of Douglas-fir on moderately productive, glacially derived soils near Tacoma, Washington. Under limited light (26% ± 16% of full sun), sapling height and diameter growth were significantly reduced by belowground competition from overstory trees. Regardless of presence or absence of belowground competition from trees, understory vegetation did not have a detectable effect on sapling growth. Nitrogen deficiency in saplings was not detected in the presence of belowground competition: where tree roots were excluded, foliar nitrogen concentration and content increased without an increase in foliar mass. Belowground competition from overstory trees had a greater negative effect on growing season soil water content than did understory vegetation. Under the conditions of restricted light availability in this study, limitations in soil water content from competition had a strong growth-limiting effect on Douglas-fir regeneration. As potential canopy trees in a future uneven-aged stand, this sapling cohort would benefit from root gaps created during harvests.
THE PREDICATES FOR THE EXACT VORONOI DIAGRAM OF ELLIPSES UNDER THE EUCLIDIEAN METRIC
Authors: EMIRIS IOANNIS Z. , TSIGARIDAS ELIAS P. , TZOUMAS GEORGE M. 
Published: December 2008

This article examines the computation of the Delaunay graph and its dual Voronoi diagram of a set of ellipses in the Euclidean plane. We propose the first complete methods, under the exact computation paradigm, for the predicates of an incremental algorithm: κ1 decides which one of two given ellipses is closest to a given exterior point; κ2 decides the position of a query ellipse relative to an external bitangent line of two given ellipses; κ3 decides the position of a query ellipse relative to a Voronoi circle of three given ellipses; κ4 determines the type of conflict between a Voronoi edge, defined by four given ellipses, and a query ellipse. The article is restricted to non-intersecting ellipses, but the extension to arbitrary ones is possible. The ellipses are input in parametric representation, i.e., constructively in terms of their axes, center and rotation. For κ1 and κ2 we derive algebraic conditions optimal in terms of the degree of the algebraic numbers involved, and provide efficient implementations in C++ . For κ3 we compute a tight bound on the number of complex tritangent circles and design an exact symbolic-numeric algorithm, which is implemented in MAPLE. This essentially answers κ4 as well. We conclude with further work on lifting the condition of non-intersecting ellipses.
Airmass Classification and Analysis of Aerosol Types at El Arenosillo (Spain)
Authors: Toledano C. , Cachorro V. E. , de Frutos A. M. , Torres B. , Berjón A. , Sorribas M. , Stone R. S. 
Published: December 2008

Abstract
The Aerosol Robotic Network (AERONET) site “El Arenosillo,” equipped with a Cimel sun photometer, has been in operation since 2000. The data collected there are analyzed to establish an aerosol synoptic climatological description that is representative of the region. Different air masses and aerosol types are present over the site depending on the synoptic conditions. The frequent intrusion of dust from the Sahara Desert at El Arenosillo suggested the use of back trajectories to determine the airmass origins of other types of aerosol observed there. The focus of this study is to classify the air masses arriving at El Arenosillo by means of back-trajectory analyses and to characterize the aerosol within each type by means of the aerosol optical depth (AOD) and its spectral signature, given as the Ångström exponent (AE). The goal is to determine how aerosols observed over the station (receptor site) differ depending on source region and transport pathways. Two classification methods are used, one based on sectors and a second based on cluster analysis. The period analyzed is from 2000 to 2004. Both methods show that maritime air masses are predominant, occurring 70% of the time and having relatively low AOD (≈0.1 at 440 nm) and a wide range of AE (from about 0 to 2.0). Air masses with continental characteristics are moderately turbid and have values of AE that average ≈1.4. Air masses arriving from the south and southwest show the distinct features of the desert dust, having moderate to high values of AOD (0.30–0.35 at 440 nm) and low values of AE.
Rhythm versus Analogy: Prosodic Form Variation in Dutch Compounds
Authors: Neijt Anneke , Schreuder Robert 
Published: December 2008

Creating compound nouns is the most productive process of Dutch morphology, with an interesting pattern of form variation. For instance, staat `nation' simply combines with kunde `art' ( staatkunde `political science, statesmanship'), but needs a linking element s or en to form staatsschuld `national debt' and statenbond `confederation'. Previous research has shown that the use of linking elements is guided by paradigmatic analogy, a factor that in the absence of other factors would lead to paradigm uniformity. However, there is considerable freedom in the use of linking elements, suggesting that other factors are relevant as well. We present studies showing that both stress and length affect their use, and that, in an experimental setting, the linking element en is less favored in lengthened compounds. However, the results observed in this experiment can only be explained satisfactorily in terms of rhythm: the preference for a recurrent pattern of stressed and unstressed syllables. The general conclusion of this study concerns the distinction between language behavior guided by stored knowledge or by processing factors. Models based on analogy (exemplar-based models) rely on stored knowledge. This study shows that apart from that, rhythm plays its own role. Rhythmic structures facilitate language processing, and a preference for perfect rhythm explains which variant of a compound (with or without the linking element) is chosen. Given the universal nature of analogy and rhythm, the issue of the balance between these two components of linguistic knowledge is relevant for a wide array of languages.
Of mice and men: an open-label pilot study for treatment of immune thrombocytopenic purpura by an inhibitor of Syk
Authors: Podolanczuk Anna , Lazarus Alan H. , Crow Andrew R. , Grossbard Elliot , Bussel James B. 
Published: December 2008

Abstract
To determine whether inhibition of Syk would be useful in FcγR-dependent cytopenias such as immune thrombocytopenic purpura (ITP) or autoimmune hemolytic anemia, mouse models were used to evaluate efficacy of R406, an inhibitor of Syk function, in treating cytopenia. Both disease models responded favorably to treatment, with amelioration of ITP being more dramatic. Thus, phase 2 clinical trial was initiated to study the effects of Syk inhibition in humans with ITP. Sixteen adults with chronic ITP were entered into an open-label, single-arm cohort dose-escalation trial beginning with 75 mg and escalating as high as 175 mg twice daily. Doses were increased until a persistent response was seen, toxicity occurred, or 175 mg twice daily was reached. Eight patients achieved persistent responses with platelet counts greater than 50 × 109/L (50 000 mm3) on more than 67% (actually 95%) of their study visits, including 3 who had not persistently responded to thrombopoietic agents. Four others had nonsustained responses. Mean peak platelet count exceeded 100 × 109/L (100 000 mm3) in these 12 patients. Toxicity was primarily GI-related with diarrhea (urgency) and vomiting; 2 patients had transaminitis. In conclusion, inhibition of Syk was an efficacious means of increasing and maintaining the platelet count in half the patients with chronic refractory ITP. (ClinicalTrials.gov, no. NCT00706342).
Complex fate of paralogs
Authors: Szklarczyk Radek , Huynen Martijn A , Snel Berend 
Published: December 2008

Abstract

Background
Thanks to recent high coverage mass-spectrometry studies and reconstructed protein complexes, we are now in an unprecedented position to study the evolution of biological systems. Gene duplications, known to be a major source of innovation in evolution, can now be readily examined in the context of protein complexes.

Results
We observe that paralogs operating in the same complex fulfill different roles: mRNA dosage increase for more than a hundred cytosolic ribosomal proteins, mutually exclusive participation of at least 54 paralogs resulting in alternative forms of complexes, and 24 proteins contributing to bona fide structural growth. Inspection of paralogous proteins participating in two independent complexes shows that an ancient, pre-duplication protein functioned in both multi-protein assemblies and a gene duplication event allowed the respective copies to specialize and split their roles.

Conclusion
Variants with conditionally assembled, paralogous subunits likely have played a role in yeast's adaptation to anaerobic conditions. In a number of cases the gene duplication has given rise to one duplicate that is no longer part of a protein complex and shows an accelerated rate of evolution. Such genes could provide the raw material for the evolution of new functions.