bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling the spread and connectivity of waterborne marine pathogens: the case of PaV1 in the Caribbean
Authors: Kough Andrew S. , Paris Claire B. , Behringer Donald C. , Butler Mark J. 
Published: November 2014

AbstractThe PaV1 virus infects spiny lobsters (Panulirus argus) throughout most of the Caribbean, where its prevalence in adult lobsters can reach 17% and where it poses a significant risk of mortality for juveniles. Recent studies indicate that vertical transmission of the virus is unlikely and PaV1 has not been identified in the phyllosoma larval stages. Yet, the pathogen appears subclinically in post-larvae collected near the coast, suggesting that lobster post-larvae may harbour the virus and perhaps have aided in the dispersal of the pathogen. Laboratory and field experiments also confirm the waterborne transmission of the virus to post-larval and early benthic juvenile stages, but its viability in the water column may be limited to a few days. Here, we coupled Lagrangian modelling with a flexible matrix model of waterborne and post-larval-based pathogen dispersal in the Caribbean to investigate how a large area with complex hydrology influences the theoretical spread of disease. Our results indicate that if the virus is waterborne and only viable for a few days, then it is unlikely to impact both the Eastern and Northwestern Caribbean, which are separated by dispersal barriers. However, if PaV1 can be transported between locations by infected post-larvae, then the entire Caribbean becomes linked by pathogen dispersal with higher viral prevalence in the North. We identify possible regions from which pathogens are most likely to spread, and highlight Caribbean locations that function as dispersal “gateways” that could facilitate the rapid spread of pathogens into otherwise isolated areas.
Distribution and habitat preferences of five species of wrasse (Family Labridae) in a Norwegian fjord
Authors: Skiftesvik Anne Berit , Durif Caroline M. F. , Bjelland Reidun M. , Browman Howard I. 
Published: November 2014

AbstractWrasse (Labridae) are used widely as cleaner fish to control sea lice infestation in commercial farming of Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) in Norway. As a result, there is an intense fishery for wrasse along the Norwegian coast. Little is known of the population ecology of wrasse and, therefore, an evaluation of their distribution, demographics, and habitat preferences was required as a baseline from which to assess the impact of the fishery. We analysed experimental catch data from a 3-year survey carried out in 1997–1999 (before the fishery began) during and after the wrasse spawning season in a Norwegian fjord. Corkwing wrasse (Symphodus melops) was always the most abundant species, ranging from 52 to 68% of the catches. Goldsinny (Ctenolabrus rupestris) and rock cook (Centrolabrus exoletus) were the second most abundant species (up to 30%). Ballan (Labrus bergylta) and cuckoo (Labrus mixtus) wrasse represented &lt;2% of the catches. Rock cook was relatively more abundant at more exposed stations, while corkwing wrasse was characteristic of more sheltered stations. Goldsinny and ballan wrasse both occupied mainly intermediate stations in the more protected areas. Smaller fish were found at the most protected areas, while larger fish were found at the more exposed stations. Sex ratio in goldsinny and rock cook varied significantly from year to year. In corkwing, the sex ratio remained the same each year, and females were always in larger proportion (61–66%). Spawning occurred mainly in June for goldsinny, rock cook, and corkwing wrasse. The fact that species composition and/or size distributions vary considerably over very small distances must be considered in monitoring programmes. Erroneous conclusions about shifts in species composition can easily be made simply because sampling gear are set in slightly different areas.
Endometriotic mesenchymal stem cells exhibit a distinct immune phenotype
Authors: Koippallil Gopalakrishnan Nair Aghila Rani , Pandit Hrishikesh , Warty Neeta , Madan Taruna 
Published: November 2014

Abstract
Endometriosis is a significant debilitating gynecological problem affecting women of the reproductive age group and post-menopause. Recent reports suggest a role for endometriotic mesenchymal stem cells (ectopic MSCs) in the pathogenesis of endometriosis. To investigate the plausible mechanisms leading to the pathogenic behavior of ectopic MSCs, we compared the immunomodulatory properties of eutopic (healthy) and ectopic MSCs. We analyzed MSC phenotypes, differentiation potential, differential gene expression for an array of pattern recognition receptors (PRRs) and pro-inflammatory cytokine release along with markers of migration and angiogenesis among eutopic and ectopic MSCs. Further, alterations in immunosuppressive functions of eutopic and ectopic MSCs were examined by co-culturing them with mitogen-activated allogeneic PBMCs. Transcripts of PRRs such as all Toll-like receptors (TLR1–10), except TLR8, collectins (CL-L1, CL-P1 and CL-K1), NOD-1 and NOD-2 receptors and secreted pro-inflammatory cytokines like IL-6, IFN-γ, vascular endothelial growth factor (VEGF), epidermal growth factor and MCP-1 were significantly up-regulated in ectopic MSCs. The anti-inflammatory cytokine transforming growth factor-β showed significant down-regulation, while IL-10 showed a significant increase in ectopic MSCs. Further, ectopic MSCs showed up-regulated expression for markers of migration and angiogenesis such as matrix metalloproteinase-2 (MMP-2), MMP-3 and MMP-9 and VEGF, respectively. We report here that proliferation of PBMCs was less inhibited upon co-culture with ectopic MSCs compared with eutopic MSCs. The findings suggest that ectopic MSCs with increased levels of TLRs, collectins, pro-inflammatory cytokines and markers of migration and angiogenesis exhibit a distinct immune phenotype compared to eutopic MSCs. This distinct phenotype may be responsible for the reduced immunosuppressive property of ectopic MSCs and may be associated with the pathogenesis of endometriosis.
AKARI infrared camera observations of the 3.3 μm PAH feature in Swift/BAT AGNs
Authors: Castro Angel , Miyaji Takamitsu , Shirahata Mai , Ichikawa Kohei , Oyabu Shinki , Clark David M. , Imanishi Masatoshi , Nakagawa Takao , Ueda Yoshihiro 
Published: November 2014

Abstract
We explore the relationships between the 3.3 μm polycyclic aromatic hydrocarbon (PAH) feature and active galactic nucleus (AGN) properties of a sample of 54 hard X-ray selected bright AGNs, including both Seyfert 1 and Seyfert 2 type objects, using the InfraRed Camera (IRC) on board the infrared astronomical satellite AKARI. The sample is selected from the nine-month Swift/BAT survey in the 14–195 keV band and all of them have measured X-ray spectra at E ≲ 10 keV. These X-ray spectra provide measurements of the neutral hydrogen column density (NH) towards the AGNs. We use the 3.3 μm PAH luminosity (L3.3μm) as a proxy for star-formation activity and hard X-ray luminosity (L14–195 keV) as an indicator of the AGN activity. We search for possible differences in star-formation activity between type 1 (unabsorbed) and type 2 (absorbed) AGNs. We have made several statistical analyses taking the upper limits of the PAH lines into account utilizing survival analysis methods. The results of our log (L14–195 keV) versus log  (L3.3 μm) regression show a positive correlation and the slope for the type 1/unobscured AGNs is steeper than that of type 2/obscured AGNs at a 3 σ level. Our analysis also shows that the circumnuclear star formation is more enhanced in type 2/absorbed AGNs than type 1/unabsorbed AGNs for low X-ray luminosity/low Eddington ratio AGNs, while there is no significant dependence of star-formation activities on the AGN type in the high X-ray luminosities/Eddington ratios.
Dwarf nova EZ Lyncis second visit to instability strip
Authors: Pavlenko Elena P. , Kato Taichi , Sosnovskij Aleksei A. , Andreev Maksim V. , Ohshima Tomohito , Sklyanov Aleksander S. , Bikmaev Ilfan F. , Galeev Almaz I. 
Published: November 2014

Abstract
The analysis of 14 periodograms of EZ Lyn for data spaced over 565 d in 2012–2014 (2–3.5 yr after the 2010 outburst) yielded the existence of a stable signal around 100 cycles/day (c/d) and three signals around 310 c/d, 338 c/d, and 368 c/d (the corresponding periods are 864 s, 279 s, 256 s, and 235 s). We interpret them as independent nonradial pulsations of the white dwarf in EZ Lyn, but the possibility that a linear combination of a frequency of 100 c/d and a harmonic of the orbital period might produce a frequency of 368 c/d also cannot be excluded. The signal at 100 c/d was detected as a transient during the first stay in the instability strip. The period at 338 c/d has been a known nonradial pulsation since EZ Lyn entered the instability strip after the 2010 outburst. We detected the signals around 310 c/d and 368 c/d for the first time. We applied the two-dimensional least absolute shrinkage and selection operator (Lasso) analysis for the first time to explore the behavior of these signals on a time scale of hours in nightly runs of observations having a duration of 6–12 hr. The Lasso analysis revealed the simultaneous existence of all three frequencies (310 c/d, 338 c/d, and 368 c/d) on a majority of nights of observations, but with variable amplitudes and variable drifts of frequencies by 2%–6% on a time scale of ∼ 5–7 hr. The largest drift we detected corresponded to 17.5 s in period in ∼ 5 hr.
Patents and Cumulative Innovation: Causal Evidence from the Courts
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Authors: Galasso Alberto , Schankerman Mark 
Published: November 2014

Abstract
Cumulative innovation is central to economic growth. Do patent rights facilitate or impede follow-on innovation? We study the causal effect of removing patent rights by court invalidation on subsequent research related to the focal patent, as measured by later citations. We exploit random allocation of judges at the U.S. Court of Appeals for the Federal Circuit to control for endogeneity of patent invalidation. Patent invalidation leads to a 50% increase in citations to the focal patent, on average, but the impact is heterogeneous and depends on characteristics of the bargaining environment. Patent rights block downstream innovation in computers, electronics, and medical instruments, but not in drugs, chemicals, or mechanical technologies. Moreover, the effect is entirely driven by invalidation of patents owned by large patentees that triggers more follow-on innovation by small firms.
Implementation of Crew Resource Management: A Qualitative Study in 3 Intensive Care Units
Authors: Kemper Peter F. , van Dyck Cathy , Wagner Cordula , de Bruijne Martine 
Published: November 2014

Objectives
Classroom-based crew resource management (CRM) training has been increasingly applied in health care to improve safe patient care. Crew resource management aims to increase participants' understanding of how certain threats can develop as well as provides tools and skills to respond to such threats. Existing literature shows promising but inconclusive results that might be explained by the quality of the implementation. The present research systematically describes the implementation from the perspective of 3 trained intensive care units (ICUs).

Methods
The design of the study was built around 3 stages of implementation: (1) the preparation, (2) the actions after the CRM training, and (3) the plans for the future. To assess all stages in 3 Dutch ICUs, 12 semistructured interviews with implementation leaders were conducted, the End-of-Course Critique questionnaire was administered, and objective measurements consisting of the number and types of plans of action were reported.

Results
The results categorize initiatives that all 3 ICUs successfully launched, including the development of checklists, each using a different implementation strategy. All ICUs have taken several steps to sustain their approach for the foreseeable future. Three similarities between the units were seen at the start of the implementation: (1) acknowledgment of a performance gap in communication, (2) structural time allocated for CRM, and (3) a clear vision on how to implement CRM.

Conclusions
This study shows that CRM requires preparation and implementation, both of which require time and dedication. It is promising to note that all 3 ICUs have developed multiple quality improvement initiatives and aim to continue doing so.
The Arabidopsis Vacuolar Sorting Receptor1 Is Required for Osmotic Stress-Induced Abscisic Acid Biosynthesis
Authors: Wang Zhen-Yu , Gehring Chris , Zhu Jianhua , Li Feng-Min , Zhu Jian-Kang , Xiong Liming 
Published: November 2014

AbstractOsmotic stress activates the biosynthesis of the phytohormone abscisic acid (ABA) through a pathway that is rate limited by the carotenoid cleavage enzyme 9-cis-epoxycarotenoid dioxygenase (NCED). To understand the signal transduction mechanism underlying the activation of ABA biosynthesis, we performed a forward genetic screen to isolate mutants defective in osmotic stress regulation of the NCED3 gene. Here, we identified the Arabidopsis (Arabidopsis thaliana) Vacuolar Sorting Receptor1 (VSR1) as a unique regulator of ABA biosynthesis. The vsr1 mutant not only shows increased sensitivity to osmotic stress, but also is defective in the feedback regulation of ABA biosynthesis by ABA. Further analysis revealed that vacuolar trafficking mediated by VSR1 is required for osmotic stress-responsive ABA biosynthesis and osmotic stress tolerance. Moreover, under osmotic stress conditions, the membrane potential, calcium flux, and vacuolar pH changes in the vsr1 mutant differ from those in the wild type. Given that manipulation of the intracellular pH is sufficient to modulate the expression of ABA biosynthesis genes, including NCED3, and ABA accumulation, we propose that intracellular pH changes caused by osmotic stress may play a signaling role in regulating ABA biosynthesis and that this regulation is dependent on functional VSR1.
ABCG26-Mediated Polyketide Trafficking and Hydroxycinnamoyl Spermidines Contribute to Pollen Wall Exine Formation in Arabidopsis
Authors: Quilichini Teagen D. , Samuels A. Lacey , Douglas Carl J. 
Published: November 2014

Abstract
Pollen grains are encased by a multilayered, multifunctional wall. The sporopollenin and pollen coat constituents of the outer pollen wall (exine) are contributed by surrounding sporophytic tapetal cells. Because the biosynthesis and development of the exine occurs in the innermost cell layers of the anther, direct observations of this process are difficult. The objective of this study was to investigate the transport and assembly of exine components from tapetal cells to microspores in the intact anthers of Arabidopsis thaliana. Intrinsically fluorescent components of developing tapetum and microspores were imaged in intact, live anthers using two-photon microscopy. Mutants of ABCG26, which encodes an ATP binding cassette transporter required for exine formation, accumulated large fluorescent vacuoles in tapetal cells, with corresponding loss of fluorescence on microspores. These vacuolar inclusions were not observed in tapetal cells of double mutants of abcg26 and genes encoding the proposed sporopollenin polyketide biosynthetic metabolon (ACYL COENZYME A SYNTHETASE5, POLYKETIDE SYNTHASE A [PKSA], PKSB, and TETRAKETIDE α-PYRONE REDUCTASE1), providing a genetic link between transport by ABCG26 and polyketide biosynthesis. Genetic analysis also showed that hydroxycinnamoyl spermidines, known components of the pollen coat, were exported from tapeta prior to programmed cell death in the absence of polyketides, raising the possibility that they are incorporated into the exine prior to pollen coat deposition. We propose a model where ABCG26-exported polyketides traffic from tapetal cells to form the sporopollenin backbone, in coordination with the trafficking of additional constituents, prior to tapetum programmed cell death.
BRASSINOSTEROID INSENSITIVE2 Interacts with ABSCISIC ACID INSENSITIVE5 to Mediate the Antagonism of Brassinosteroids to Abscisic Acid during Seed Germination inArabidopsis
Authors: Hu Yanru , Yu Diqiu 
Published: November 2014

AbstractSeed germination and postgerminative growth are regulated by a delicate hormonal balance. Abscisic acid (ABA) represses Arabidopsis thaliana seed germination and postgerminative growth, while brassinosteroids (BRs) antagonize ABA-mediated inhibition and promote these processes. However, the molecular mechanism underlying BR-repressed ABA signaling remains largely unknown. Here, we show that the Glycogen Synthase Kinase 3-like kinase BRASSINOSTEROID INSENSITIVE2 (BIN2), a critical repressor of BR signaling, positively regulates ABA responses during seed germination and postgerminative growth. Mechanistic investigation revealed that BIN2 physically interacts with ABSCISIC ACID INSENSITIVE5 (ABI5), a bZIP transcription factor. Further genetic analysis demonstrated that the ABA-hypersensitive phenotype of BIN2-overexpressing plants requires ABI5. BIN2 was found to phosphorylate and stabilize ABI5 in the presence of ABA, while application of epibrassinolide (the active form of BRs) inhibited the regulation of ABI5 by BIN2. Consistently, the ABA-induced accumulation of ABI5 was affected in BIN2-related mutants. Moreover, mutations of the BIN2 phosphorylation sites on ABI5 made the mutant protein respond to ABA improperly. Additionally, the expression of several ABI5 regulons was positively modulated by BIN2. These results provide evidence that BIN2 phosphorylates and stabilizes ABI5 to mediate ABA response during seed germination, while BRs repress the BIN2-ABI5 cascade to antagonize ABA-mediated inhibition.
Helping Hands for Budding Prospects: ENTH/ANTH/VHS Accessory Proteins in Endocytosis, Vacuolar Transport, and Secretion
Authors: Zouhar Jan , Sauer Michael 
Published: November 2014

Abstract
Coated vesicles provide a major mechanism for the transport of proteins through the endomembrane system of plants. Transport between the endoplasmic reticulum and the Golgi involves vesicles with COPI and COPII coats, whereas clathrin is the predominant coat in endocytosis and post-Golgi trafficking. Sorting of cargo, coat assembly, budding, and fission are all complex and tightly regulated processes that involve many proteins. The mechanisms and responsible factors are largely conserved in eukaryotes, and increasing organismal complexity tends to be associated with a greater numbers of individual family members. Among the key factors is the class of ENTH/ANTH/VHS domain-containing proteins, which link membrane subdomains, clathrin, and other adapter proteins involved in early steps of clathrin coated vesicle formation. More than 30 Arabidopsis thaliana proteins contain this domain, but their generally low sequence conservation has made functional classification difficult. Reports from the last two years have greatly expanded our knowledge of these proteins and suggest that ENTH/ANTH/VHS domain proteins are involved in various instances of clathrin-related endomembrane trafficking in plants. This review aims to summarize these new findings and discuss the broader context of clathrin-dependent plant vesicular transport.
Remodeling American Sentencing: A Ten‐Step Blueprint for Moving Past Mass Incarceration
Authors: Tonry Michael 
Published: November 2014

SummaryWhen and if the will to roll back mass incarceration and to create just, fair, and effective sentencing systems becomes manifest, the way forward is clear.First, three‐strikes, mandatory minimum sentence, and comparable laws should be repealed.Second, any three‐strikes, mandatory minimum sentence, and comparable laws that are not repealed should be substantially narrowed in scope and severity.Third, any three‐strikes, mandatory minimum sentence, and comparable laws that are not repealed should be amended to include provisions authorizing judges to impose some other sentence “in the interest of justice.”Fourth, life‐without‐possibility‐of‐parole laws should be repealed or substantially narrowed.Fifth, truth‐in‐sentencing laws should be repealed.Sixth, criminal codes should be amended to set substantially lower maximum sentences scaled to the seriousness of crimes.Seventh, every state that does not already have one should establish a sentencing commission and promulgate presumptive sentencing guidelines.Eighth, every state that does not already have one should establish a parole board and every state should establish a parole guidelines system.Ninth, every state and the federal government should reduce its combined rate of jail and prison confinement to half its 2014 level by 2020.Tenth, every state should enact legislation making all prisoners serving fixed terms longer than 5 years, or indeterminate terms, eligible for consideration for release at the expiration of 5 years, and making all prisoners 35 years of age or older eligible for consideration for release after serving 3 years.These proposals are evidence‐based and mostly technocratic. Those calling for prison population targets and reducing the lengths of sentences being served may seem bold to some. Relative to the problems they address, they are modest and partial. Decreasing rates of imprisonment by half in the United States, a country with comparatively low crime rates, to a level that will remain 3 to 3.5 times those of other developed Western countries, can hardly be considered overly ambitious.
Barcoding Neotropical birds: assessing the impact of nonmonophyly in a highly diverse group
Authors: Chaves Bárbara R. N. , Chaves Anderson V. , Nascimento Augusto C. A. , Chevitarese Juliana , Vasconcelos Marcelo F. , Santos Fabrício R. 
Published: November 2014

AbstractIn this study, we verified the power of DNA barcodes to discriminate Neotropical birds using Bayesian tree reconstructions of a total of 7404 COI sequences from 1521 species, including 55 Brazilian species with no previous barcode data. We found that 10.4% of species were nonmonophyletic, most likely due to inaccurate taxonomy, incomplete lineage sorting or hybridization. At least 0.5% of the sequences (2.5% of the sampled species) retrieved from GenBank were associated with database errors (poor‐quality sequences, NuMTs, misidentification or unnoticed hybridization). Paraphyletic species (5.8% of the total) can be related to rapid speciation events leading to nonreciprocal monophyly between recently diverged sister species, or to absence of synapomorphies in the small COI region analysed. We also performed two series of genetic distance calculations under the K2P model for intraspecific and interspecific comparisons: the first included all COI sequences, and the second included only monophyletic taxa observed in the Bayesian trees. As expected, the mean and median pairwise distances were smaller for intraspecific than for interspecific comparisons. However, there was no precise ‘barcode gap’, which was shown to be larger in the monophyletic taxon data set than for the data from all species, as expected. Our results indicated that although database errors may explain some of the difficulties in the species discrimination of Neotropical birds, distance‐based barcode assignment may also be compromised because of the high diversity of bird species and more complex speciation events in the Neotropics.