bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Extinction of Birds Drives Rapid Evolutionary Changes in Seed Size
Authors: Galetti Mauro , Guevara Roger , Côrtes Marina C. , Fadini Rodrigo , Von Matter Sandro , Leite Abraão B. , Labecca Fábio , Ribeiro Thiago , Carvalho Carolina S. , Collevatti Rosane G. , Pires Mathias M. , Guimarães Paulo R. , Brancalion Pedro H. , Ribeiro Milton C. , Jordano Pedro 
Published: May 2013

The Birds and the SeedsWhen species are lost from ecosystems through local extinction, the pattern of ecological interactions changes.Galettiet al.(p.1086) show how the loss of large fruit-eating birds from tropical forest fragments in Brazil affects the reduction of seed size in a palm species. A data set was compiled that consisted of >9000 seeds measured in 22 populations over a large area of Atlantic rainforest, including seven areas where large-seed dispersers (toucans, cracids, and large cotingas) were extinct and 15 areas where they are still common.
Echinocandin and Triazole Antifungal Susceptibility Profiles for Clinical Opportunistic Yeast and Mold Isolates Collected from 2010 to 2011: Application of New CLSI Clinical Breakpoints and Epidemiological Cutoff Values for Characterization of Geographic and Temporal Trends of Antifungal Resistance
Authors: Pfaller Michael A. , Messer Shawn A. , Woosley Leah N. , Jones Ronald N. , Castanheira Mariana 
Published: May 2013

ABSTRACT

The SENTRY Antimicrobial Surveillance Program monitors global susceptibility and resistance rates of newer and established antifungal agents. We report the echinocandin and triazole antifungal susceptibility patterns for 3,418 contemporary clinical isolates of yeasts and molds. The isolates were obtained from 98 laboratories in 34 countries during 2010 and 2011. Yeasts not presumptively identified by CHROMagar, the trehalose test, or growth at 42°C and all molds were sequence identified using internal transcribed spacer (ITS) and 28S (yeasts) or ITS, translation elongation factor (TEF), and 28S (molds) genes. Susceptibility testing was performed against 7 antifungals (anidulafungin, caspofungin, micafungin, fluconazole, itraconazole, posaconazole, and voriconazole) using CLSI methods. Rates of resistance to all agents were determined using the new CLSI clinical breakpoints and epidemiological cutoff value criteria, as appropriate. Sequencing of
fks
hot spots was performed for echinocandin non-wild-type (WT) strains. Isolates included 3,107 from 21
Candida
spp., 146 from 9
Aspergillus
spp., 84 from
Cryptococcus neoformans
, 40 from 23 other mold species, and 41 from 9 other yeast species. Among
Candida
spp., resistance to the echinocandins was low (0.0 to 1.7%).
Candida albicans
and
Candida glabrata
that were resistant to anidulafungin, caspofungin, or micafungin were shown to have
fks
mutations. Resistance to fluconazole was low among the isolates of
C. albicans
(0.4%),
Candida tropicalis
(1.3%), and
Candida parapsilosis
(2.1%); however, 8.8% of
C. glabrata
isolates were resistant to fluconazole. Among echinocandin-resistant
C. glabrata
isolates from 2011, 38% were fluconazole resistant. Voriconazole was active against all
Candida
spp. except
C. glabrata
(10.5% non-WT), whereas posaconazole showed decreased activity against
C. albicans
(4.4%) and
Candida krusei
(15.2% non-WT). All agents except for the echinocandins were active against
C. neoformans
, and the triazoles were active against other yeasts (MIC
90
, 2 μg/ml). The echinocandins and triazoles were active against
Aspergillus
spp. (MIC
90
/minimum effective concentration [MEC
90
] range, 0.015 to 2 μg/ml), but the echinocandins were not active against other molds (MEC
90
range, 4 to >16 μg/ml). Overall, echinocandin and triazole resistance rates were low; however, the fluconazole and echinocandin coresistance among
C. glabrata
strains warrants continued close surveillance.
Use of Vitek 2 Antimicrobial Susceptibility Profile To Identify
mecC
in Methicillin-Resistant Staphylococcus aureus
Authors: Cartwright Edward J. P. , Paterson Gavin K. , Raven Kathy E. , Harrison Ewan M. , Gouliouris Theodore , Kearns Angela , Pichon Bruno , Edwards Giles , Skov Robert L. , Larsen Anders R. , Holmes Mark A. , Parkhill Julian , Peacock Sharon J. , Török M. Estée 
Published: May 2013

ABSTRACT

The emergence of
mecC
methicillin-resistant
Staphylococcus aureus
(MRSA) poses a diagnostic challenge for clinical microbiology laboratories. Using the Vitek 2 system, we tested a panel of 896
Staphylococcus aureus
isolates and found that an oxacillin-sensitive/cefoxitin-resistant profile had a sensitivity of 88.7% and a specificity of 99.5% for the identification of
mecC
MRSA isolates. The presence of the
mecC
gene, determined by bacterial whole-genome sequencing, was used as the gold standard. This profile could provide a zero-cost screening method for identification of
mecC
-positive MRSA strains.
Lipid Raft- and Src Family Kinase-Dependent Entry of Coxsackievirus B into Human Placental Trophoblasts
Authors: Delorme-Axford Elizabeth , Sadovsky Yoel , Coyne Carolyn B. 
Published: May 2013

ABSTRACTMaternal-fetal transmission of group B coxsackieviruses (CVB) during pregnancy has been associated with a number of diverse pathological outcomes, including hydrops fetalis, fetal myocarditis, meningoencephalitis, neurodevelopmental delays, congenital skin lesions, miscarriage, and/or stillbirth. Throughout pregnancy, the placenta forms a critical antimicrobial protective barrier at the maternal-fetal interface. Despite the severity of diseases accompanying fetal CVB infections, little is known regarding the strategies used by CVB to gain entry into placental trophoblasts. Here we used both a trophoblast cell line and primary human trophoblasts to demonstrate the mechanism by which CVB gains entry into polarized placental trophoblasts. Our studies revealed that the kinetics of CVB entry into placental trophoblasts are similar to those previously described for polarized intestinal epithelial cells. Likewise, CVB entry into placental trophoblasts requires decay-accelerating factor (DAF) binding and involves relocalization of the virus from the apical surface to intercellular tight junctions. In contrast, we have identified a divergent mechanism for CVB entry into polarized trophoblasts that is clathrin, caveolin-1, and dynamin II independent but requires intact lipid rafts. In addition, we found that members of the Src family of tyrosine kinases were required for CVB entry. Our studies highlight the complexity of viral entry into human placental trophoblasts and may serve as a model for mechanisms used by diverse pathogens to penetrate the placental barrier.
Antibody and Antiretroviral Preexposure Prophylaxis Prevent Cervicovaginal HIV-1 Infection in a Transgenic Mouse Model
Authors: Gruell Henning , Bournazos Stylianos , Ravetch Jeffrey V. , Ploss Alexander , Nussenzweig Michel C. , Pietzsch John 
Published: May 2013

ABSTRACT

The development of an effective vaccine preventing HIV-1 infection remains elusive. Thus, the development of novel approaches capable of preventing HIV-1 transmission is of paramount importance. However, this is partly hindered by the lack of an easily accessible small-animal model to rapidly measure viral entry. Here, we report the generation of a human CD4- and human CCR5-expressing transgenic luciferase reporter mouse that facilitates measurement of peritoneal and genitomucosal HIV-1 pseudovirus entry
in vivo
. We show that antibodies and antiretrovirals mediate preexposure protection in this mouse model and that the serum antibody concentration required for protection from cervicovaginal infection is comparable to that required to protect macaques. Our results suggest that this system represents a model for the preclinical evaluation of prophylactic or vaccine candidates. It further supports the idea that broadly neutralizing antibodies should be evaluated for use as preexposure prophylaxis in clinical trials.
Natural Variation in the Heparan Sulfate Binding Domain of the Eastern Equine Encephalitis Virus E2 Glycoprotein Alters Interactions with Cell Surfaces and Virulence in Mice
Authors: Gardner Christina L. , Choi-Nurvitadhi Jo , Sun Chengqun , Bayer Avraham , Hritz Jozef , Ryman Kate D. , Klimstra William B. 
Published: May 2013

ABSTRACT
Recently, we compared amino acid sequences of the E2 glycoprotein of natural North American eastern equine encephalitis virus (NA-EEEV) isolates and demonstrated that naturally circulating viruses interact with heparan sulfate (HS) and that this interaction contributes to the extreme neurovirulence of EEEV (C. L. Gardner, G. D. Ebel, K. D. Ryman, and W. B. Klimstra, Proc. Natl. Acad. Sci. U. S. A., 108:16026–16031, 2011). In the current study, we have examined the contribution to HS binding of each of three lysine residues in the E2 71-to-77 region that comprise the primary HS binding site of wild-type (WT) NA-EEEV viruses. We also report that the original sequence comparison identified five virus isolates, each with one of three amino acid differences in the E2 71-to-77 region, including mutations in residues critical for HS binding by the WT virus. The natural variant viruses, which possessed either a mutation from lysine to glutamine at E2 71, a mutation from lysine to threonine at E2 71, or a mutation from threonine to lysine at E2 72, exhibited altered interactions with heparan sulfate and cell surfaces and altered virulence in a mouse model of EEEV disease. An electrostatic map of the EEEV E1/E2 heterotrimer based upon the recent Chikungunya virus crystal structure (J. E. Voss, M. C. Vaney, S. Duquerroy, C. Vonrhein, C. Girard-Blanc, E. Crublet, A. Thompson, G. Bricogne, and F. A. Rey, Nature, 468:709–712, 2010) showed the HS binding site to be at the apical surface of E2, with variants affecting the electrochemical nature of the binding site. Together, these results suggest that natural variation in the EEEV HS binding domain may arise during EEEV sylvatic cycles and that this variation may influence receptor interaction and the severity of EEEV disease.
Cytomegalovirus UL91 Is Essential for Transcription of Viral True Late (γ2) Genes
Authors: Omoto Shinya , Mocarski Edward S. 
Published: May 2013

ABSTRACT
Human cytomegalovirus-encoded UL91 is a betagamma gene that is essential for viral replication. Here we show that the 111-amino-acid (aa) UL91 protein controls accumulation of true-late (γ2) viral transcripts. The primate betaherpesvirus conserved N-terminal region from aa 1 to 71 is sufficient to fully reconstitute function. Evaluation of viral DNA, RNA, and antigen revealed that UL91 protein is expressed with leaky-late (γ1) kinetics, localizes in the nucleus without influencing viral DNA synthesis, and must be present from 48 h postinfection to support full expression of late viral transcripts and proteins. In the absence of UL91, viral capsid assembly in the nucleus of infected cells is significantly reduced, and mature, cytoplasmic virions fail to form. Taken together, the evidence shows that UL91 regulates late viral gene expression by a mechanism that is apparently conserved in betaherpesviruses and gammaherpesviruses.
Genetic Characterization of Betacoronavirus Lineage C Viruses in Bats Reveals Marked Sequence Divergence in the Spike Protein of Pipistrellus Bat Coronavirus HKU5 in Japanese Pipistrelle: Implications for the Origin of the Novel Middle East Respiratory Syndrome Coronavirus
Authors: Lau Susanna K. P. , Li Kenneth S. M. , Tsang Alan K. L. , Lam Carol S. F. , Ahmed Shakeel , Chen Honglin , Chan Kwok-Hung , Woo Patrick C. Y. , Yuen Kwok-Yung 
Published: May 2013

ABSTRACT

While the novel Middle East respiratory syndrome coronavirus (MERS-CoV) is closely related to
Tylonycteris
bat CoV HKU4 (Ty-BatCoV HKU4) and
Pipistrellus
bat CoV HKU5 (Pi-BatCoV HKU5) in bats from Hong Kong, and other potential lineage C betacoronaviruses in bats from Africa, Europe, and America, its animal origin remains obscure. To better understand the role of bats in its origin, we examined the molecular epidemiology and evolution of lineage C betacoronaviruses among bats. Ty-BatCoV HKU4 and Pi-BatCoV HKU5 were detected in 29% and 25% of alimentary samples from lesser bamboo bat (
Tylonycteris pachypus
) and Japanese pipistrelle (
Pipistrellus abramus
), respectively. Sequencing of their RNA polymerase (RdRp), spike (S), and nucleocapsid (N) genes revealed that MERS-CoV is more closely related to Pi-BatCoV HKU5 in RdRp (92.1% to 92.3% amino acid [aa] identity) but is more closely related to Ty-BatCoV HKU4 in S (66.8% to 67.4% aa identity) and N (71.9% to 72.3% aa identity). Although both viruses were under purifying selection, the S of Pi-BatCoV HKU5 displayed marked sequence polymorphisms and more positively selected sites than that of Ty-BatCoV HKU4, suggesting that Pi-BatCoV HKU5 may generate variants to occupy new ecological niches along with its host in diverse habitats. Molecular clock analysis showed that they diverged from a common ancestor with MERS-CoV at least several centuries ago. Although MERS-CoV may have diverged from potential lineage C betacoronaviruses in European bats more recently, these bat viruses were unlikely to be the direct ancestor of MERS-CoV. Intensive surveillance for lineage C betaCoVs in
Pipistrellus
and related bats with diverse habitats and other animals in the Middle East may fill the evolutionary gap.
High-Throughput Sequencing Reveals Principles of Adeno-Associated Virus Serotype 2 Integration
Authors: Janovitz Tyler , Klein Isaac A. , Oliveira Thiago , Mukherjee Piali , Nussenzweig Michel C. , Sadelain Michel , Falck-Pedersen Erik 
Published: May 2013

ABSTRACT
Viral integrations are important in human biology, yet genome-wide integration profiles have not been determined for many viruses. Adeno-associated virus (AAV) infects most of the human population and is a prevalent gene therapy vector. AAV integrates into the human genome with preference for a single locus, termed AAVS1. However, the genome-wide integration of AAV has not been defined, and the principles underlying this recombination remain unclear. Using a novel high-throughput approach, integrant capture sequencing, nearly 12 million AAV junctions were recovered from a human cell line, providing five orders of magnitude more data than were previously available. Forty-five percent of integrations occurred near AAVS1, and several thousand novel integration hotspots were identified computationally. Most of these occurred in genes, with dozens of hotspots targeting known oncogenes. Viral replication protein binding sites (RBS) and transcriptional activity were major factors favoring integration. In a first for eukaryotic viruses, the data reveal a unique asymmetric integration profile with distinctive directional orientation of viral genomes. These studies provide a new understanding of AAV integration biology through the use of unbiased high-throughput data acquisition and bioinformatics.
Characterizing durability of mudrocks for slope stability purposes
Authors: Dick Jeffrey C. , Shakoor Abdul 
Published: May 2013

Abstract
The lithologic characteristics and slake durability of mudrocks from 48 natural and human-made slopes were investigated with the objective of developing a classification of mudrock durability for slope stability purposes. Slopes from which samples were taken ranged from long-term stable to highly unstable. Samples included 10 claystones, 17 shales, and 21 mudstones. The durability of mudrocks was classified as high, medium, or low on the basis of relationships between lithologic characteristics, slake durability, and slope conditions, as observed in the field. The three classes of durability were then used to evaluate the likelihood of occurrence of the four commonly recognized types of instability that affect slopes in mudrocks: excessive erosion, slumps, debris flows, and undercutting-induced failures. High-durability mudrocks were found to be susceptible to undercutting only, medium-durability mudrocks to slumps, debris flows, and undercutting-induced failures, and low-durability mudrocks to all four types of slope instability.
Effect of test method and procedure on measurements of residual shear strength of bentonite from the Portuguese Bend landslide
Authors: Watry Stephen M. , Ehlig Perry L. 
Published: May 2013

Abstract
Palos Verdes Peninsula contains large landslides in areas that are otherwise desirable for residential development. The landslides can be developed providing the factor of safety is at least 1.5 or can be raised to 1.5 during development. The greatest uncertainty in the calculated factor of safety is the residual shear strength of bentonite that forms the bases of slides. The use of too high a shear strength inflates the calculated factor of safety and can result in landslide failure after development. Tests by various investigators yield a wide range of residual shear strengths for bentonite samples from Palos Verdes Peninsula. Most residual friction angles (4φr) range between 6° and 14° with one lower value (3.5°) and several higher values reported. Residual cohesions (Cr) range mostly between 0 and 36 kPa (0 to 750 lb/ft2). Data for various bentonite samples from Palos Verdes Peninsula indicate they have similar compositions and Atterberg limits. Calcium montmorillonite is the principal clay mineral; the liquid limit is generally between 80% and 110% with the plasticity index between 40% and 70%. The data suggest that much of the reported variation in residual shear strength is the result of differences in sample preparation, testing methods, and interpretation of results rather than true differences in strength. Bulk samples of bentonite from the base of the Portuguese Bend landslide were remolded and tested by conventional direct shear, long sample direct shear, and ring shear devices to determine the effect of testing method on residual shear strength measurements. The three devices gave similar results—for conventional direct shear, φr = 6.9° and Cr = 33.0 kPa (690 lb/ft2); for long sample shear, tyr = 6.8° and Cr = 23.8 kPa (497 lb/ft2); for ring shear, tyr = 6.7° and Cr = 7.2 kPa (150 lb/ft2). Back calculations indicate the ring shear results most closely simulate the residual strength along the base of the Portuguese Bend landslide. For all those devices, the residual shear envelope is a curve whose slope reaches an asymptote near a confining pressure of 200 kPa (approximately 4,000 lb/ft2). Reported φr angles are commonly too high because samples were not tested at sufficient confining pressure to define the asymptote and a best fit straight line was drawn through the data points.
Evaluation of viscoplastic slope movement based on triaxial tests
Authors: Wong Wylie W.-H. , Ho Carlton L. , Iverson Richard M. , Hovind Cynthia L. 
Published: May 2013

Abstract
Viscoplastic soil parameters are used in a nonlinear viscoplastic constitutive model to predict time-dependent displacement of slow-moving landslides. The viscoplastic material parameters are determined by a novel method that uses a standard triaxial apparatus. This method employs data obtained from consolidated drained triaxial tests and consolidated drained stress-controlled strain-rate tests. The methodology was applied to undisturbed samples from the Minor Creek landslide in the Franciscan Terrane of northern California. Viscoplastic parameters determined from the laboratory tests were combined with boring log data to calculate the landslide’s vertical velocity profile. This profile provided a reasonable match to a measured velocity profile obtained from repetitive inclinometer surveys.
Stability of slopes
Authors: Michalowski Radoslaw L. 
Published: May 2013

Abstract
Traditional analyses of earth slope stability are based on equilibrium considerations of “slices” into which the collapsing soil mass is divided. Such analyses require some static assumptions so that the system of equilibrium equations becomes determinate. It is proposed that the kinematics-based limit analysis be used to calculate the stability (factor of safety or the critical height), rather than using the limit equilibrium technique with arbitrary static assumptions (such as, for instance, inclination of forces between slices). The method described is straightforward, the analysis has a clear mechanical interpretation, and it stands on its own as a means of performing stability analyses for earth slopes. The method proposed, when used with identical failure mechanisms as in traditional slice methods, can be used to assess the static assumptions used in these conventional methods. It can be argued that all solutions using conventional slice methods can be bound by a rigorous upper bound solution and another approximate solution, both presented in this paper. Traditional solutions which fall beyond the range indicated lead to unrealistic consequences when interpreted in view of the collapse mechanism.
A convenient technique for including the influence of the pore pressure on stability of slopes is shown, and results of critical height calculations for homogeneous slopes are presented.
Geology education in the U.S. Army
Authors: Jens John C. , Stevens M. Merrill 
Published: May 2013

Abstract
The U.S. Army trains soldiers in geology under the guise of related topics. Thus, instructional responsibilities are disjointed.
The army considers geologic matters to be the responsibility of Engineer officers. Familiarization of topographic requirements and construction practices, both military and civil, is given in the Engineer Officer Basic Course, with specific concepts included in the Engineer Officer Advanced Course. Officers wanting more depth in topographic matters take the Mapping, Charting, and Geodesy Officers Course that emphasizes terrain analysis.
Enlisted personnel have more direct contact with geology. Construction materials specialists and quarry operations specialists receive instruction in rock identification and properties about quarrying and construction. On the topographic side, Basic Terrain Analysis teaches mineral and rock identification—weathering and soils are the targeted tasks. Sergeants learn more advanced geology concepts within an imagery analysis and interpretation block of classes in the Advanced Terrain Analysis Course.
Warrant officers, normally selected from the enlisted ranks, provide technical expertise in terrain analysis. Although they receive no formal training, the competitive selection process generally chooses those with the most extensive computer knowledge and field experience in terrain analysis. Geology skills per se are not a criterion.
The Topographic Engineering Center provides, when needed, a two-week intensive interdisciplinary imagery analysis and interpretation short course, which is primarily for federal agencies.
Location of sites for airstrips in North Greenland
Authors: Krinsley Daniel B. 
Published: May 2013

Abstract
Engineering geological investigations of North Greenland for the purpose of locating sites suitable for airstrips were conducted by earth scientists of the U.S. Geological Survey, Air Force Cambridge Research Laboratories, and the U.S. Army Corps of Engineers in 1956–1960. Potential sites that were approximately 5,000 ft (1,524 m) long with clear approaches, delineated through photogeologic studies and aerial reconnaissance, received on-site examination of their relief, frost features, drainage, depth to permafrost, soil composition, strength, and other engineering properties. The resulting favorable sites that required only a minimal amount of surface modification were selected for the test landings of heavy aircraft such as the C-124 and C-130. Successful landings were made at Bronlunds Fjord in 1957, at Polaris Promontory in 1959, and at Centrum Lake in 1960.
Soils are strong enough to support heavy aircraft at these tested sites except during the spring thaw in June and July. Permafrost conditions at the North Greenland sites do not impose severe restrictions on minor grading and light construction if the surficial materials on and immediately adjacent to the airstrips are not extensively removed.