bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurements of total hydroxyl radical reactivity during CABINEX 2009 – Part 1: Field measurements
Authors: Hansen R. F. , Griffith S. M. , Dusanter S. , Rickly P. S. , Stevens P. S. , Bertman S. B. , Carroll M. A. , Erickson M. H. , Flynn J. H. , Grossberg N. , Jobson B. T. , Lefer B. L. , Wallace H. W.
Published: June 2013

Abstract. Total hydroxyl radical (OH) reactivity was measured at the PROPHET (Program for Research on Oxidants: PHotochemistry, Emissions, and Transport) forested field site in northern Michigan during the 2009 Community Atmosphere–Biosphere INteraction EXperiment (CABINEX). OH reactivity measurements were made with a turbulent-flow reactor instrument at three heights from the forest floor above (21 m, 31 m) and below (6 m) the canopy. In addition to total OH reactivity measurements, collocated measurements of Volatile Organic Compounds (VOCs), inorganic species, and ambient temperature were made at the different heights. These ancillary measurements were used to calculate the total OH reactivity, which was then compared to the measured values. Discrepancies between the measured and calculated OH reactivity, on the order of 1–20 s−1, were observed during the daytime above the canopy at the 21 and 31 m heights, as previously reported for this site. In contrast, the measured OH reactivity during the day was in better agreement with the calculated reactivity below the canopy at the 6 m level during the day. These results suggest that emissions of isoprene and monoterpenes and some measured oxidation products from these primary emissions can explain the measured daytime OH reactivity at the 6 m height, while additional unmeasured trace gases, likely oxidation products, are needed to account for the measured OH reactivity at the 21 m and 31 m heights as well as the nighttime OH reactivity for the 6 m height.
Parameterization of vertical chlorophyll a in the Arctic Ocean: impact of the subsurface chlorophyll maximum on regional, seasonal, and annual primary production estimates
Authors: Ardyna M. , Babin M. , Gosselin M. , Devred E. , Bélanger S. , Matsuoka A. , Tremblay J.-É.
Published: June 2013

Abstract. Predicting water-column phytoplankton biomass from near-surface measurements is a common approach in biological oceanography, particularly since the advent of satellite remote sensing of ocean color (OC). In the Arctic Ocean, deep subsurface chlorophyll maxima (SCMs) that significantly contribute to primary production (PP) are often observed. These are neither detected by ocean color sensors nor accounted for in the primary production models applied to the Arctic Ocean. Here, we assemble a large database of pan-Arctic observations (i.e., 5206 stations) and develop an empirical model to estimate vertical chlorophyll a (Chl a) according to (1) the shelf–offshore gradient delimited by the 50 m isobath, (2) seasonal variability along pre-bloom, post-bloom, and winter periods, and (3) regional differences across ten sub-Arctic and Arctic seas. Our detailed analysis of the dataset shows that, for the pre-bloom and winter periods, as well as for high surface Chl a concentration (Chl asurf; 0.7–30 mg m−3) throughout the open water period, the Chl a maximum is mainly located at or near the surface. Deep SCMs occur chiefly during the post-bloom period when Chl asurf is low (0–0.5 mg m−3). By applying our empirical model to annual Chl asurf time series, instead of the conventional method assuming vertically homogenous Chl a, we produce novel pan-Arctic PP estimates and associated uncertainties. Our results show that vertical variations in Chl a have a limited impact on annual depth-integrated PP. Small overestimates found when SCMs are shallow (i.e., pre-bloom, post-bloom > 0.7 mg m−3, and the winter period) somehow compensate for the underestimates found when SCMs are deep (i.e., post-bloom < 0.5 mg m−3). SCMs are, however, important seasonal features with a substantial impact on depth-integrated PP estimates, especially when surface nitrate is exhausted in the Arctic Ocean and where highly stratified and oligotrophic conditions prevail.
Strong stimulation of N2 fixation in oligotrophic Mediterranean Sea: results from dust addition in large in situ mesocosms
Authors: Ridame C. , Guieu C. , L'Helguen S.
Published: June 2013

Abstract. The response of N2 fixation to contrasted (wet and dry) Saharan dust deposition was studied in the framework of the DUNE project "a DUst experiment in a low-Nutrient, low-chlorophyll Ecosystem" during which realistic simulations of dust deposition (10 g m
A total quasi-steady-state formulation of substrate uptake kinetics in complex networks and an example application to microbial litter decomposition
Authors: Tang J. Y. , Riley W. J.
Published: June 2013

Abstract. We demonstrate that substrate uptake kinetics in any consumer-substrate network subject to the total quasi-steady-state assumption can be formulated as an equilibrium chemistry (EC) problem. If the consumer-substrate complexes equilibrate much faster than other metabolic processes, then the relationships between consumers, substrates, and consumer-substrate complexes are in quasi-equilibrium and the change of a given total substrate (free plus consumer-bounded) is determined by the degradation of all its consumer-substrate complexes. In this EC formulation, the corresponding equilibrium reaction constants are the conventional Michaelis–Menten (MM) substrate affinity constants. When all of the elements in a given network are either consumer or substrate (but not both), we derived a first-order accurate EC approximation (ECA). The ECA kinetics is compatible with almost every existing extension of MM kinetics. In particular, for microbial organic matter decomposition modeling, ECA kinetics explicitly predicts a specific microbe's uptake for a specific substrate as a function of the microbe's affinity for the substrate, other microbes' affinity for the substrate, and the shielding effect on substrate uptake by environmental factors, such as mineral surface adsorption. By taking the EC solution as a reference, we evaluated MM and ECA kinetics for their abilities to represent several differently configured enzyme-substrate reaction networks. In applying the ECA and MM kinetics to microbial models of different complexities, we found (i) both the ECA and MM kinetics accurately reproduced the EC solution when multiple microbes are competing for a single substrate; (ii) ECA outperformed MM kinetics in reproducing the EC solution when a single microbe is feeding on multiple substrates; (iii) the MM kinetics failed, while the ECA kinetics succeeded, in reproducing the EC solution when multiple consumers (i.e., microbes and mineral surfaces) were competing for multiple substrates. We then applied the EC and ECA kinetics to a guild based C-only microbial litter decomposition model and found that both approaches successfully simulated the commonly observed (i) two-phase temporal evolution of the decomposition dynamics; (ii) final asymptotic convergence of the lignocellulose index to a constant that depends on initial litter chemistry and microbial community structure; and (iii) microbial biomass proportion of total organic biomass (litter plus microbes). In contrast, the MM kinetics failed to realistically predict these metrics. We therefore conclude that the ECA kinetics is more robust than the MM kinetics in representing complex microbial, C substrate, and mineral surface interactions. Finally, we discuss how these concepts can be applied to other consumer-substrate networks.
Modeling dissolved organic carbon in temperate forest soils: TRIPLEX-DOC model development and validation
Authors: Wu H. , Peng C. , Moore T. R. , Hua D. , Li C. , Zhu Q. , Peichl M. , Arain M. A. , Guo Z.
Published: June 2013

Abstract. Even though dissolved organic carbon (DOC) is the most active carbon (C) cycling that takes place in soil organic carbon (SOC) pools, it is missing from the global C budget. Fluxes in DOC are critical to aquatic ecosystem inputs and contribute to C balances of terrestrial ecosystems. Only a few ecosystem models have attempted to integrate DOC dynamics into terrestrial C cycling. This study introduces a new process-based model, TRIPLEX-DOC that is capable of estimating DOC dynamics in forest soils by incorporating both ecological drivers and biogeochemical processes. TRIPLEX-DOC was developed from Forest-DNDC, a biogeochemical model simulating C and nitrogen (N) dynamics, coupled with a new DOC process module that predicts metabolic transformations, sorption/desorption, and DOC leaching in forest soils. The model was validated against field observations of DOC concentrations and fluxes at white pine forest stands located in southern Ontario, Canada. The model was able to simulate seasonal dynamics of DOC concentrations and the magnitudes observed within different soil layers, as well as DOC leaching in the age-sequence of these forests. Additionally, TRIPLEX-DOC estimated the effect of forest harvesting on DOC leaching, with a significant increase following harvesting, illustrating that change in land use is of critical importance in regulating DOC leaching in temperate forests as an important source of C input to aquatic ecosystems.
A coupled two-dimensional hydrodynamic and terrestrial input model to simulate CO2 diffusive emissions from lake systems
Authors: Wu H. , Peng C. , Lucotte M. , Soumis N. , Gélinas Y. , Duchemin É. , Plouhinec J.-B. , Ouellet A. , Guo Z.
Published: June 2013

Abstract. Most lakes worldwide are supersaturated with carbon dioxide (CO2) and consequently act as atmospheric net sources. Since CO2 is a major greenhouse gas (GHG), the accurate estimation of CO2 exchanges at air/water interfaces of aquatic ecosystems is vital in quantifying the carbon budget of aquatic ecosystems overall. To date, lacustrine CO2 emissions are poorly understood, and lake carbon source proportions remain controversial, largely due to a lack of integration between aquatic and terrestrial ecosystems. In this paper a new process-based model (TRIPLEX-Aquatic) is introduced incorporating both terrestrial inputs and aquatic biogeochemical processes to estimate diffusive emissions of CO2 from lake systems. The model was built from a two-dimensional hydrological and water quality model coupled with a new lacustrine CO2 diffusive flux model. For calibration and validation purposes, two years of data collected in the field from two small boreal oligotrophic lakes located in Québec (Canada) were used to parameterize and test the model by comparing simulations with observations for both hydrodynamic and carbon process accuracy. Model simulations were accordant with field measurements in both calibration and verification. Consequently, the TRIPLEX-Aquatic model was used to estimate the annual mean CO2 diffusive flux and predict terrestrial dissolved organic carbon (DOC) impacts on the CO2 budget for both lakes. Results show a significant fraction of the CO2 diffusive flux (~30–45%) from lakes was primarily attributable to the input and mineralization of terrestrial DOC, which indicated terrestrial organic matter was the key player in the diffusive flux of CO2 from oligotropical lake systems in Québec, Canada.
Estimating root zone soil moisture using near-surface observations from SMOS
Authors: Ford T. W. , Harris E. , Quiring S. M.
Published: June 2013

Abstract. Satellite-derived soil moisture provides more spatially and temporally extensive data than in situ observations. However, satellites can only measure water in the top few centimeters of the soil. Therefore estimates of root zone soil moisture must be inferred from near-surface soil moisture retrievals. The accuracy of this inference is contingent on the relationship between soil moisture in the near-surface and at greater depths. This study uses cross correlation analysis to quantify the association between near-surface and root zone soil moisture using in situ data from the United States Great Plains. Our analysis demonstrates that there is generally a strong relationship between near-surface (5 to 10 cm) and root zone (25 to 60 cm) soil moisture. An exponential decay filter is applied to estimate root zone soil moisture from near-surface observations. Reasonably skillful predictions of root zone soil moisture can be made using near-surface observations. The same method is then applied to evaluate whether soil moisture derived from the Soil Moisture and Ocean Salinity (SMOS) satellite can be used to accurately estimate root zone soil moisture. We conclude that the exponential filter method is a useful approach for accurately predicting root zone soil moisture from SMOS surface retrievals.
Tephra hazard assessment at Mt. Etna (Italy)
Authors: Scollo S. , Coltelli M. , Bonadonna C. , Del Carlo P.
Published: June 2013

Abstract. In this paper we present a probabilistic hazard assessment for tephra fallout at Mt. Etna (Italy) associated with both short- and long-lived eruptions. We analyzed wind data from the atmospheric soundings of the Italian Air Force at Trapani Birgi (western Sicily), and use the TEPHRA advection-diffusion-sedimentation model to capture the variation of wind speed and direction with time. Two different typologies of eruptions were considered in our analysis: eruptions forming strong short-lived plumes (SSL eruptions) and eruptions forming weak long-lived plumes (WLL eruptions). One Eruption Scenario (OES) for both typologies and the Eruption Range Scenario (ERS) for WLL eruptions were identified based on well documented past activity of Etna since the '90. First, model calibration was carried out for two well-known Etna explosive eruptions: the 22 July 1998 and July 2001 Etna eruptions. Second, probabilistic maps were compiled. Results clearly show that the eastern flanks are significantly affected by tephra deposition and that the WLL eruptions and the Plinian eruption of 122 BC represent the largest threat for both infrastructures and agriculture.
Assessment of tsunami hazard for the American Pacific coast from southern Mexico to northern Peru
Authors: Brizuela B. , Armigliato A. , Tinti S.
Published: June 2013

Abstract. Central America has been struck by at least 49 tsunamis between 1539 and 1996. As many as 37 of these events occurred at the Pacific Coast, and 31 were generated by earthquakes. Some of the events have been destructive, but despite this, tsunamis are an underrated hazard in Central America: people are not aware that they are at risk and even recent tsunami events have been forgotten. Recent studies, following the destructive tsunami occurred in Nicaragua in 1992, have revealed that Central America is a moderately tsunamigenic zone that is mainly affected by tsunamis triggered by earthquakes, especially at the Pacific coast where the Middle American Trench runs parallel to the coast. In this study, a statistical first and then a deterministic analysis for the Pacific coast of Central America has been carried out. The statistical approach aims to estimate the Gutenberg-Richter coefficients of the main seismic tsunamigenic regions of the area in order to assess the annual rate of occurrence of tsunamigenic earthquakes and their corresponding return period. A deterministic approach is then used to compute the tsunami run-up distribution along the coast corresponding to a given annual rate of occurrence of tsunamigenic earthquakes.
High sensitivity of tidewater outlet glacier dynamics to shape
Authors: Enderlin E. M. , Howat I. M. , Vieli A.
Published: June 2013

Abstract. Variability in tidewater outlet glacier behavior under similar external forcing has been attributed to differences in outlet shape (i.e., bed elevation and width), but this dependence has not been investigated in detail. Here we use a numerical ice flow model to show that the dynamics of tidewater outlet glaciers under external forcing are highly sensitive to width and bed topography. Our sensitivity tests indicate that for glaciers with similar discharge, the trunks of wider glaciers and those grounded over deeper basal depressions tend to be closer to flotation, so that less dynamically induced thinning results in rapid, unstable retreat following a perturbation. The lag time between the onset of the perturbation and unstable retreat varies with outlet shape, which may help explain intra-regional variability in tidewater outlet glacier behavior. Further, because the perturbation response is dependent on the thickness relative to flotation, varying the bed topography within the range of observational uncertainty can result in either stable or unstable retreat due to the same perturbation. Thus, extreme care must be taken when interpreting the future behavior of actual glacier systems using numerical ice flow models that are not accompanied by comprehensive sensitivity analyses.
Sovereigns as Trustees of Humanity: On the Accountability of States to Foreign Stakeholders
Authors: Benvenisti Eyal
Published: June 2013

We live in a shrinking world where interdependence between countries and communities is increasing. These changes also affect—as they should—the concept of sovereignty. In past decades the predominant conception of sovereignty was akin to owning a large estate separated from other properties by rivers or deserts. By contrast, today’s reality is more analogous to owning a small apartment in one densely packed high-rise that is home to two hundred separate families. The sense of interdependency is heightened when we recognize the absence of any alternative to this shared home, of any exit from this global high-rise. The privilege of bygone days of opting out, of retreating into splendid isolation, of adopting mercantilist policies or erecting iron curtains is no longer realistically available.
No Thank You to a Radical Rewrite of the Jus ad Bellum
Authors: Rona Gabor , Wala Raha
Published: June 2013

Just as a newspaper must separate its reporting from its editorials, legal
scholarship must distinguish between representations of what the law is and what
the author might like it to be. Daniel Bethlehem’s proposed principles and his
arguments in support of them are an amalgam of the two that, if actualized under
international law, would reverse more than a century of humanitarian and human
rights progress: they would undermine the general prohibition against the use of
force in international relations as well as the right to life and the scope of a
state’s obligation of due process in the deprivation of life.
“You Turn Me into Nothing”: Reformation of Queenship on the Jacobean Stage
Authors: Moore Gaywyn
Published: June 2013

Henry VIII's divorce of Katherine of Aragon and execution of Anne Boleyn mark the beginning of the English Reformation and a substantial alteration of the queen consort role. Early modern plays that feature Henry VIII's queens, such as Samuel Rowley's When You See Me, You Know Me and William Shakespeare and John Fletcher's King Henry VIII, focus on the transition from a medieval to an early modern notion of queenship and represent the dismantled position of the queen consort in early sixteenth-century England. They also highlight the unstable and reduced position that future English queens would inherit.
The Possibility of Justice: Bárbara Colio's Antigone in Usted está aquí
Authors: Vargas Margarita
Published: June 2013

In her play, Usted está aquí (You Are Here, 2009) Bárbara Colio creates an Antigone-type character to address questions of justice and social responsibility. The play is based on the story of Isabel Miranda de Wallace, who relentlessly sought justice for her son, Hugo Alberto Wallace Miranda, who was kidnapped and killed in Mexico City in 2005. The return to antiquity draws attention to the perennial existence of power struggles and violence, but the references to a twenty-first-century Mexican reality and the use of metatheatrical devices reveal Colio's conviction that through activism justice can be achieved.
EXACT SIMULATION OF A BOOLEAN MODEL
Authors: Lantuéjoul Christian
Published: June 2013

A Boolean model is a union of independent objects (compact random subsets) located at Poisson points. Two algorithms are proposed for simulating a Boolean model in a bounded domain. The first one applies only to stationary models. It generates the objects prior to their Poisson locations. Two examples illustrate its applicability. The second algorithm applies to stationary and non-stationary models. It generates the Poisson points prior to the objects. Its practical difficulties of implementation are discussed. Both algorithms are based on importance sampling techniques, and the generated objects are weighted.
3D RECONSTRUCTION AND ANALYSIS OF THE FRAGMENTED GRAINS IN A COMPOSITE MATERIAL
Authors: Gillibert Luc , Jeulin Dominique
Published: June 2013

X-ray microtomography from solid propellant allows studying the microstructure of fragmented grains in damaged samples. A new reconstruction algorithm of fragmented grains for 3D images is introduced. Based on a watershed transform of a morphological closing of the input image, the algorithm can be used  with different sets of markers. Two of them are compared. After the grain reconstruction, a multiscale segmentation  algorithm is used to extract each fragment of the damaged grains. This allows an original quantitative study of the  fragmentation of each grain in 3D. Experimental results on X-ray microtomographic images of a solid propellant fragmented under compression are presented and validated.
CHARACTERIZATION OF THE FORMATION OF FILTER PAPER USING THE BARTLETT SPECTRUM OF THE FIBER STRUCTURE
Authors: Lehmann Martin , Eisengräber-Pabst Jobst , Ohser Joachim , Moghiseh Ali
Published: June 2013

The formation index of filter paper is one of the most important characteristics used in industrial quality control. Its estimation is often based on subjective comparison chart rating or, even more objective, on the power spectrum of the paper structure observed on a transmission light table. It is shown that paper formation can be modeled as Gaussian random fields with a well defined class of correlation functions, and a formation index can be derived from the density of the Bartlett spectrum estimated from image data. More precisely, the formation index is the mean of the Bessel transform of the correlation taken for wave lengths between 2 and 5 mm.
AUTOMATIC OBJECT DETECTION AND SEGMENTATION OF THE HISTOCYTOLOGY IMAGES USING RESHAPABLE AGENTS
Authors: Alilou Mehdi , Kovalev Vassili
Published: June 2013

The aim of this study is to suggest a method for automatic detection and segmentation of the target objects in the microscopic histology/cytology images. The detection is carried out by rectangular shapes then segmentation process starts utilizing flexible agents which are able to move and change their shapes according to a cost function. The agents are rectangular at the beginning then they gradually fit to the corresponding objects using a stochastic reshaping algorithm. The iterative reshaping process is controlled by a cost function and it is resulted in a finer segmentation of the target objects. The cost functional of the proposed method comprised of three terms including the prior shape, regional texture and gradient information. The experiments were carried out using a publicly available microscopy image dataset which contains 510 manually-labeled target cells. The segmentation performance of the proposed method is compared with another state of the art segmentation method. The results demonstrate satisfactory detection and segmentation performance of the proposed method.
Extranodal Rosai-Dorfman Disease Associated With Increased Numbers of Immunoglobulin G4 Plasma Cells Involving the Colon: Case Report With Literature Review
Authors: Wimmer Daniel B. , Ro Jae Y. , Lewis Annisa , Schwartz Mary R. , Caplan Richard , Schwarz Peter , Ayala Alberto G.
Published: June 2013

A 49-year-old woman presented with fever, weight loss, night sweats, hematochezia, and acid reflux symptoms. Two large, firm cecal lesions were seen at colonoscopy, but multiple biopsies were inconclusive. The patient underwent a right hemicolectomy for a clinical diagnosis of colon cancer. Noncaseating granulomatous inflammation with background lymphocytes, plasma cells, and histiocytes exhibiting emperipolesis were identified. With these histologic features and immunoreactivity for S-100 protein and CD68, a diagnosis of Rosai-Dorfman disease was rendered. Other areas had storiform fibrosis admixed with numerous immunoglobulin G4 (IgG4)–positive plasma cells. Although a few preliminary reports have noted an increased number of IgG4-positive plasma cells in Rosai-Dorfman disease, the relationship between these 2 conditions is unclear. To our knowledge, this is the first case report of a possible association of colonic Rosai-Dorfman disease with an increased number of IgG4-positive plasma cells. Reviews of colonic Rosai-Dorfman disease and IgG4-related sclerosis are presented to heighten awareness of this rare presentation.
Comparison Between 1-Needle Technique Versus 2-Needle Technique for Bone Marrow Aspiration and Biopsy Procedures
Authors: Al-Ibraheemi Alyaa , Pham Tiffany , Chen Lei , Syklawer Erica , Quesada Andres , Wahed Amer , Nedelcu Elena , Nguyen Andy N. D.
Published: June 2013

Context.—Bone marrow examination is essential for diagnosis and staging of hematologic disorders. Traditionally, the bone marrow biopsy and aspirate are obtained with 2 needles at 2 separate sites. This approach is associated with significant discomfort, procedural time, and occasionally, morbidity. Although previous observations had suggested that a single-needle technique at one site is a simpler and less-painful procedure, there had been concern that the 1-needle technique may yield a suboptimal biopsy for diagnosis.

Objective.—To conduct a systematic comparison of multiple parameters of bone marrow biopsy specimens obtained by the traditional 2-needle technique versus the 1-needle technique for bone marrow collection.

Design.—We retrospectively evaluated 20 biopsy specimens obtained by each of the 2 mentioned techniques by comparing the morphologic quality of the biopsy, biopsy length, and biopsy cellularity.

Results.—We found that the 1-needle technique yielded an adequate biopsy for diagnosis. The measured parameters of the samples obtained by the 1-needle versus 2-needle techniques were similar.

Conclusion.—This study suggests that the 1-needle technique may be preferred for bone marrow aspirate and biopsy.
Prevalence of Terminal Duct Lobular Units and Frequency of Neoplastic Involvement of the Nipple in Mastectomy
Authors: Kryvenko Oleksandr N. , Yoon Ji Yoon , Chitale Dhananjay A. , Lee Min W.
Published: June 2013

Context.—Breast cancer treatment has greatly evolved from radical mastectomy to more cosmetically acceptable and less-debilitating surgeries. Nipple-sparing mastectomy is increasingly done for both cancer treatment and risk reduction. The frequency of terminal duct lobular units (TDLUs) and occult neoplastic epithelial proliferation in grossly/clinically unremarkable nipples (GUNs) is not well investigated.

Objective.—To describe frequency of TDLUs and occult and overt neoplastic nipple involvement.

Design.—Nipples from 105 consecutive specimens (90 therapeutic, 15 prophylactic) were studied. Sixty-five nipples were entirely submitted to evaluate frequency of TDLUs; the rest had 1 vertical section submitted.

Results.—Terminal duct lobular unit was seen in 17 GUNs (26%). Six had TDLU in the base, 6 had it in the papilla, and 5 in both. Four GUNs showed lobular carcinoma in situ (1), Paget disease (1), and pagetoid extension of underlying malignancy (2). Grossly/clinically abnormal nipples had Paget disease (2), lymphovascular invasion (2), invasive carcinoma (4), and pagetoid extension (5). Involved nipples were closer to tumor (mean, 1.1 versus 3.2 cm, P < .001), had larger underlying tumors (mean, 4.3 versus 2.6 cm, P = .03) and of higher grade (P = .04), and more often had lymph node metastases (91% versus 44%, P = .007). No pathologic abnormalities were found in prophylactic mastectomy nipples.

Conclusions.—Terminal duct lobular units were seen in 26% of nipples. They were frequently seen in the nipple papilla. Occult neoplastic epithelial proliferation was seen in 5% of grossly/clinically unremarkable therapeutic mastectomy nipples. Pagetoid extension was the dominant spread of underlying malignancy. Overall, the nipple was more often involved by larger and higher-grade tumors located closer to the nipple. All prophylactic mastectomies had unremarkable nipples. These findings should be considered while selecting patients for nipple-sparing mastectomy.
Direct Thrombin Inhibitors and Factor Xa Inhibitors Can Influence the Diluted Prothrombin Time Used as the Initial Screen for Lupus Anticoagulant
Authors: Olah Zsolt , Szarvas Mariann , Bereczky Zsuzsanna , Kerenyi Adrienne , Kappelmayer Janos , Boda Zoltan
Published: June 2013

Context.—Lupus anticoagulant (LA) is a heterogeneous group of antiphospholipid antibodies. Among others, diluted prothrombin time (dPT) is a sensitive screening test for LA; however, the interpretation of LA tests is difficult in patients treated with anticoagulants. The effect of different types of anticoagulants on the result of LA tests, particularly on dPT, has not been studied extensively.

Objective.—To determine whether the direct thrombin inhibitors lepirudin and argatroban and the predominantly factor Xa inhibitors enoxaparin, danaparoid, and fondaparinux could interfere with LA screening based on dPT.

Design.—Each drug was added to normal and LA-positive plasmas in clinically relevant concentrations. Each sample was tested for dPT. Samples with factor Xa inhibitors were investigated before and after addition of heparinase. Mixing and confirmatory tests for LA were not performed.

Results.—In the presence of lepirudin or argatroban, dPT increased notably and the dPT ratio exceeded the cutoff value even at subtherapeutic concentrations resulting in false positivity. With increasing factor Xa inhibitor concentrations, a linear increase of dPT ratios and false-positive results were also demonstrated. Although heparinase could almost completely neutralize the anti-Xa effect of all investigated factor Xa inhibitors, dPT ratio returned to the basal level only in case of enoxaparin.

Conclusions.—Here we provide evidence that both the direct thrombin and indirect factor Xa inhibitors influence dPT assay for LA, causing false positivity. This should be considered when interpreting LA results during anticoagulant therapy. However, dPT seems to be a reliable test for LA screening under enoxaparin therapy after neutralization by heparinase.
Prevalence and Types of Misrepresentation of Publication Record by Pathology Residency Applicants
Authors: Kaley Jennifer Raible , Bornhorst Joshua , Wiggins Michael , Yared Marwan
Published: June 2013

Context.—Publication misrepresentation among residency applicants has been demonstrated in various specialties. This study examines the prevalence of publication misrepresentation among US-trained and non–US-trained pathology residency applicants.

Objective.—To determine the prevalence of publication misrepresentation in the pathology applicant pool at our institution, to compare the rates of misrepresentation among US-trained and non–US-trained applicants, and to compare results to published results from other medical specialties.

Design.—All peer-reviewed journal articles reported on applications to our program in 2010 and 2011 were examined for veracity. Applications from current or past trainees and applications with unverifiable manuscripts were excluded. The type of misrepresentation and the country in which the applicant trained were recorded.

Results.—Seven hundred applications were reviewed. Of 319 (46%) reported publications, 25 were from US graduates (8%) and 294 (92%) were from non-US graduates. Eighty-six applications were excluded owing to unverifiable manuscripts. Publication misrepresentations were found in 42 (18%) of the remaining 233 applications. The most common misrepresentations were omission of authors (69%), nonauthorship (14%), and self-promotion on the author list (12%). A significantly higher percentage of foreign medical graduates listed publications (P < .001). The misrepresentation rate by foreign graduates (19%) did not differ significantly from that of US-trained graduates (13%) (P = .45).

Conclusions.—Publication misrepresentation was present among pathology residency applicants. Similar rates were seen among US and non-US applicants. Percentages of misrepresentation among applicants to our pathology program and applicants to other medical specialties (18% and 17%, respectively) were comparable.
A Multiplex Technology Platform for the Rapid Analysis of Clinically Actionable Genetic Alterations and Validation for BRAF p.V600E Detection in 1549 Cytologic and Histologic Specimens
Authors: Smith David L. , Lamy Aude , Beaudenon-Huibregtse Sylvie , Sesboüé Richard , Laosinchai-Wolf Walairat , Sabourin Jean-Christophe , Labourier Emmanuel
Published: June 2013

Context.—Current clinicopathologic assessment of malignant neoplastic diseases entails the analysis of specific genetic alterations that provide diagnostic, prognostic, or therapy-determining information.

Objective.—To develop and validate a robust molecular method to detect clinically relevant mutations in various tissue types and anatomic pathology specimens.

Design.—Genes of interest were amplified by multiplex polymerase chain reaction and sequence variants identified by liquid bead array cytometry. The BRAF assay was fully characterized by using plasmids and genomic DNA extracted from cell lines, metastatic colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissues, and thyroid nodule fine-needle aspirates.

Results.—Qualitative multiplex assays for 22 different mutations in the BRAF, HRAS, KRAS, NRAS, or EGFR genes were established. The high signal-to-noise ratio of the technology enabled reproducible detection of BRAF c.1799T>A (p.V600E) at 0.5% mutant allele in 20 ng of genomic DNA. Precision studies with multiple operators and instruments showed very high repeatability and reproducibility with 100% (98.7%–100%) qualitative agreement among 292 individual measures in 38 runs. Evaluation of 1549 representative pathologic specimens in 2 laboratories relative to independent reference methods resulted in 99.0% (97.6%–99.6%) agreement for colorectal FFPE tissues (n = 416) and 98.9% (98.2%–99.4%) for thyroid fine-needle aspiration specimens (n = 1133) with an overall diagnostic odds ratio of 10 856 (2451–48 078).

Conclusions.—The multiplex assay system is a sensitive and reliable method to detect BRAF c.1799T>A mutation in colorectal and thyroid lesions. This optimized technology platform is suitable for the rapid analysis of clinically actionable genetic alterations in cytologic and histologic specimens.
Characterization of MgO Thin Films Grown on Carbon Materials by Molecular Beam Epitaxy
Authors: Kobayashi Satoshi , Miwa Shinji , Bonell Frédéric , Yoshikuni Shota , Seki Takeshi , Shiraishi Masashi , Shinjo Teruya , Mizuochi Norikazu , Suzuki Yoshishige
Published: June 2013

MgO thin films were grown on highly oriented pyrolytic graphite (HOPG) and (001)-oriented diamond substrates by molecular beam epitaxy. The crystal structure of MgO was characterized by reflection high-energy electron diffraction and X-ray diffraction. We found that the MgO grew as (001)- and (111)-oriented textured structures on the HOPG and diamond substrates, respectively. The MgO(001) showed a smaller misalignment of the crystal orientation on the HOPG than on amorphous CoFeB, which indicates that the MgO(001) on graphene can be useful as a tunnel barrier for efficient spin injection into semiconductors.
Scanning Transmission Electron Microscopy and Thermoelectric Properties of Sr-Doped Misfit Cobalt Oxide
Authors: Morimura Takao , Sato Yukio , Ikuhara Yuichi , Yamaguchi Takahiro , Hasaka Masayuki
Published: June 2013

In order to clarify the role of Sr doping in the themoelectric properties of Ca3Co4O9, Ca3-x
Sr
x
Co4O9 samples were fabricated by uniaxial compression molding and sintering in atmosphere. Their thermoelectric properties and atomic-scale structures were investigated. For x<0.3, the dimensionless figure of merit (Z
T) increases with x through a decrease in the thermal conductivity κ despite the nearly constant Seebeck coefficient α and electrical resistivity ρ. Scanning transmission electron microscopy images and energy-dispersive X-ray spectroscopy maps have revealed that Sr mainly substitutes in the Ca site in the rocksalt layer. These results suggest that Sr doping enhances Z
T by decreasing κ in the rocksalt layer, but it does not significantly affect electrical properties because it is an isovalent substitution.
Photoluminescence from Eu3+ Ions Doped in ZnO Films Sputter-Deposited with H2O Vapor Gas
Authors: Akazawa Housei , Shinojima Hiroyuki
Published: June 2013

We found that ZnO:Eu films sputter-deposited with H2O vapor gas produce intense photoluminescence from Eu3+ ions through excitation of ZnO host crystals with a 325-nm laser light, whereas those deposited with O2 gas do not. At optimum annealing temperatures of 300–500 °C, the primary luminescence from Eu3+ ions appeared at 612 nm, which was much stronger than the near-band edge and defect emissions from ZnO. After annealing at higher temperatures, the 612-nm peak attenuated, and two emission lines at 612 and 620 nm, corresponding to two distinct chemical sites, had comparable intensities. These observations suggest that incorporating H+ and/or OH- species in ZnO crystals are prerequisite for emissions from Eu3+ ions to occur. Characterization with infrared absorption spectroscopy and X-ray diffraction suggested that Eu3+ ions substitute Zn2+ sites when OH- (H+) species are contained in ZnO crystals. The role of H+ and/or OH- species may be either charge compensation when substituting Zn2+ sites with Eu3+ ions or creation of trapping centers of excited energies that mediate efficient energy transfer from ZnO to Eu3+ ions.
Optimization of Surface Layers for Suppression of Agglomeration in Ag Films
Authors: Zhang Ziyang , Kawamura Midori , Abe Yoshio , Kim Kyung Ho
Published: June 2013

We previously reported that Al, Ti, and Nb surface layers can effectively suppress agglomeration in Ag films, which is dominated by the surface diffusion of Ag atoms. In this study, Ag films with Pd, Ni, and W surface layers were prepared by RF magnetron sputtering, and the properties of these films were compared with previous observations of the effects of Ti and Nb surface layers. The most important properties of the appropriate surface layers for the suppression of agglomeration in Ag films are a high cohesive energy or a high Gibbs free energy of formation of the oxide, and a low solid solubility in Ag.
Photo‐Activatable Surfaces for Cell Migration Assays
Authors: Salierno Marcelo J. , García Andrés J. , del Campo Aránzazu
Published: June 2013

A simple material platform for advanced cell migration studies is presented. It relies on surfaces modified with photo‐activatable adhesion peptides and two light exposure steps to independently trigger attachment and migration. The light‐controlled exposure of adhesive ligands allows precise and selective control over integrin‐mediated adhesion and migration events, including their dynamic variation. By using a microscope‐coupled scanning laser, user‐defined geometry, size and composition of the adhesion and migration spaces are possible and simply defined by the laser scanning parameters. Time lapse and high resolution microscopy are possible during the complete process. The miniaturization capabilities of this assay also allow (i) parallel or sequential migration experiments and controls on the same view field of the microscope, (ii) migration studies in confined and unconventional geometries or (iii) activation of migration spaces at subcellular resolution, all of these with minimum material and time consumption. The photo‐activatable surfaces will allow studies of the dynamics of integrin‐dependent migration processes with unprecedented flexibility, multiplexing, reproducibility, and spatiotemporal resolution.
Surface Coatings that Promote Rapid Release of Peptide‐Based AgrC Inhibitors for Attenuation of Quorum Sensing in Staphylococcus aureus
Authors: Broderick Adam H. , Stacy Danielle M. , Tal‐Gan Yftah , Kratochvil Michael J. , Blackwell Helen E. , Lynn David M.
Published: June 2013

Staphylococcus aureus is a major human pathogen responsible for a variety of life‐threatening infections. The pathogenicity of this organism is attributed to its ability to produce a range of virulence factors and toxins, including the superantigen toxic shock syndrome toxin‐1 (TSST‐1). While many S. aureus infections can be treated using conventional antibiotics, strains resistant to these bactericidal agents have emerged. Approaches that suppress pathogenicity through mechanisms that are nonbactericidal (i.e., antivirulence approaches) could provide new options for treating infections, including those caused by resistant strains. Here, we report a nonbactericidal approach to suppressing pathogenicity based on the release of macrocyclic peptides (1 and 2) that inhibit the agr quorum sensing (QS) circuit in group‐III S. aureus. It is demonstrated that these peptides can be immobilized on planar and complex objects (on glass slides, nonwoven meshes, or within absorbent tampons) using the rapidly dissolving polymer carboxymethylcellulose (CMC). Peptide‐loaded CMC films released peptide rapidly (<5 min) and promoted strong (>95%) inhibition of the agr QS circuit without inducing cell death when incubated in the presence of a group‐III S. aureus gfp‐reporter strain. Peptide 1 is among the most potent inhibitors of QS in S. aureus reported to date, and the group‐III QS circuit regulates production of TSST‐1, the primary cause of toxic shock syndrome (TSS). These results thus suggest approaches to treat the outer covers of tampons, wound dressings, or other objects to suppress toxin production and reduce the severity of TSS in clinical and personal care contexts. Because peptide 1 also inhibits QS in S. aureus groups‐I, ‐II, and ‐IV, this approach could also provide a pathway for attenuation of QS and associated virulence phenotypes in a broader range of contexts.
Development and Performance of MnFeCrO4‐Based Electrodes for Solid Oxide Fuel Cells
Authors: Stefan Elena , Tsekouras George , Irvine John T.S.
Published: June 2013

Important advances have been made in SOFC development utilizing a ceramic framework based upon yttria zirconia (YSZ) electrolytes supported upon porous YSZ electrode skeletons. This ceramic framework is sintered at high temperatures with subsequent impregnation and low temperature processing of the active electrode materials. Here we seek to develop this impregnated electrode concept by investigating a novel scaffold material similar to the main corrosion product of ferritic stainless steel. The chromium rich spinel (MnFeCrO4) was used as an electrode support material, either alone or impregnated with (La0.75Sr0.25)0.97Cr0.5Mn0.5O3‐δ, La0.8Sr0.2FeO3‐δ, Ce0.9Gd0.1O2‐δ, CeO2 and/or Pd. In these initial studies it was found that all of the impregnated phases adhere very well to the spinel and considerably enhance performance and stability to a level sufficient for SOFC applications.
Severe infantile leigh syndrome associated with a rare mitochondrial ND6 mutation, m.14487T>C
Authors: Tarnopolsky Mark , Meaney Brandon , Robinson Brian , Sheldon Katherine , Boles Richard G.
Published: June 2013

We describe a case of severe infantile‐onset complex I deficiency in association with an apparent de novo near‐homoplasmic mutation (m.14487T>C) in the mitochondrial ND6 gene, which was previously associated with Leigh syndrome and other neurological disorders. The mutation was near‐homoplasmic in muscle by NextGen sequencing (99.4% mutant), homoplasmic in muscle by Sanger sequencing, and it was associated with a severe complex I deficiency in both muscle and fibroblasts. This supports previous data regarding Leigh syndrome being on the severe end of a phenotypic spectrum including progressive myoclonic epilepsy, childhood‐onset dystonia, bilateral striatal necrosis, and optic atrophy, depending on the proportion of mutant heteroplasmy. While the mother in all previously reported cases was heteroplasmic, the mother and brother of this case were homoplasmic for the wild‐type, m.14487T. Importantly, the current data demonstrate the potential for cases of mutations that were previously reported to be homoplasmic by Sanger sequencing to be less homoplasmic by NextGen sequencing. This case underscores the importance of considering mitochondrial DNA mutations in families with a negative family history, even in offspring of those who have tested negative for a specific mtDNA mutation. © 2013 Wiley Periodicals, Inc.
Human and natural drivers of changing macrophyte community dynamics over 12 years in a Neotropical riverine floodplain system
Authors: Martins Sara Varandas , Milne Judith , Thomaz Sidinei Magela , McWaters Stephanie , Mormul Roger Paulo , Kennedy Michael , Murphy Kevin
Published: June 2013

The Rio Paraná is the world's tenth largest river (discharge in the upper river, studied here, during major flood events exceeds 12 700 m3s‐1). Together with its associated floodplain water bodies, this Neotropical river system supports a freshwater biodiversity of worldwide conservation significance, but one increasingly affected by human pressures, particularly the effects of river impoundment.

Multivariate analysis of data from repeated (2000–2002 and 2011) macrophyte–environment surveys of a set of stations within a 230 km stretch of functioning riverine floodplain, downstream of the most recently completed dam on the Upper Paraná, the Porto Primavera Dam, together with published data (from 1999 and 2005–2007), was used to test the hypothesis that human influences might outweigh the importance of natural factors in driving the aquatic vegetation dynamics (macrophyte community composition, alpha‐diversity, and abundance) of this system during the period 1999–2011.

The macrophyte communities present showed differences of species composition and abundance that could be strongly related to the scale and duration of the immediately preceding annual flood pulse, as well as local variations in physico‐chemical conditions. For rare Neotropical endemic species, which are a good marker of the conservation status of the system, there was a reasonable degree of stability between the 2000–2002 and 2011 survey periods, with eight of 16 such species being present in both surveys, three present in 2000–2002 only, but an additional five such species found only in 2011.

The conclusion is that vegetation changes in the system can be referred both to direct human impacts (river regulation), and to indirect human or natural impacts (floods, alien species invasion byHydrilla verticillata, and local environmental factors). Overall there was evidence that major floods associated with El Niño ‐ Southern Oscillation (ENSO) climatic events had a much greater impact than other drivers, whether natural or anthropogenic.

Copyright © 2013 John Wiley & Sons, Ltd.