bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational Electromagnetism and Acoustics
Authors: Hiptmair Ralf , Hoppe Ronald H.W. , Joly Patrick , Langer Ulrich
Published: November 2013

Computational electromagnetics and acoustics revolve around a few key challenges, among which are the non-local nature of the underlying phenomena and resonance effects. The bulk of the contributions to the workshop addressed mathematical and numerical approaches meant to grapple with these two difficulties. Frequency domain integral equation methods continue to receive much attention, with a particular focus on (i) frequency robust matrix compression algorithms through so-called directional schemes or “butterfly algorithms”, and (ii) domain decomposition approaches. Time domain integral equation methods still enjoy rapid development and much progress was made in their numerical analysis. Of course, efficient and accurate absorbing boundary conditions remain a persistent topic and were covered in a few contributions. Resonance induced phenomena in a broad sense affect the analytical and numerical model for meta-materials, periodic structures, and micro-structured media. There is a lot left to be explored in this field in terms of analysis and algorithm development and a few presentations were devoted to such issues.
Numerical Methods for PDE Constrained Optimization with Uncertain Data
Authors: Heinkenschloss Matthias , Schulz Volker
Published: November 2013

Optimization problems governed by partial differential equations (PDEs) arise in many applications in the form of optimal control, optimal design, or parameter identification problems. In most applications, parameters in the governing PDEs are not deterministic, but rather have to be modeled as random variables or, more generally, as random fields. It is crucial to capture and quantify the uncertainty in such problems rather than to simply replace the uncertain coefficients with their mean values. However, treating the uncertainty adequately and in a computationally tractable manner poses many mathematical challenges. The numerical solution of optimization problems governed by stochastic PDEs builds on mathematical subareas, which so far have been largely investigated in separate communities: Stochastic Programming, Numerical Solution of Stochastic PDEs, and PDE Constrained Optimization. The workshop achieved an impulse towards cross-fertilization of those disciplines which also was the subject of several scientific discussions. It is to be expected that future exchange of ideas between these areas will give rise to new insights and powerful new numerical methods.
Integral Geometry and its Applications
Authors: Alesker Semyon , Bernig Andreas , Schuster Franz E.
Published: November 2013

In recent years there has been a series of striking developments in modern integral geometry which has, in particular, lead to the discovery of new relations to several branches of pure and applied mathematics. A number of examples were presented at this meeting, e.g. the work of Bernig, Solanes, and Fu on kinematic formulas on complex projective and complex hyperbolic spaces, that of Schneider and Vedel Jensen on tensor valuations and a series of results on convex body valued valuations by Abardia, Ludwig, Parapatits, and Wannerer.
Mini-Workshop: Numerical Upscaling for Media with Deterministic and Stochastic Heterogeneity
Authors: Efendiev Yalchin , Iliev Oleg , Vassilevski Panayot S.
Published: November 2013

This minisymposium was third in series of similar events, after two very successful meetings in 2005 and 2009. The aim was to provide a forum for an extensive discussion on the theoretical aspects and on the areas of application and validity of numerical upscaling approaches for heterogeneous problems with deterministic and stochastic coefficients. The intensive discussions during the meeting contributed to a better understanding of upscaling approaches for multiscale problems with stochastic coefficients, and for synergy between scientists coming to this topic from the area of deterministic multiscale problems on one hand, and those coming from the area of SPDE on the other hand. Recent advanced results on upscaling approaches for deterministic multiscale problems were presented, well mixed with strong presentations on SDE and SPDE. The open problems in these areas were discussed, with emphasis on the case of stochastic coefficients brainstorming numerous numerical upscaling approaches. A number of young researchers, very actively working in these areas, were involved in the workshop discussing the links between scales., thus ensuring the continuity between the generations of researchers.
Mini-Workshop: Stochastic Analysis for Poisson Point Processes: Malliavin Calculus, Wiener-Ito Chaos Expansions and Stochastic Geometry
Authors: Reitzner Matthias , Peccati Giovanni
Published: November 2013

Malliavin calculus plays an important role in the stochastic analysis for Poisson point processes. This technique is tightly connected with chaotic expansions, that were introduced in the first half of the last century by Itˆo and Wiener. These techniques found an increasing number of applications, in particular in the field of stochastic geometry. This in turn inspired new research in stochastic analysis. Leading experts and young researchers of both fields met for a week for fruitful discussions and new cooperations.
Geophysical Fluid Dynamics
Authors: Giga Yoshikazu , Hieber Matthias , Titi Edriss S.
Published: November 2013

The workshop “Geophysical Fluid Dynamics” addressed recent advances in analytical, stochastic, modeling and computational studies of geophysical rotating fluids models. Of particular interest on the analytical and stochastic sides were the contributions concerning dispersive mechanism, regularity verses finite-time formation of singularities of certain viscous and inviscid geostrophic models, the primitive equations, Boussinesq approximation, boundary layers and fast rotating fluids. Model reductions, based on asymptotic, scaling analysis and variational methods, were presented. In addition, computational investigations were provided in support of the claim that three-dimensional geophysical turbulent flows exhibit two-dimensional features, at small Rosby numbers.
Representations of Lie Groups and Supergroups
Authors: Hilgert Joachim , Kobayashi Toshiyuki , Neeb Karl-Hermann , Ratiu Tudor S.
Published: November 2013

The workshop focussed on recent developments in the representation theory of group objects in several categories, mostly finite and infinite dimensional smooth manifolds and supermanifolds. The talks covered a broad range of topics, with a certain emphasis on benchmark problems and examples such as branching, limit behavior, and dual pairs. In many talks the relation to physics played an important role.
Interplay of Theory and Numerics for Deterministic and Stochastic Homogenization
Authors: Bal Guillaume , Engquist Björn , Le Bris Claude , Owhadi Houman
Published: November 2013

The workshop has brought together experts in the broad field of partial differential equations with highly heterogeneous coefficients. Analysts and computational and applied mathematicians have shared results and ideas on a topic of considerable interest both from the theoretical and applied viewpoints. A characteristic feature of the workshop has been to encourage discussions on the theoretical as well as numerical challenges in the field, both from the point of view of deterministic as well as stochastic modeling of the heterogeneities.
Phytoplankton competition during the spring bloom in four plankton functional type models
Authors: Hashioka T. , Vogt M. , Yamanaka Y. , Le Quéré C. , Buitenhuis E. T. , Aita M. N. , Alvain S. , Bopp L. , Hirata T. , Lima I. , Sailley S. , Doney S. C.
Published: November 2013

Abstract. We investigated the mechanisms of phytoplankton competition during the spring bloom, one of the most dramatic seasonal events in lower-trophic-level ecosystems, in four state-of-the-art plankton functional type (PFT) models: PISCES, NEMURO, PlankTOM5 and CCSM-BEC. In particular, we investigated the relative importance of different ecophysiological processes on the determination of the community structure, focusing both on the bottom-up and the top-down controls. The models reasonably reproduced the observed global distribution and seasonal variation of phytoplankton biomass. The fraction of diatoms with respect to the total phytoplankton biomass increases with the magnitude of the spring bloom in all models. However, the governing mechanisms differ between models, despite the fact that current PFT models represent ecophysiological processes using the same types of parameterizations. The increasing trend in the percentage of diatoms with increasing bloom magnitude is mainly caused by a stronger nutrient dependence of diatom growth compared to nanophytoplankton (bottom-up control). The difference in the maximum growth rate plays an important role in NEMURO and PlankTOM5 and determines the absolute values of the percentage of diatoms during the bloom. In CCSM-BEC, the light dependency of growth plays an important role in the North Atlantic and the Southern Ocean. The grazing pressure by zooplankton (top-down control), however, strongly contributes to the dominance of diatoms in PISCES and CCSM-BEC. The regional differences in the percentage of diatoms in PlankTOM5 are mainly determined by top-down control. These differences in the mechanisms suggest that the response of marine ecosystems to climate change could significantly differ among models, even if the present-day ecosystem is reproduced to a similar degree of confidence. For further understanding of plankton competition and for the prediction of future change in marine ecosystems, it is important to understand the relative differences in each physiological rate and life history rate in the bottom-up and the top-down controls between PFTs.
Comparison between eddy covariance and automatic chamber techniques for measuring net ecosystem exchange of carbon dioxide in cotton and wheat fields
Authors: Wang K. , Liu C. , Zheng X. , Pihlatie M. , Li B. , Haapanala S. , Vesala T. , Liu H. , Wang Y. , Liu G. , Hu F.
Published: November 2013

Abstract. Static and transparent automatic chamber (AC) technique is a necessary choice for measuring net ecosystem exchange (NEE) of carbon dioxide (CO2) in circumstances where eddy covariance (EC) technique is not applicable. However, a comparison of the two techniques for measurements on croplands has seldom been undertaken. We carried out NEE observations in a cotton field (for one year) and a winter wheat field (for one cropping season) using both AC and EC techniques, to (a) compare the NEE fluxes measured using each technique, and (b) test the NEE measurement performance of an automatic chamber system (AMEG), which was designed for simultaneous flux measurements of multiple gases. The half-hourly NEE fluxes measured with the two techniques were in approximate agreement, with the AC fluxes being 0.78 (cotton) and 1.06 (wheat) times the size of the EC fluxes. When integrated to daily timescale, the fluxes of the two techniques were in better agreement, showing an average ratio of 0.94 and 1.00 for the cotton and wheat, respectively. During the periods with comparable field conditions and normal performance of both instruments, the cumulative NEE fluxes revealed small differences between the two techniques (−9.0% ~ 7%, with a mean of 0.1%). The measurements resulted in an annual cumulative NEE of −40 g C m−2 yr−1 (EC) and −42 g C m−2 yr−1 (AC) in the cotton field, and a seasonal cumulative NEE of −251 g C m−2 (EC) and −205 g C m−2 (AC) in the wheat field. Our results indicate that, for cropland populated by short plants, the AMEG system and the data processing procedures applied in this study are able to provide NEE estimates comparable to those from EC measurements.
Sink or link? The bacterial role in benthic carbon cycling in the Arabian Sea's oxygen minimum zone
Authors: Pozzato L. , Van Oevelen D. , Moodley L. , Soetaert K. , Middelburg J. J.
Published: November 2013

Abstract. The bacterial loop, the consumption of dissolved organic matter (DOM) by bacteria and subsequent transfer of bacterial carbon to higher trophic levels, plays a prominent role in pelagic food webs. However, its role in sedimentary ecosystems is not well documented. Here we present the results of isotope tracer experiments performed under in situ oxygen conditions in sediments from inside and outside the Arabian Sea's oxygen minimum zone (OMZ) to study the importance of the microbial loop in this setting. Particulate organic matter, added as phytodetritus, was processed by bacteria, protozoa and metazoans, while dissolved organic matter was processed only by bacteria and there was very little, if any, transfer to higher trophic levels within the 7 day experimental period. This lack of significant transfer of bacterial-derived carbon to metazoan consumers indicates that the bacterial loop is rather inefficient, in sediments both inside and outside the OMZ. Moreover, metazoans directly consumed labile particulate organic matter resources and thus competed with bacteria for phytodetritus.
In-hospital mortality and length-of-stay in a cohort of ED patients admitted to internistic units
Authors: Giorgi Alfredo De , Fabbian Fabio , Ferro Jadran , Menegatti Alessandra Mallozzi , Salmi Raffaella , Melandri Roberto , Gardini Andrea , Rinaldi Gabriele , Gallerani Massimo , Manfredini Roberto
Published: November 2013

Background: Several life-threatening acute diseases exhibit precise preferred times of onset, during the day (morning), the month or season of the year (winter), and the day of the week (Monday). Moreover, admission to the hospital during nighttime and weekend (WE) is associated with increased risk of in-hospital mortality (IHM) and length-of-hospital stay (LOS). Since most of these data have been obtained in North American settings, the aim of this study was to verify also in an Italian setting whether some factors related to ED evaluation, including time of arrival, and disease’s severity evaluated by a colour code, could be associated with IHM and LOS in ED patients admitted to internal medicine units. Methods: This study was conducted between January 1, 2010 and July 31, 2012, at the St Anna Hospital of Ferrara. We analyzed age, sex, time of arrival to the ED, ED boarding time, and triage colour code of all patients admitted to the Department of Medicine. Friday to midnight Sunday was considered as WE, and the nine main national festive days were always considered as Sunday-WE. Thus, the time period was classified into holidays (WE + festive days) and weekdays (WD), and daytime (8:00 am - 8:00 pm) and nighttime (8:00 pm - 8:00 am). IHM and LOS were assumed as primary and secondary objectives, respectively. Patients were classified into deceased and survivors, and LOS was classified depending on length lower or higher than the median (seven days). T-test, chi-squared test, U Mann-Whitney test, and logistic regression analysis were performed. Results: During the 18-month period, 13,237 consecutive patients visiting the ED (43.4% males, mean age 74.8 ± 13.6 years, 56.6% females, mean age 78.0 ± 13.3 years), were considered. IHM was related to: time of admission (daytime vs. nighttime, p = .015; WE vs. WD, p = .026, holidays vs. no holidays, p = .021), colour code (p < .001), and age (p < .001). Multivariate analysis showed an independent association with IHM for colour code (p < .001), and age (p < .001). LOS >7 days was related to: time of admission (daytime vs. nighttime, p < .001; WE or WD, p = .001; holidays vs. no holidays, p = .002). Furthermore, LOS >7 days depended on both colour code of admission (p < .001), and age (p < .001). Multivariate analysis showed a significant correlation with LOS >7 days for yellow colour code (p < .001), and age (p < .001). Conclusions: Although several factors, such as admission colour code and age, influence some parameters of clinical outcome, i.e., IHM and LOS, a striking weekend effect is not evident in a cohort of consecutive patients admitted to an Italian Medical Department, characterized by intermediate-high level of urgency.
Dessler, Jimenez, Klein, and Nenes Receive 2012 Atmospheric Sciences Ascent Awards: Citation for Andrew E. Dessler
Authors: Webster Peter J.
Published: November 2013

The Atmospheric Sciences section of AGU awards one of the four Ascent Awards to Professor Andrew E. Dessler of the Department of Atmospheric Sciences at Texas A&M University for fundamental contributions to the understanding of stratospheric‐tropospheric exchange processes and the physics of ozone depletion and for attempts to unravel water vapor and cloud feedbacks in the climate system. In addition, he is commended for his ceaseless work in communicating the science of climate change to the public.
Dessler, Jimenez, Klein, and Nenes Receive 2012 Atmospheric Sciences Ascent Awards: Citation for Stephen A. Klein
Authors: Webster Peter J.
Published: November 2013

The Atmospheric Sciences section of AGU awards one of the four Ascent Awards to Dr. Stephen Klein of the Lawrence Livermore National Laboratory. The award is made for the substantial contributions Dr. Klein has made toward understanding some of the field's most important problems, the interaction of clouds and climate through (as noted in his nomination) “the careful analysis of observations, the insightful use of models of varying complexity and his ability to synthesize diverse strands of knowledge.”
Implications of a long‐lived basal magma ocean in generating Earth's ancient magnetic field
Authors: Ziegler L. B. , Stegman D. R.
Published: November 2013

Observations of Earth's magnetic field extending back to 3.45 billion years ago indicate that generation by a core dynamo must be sustained over most of Earth's history. However, recent estimates of thermal and electrical conductivity of liquid iron at core conditions from mineral physics experiments indicate that adiabatic heat flux is approximately 15 TW, nearly three times larger than previously thought, exacerbating difficulties for driving a core dynamo throughout Earth history by convective core cooling alone. Here, we explore the geomagnetic consequences of a basal magma ocean layer in the lowermost mantle, hypothesized to exist in the early Earth and perhaps surviving until well after the Archean. While the modern, solid lower mantle is an electromagnetic insulator, electrical conductivities of silicate melts are known to be higher, though as yet they are unconstrained for lowermost mantle conditions. We consider a range of possible electrical conductivities and find that for the highest electrical conductivities considered, a long‐lived basal magma ocean could be a primary dynamo source region. This would suggest the proposed three magnetic eras observed in paleomagnetic data originate from distinct sources for dynamo generation: from 4.5 to 2.45 Ga within a basal magma ocean, from 2.25 to 0.4 Ga within a superadiabatically cooled liquid core, and from 0.4 Ga to present within a quasi‐adiabatic core that includes a solidifying inner core.
Effects of vegetation distribution on experimental river channel dynamics
Authors: van Dijk W. M. , Teske R. , van de Lageweg W. I. , Kleinhans M. G.
Published: November 2013

Strong feedbacks exist between channel dynamics, floodplain development, and riparian vegetation. Earlier experimental studies showed how uniformly distributed riparian vegetation causes a shift from a braided to a single‐thread river because riparian vegetation stabilizes the banks and focuses discharge off the floodplains into channels. These experiments tested anemochorously distributed vegetation, i.e., by wind, whereas many riparian species in nature are also distributed hydrochorously, i.e., by flowing water. The objective of this study is to test experimentally what the different effects are of hydrochorously and anemochorously distributed vegetation on channel pattern and dynamics. The experiments were carried out in a flume of 3 m wide and 10 m long. We compared experiments with the two forms of vegetation distribution methods to control experiments without vegetation. To independently quantify bank retreat rate as a function of seed density and vegetation age, we used a small bank erosion test. In agreement with other work, the uniformly distributed vegetation decreased bank retreat, often stabilized banks and tightened meander bends. Vegetation seeds distributed by the flow during floods settled at lower elevations compared to the uniformly distributed vegetation. Inner bend vegetation stabilized a part of the point bar and hydraulic resistance of the vegetated bar forced water into the channel and over the floodplain. As a result, sediment was deposited upstream of vegetation patches. We conclude that seeds distributed by the flow during floods lead to island braiding: a patchy multithread river with stable vegetated bars, whereas vegetation uniformly distributed on the floodplain of a single‐thread meandering river increases sinuosity and decreases bend wavelength. This implies that the combination of discharge variations and vegetation settling behavior has a large effect on the morphology and dynamics of rivers. The experimental approach opens up a wide range of possibilities to explore hydro‐bio‐geomorphological interactions with a high degree of control.
Care and Handling of Laboratory Mice
Authors: Donovan John , Brown Patricia
Published: November 2013

The importance of laboratory mice in experimental microbiology and biomedical research is indisputable, and their care and handling is a contributing factor to the quality of the science resulting from their use. This unit provides guidelines for practical housing, handling, and the methodology for sample collection to ensure animal health and minimize variable experimental parameters. Curr. Protoc. Microbiol. 31:A.3N.1‐A.3N.18. © 2013 by John Wiley & Sons, Inc.
Cognitive, sensory, and psychosocial characteristics in patients with Bardet–Biedl syndrome
Authors: Brinckman Danielle D. , Keppler‐Noreuil Kim M. , Blumhorst Catherine , Biesecker Leslie G. , Sapp Julie C. , Johnston Jennifer J. , Wiggs Edythe A.
Published: November 2013

Forty‐two patients with a clinical diagnosis of Bardet–Biedl syndrome ages 2–61 years were given a neuropsychological test battery to evaluate cognitive, sensory, and behavioral functioning. These tests included the Wechsler scales of intelligence, Rey Auditory Verbal Learning Test, Boston Naming Test, D‐KEFS Verbal Fluency Test, D‐KEFS Color‐Word Interference Test, D‐KEFS Sorting Test, Wide Range Achievement Test: Math and Reading Subtests, Purdue Pegboard, The University of Pennsylvania Smell Identification Test, Social Communication Questionnaire, Social Responsiveness Scale, and Behavior Assessment System for Children, Second Edition, Parent Rating Scale. On the age appropriate Wechsler scale, the mean Verbal Comprehension was 81 (n = 36), Working Memory was 81 (n = 36), Perceptual Reasoning was 78 (n = 24) and Full Scale IQ was 75 (n = 26). Memory for a word list (Rey Auditory Verbal Learning Test) was in the average range with a mean of 89 (n = 19). Fine motor speed was slow on the Purdue with mean scores 3–4 standard deviations below norms. All subjects were microsmic on the University of Pennsylvania Smell Identification Test. Of these 42 patients, only 6 were able to complete all auditory and visual tests; 52% were unable to complete the visual tests due to impaired vision. A wide range of behavioral issues were endorsed on questionnaires given to parents. Most had social skill deficits but no pattern of either externalizing or internalizing problems. We identify a characteristic neuro‐behavioral profile in our cohort comprised of reduced IQ, impaired fine‐motor function, and decreased olfaction. © 2013 Wiley Periodicals, Inc.
Hydrogen‐Bonding Effect on Spin‐Center Transfer of Tetrathiafulvalene‐Linked 6‐Oxophenalenoxyl Evaluated Using Temperature‐Dependent Cyclic Voltammetry and Theoretical Calculations
Authors: Nishida Shinsuke , Fukui Kozo , Morita Yasushi
Published: November 2013

The stable tetrathiafulvalene (TTF)‐linked 6‐oxophenalenoxyl neutral radical exhibits a spin‐center transfer with a continuous color change in solution caused by an intramolecular electron transfer, which is dependent on solvent and temperature. Cyclic voltammetry measurements showed that addition of 2,2,2‐trifluoroethanol (TFE) to a benzonitrile solution of the neutral radical induces a redox potential shift that is favorable for the spin‐center transfer. Temperature‐dependent cyclic voltammetry of the neutral radical using a novel low‐temperature electrochemical cell demonstrated that the redox potentials change with decreasing temperature in a 199:1 CH2Cl2/TFE mixed solvent. Furthermore, theoretical calculation revealed that the energy levels of the frontier molecular orbitals involved in the spin‐center transfer are lowered by the hydrogen‐bonding interaction of TFE with the neutral radical. These results indicate that the hydrogen‐bonding effect is a key factor for the occurrence of the spin‐center transfer of TTF‐linked 6‐oxophenalenoxyl.
Numerical Investigation of the Gas‐Solid Flow Characteristics in a Three‐Dimensional Spouted Bed with a Draft Tube
Authors: Yang S.‐L. , Luo K. , Fang M.‐M. , Zhang K. , Fan J.‐R.
Published: November 2013

Gas‐solid motions in a three‐dimensional conical spouted bed with a draft tube are investigated based on a simulation carried out by the coupling approach of computational fluid dynamics combined with the discrete‐element method. The distribution properties of the velocity, the concentration, and the flux of the solid phase are discussed. The vertical solid velocity in the central region initially increases, diminishes gradually, and finally decreases sharply in the region above the draft tube. Vigorous lateral solid motion occurs in the periphery of the fountain and the spout‐annulus interface. In addition, the vertical solid flux shows a large value in the spout. A larger vertical velocity but a more dilute solid concentration can be detected along the axial direction when enlarging the gas flow rate.
Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes
Authors: Navrátil Václav , Klusák Vojtěch , Rulíšek Lubomír
Published: November 2013

Activation and reaction energies for four model systems capturing the essential physicochemical features of the hydrolysis of the peptide bond have been calculated at various level of theory, including the presumably accurate CCSD(T) calculations. The models studied covered a part of the spectrum encountered in biological systems: the hydrolysis in the absence of metal ions (represented by formamide and Ala–Ala) and the hydrolysis in the presence of one and two zinc(II) ions, mimicking the active sites of mono‐ and dizinc metallopeptidases, respectively (by using thermolysin and glutamate carboxypeptidase II as the model catalytic systems and formamide as the model substrate). The results obtained using CCSD(T)/def2‐TZVP and CCSD(T)/aug‐cc‐pVTZ calculations were used as the benchmark values to which the set of cheaper methods, such as (RI‐)DFT, (RI‐)MP2, and SCS‐MP2, were referenced. It was shown that deviations of 3–5 kcal mol−1 (translating to 2–3 orders in reaction constants) with respect to the reference CCSD(T) barriers are frequently encountered for many correlated methods and most of studied DFT functionals. It has been concluded that from the set of wave‐function methods, both MP2 and SCS‐MP2 methods can be recommended for smaller models (measured by the mean absolute deviation of the activation barriers over the four systems studied), whereas among the popular DFT functionals, B3LYP and especially M06‐2X are likely to be reasonable choices for calculating the activation barriers of zinc metallopeptidases. Finally, with the model of glutamate carboxypeptidase II, issues related to the convergence of the calculated barriers with the size of the model system used as the representative of the enzyme active site were addressed. The intricacies related to system truncation are demonstrated, and suggest that the correlated wave‐function methods may suffer from problems, such as intramolecular BSSE, which make their usage for the larger system questionable. Altogether, the presented data should contribute to efforts to understand enzymatic catalysis more deeply and to gain control of the accuracy and deficiencies of the available theoretical methods and computational approaches.
Nomogram for predicting the benefit of neoadjuvant chemoradiotherapy for patients with esophageal cancer: A SEER‐Medicare analysis
Authors: Eil Robert , Diggs Brian S. , Wang Samuel J. , Dolan James P. , Hunter John G. , Thomas Charles R.
Published: November 2013

BACKGROUND

The survival impact of neoadjuvant chemoradiotherapy (CRT) on esophageal cancer remains difficult to establish for specific patients. The aim of the current study was to create a Web‐based prediction tool providing individualized survival projections based on tumor and treatment data.

METHODS

Patients diagnosed with esophageal cancer between 1997 and 2005 were selected from the Surveillance, Epidemiology, and End Results (SEER)‐Medicare database. The covariates analyzed were sex, T and N classification, histology, total number of lymph nodes examined, and treatment with esophagectomy or CRT followed by esophagectomy. After propensity score weighting, a log‐logistic regression model for overall survival was selected based on the Akaike information criterion.

RESULTS

A total of 824 patients with esophageal cancer who were treated with esophagectomy or trimodal therapy met the selection criteria. On multivariate analysis, age, sex, T and N classification, number of lymph nodes examined, treatment, and histology were found to be significantly associated with overall survival and were included in the regression analysis. Preoperative staging data and final surgical margin status were not available within the SEER‐Medicare data set and therefore were not included. The model predicted that patients with T4 or lymph node disease benefitted from CRT. The internally validated concordance index was 0.72.

CONCLUSIONS

The SEER‐Medicare database of patients with esophageal cancer can be used to produce a survival prediction tool that: 1) serves as a counseling and decision aid to patients and 2) assists in risk modeling. Patients with T4 or lymph node disease appeared to benefit from CRT. This nomogram may underestimate the benefit of CRT due to its variable downstaging effect on pathologic stage. It is available at skynet.ohsu.edu/nomograms. Cancer 2014;120:492–498. © 2013 American Cancer Society.
Integrated Catalytic Process to Directly Convert Furfural to Levulinate Ester with High Selectivity
Authors: Chen Bingfeng , Li Fengbo , Huang Zhijun , Lu Tao , Yuan Yin , Yuan Guoqing
Published: November 2013

Levulinic acid is an important platform molecule from biomass‐based renewable resources. A sustainable manufacturing process for this chemical and its derivatives is the enabling factor to harness the renewable resource. An integrated catalytic process to directly convert furfural to levulinate ester was developed based on a bifunctional catalyst of Pt nanoparticles supported on a ZrNb binary phosphate solid acid. The hydrogenation of furfural and the following alcoholysis of furfuryl alcohol were performed over this catalyst in a one‐pot conversion model. Mesoporous ZrNb binary phosphate was synthesized by a sol–gel method and had a high surface area of 170.1 m2 g−1 and a large average pore size of around 8.0 nm. Pt nanoparticles remained in a monodisperse state on the support, and the reaction over Pt/ZrNbPO4 (Pt loading: 2.0 wt %; Zr/Nb, 1:1) gave a very high selectivity to levulinate derivatives (91 % in total). The sustainability of this conversion was greatly improved by the process intensification based on the new catalyst, mild reaction conditions, cost abatement in separation and purification, and utilization of green reagents and solvents.
Polyvinylidene Fluoride/Siloxane Nanofibrous Membranes for Long‐Term Continuous CO2‐Capture with Large Absorption‐Flux Enhancement
Authors: Lin Yi‐Feng , Wang Chi‐Sen , Ko Chia‐Chieh , Chen Chien‐Hua , Chang Kai‐Shiun , Tung Kuo‐Lun , Lee Kueir‐Rarn
Published: November 2013

In a CO2 membrane contactor system, CO2 passes through a hydrophobic porous membrane in the gas phase to contact the amine absorbent in the liquid phase. Consequently, additional CO2 gas is absorbed by amine absorbents. This study examines highly porous polyvinylidene fluoride (PVDF)/siloxane nanofibrous layers that are modified with hydrophobic fluoroalkylsilane (FAS) functional groups and successfully coated onto a macroporous Al2O3 membrane. The performance of these materials in a membrane contactor system for CO2 absorption is also investigated. Compared with pristine PVDF nanofibrous membranes, the PVDF/siloxane nanofibrous membranes exhibit greater solvent resistance and mechanical strength, making them more suitable for use in CO2 capture by the membrane contactor. The PVDF/siloxane nanofibrous layer in highly porous FAS‐modified membranes can prevent the wetting of the membrane by the amine absorbent; this extends the periods of continuous CO2 absorption and results in a high CO2 absorption flux with a minimum of 500 % enhancement over that of the uncoated membranes. This study suggests the potential use of an FAS‐modified PVDF/siloxane nanofibrous membrane in a membrane contactor system for CO2 absorption. The resulting hydrophobic membrane contactor also demonstrates the potential for large‐scale CO2 absorption during post‐combustion processes in power plants.
Exomic analysis of myxoid liposarcomas, synovial sarcomas, and osteosarcomas
Authors: Joseph Christine G. , Hwang Heejung , Jiao Yuchen , Wood Laura D. , Kinde Isaac , Wu Jian , Mandahl Nils , Luo Jinyong , Hruban Ralph H. , Diaz Luis A. , He Tong‐Chuan , Vogelstein Bert , Kinzler Kenneth W. , Mertens Fredrik , Papadopoulos Nickolas
Published: November 2013

Bone and soft tissue sarcomas are a group of histologically heterogeneous and relatively uncommon tumors. To explore their genetic origins, we sequenced the exomes of 13 osteosarcomas, eight myxoid liposarcomas (MLPS), and seven synovial sarcomas (SYN). These tumors had few genetic alterations (median of 10.8). Nevertheless, clear examples of driver gene mutations were observed, including canonical mutations in TP53, PIK3CA, SETD2, AKT1, and subclonal mutation in FBXW7. Of particular interest were mutations in H3F3A, encoding the variant histone H3.3. Mutations in this gene have only been previously observed in gliomas. Loss of heterozygosity of exomic regions was extensive in osteosarcomas but rare in SYN and MLPS. These results provide intriguing nucleotide‐level information on these relatively uncommon neoplasms and highlight pathways that help explain their pathogenesis. © 2013 Wiley Periodicals, Inc.
The role of topoisomerase II beta on breakage and proximity of RUNX1 to partner alleles RUNX1T1 and EVI1
Authors: Smith Kayleigh A. , Cowell Ian G. , Zhang Yanming , Sondka Zbyslaw , Austin Caroline A.
Published: November 2013

Rearrangements involving the RUNX1 gene account for approximately 15% of balanced translocations in therapy‐related acute myeloid leukemia (t‐AML) patients and are one of the most common genetic abnormalities observed in t‐AML. Drugs targeting the topoisomerase II (TOP2) enzyme are implicated in t‐AML; however, the mechanism is not well understood and to date a single RUNX1‐RUNX1T1 t‐AML breakpoint junction sequence has been published. Here we report an additional five breakpoint junction sequences from t‐AML patients with the RUNX1‐ RUNX1T1 translocation. Using a leukemia cell line model, we show that TOP2 beta (TOP2B) is required for induction of RUNX1 chromosomal breaks by the TOP2 poison etoposide and that, while TOP2 alpha (TOP2A) and TOP2B proteins are both present on RUNX1 and RUNX1T1 chromatin, only the TOP2B enrichment reached significance following etoposide exposure at a region on RUNX1 where translocations occur. Furthermore, we demonstrate that TOP2B influences the separation between RUNX1 and two translocation partners (RUNX1T1 and EVI) in the nucleus of lymphoid cells. Specifically, we identified a TOP2B‐dependent increase in the number of nuclei displaying juxtaposed RUNX1 and RUNX1T1 loci following etoposide treatment. © 2013 Wiley Periodicals, Inc.
Analysis of αSMA-Labeled Progenitor Cell Commitment Identifies Notch Signaling as an Important Pathway in Fracture Healing
Authors: Matthews Brya G , Grcevic Danka , Wang Liping , Hagiwara Yusuke , Roguljic Hrvoje , Joshi Pujan , Shin Dong-Guk , Adams Douglas J , Kalajzic Ivo
Published: November 2013

Fracture healing is a regenerative process that involves coordinated responses of many cell types, but characterization of the roles of specific cell populations in this process has been limited. We have identified alpha smooth muscle actin (αSMA) as a marker of a population of mesenchymal progenitor cells in the periosteum that contributes to osteochondral elements during fracture healing. Using a lineage tracing approach, we labeled αSMA-expressing cells, and characterized changes in the periosteal population during the early stages of fracture healing by histology, flow cytometry, and gene expression profiling. In response to fracture, the αSMA-labeled population expanded and began to differentiate toward the osteogenic and chondrogenic lineages. The frequency of mesenchymal progenitor cell markers such as Sca1 and PDGFRα increased after fracture. By 6 days after fracture, genes involved in matrix production and remodeling were elevated. In contrast, genes associated with muscle contraction and Notch signaling were downregulated after fracture. We confirmed that activating Notch signaling in αSMA-labeled cells inhibited differentiation into osteogenic and adipogenic lineages in vitro and ectopic bone formation in vivo. By characterizing changes in a selected αSMA-labeled progenitor cell population during fracture callus formation, we have shown that modulation of Notch signaling may determine osteogenic potential of αSMA-expressing progenitor cells during bone healing. © 2014 American Society for Bone and Mineral Research.
Reproducibility of MRI renal artery blood flow and BOLD measurements in patients with chronic kidney disease and healthy controls
Authors: Khatir Dinah S. , Pedersen Michael , Jespersen Bente , Buus Niels H.
Published: November 2013

Purpose

Determine the reproducibility of renal artery blood flow (RABF) and blood‐oxygenation level dependent (R2*) in patients with chronic kidney disease (CKD) and healthy controls.

Materials and Methods

RABF and R2* were measured in 11 CKD patients and 9 controls twice with 1‐ to 2‐week interval. R2* in the cortex and medulla were determined after breathing atmospheric air and 100% oxygen. Reproducibility was evaluated by coefficients of variation (CV), limits of agreements and intra‐class coefficient calculated by variance components by maximum likelihood modeling.

Results

Single‐kidney RABF (mL/min) for patients was: 170 ± 130 and 186 ± 137, and for controls: 365 ± 119 and 361 ± 107 (P < 0.05 versus patients), for first and second scans, respectively. RABF measurements were reproducible with a CV of 12.9% and 8.3% for patients and controls, respectively. Renal cortical R2* was: 13.6 ± 0.9 and 13.5 ± 1.2 in patients (CV = 8.0%), and 13.8 ± 1.6 and 14.0 ± 1.5 in controls (CV = 5.6%), while medullary R2*(s−1) was: 26.9 ± 2.0 and 27.0 ± 4.0 (CV = 8.0%) in patients, and 26.0 ± 2.4 and 26.1 ± 2.1 (CV = 3.6%) in controls, for first and second scans, respectively. In both groups R2* in medulla decreased after breathing 100% oxygen.

Conclusion

The reproducibility was high for both RABF and R2* in patients and controls, particularly in the cortex. Inhalation of 100% oxygen reduced medullary R2*. J. Magn. Reson. Imaging 2014;40:1091–1098. © 2013 Wiley Periodicals, Inc.
Hydration of nitriles: an examination in terms of No Barrier Theory
Authors: Guthrie J. Peter , Yim Jacky C.‐H. , Wang Qiang
Published: November 2013

Nitriles pose an interesting problem to the explanatory powers of organic chemistry because, despite the favorable overall thermodynamics of hydrolysis to the corresponding amides, the reactions are inherently slow. The rate determining step is hydration of the nitrile to give the imidic acid, which quickly tautomerizes to the amide. In terms of Marcus Theory, the intrinsic barriers for acid and base‐catalyzed hydration are higher for nitriles than for amides, which are themselves slow reactions. It is remarkable that hydration of a nitrile, for which the free energy change is close to zero except for polyhaloacetonitriles, is much slower than hydration of an amide, which is energetically unfavorable. This can be explained by No Barrier Theory in terms of the high energetic cost of the geometrical distortions in “one thing at a time” corner species.

There are no experimental equilibrium constants for this initial hydration step, so we have determined them computationally. The free energy change for the initial hydration is small; it is the fast and energetically downhill second step, tautomerization to the amide, which makes the overall hydrolysis of nitrile to amide thermodynamically favorable. Very few of the pKa values needed in the acid and base‐catalyzed mechanisms are known, so we used linear free energy relations and treat the parent pKa values as adjustable parameters. This procedure leads to pKa values in accord with expectation based on such data as are available and permits calculation of rate constants in satisfactory agreement with experiment. Copyright © 2013 John Wiley & Sons, Ltd.
Quantitative analysis of γ‐ and δ‐lactones in wines using gas chromatography with selective tandem mass spectrometric detection
Authors: Langen Johannes , Wang Chen‐Yin , Slabizki Petra , Wall Kristina , Schmarr Hans‐Georg
Published: November 2013

RATIONALE

Aroma relevant γ‐ and δ‐lactones are important flavor compounds in various foodstuffs. Their quantitative determination is essential for evaluating food sensory properties as well as food authenticity studies.

METHODS

High‐throughput head‐space solid‐phase microextraction as sample preparation, separation by capillary gas chromatography coupled with triple stage quadrupole mass spectrometry has been evaluated as the analytical method.

RESULTS

Monitoring selected reaction mass fragments allowed sub‐µg/L quantification of γ‐ and δ‐lactones in complex wine matrices.

CONCLUSIONS

Tandem mass spectrometry improves specific detection of γ‐ and δ‐lactones, a prerequisite for reliable quantification at low‐µg/L concentration levels in complex wine matrices. Copyright © 2013 John Wiley & Sons, Ltd.
The influence of growth conditions on strain differentiation within the Lactobacillus acidophilus group using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry profiling
Authors: Šedo Ondrej , Vávrová Andrea , Vad'urová Marta , Tvrzová Ludmila , Zdráhal Zbyněk
Published: November 2013

RATIONALE

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) profiling of bacteria is often used to distinguish isolates beyond the species level, even to the level of individual strains. However, the influence of bacterial growth conditions on the discriminatory power of the method to the strain level has not yet been properly evaluated.

METHODS

For the purpose of this study, we used an extraction protocol recommended for clinical laboratories for MALDI‐TOF MS profiling of bacteria. Seventeen closely related strains of the Lactobacillus acidophilus group were cultivated under various growth conditions (growth medium, time, and temperature) and analyzed.

RESULTS

Out of a total of 327 samples, 80 % were correctly assigned to the species level and 13 % only to the genus level. When using data obtained from strains cultured for lengthy periods (7 days), the identification success rate was reduced due to poor signal quality, whereas with shorter cultivation times there was no influence of growth conditions on the assignment of particular strains to their corresponding species. However, variations in certain cultivation parameters were found to influence identification and differentiation of most of the examined strains. Strain discrimination was frequently found to be dependent on the selection of culture conditions. MALDI‐TOF MS data treatment (strain‐specific peak detection, BioTyper scoring, subtyping, or cluster analysis) also contributed to the discriminatory power of the method.

CONCLUSIONS

When MALDI‐TOF MS profiling of bacteria is used for strain discrimination, the cultivation conditions should be properly optimized and controlled as they significantly contribute to the discriminatory power of the method. Copyright © 2013 John Wiley & Sons, Ltd.
On‐line HfF5−/WF5− separation in an O2‐filled radiofrequency quadrupole gas cell
Authors: Zhao X.‐L. , Eliades J. , Litherland A. E. , Kieser W. E. , Cornett J. , Charles C. R. J.
Published: November 2013

RATIONALE

An experimental Isobar Separator for Accelerator Mass Spectrometry (ISAMS) instrument has been used to demonstrate an on‐line separation of HfF5− from its isobar WF5−. This is necessary, in addition to sample preparation chemistry, for measuring 182Hf at natural levels by Accelerator Mass Spectrometry (AMS).

METHODS

The device utilizes a radiofrequency quadrupole (RFQ) controlled gas cell, wherein anion‐gas reactions at eV energies attenuate the interfering isobars of the analyte molecular anions, leaving HfF5− for AMS analysis. The RFQ also helps to control the multiple scattering resulting from the ion‐gas collisions.

RESULTS

O2 gas was used in the HfF5−/WF5− separation and WF5− was attenuated by nearly 3 orders of magnitude while maintaining ~75% transmission of HfF5−. It is expected that the transmission and attenuation can be increased by further research.

CONCLUSIONS

This result advances the possibility of detecting natural 182Hf when AMS is supplemented with an isobar separator in the injection system. Copyright © 2013 John Wiley & Sons, Ltd.