bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co‐occurring grazing and climate stressors have different effects on the total seed bank when compared to the persistent seed bank
Authors: Espinosa Carlos I. , Luzuriaga Arantzazu L. , de la Cruz Marcelino , Montero Marianne , Escudero Adrián 
Published: January 2013

AbstractQuestions(1) Does climate amelioration in semi‐arid ecosystems increase seed bank richness and seed density in both total and persistent seed banks? (2) Does herbivory modulate climate effects on soil seed banks? (3) Is this effect mediated by changes in the above‐ground vegetation? (4) To what extent do environmental conditions affect similarity between the total and persistent seed banks, and between above‐ground (vegetation) vs below‐ground (seed bank) community compartments?LocationEcuadorian Dry Mountain Scrub Ecosystem.MethodsOur study was conducted along a climatic gradient (altitude) under two different management conditions: undisturbed and grazed. The effect of grazing, altitude and their interaction on seed abundance and richness of the total and persistent soil seed banks were evaluated with non‐linear mixed models.ResultsAltitude, grazing and their interaction exerted a significant effect on richness and abundance of the total seed bank, but not on the persistent seed bank. At highly stressful climate conditions, differences in species richness between the total and persistent seed banks were small or absent, while at milder environmental conditions the total seed bank showed greater seed species richness and abundance than the persistent one. However, under grazing conditions, species richness in both seed banks was rather similar along the climatic gradient. Relationships in terms of species richness between above‐ground vs below‐ground compartments, shifted from being dominated by the above‐ground component at low altitudes (more stress) to being dominated by the seed bank component at higher elevations (milder conditions). In grazed locations, vegetation and seed bank showed similar species richness throughout the altitudinal gradient.ConclusionsThis study demonstrates that not only climate acted as a key environmental filter on soil seed bank properties, but also that grazing greatly modulated the primary effect of climate. Nevertheless, the effect of climate and grazing was restricted to the total seed bank (the fertility compartment) and no effect was observed in the persistent seed bank (longevity compartment). In this tropical dry scrub, richness and abundance of seeds increased upwards along the altitudinal gradient, most likely because at higher altitudes environmental conditions improve and become more benign for plant development.
North Atlantic Islands with native and alien trees: are there differences in diversity and species‐area relationships?
Authors: Vetaas Ole R. , Vikane Jan H. , Saure Heidi I. , Vandvik Vigdis 
Published: January 2013

AbstractQuestionsAre there differences in species composition and richness between islands that were reforested more than 70 yr ago with the introduced Pinus mugo compared with islands supporting the native Pinus sylvestris? Do the results depend on autocorrelation in geographical space and species ordination space? Species richness is expected to increase as a function of the size of an island; are the responses to island size different between P. mugo and P. sylvestris islands. Does the land‐use history have an impact on the current species composition and richness pattern?LocationThe archipelago is in the oceanic section of the Atlantic bioclimatic zone, west Norway. This archipelago was part of the ancient and widespread treeless heathland found along the European west coast.MethodsData on vascular plants were compiled from the forested islands, and their differences in species composition were analysed by ordination. The hypotheses were tested by means of t‐tests and generalized linear models, the spatial component was accounted for by means of Moran's I and spatial autoregression with the moving average approach. This was done both in geographical space and species ordination space.ResultsThere are more vascular plants on the islands with introduced P. mugo than on the islands with native P. sylvestris. The latter have rather homogenous undergrowth dominated by bryophytes. This may explain lower richness on islands with native forest and why island size is not correlated with species richness on these islands. In contrast, P. mugo is easily wind‐felled in autumn storms, which keeps rocky microhabitats exposed to air and new forest habitats are created. Species that are associated with the previous land‐use system (grazing) prevail on islands with introduced pine, and thus contribute to higher plant richness.ConclusionsThe difference in species richness and island species–area relationship (ISAR) between P. mugo and P. sylvestris islands may relate to the same underpinning causes. Species from the old land‐use system have survived on P. mugo islands, but not in the late‐successional forest with a more closed canopy that has developed on P. sylvestris islands. Thus habitat and species richness is higher and increases with area on P. mugo islands but not on P. sylvestris islands.
Grazing effects on plant community succession of early‐ and mid‐seral seeded grassland compared to shortgrass steppe
Authors: Milchunas Daniel G. , Vandever Mark W. 
Published: January 2013

AbstractQuestionsGrazing may speed or slow secondary succession, and the direction may depend on seral stage and relative tolerance of native perennial grasses compared with annual invasive species. How does grazing affect succession where undisturbed communities have a long evolutionary history of grazing by native herbivores and are tolerant to livestock grazing?LocationShortgrass steppe, North American Great Plains, Colorado (40°49′N, 104°46′W), USA.MethodsUngrazed and grazed early‐seral (4–6 yr) and mid‐seral (18–20 yr) seeded fields (Conservation Reserve Program) and traditionally grazed native steppe were compared for effects on plant composition in relation to changes expected from regional succession models.ResultsRecovery towards undisturbed native shortgrass steppe for early‐ and mid‐seral communities, respectively, was 19% and 36% for total vegetation cover, 5% and 21% for planted native species, 10% and 88% for non‐planted native perennial grasses, only 0.2% and 13% for short grasses, and overall dissimilarity in community species compositions was 97% and 68%. In general, grazing effects were neutral or most often not significant in all years and/or were small in overall community magnitude. The early‐seral community displayed more changes indicative of a slowing of succession with grazing (total vegetative and grass basal cover) rather than reducing invasive species (species targeted by timing of grazing), although drought had limited the establishment of grazing‐tolerant short grasses. The mid‐seral community showed more changes consistent with advancing successional recovery with grazing (overall community dissimilarity, forbs, planted native perennial grasses, tall grasses and target species). However, non‐planted native perennial grasses responded negatively to grazing in the mid‐seral community and positively in native shortgrass steppe where outside seed would originate.ConclusionsGrazing effects on particular functional groups and species were not the same across seral stages, were mixed in terms of speeding or slowing succession, and were generally not large at the community level. Evolutionary history of grazing may serve as a general guide but decisions on whether to graze successional grasslands may best be made after assessing whether tolerant perennial short grass species are significant components. Monitoring may then be necessary to determine species responses in particular community matrixes and effects on subsequent immigration of non‐seeded native perennial species.
Shades of red: bird‐pollinated flowers target the specific colour discrimination abilities of avian vision
Authors: Shrestha Mani , Dyer Adrian G. , Boyd‐Gerny Skye , Wong Bob B. M. , Burd Martin 
Published: January 2013

Summary

Colour signals are a major cue in putative pollination syndromes. There is evidence that the reflectance spectra of many flowers target the distinctive visual discrimination abilities of hymenopteran insects, but far less is known about bird‐pollinated flowers. Birds are hypothesized to exert different selective pressures on floral colour compared with hymenopterans because of differences in their visual systems.

We measured the floral reflectance spectra of 206 Australian angiosperm species whose floral visitors are known from direct observation rather than inferred from floral characteristics. We quantified the match between these spectra and the hue discrimination abilities of hymenopteran and avian vision, and analysed these metrics in a phylogenetically informed comparison of flowers in different pollination groups.

We show that bird‐visited flowers and insect‐visited flowers differ significantly from each other in the chromatic cues they provide, and that the differences are concentrated near wavelengths of optimal colour discrimination by whichever class of pollinator visits the flowers.

Our results indicate that angiosperms have evolved the spectral signals most likely to reinforce their pollinators' floral constancy (the tendency of individual pollinators to visit flowers of the same species) in communities of similarly coloured floral competitors.
Gamete fertility and ovule number variation in selfed reciprocal F1 hybrid triploid plants are heritable and display epigenetic parent‐of‐origin effects
Authors: Duszynska Dorota , McKeown Peter C. , Juenger Thomas E. , Pietraszewska‐Bogiel Anna , Geelen Danny , Spillane Charles 
Published: January 2013

Summary

Polyploidy and hybridization play major roles in plant evolution and reproduction. To investigate the reproductive effects of polyploidy and hybridization in Arabidopsis thaliana, we analyzed fertility of reciprocal pairs of F1 hybrid triploids, generated by reciprocally crossing 89 diploid accessions to a tetraploid Ler‐0 line.

All F1 hybrid triploid genotypes exhibited dramatically reduced ovule fertility, while variation in ovule number per silique was observed across different F1 triploid genotypes. These two reproductive traits were negatively correlated suggesting a trade‐off between increased ovule number and ovule fertility. Furthermore, the ovule fertility of the F1 hybrid triploids displayed both hybrid dysgenesis and hybrid advantage (heterosis) effects.

Strikingly, both reproductive traits (ovule fertility, ovule number) displayed epigenetic parent‐of‐origin effects between genetically identical reciprocal F1 hybrid triploid pairs. In some F1 triploid genotypes, the maternal genome excess F1 hybrid triploid was more fertile, whilst for other accessions the paternal genome excess F1 hybrid triploid was more fertile.

Male gametogenesis was not significantly disrupted in F1 triploids. Fertility variation in the F1 triploid A. thaliana is mainly the result of disrupted ovule development. Overall, we demonstrate that in F1 triploid plants both ovule fertility and ovule number are subject to parent‐of‐origin effects that are genome dosage‐dependent.
Serotype Sensitivity of a Lateral Flow Immunoassay for Cryptococcal Antigen
Authors: Gates-Hollingsworth Marcellene A. , Kozel Thomas R. 
Published: January 2013

ABSTRACT
To meet the needs of a global community, an immunoassay for cryptococcal antigen (CrAg) must have high sensitivity for CrAg of all major serotypes. A new immunoassay for CrAg in lateral flow format was evaluated and found to have a high sensitivity for detection of serotypes A, B, C, and D.
Cerebrospinal Fluid (1,3)-β-
d
-Glucan Detection as an Aid for Diagnosis of Iatrogenic Fungal Meningitis
Authors: Lyons Jennifer L. , Roos Karen L. , Marr Kieren A. , Neumann Henry , Trivedi Julie B. , Kimbrough Dorlan J. , Steiner Lisa , Thakur Kiran T. , Harrison Daniel M. , Zhang Sean X. 
Published: January 2013

ABSTRACT

This case series highlights our experience with use of the Fungitell assay for quantifying (1,3)-β-
d
-glucan in cerebrospinal fluid during the current U.S. outbreak of fungal meningitis related to contaminated methylprednisolone acetate. This test may prove a useful adjunct in diagnosis and management of exposed patients.
Whole-Genome Mapping: a New Paradigm in Strain-Typing Technology
Authors: Miller J. Michael 
Published: January 2013

ABSTRACT
Strain-typing technology in support of outbreak identification and resolution has evolved from phenotypic analysis, such as serology and biotypes, to much-more-robust molecular genetic approaches, such as pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. Whole-genome mapping (WGM) has been recently applied to subtyping analysis, and it bridges the gap between PFGE (∼20 bands sorted by size) and whole-genome sequencing. WGM utilizes restriction site analysis but arranges 200 to 500 bands in the order they appear on the chromosome. WGM is able to quickly and cost-effectively generate high-resolution, ordered whole-genome maps of bacteria.
Direct Sequencing and RipSeq Interpretation as a Tool for Identification of Polymicrobial Infections
Authors: Wolff Tine Y. , Eickhardt Steffen , Björnsdottir Maria K. , Moser Claus , Bjarnsholt Thomas , Høiby Niels , Thomsen Trine R. 
Published: January 2013

ABSTRACT
In this study, RipSeq Mixed, a software resolving uninterpretable mixed DNA sequencing chromatograms, revealed the bacterial content of 15 polymicrobial samples. Direct sequencing combined with RipSeq Mixed constitutes a valuable supplement to cultivation, particularly when cultivation is negative and direct sequencing is inconclusive despite continued clinical indications of infection.
Comparison of (1→3)-β-
d
-Glucan, Mannan/Anti-Mannan Antibodies, and Cand-Tec Candida Antigen as Serum Biomarkers for Candidemia
Authors: Held Jürgen , Kohlberger Isabelle , Rappold Elfriede , Busse Grawitz Andrea , Häcker Georg 
Published: January 2013

ABSTRACT

We conducted a case-control study using the Fungitell assay, the novel Platelia
Candida
Antigen (Ag) Plus and
Candida
Antibody (Ab) Plus assays, and the Cand-Tec latex agglutination test to evaluate the usefulness of (1→3)-β-
d
-glucan (BDG), mannan antigen with/without anti-mannan antibody, and Cand-Tec
Candida
antigen measurement for the diagnosis of candidemia. A total of 56 patients fulfilled the inclusion criteria and were enrolled. One hundred patients with bacteremia and 100 patients with sterile blood cultures served as negative controls. In the candidemia group, median (1→3)-β-
d
-glucan, mannan antigen, and anti-mannan antibody levels were 427 pg/ml, 190 pg/ml, and 18.6 antibody units (AU)/ml, respectively. All three parameters were significantly elevated in patients with candidemia. The sensitivity and specificity were, respectively, 87.5% and 85.5% for (1→3)-β-
d
-glucan, 58.9% and 97.5% for mannan antigen, 62.5% and 65.0% for anti-mannan antibody, 89.3% and 63.0% for mannan antigen plus anti-mannan antibody, 89.3% and 85.0% for BDG plus mannan antigen, and 13.0% and 93.9% for Cand-Tec
Candida
antigen. The low mannan antigen sensitivity was in part caused by
Candida parapsilosis
and
Candida guilliermondii
fungemias, which were not detected by the Platelia
Candida
Ag Plus assay. When the cutoff was lowered from 125 pg/ml to 50 pg/ml, mannan antigen sensitivity increased to 69.6% without severely affecting the specificity (93.5%). Contrary to recently published data, superficial candidiasis was not associated with elevated mannan antigen levels, not even after the cutoff was lowered. Combining procalcitonin (PCT) with (1→3)-β-
d
-glucan to increase specificity provided a limited advantage because the benefit of the combination did not outweigh the loss of sensitivity. Our results demonstrate that the Cand-Tec
Candida
antigen and the mannan antigen plus anti-mannan antibody measurements have unacceptably low sensitivity or specificity. Of the four tests compared, (1→3)-β-
d
-glucan and mannan antigen are the superior biomarkers, depending on whether a sensitivity-driven or specificity-driven approach is used.
Invasive Pulmonary Aspergillosis Due to Emericella nidulans var. echinulata, Successfully Cured by Voriconazole and Micafungin
Authors: Yu Jin , Mu Xiangdong , Li Ruoyu 
Published: January 2013

ABSTRACT

A 78-year-old male who was undergoing prolonged glucocorticoid treatment experienced cough and expectoration for 2 weeks. Galactomannan antigen analysis and a chest computed tomography (CT) scan suggested a diagnosis of invasive pulmonary aspergillosis. DNA sequencing indicated that
Emericella nidulans
var.
echinulata
was the causative agent. A combination of voriconazole and micafungin successfully treated the illness.
Comparison of Anyplex II RV16 with the xTAG Respiratory Viral Panel and Seeplex RV15 for Detection of Respiratory Viruses
Authors: Kim Hyun-Ki , Oh Sung-Hee , Yun Kyung Ah , Sung Heungsup , Kim Mi-Na 
Published: January 2013

ABSTRACT

A novel multiplex real-time PCR approach (Anyplex II RV16 [RV16]; Seegene, South Korea) was compared with a multiplex endpoint PCR kit (Seeplex RV15 ACE detection kit [RV15]; Seegene) and a liquid bead-based assay (xTAG respiratory viral panel [xTAG]; Abbott, United States). Of nasopharyngeal swabs or aspirates and bronchoalveolar lavage fluid samples submitted for RV15 testing, 199 retrospectively collected positive specimens and 283 prospectively collected specimens were further tested with RV16 and xTAG. A true-positive result was defined as a positive result from all three methods or RV16 and xTAG or RV15 and xTAG. For specimens with discrepant results, monoplex PCR and sequencing of the target viruses were performed. In total, 300 virus-positive specimens yielded 386 viruses. When the bocavirus results were excluded, the overall sensitivities of RV16, RV15, and xTAG were 95.2%, 93.3%, and 87.2%, respectively (95% confidence intervals, 93.0 to 97.4%, 90.8 to 95.8%, and 83.8 to 90.6%, respectively). RV16 was more sensitive than xTAG for coronavirus OC43/HKU1 (100% versus 26.1%;
P
< 0.0001) and adenovirus (100% versus 79.5%;
P
< 0.01) but was less sensitive than xTAG for rhinovirus/enterovirus (89.4% versus 97.9%;
P
< 0.05). RV16 demonstrated higher sensitivity than RV15 for the detection of adenovirus (100% versus 82.1%;
P
< 0.05). The specificities of all three methods ranged from 98.6% to 100%. Sequencing analysis of 64 rhinovirus-positive samples revealed that RV16 accurately differentiated between rhinovirus and enterovirus. RV16 most frequently missed rhinovirus C. In conclusion, the overall sensitivity of RV16 was better than that of xTAG. However, improvement of the sensitivity for rhinovirus is required.
A Deceptive Case of Cellulitis Caused by a Gram-Negative Pathogen
Authors: Bhowmick T. , Weinstein M. P. 
Published: January 2013

ABSTRACT

Yokenella regensburgei
is a member of the family
Enterobacteriaceae
that has rarely been implicated in clinical disease. We report here a case of septicemia with a skin and soft tissue source caused by
Y. regensburgei
in an immunocompromised host.
Evaluation of a Microarray-Based Assay for Rapid Identification of Gram-Positive Organisms and Resistance Markers in Positive Blood Cultures
Authors: Samuel Linoj P. , Tibbetts Robert J. , Agotesku Adam , Fey Margaret , Hensley Rhonda , Meier Frederick A. 
Published: January 2013

ABSTRACT

Rapid identification of pathogens directly from positive blood cultures can play a major role in reducing patient mortality rates. We evaluated the performance of the Verigene Gram-Positive Blood Culture (BC-GP) assay (Nanosphere Inc., Northbrook, IL) for detection of commonly isolated Gram-positive organisms as well as associated resistance markers from positive blood cultures. Positive blood cultures (VersaTREK; Trek Diagnostic Systems, Independence, OH) from 203 patients with Gram-positive organism infections were analyzed using the BC-GP assay within 12 h for the detection of 12 different organisms, including staphylococci, streptococci, and enterococci, as well as for the presence of 3 resistance markers (
mecA
,
vanA
, and
vanB
). Results were compared to those of routine laboratory methods for identification and susceptibility testing. For identification of organisms and detection of resistance markers in 178 monomicrobial positive blood cultures, the BC-GP assay showed 94% and 97% concordance, respectively, with routine methods. After 25 polymicrobial cultures were included, the results showed 92% and 96% agreement for identification and resistance markers, respectively, for a total of 203 positive cultures. In 6/25 polymicrobial cultures, at least 1 isolate was not detected. Concordance levels for detection of major pathogens such
Staphylococcus aureus
(
n
= 45) and enterococci (
n
= 19) were 98% and 95%, respectively. Agreement levels for detection of resistance markers such as
mecA
and
vanA
/
B
were 92% and 100%, respectively. The BC-GP assay is capable of providing rapid identification of Gram-positive cocci as well as detection of resistance markers directly from positive blood cultures at least 24 to 48 h earlier than conventional methods.
Prevalence and Characterization of Methicillin-Resistant Staphylococcus aureus Isolates from Retail Meat and Humans in Georgia
Authors: Jackson Charlene R. , Davis Johnnie A. , Barrett John B. 
Published: January 2013

ABSTRACT

There is increasing interest in the presence of
Staphylococcus aureus
, specifically methicillin-resistant
S. aureus
(MRSA), on retail meat products. In this study, staphylococci were isolated from retail pork and retail beef in Georgia, and MRSA from the products was compared to human MRSA from the same geographic area using broth microdilution antimicrobial susceptibility testing, multilocus sequence typing (MLST),
spa
typing, SCC
mec
typing, and pulsed-field gel electrophoresis (PFGE).
S. aureus
was isolated from 45% (45/100) of pork products and 63% (63/100) of beef products;
mecA
was detected in
S. aureus
from both pork (3/100; 3%) and beef (4/100; 4%). Fifty percent (50/100) of human
S. aureus
also contained
mecA
. Multidrug resistance was detected among MRSA from all sources. All MRSA (
n
= 57) was SCC
mec
type IV, and nine different
spa
types were present among the isolates (t002, t008, t012, t024, t179, t337, t548, t681, and t1062). Four sequence types (ST5, ST8, ST9, and ST30) were detected using MLST; the majority of MRSA isolates belonged to ST8, followed by ST5. One retail beef MRSA isolate belonged to ST8, while the remaining three were ST5. In retail pork MRSA, ST5, ST9, and ST30 were observed. The majority of human MRSA isolates belonged to ST8. Thirty-seven MRSA isolates, one of which was a retail beef MRSA isolate, were
pvl
+
. Using PFGE, MLST, and
spa
typing, three retail beef MRSA isolates were found to be identical in PFGE pattern, ST, and
spa
type to two human clonal MRSA isolates (USA100 and USA300). One additional retail beef MRSA isolate had a PFGE pattern similar to that of a human MRSA isolate, whereas none of the retail pork MRSA isolates had PFGE patterns similar to those of human MRSA isolates. These data suggest that the retail beef samples were contaminated by a human source, possibly during processing of the meat, and may present a source of MRSA for consumers and others who handle raw meat.