bluuebunny/crossref_metadata_2025_split huggingface dataset:
lck-Driven Cre Expression Alters T Cell Development in the Thymus and the Frequencies and Functions of Peripheral T Cell Subsets
Authors: Carow Berit , Gao Yu , Coquet Jonathan , Reilly Marie , Rottenberg Martin E. 
Published: August 2016

Abstract
Conditional gene targeting using the bacteriophage-derived Cre recombinase is widely applied for functional gene studies in mice. Mice transgenic for Cre under the control of the lck gene promoter are used to study the role of loxP-targeted genes in T cell development and function. In this article, we show a striking 65% reduction in cellularity, preferential development of γδ versus αβ T cells, and increased expression of IL-7R in the thymus of mice expressing Cre under the proximal lck promoter (lck-cre+ mice). The transition from CD4/CD8 double-negative to double-positive cells was blocked, and lck-cre+ double-positive cells were more prone to apoptosis and showed higher levels of Cre expression. Importantly, numbers of naive T cells were reduced in spleens and lymph nodes of lck-cre+ mice. In contrast, frequencies of γδ T cells, CD44+CD62L− effector T cells, and Foxp3+ regulatory T cells were elevated, as was the frequency of IFN-γ–secreting CD4+ and CD8+ T cells. A literature survey of 332 articles that used lck-cre+ mice for deletion of floxed genes indicated that results are statistically influenced by the control used (lck-cre+ or lck-cre−), more frequently resembling the lck-cre+ phenotype described in this article if lck-cre− controls were used. Altogether, care should be taken when interpreting published results and to properly control targeted gene deletions using the lck-cre+ strain.
NUTRIENTS AND CARBON DIOXIDE IN THE COLUMBIA RIVER1,2
Authors: Park P. Kilho , Catalfomo Magdalena , Webster George R. , Reid Barry H. 
Published: August 2016

During 1966, 1.8 × 1014 liters of water; 8.3 × 107, 2.1 × 109, and 2.7 × 1010 moles of phosphate, nitrate, and reactive silicate; 1.9 × 1011 equivalents of alkalinity; and 1.9 × 1011 moles of total carbon dioxide passed through Clatskanie, 87 km above the mouth of the Columbia River into the Astoria estuary and the Pacific Ocean. Along the main stream, phosphate, nitrate, and silicate concentrations show a definite seasonal change; their maxima occur in winter and minima in summer. On‐stream primary production greatly affects the formation of the summer minima. At Clatskanie, the nitrate: phosphate ratio is 3:1 during summer months and over 19:1 at other seasons.Bicarbonate ion is the major dissolved carbon dioxide species in the entire Columbia River system, where water pH measured at 20C ranges from 6.63 to 8.68. The major portion of the river system is undersaturated with respect to calcite solubility. Along the main stream, the river is supersaturated with respect to the atmospheric carbon dioxide pressure of 320 ppm.
Two sediment trap designs for use in small rivers and streams1
Authors: Welton J. S. , Ladle M. 
Published: August 2016

Two sediment traps designed foruse in riverine gravels to assess rates, size, and gross quantities of sedimenting material and each having a collecting area of 40 cm2 are small, easy to construct and to handle. The results of the two types of traps used in the gravel bed of a recirculating channel are compared and recovery efficiencies are given based on laboratory experiments.
Nuisance phytoplankton blooms in coastal, estuarine, and inland waters1
Authors: Paerl Hans W. 
Published: August 2016

Multiple interacting physical, chemical, and biotic factors, in proper combination, lead to the development and persistence of nuisance algal blooms. Upon examining combinations of environmental conditions most likely to elicit nuisance blooms, commonalities and analog situations become more apparent among coastal marine (dinoflagellate‐dominated), estuarine (dinoflagellate‐ and cyanobacteria‐dominated), and freshwater (cyanobacteria‐dominated) ecosystems. A combination of the following hydrological, chemical, and biotic factors will most likely lead to bloom‐sensitive waters: a horizontally distinct water mass; a vertically stratified water column; warm weather conditions, as typified by dry monsoon tropical climates and summer seasons in temperate zones; high incident photosynthetically active radiation (PAR); enhanced allochthonous organic matter loading (both as DOC and POC); enhanced allochthonous inorganic nutrient loading (nitrogen and/or phosphorus); adequate availability of essential metals, supplied by terrigenous inputs or upwelling; underlying sediments physically and nutritionally suitable as “seed beds” for resting cysts and akinetes; algal‐bacterial synergism, which exhibits positive impacts on phycosphere nutrient cycling; algal‐micrograzer (protists and rotifers) synergism, which also enhances nutrient cycling without consumption of filamentous and colonial nuisance taxa; and selective (for non‐nuisance taxa) activities of macrograzers (crustacean zooplankton, larval fish).Nuisance bloom taxa share numerous additional physiological and ecological characteristics, including limited heterotrophic capabilities, high degrees of motility, and toxicity. Given such a set of commonalities, it would appear useful and timely to identify and address generally applicable criteria for deeming a water body “bloom sensitive” and to incorporate such criteria into the design of water quality management strategies applicable to both coastal marine and freshwater habitats.
Comparative ecology of the macrofauna of freshwater and marine muds1
Authors: Lopez Glenn R. 
Published: August 2016

There are many striking similarities between the benthic macrofauna inhabiting marine and lacustrine sediments. Most of the same trophic/functional groups are well represented in both habitats. There is no obvious difference between the types of particulate food sources available for microphagous animals. Temperate lakes and neritic environments support a similar standing stock of macrofauna, which is a function of similar detrital input to the benthos. There is no characteristic difference in P : B ratios between marine and freshwater macrobenthos. Predation and competition have similar important effects on community structure. Likewise, community succession appears to follow the same pattern.There are certain differences between marine and freshwater macrobenthos, however, that appear to relate to fundamental habitat differences. The major difference is that low salinity and the closed, ephemeral nature of most lakes have resulted in little taxonomic similarity between the two faunas. Tentaculate deposit feeders are found only in marine sediments, and interstitial suspension feeders are common only in freshwater muds. The ability to use dissolved organic matter is well developed only in marine animals, which is a consequence of the osmotic problems faced by freshwater animals. The ability of many limnetic species to survive prolonged anoxia relates to the lack of tidal mixing in lakes.
Accounting for effort when comparing tropical fisheries in lakes, river‐floodplains, and lagoons
Authors: Bayley Peter B. 
Published: August 2016

Data from 59 tropical fisheries which were artisanal and multispecies in character indicated that fishing effort was a major determinant of yield. Effort was defined as number of full‐ and part‐time fishermen.The largest subset, which comprised 31 African lake fisheries, conformed to a function related to the Schaefer model. Data from different lakes were thus treated as samples from a hypothetical multispecies fishery. The model explained 75% of the variance in log(yield). The residuals were correlated (P < 0.05) with log(morphoedaphic index). The effort model and the morphoedaphic index jointly explained 80% of the variance in log(yield). A function to account for the nonlinear effect of fishing effort was proposed for sets of fisheries conforming to the model.Data from river‐floodplain and lagoon fisheries were very similar and were best described by the same effort model. Differences in the model parameters for these fisheries compared to those of lakes suggested differences in effective effort.A “precision improvement index” was proposed to compare the predictive value of models with different predictors and transformations. A comparison of the predictability of yields revealed that, despite variation in socioeconomics, commercialization, and biological productivity between fisheries, this crude effort measurement was more important than indices of productivity for these sets of fisheries.Future progress in predicting and understanding fisheries yields depends on the synchronized collection of variables that relate to the fishery and to biological productivity in numerous comparable systems.
Fine spatial structure of genetically distinct picocyanobacterial populations across environmental gradients in the Costa Rica Dome
Authors: Gutiérrez-Rodríguez Andrés , Slack Gillian , Daniels Emy F. , Selph Karen E. , Palenik Brian , Landry Michael R. 
Published: August 2016

We investigated the spatial variability of picocyanobacterial community structure across the Costa Rica Dome (CRD), an offshore upwelling system characterized by high seasonal abundance of Synechococcus spp. We constructed clone libraries of the rpoC1 gene to survey picocyanobacterial diversity and developed specific real‐time quantitative polymerase chain reaction assays to assess the distribution of genetically distinct Synechococcus (SYN) and Prochlorococcus (PRO) populations across vertical and horizontal physicochemical gradients. Flow cytometry data showed that cell abundances for both SYN and PRO were highest near the dome center. Phylogenetic analysis of rpoC1 sequences revealed a remarkably high and distinctive picocyanobacterial diversity (FLU1‐3, CRD1, Clade II, XV, XVI) that included “novel” SYN and PRO genotypes. Furthermore, genetically different populations exhibited vertical and horizontal spatial partitioning. Abundances of distinct SYN genotypes peaked at subsequent depth horizons, leading to a fine vertical structure with at least three populations stacked within the upper 30–40 m at the dome. Clade II and FLU1A peaked in surface waters, while maximum concentrations of CRD1, FLU1B, and Clade XVI occurred in the upper and lower thermocline, respectively. Horizontally, Clade II abundance in surface waters remained high across the entire region, while SYN genotypes CRD1 and FLU1A increased with shoaling of the thermo‐ and nutricline toward the center of the dome to become the dominant genotypes of the SYN assemblage in the dome. Below the mixed layer, Clade XVI and PRO genotype FLU2, virtually absent outside the dome, became abundant components of the picocyanobacterial assemblage. Despite their phylogenetic relatedness, FLU1A and FLU1B subclades followed different distributional patterns, suggesting ecological significance of the microdiversity within the clade. The unprecedented fine vertical structure demonstrated for SYN genotypes is driven by sharp physicochemical gradients (e.g., density, nutrient, oxygen, and trace metals) created by the dome and the presence of a shallow oxycline that enhances habitat diversification.
A review of marine geomorphometry, the quantitative study of the seafloor
Authors: Lecours Vincent , Dolan Margaret F. J. , Micallef Aaron , Lucieer Vanessa L. 
Published: August 2016

Abstract. Geomorphometry, the science of quantitative terrain characterization, has traditionally focused on the investigation of terrestrial landscapes. However, the dramatic increase in the availability of digital bathymetric data and the increasing ease by which geomorphometry can be investigated using geographic information systems (GISs) and spatial analysis software has prompted interest in employing geomorphometric techniques to investigate the marine environment. Over the last decade or so, a multitude of geomorphometric techniques (e.g. terrain attributes, feature extraction, automated classification) have been applied to characterize seabed terrain from the coastal zone to the deep sea. Geomorphometric techniques are, however, not as varied, nor as extensively applied, in marine as they are in terrestrial environments. This is at least partly due to difficulties associated with capturing, classifying, and validating terrain characteristics underwater. There is, nevertheless, much common ground between terrestrial and marine geomorphometry applications and it is important that, in developing marine geomorphometry, we learn from experiences in terrestrial studies. However, not all terrestrial solutions can be adopted by marine geomorphometric studies since the dynamic, four-dimensional (4-D) nature of the marine environment causes its own issues throughout the geomorphometry workflow. For instance, issues with underwater positioning, variations in sound velocity in the water column affecting acoustic-based mapping, and our inability to directly observe and measure depth and morphological features on the seafloor are all issues specific to the application of geomorphometry in the marine environment. Such issues fuel the need for a dedicated scientific effort in marine geomorphometry.This review aims to highlight the relatively recent growth of marine geomorphometry as a distinct discipline, and offers the first comprehensive overview of marine geomorphometry to date. We address all the five main steps of geomorphometry, from data collection to the application of terrain attributes and features. We focus on how these steps are relevant to marine geomorphometry and also highlight differences and similarities from terrestrial geomorphometry. We conclude with recommendations and reflections on the future of marine geomorphometry. To ensure that geomorphometry is used and developed to its full potential, there is a need to increase awareness of (1) marine geomorphometry amongst scientists already engaged in terrestrial geomorphometry, and of (2) geomorphometry as a science amongst marine scientists with a wide range of backgrounds and experiences.
Enhancement of field-effect mobility in molybdenum-disulfide transistor through the treatment of low-power oxygen plasma
Authors: Chen Kuan-Chao , Wu Chong-Rong , Chang Xiang-Rui , Chang Shu-Wei , Lee Si-Chen , Lin Shih-Yen 
Published: August 2016

Abstract
We experimentally demonstrate that the treatment with low-power oxygen plasma can raise the field-effect mobility in molybdenum-sulfide (MoS2) transistors from 0.01 to 9.6 cm2 V−1 s−1, which is an increment of about three orders of magnitude. The decrease in threshold voltage and the increase in the drain current of the devices indicate that the electron density increases significantly after the mild plasma treatment. The emergence of Mo–O characteristics but the suppression of Mo–S features on the X-ray photoelectron spectrum of the plasma-treated sample suggests that a portion of the MoS2 film becomes conductive molybdenum oxide. This transformation may considerably upgrade the performance of MoS2 transistors.
Visible–infrared achromatic imaging by wavefront coding with wide-angle automobile camera
Authors: Ohta Mitsuhiko , Sakita Koichi , Shimano Takeshi , Sugiyama Takashi , Shibasaki Susumu 
Published: August 2016

Abstract
We perform an experiment of achromatic imaging with wavefront coding (WFC) using a wide-angle automobile lens. Our original annular phase mask for WFC was inserted to the lens, for which the difference between the focal positions at 400 nm and at 950 nm is 0.10 mm. We acquired images of objects using a WFC camera with this lens under the conditions of visible and infrared light. As a result, the effect of the removal of the chromatic aberration of the WFC system was successfully determined. Moreover, we fabricated a demonstration set assuming the use of a night vision camera in an automobile and showed the effect of the WFC system.
A horizon scan of future threats and opportunities for pollinators and pollination
Authors: Brown Mark J.F. , Dicks Lynn V. , Paxton Robert J. , Baldock Katherine C.R. , Barron Andrew B. , Chauzat Marie-Pierre , Freitas Breno M. , Goulson Dave , Jepsen Sarina , Kremen Claire , Li Jilian , Neumann Peter , Pattemore David E. , Potts Simon G. , Schweiger Oliver , Seymour Colleen L. , Stout Jane C. 
Published: August 2016

Background.Pollinators, which provide the agriculturally and ecologically essential service of pollination, are under threat at a global scale. Habitat loss and homogenisation, pesticides, parasites and pathogens, invasive species, and climate change have been identified as past and current threats to pollinators. Actions to mitigate these threats, e.g., agri-environment schemes and pesticide-use moratoriums, exist, but have largely been applied post-hoc. However, future sustainability of pollinators and the service they provide requires anticipation of potential threats and opportunities before they occur, enabling timely implementation of policy and practice to prevent, rather than mitigate, further pollinator declines.Methods.Using a horizon scanning approach we identified issues that are likely to impact pollinators, either positively or negatively, over the coming three decades.Results.Our analysis highlights six high priority, and nine secondary issues. High priorities are: (1) corporate control of global agriculture, (2) novel systemic pesticides, (3) novel RNA viruses, (4) the development of new managed pollinators, (5) more frequent heatwaves and drought under climate change, and (6) the potential positive impact of reduced chemical use on pollinators in non-agricultural settings.Discussion.While current pollinator management approaches are largely driven by mitigating past impacts, we present opportunities for pre-emptive practice, legislation, and policy to sustainably manage pollinators for future generations.
Hepatic Vein Arrival Time for Diagnosis of Liver Cirrhosis
Authors: Abbattista Teresa , Ridolfi Francesco , Consalvo Giovanni Traina , Brunelli Eugenio 
Published: August 2016

ObjectivesTo evaluate the performance of contrast‐enhanced sonography with a second‐generation contrast agent in assessing the severity of chronic diffuse liver disease and differentiating cirrhotic from noncirrhotic liver disease.MethodsContrast‐enhanced sonography was performed after intravenous bolus injection of a second‐generation contrast agent in 14 healthy control participants and 160 consecutive patients with cirrhotic and noncirrhotic liver disease (n = 78 and 82, respectively) enrolled between March 2004 and April 2014. The intensity of enhancement in a main hepatic vein was used to determine hepatic vein arrival time, time to peak intensity, and peak contrast enhancement.ResultsThe hepatic vein arrival time was lower in cirrhotic patients compared with both noncirrhotic patients and controls (mean ± SD, 15.0 ± 2.8, 21.5 ± 3.4, and 25.6 ± 4.7 seconds, respectively; P < .05). The hepatic vein arrival time in noncirrhotic patients was also significantly lower than that in controls (P < .05). The time to peak intensity was significantly lower in cirrhotic patients compared with noncirrhotic patients and controls (40.7 ± 13.7, 49.4 ± 12.8, and 51.2 ± 13.7 seconds; P < .05). A receiver operating characteristic curve analysis revealed that the hepatic vein arrival time more accurately excluded a diagnosis of liver cirrhosis than the time to peak intensity (area under the receiver operating characteristic curve, 0.953 versus 0.694). Specifically, a hepatic vein arrival time cutoff value of 17 seconds excluded liver cirrhosis with 91.1% sensitivity and 93.6% specificity.ConclusionsContrast‐enhanced sonography is a valid alternative method for noninvasive staging of liver diseases. The hepatic vein arrival time could be used to exclude liver cirrhosis in a clinical setting.
Prospective Study Comparing Two Second‐Look Ultrasound Techniques
Authors: Kim Yoonsoo , Kang Bong Joo , Kim Sung Hun , Lee Eun Jae 
Published: August 2016

ObjectivesThe aim of this study was to compare the diagnostic performance of handheld ultrasound (US) and an automated breast volume scanner (ABVS) as second‐look US techniques subsequent to preoperative breast magnetic resonance imaging (MRI).MethodsWe prospectively enrolled patients with breast cancer who underwent handheld US and ABVS examinations as second‐look US modalities for additional suspicious lesions found via preoperative breast MRI. We reviewed each second‐look US modality independently and evaluated the detection rate of each modality. We then analyzed the correlation between the detection rate and the MRI factors (size, distance, and enhancement type).ResultsFrom March to September 2014, both types of second‐look US examinations were performed on 40 patients with breast cancer who had 76 additional suspicious lesions detected via preoperative breast MRI. The detection rate of the ABVS was higher than that of handheld US for the second‐look examination (94.7% versus 86.8%; P< .05). Among the 76 total lesions, 7 were only identified by the ABVS, 1 was only found by handheld US, and 3 were not detected by either the ABVS or handheld US. When we analyzed the correlation between the detection rate and MRI factors, the only meaningful factor was the enhancement type. The ability to detect a nonmass lesion was lower than the ability to detect a mass‐type lesion (P < 0.05) for both the ABVS and handheld US.ConclusionsFor a second‐look US examination subsequent to preoperative breast MRI in patients with breast cancer, the ABVS is a more efficient modality than handheld US for preoperative evaluations. However, both techniques have limitations in detecting nonmass lesions.
Reconstruction of hydrographic changes in the southern Norwegian Sea during the past 135 kyr and the impact of different foraminiferal Mg/Ca cleaning protocols
Authors: Ezat Mohamed M. , Rasmussen Tine L. , Groeneveld Jeroen 
Published: August 2016

AbstractThe shallow subsurface hydrography in the southern Norwegian Sea during the past 135,000 years was investigated using parallel measurements of Mg/Ca and δ18O in shells of the planktic foraminiferal species Neogloboquadrina pachyderma. Two cleaning methods were applied prior to Mg/Ca analysis, “Mg cleaning” and “full cleaning” methods. Different results were obtained, which are most likely due to a more efficient removal of Mn‐contaminant coatings of the shells, when the “full cleaning” procedure was applied. We further combined Mg/Ca and B/Ca from the “full cleaning” method with δ18O values to constrain the calcification temperature and seawater‐δ18O (δ18Osw) in the past. During Heinrich Stadial (HS)1 (∼18.5–15 ka) N. pachyderma constituted >80% of the planktic foraminiferal population, δ18Osw decreased by ∼1.5‰, and shallow subsurface temperature increased by ∼1.5–3°C, suggesting strong stratification in the upper water column and a possible subsurface inflow of Atlantic water below a well‐developed halocline during the calcification seasons of N. pachyderma. Similar decreases in δ18Osw are also recorded for other Heinrich stadials (HS2, 3, 4, 6, and 11). Our temperature estimates confirm previous observations of the delay of the last interglacial “Eemian” warm peak in the eastern Nordic Seas compared to the North Atlantic, and a late warming coinciding with the summer insolation minimum at 60°N. In addition, relatively high values of δ18Osw during the early Eemian suggest a shallow subsurface inflow of Atlantic water below a thin layer of Arctic surface water.