bluuebunny/crossref_metadata_2025 huggingface dataset:
Crossing Paths in Human Renal Cell Carcinoma (hRCC)
Authors: Gallego Guadalupe , Villaamil Vanessa , Grande Enrique , Caínzos Isabel , Aparicio Luís
Published: October 2012

Historically, cell-signaling pathways have been studied as the compilation of isolated elements into a unique cascade that transmits extracellular stimuli to the tumor cell nucleus. Today, growing evidence supports the fact that intracellular drivers of tumor progression do not flow in a single linear pathway, but disseminate into multiple intracellular pathways. An improved understanding of the complexity of cancer depends on the elucidation of the underlying regulatory networks at the cellular and intercellular levels and in their temporal dimension. The high complexity of the intracellular cascades causes the complete inhibition of the growth of one tumor cell to be very unlikely, except in cases in which the so-called “oncogene addiction” is known to be a clear trigger for tumor catastrophe, such as in the case of gastrointestinal stromal tumors or chronic myeloid leukemia. In other words, the separation and isolation of the driver from the passengers is required to improve accuracy in cancer treatment. This review will summarize the signaling pathway crossroads that govern renal cell carcinoma proliferation and the emerging understanding of how these pathways facilitate tumor escape. We outline the available evidence supporting the putative links between different signaling pathways and how they may influence tumor proliferation, differentiation, apoptosis, angiogenesis, metabolism and invasiveness. The conclusion is that tumor cells may generate their own crossroads/crosstalk among signaling pathways, thereby reducing their dependence on stimulation of their physiologic pathways.
Brockman, M.A., et al., Human Leukocyte Antigen (HLA) Class I Down-Regulation by Human Immunodeficiency Virus Type 1 Negative Factor (HIV-1 Nef): What Might We Learn From Natural Sequence Variants? Viruses 2012, 4, 1711-1730
Authors: Mwimanzi Philip , Markle Tristan J. , Ueno Takamasa , Brockman Mark A.
Published: October 2012

In the original manuscript, the text in figure 1 is illegible. Furthermore, there is an unnecessary carriage return (page 1716, ~line 18) "crystallographic ... methods". [...]
A Generic Framework for Modeling Brain Deformation as a Constrained Parametric Optimization Problem to Aid Non-diffeomorphic Image Registration in Brain Tumor Imaging
Authors: Mang A. , Toma A. , Schuetz T. A. , Becker S. , Buzug T. M.
Published: October 2012

Objectives: In the present paper a novel computational framework for modeling tumor induced brain deformation as a biophysical prior for non-rigid image registration is described. More precisely, we aim at providing a generic building block for non-rigid image registration that can be used to resolve inherent irregularities in non-diffeomorphic registration problems that naturally arise in serial and cross-population brain tumor imaging studies due to the presence (or progression) of pathology.

Methods: The model for the description of brain cancer dynamics on a tissue level is based on an initial boundary value problem (IBVP). The IBVP follows the accepted assumption that the progression of primary brain tumors on a tissue level is governed by proliferation and migration of cancerous cells into surrounding healthy tissue. The model of tumor induced brain deformation is phrased as a parametric, constrained optimization problem. As a basis of comparison and to demonstrate generalizability additional soft constraints (penalties) are considered. A backtracking line search is implemented in conjunction with a limited memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) method in order to handle the numerically delicate log-barrier strategy for confining volume change.

Results: Numerical experiments are performed to test the flexible control of the computed deformation patterns in terms of varying model parameters. The results are qualitatively and quantitatively related to patterns in patient individual magnetic resonance imaging data.

Conclusions: Numerical experiments demonstrate the flexible control of the computed deformation patterns. This in turn strongly suggests that the model can be adapted to patient individual imaging patterns of brain tumors. Qualitative and quantitative comparison of the computed cancer profiles to patterns in medical imaging data of an exemplary patient demonstrates plausibility. The designed optimization problem is based on computational tools widely used in non-rigid image registration, which in turn makes the model generally applicable for integration into non-rigid image registration algorithms.
De la conservation conflictuelle à l'aménagement durable : le paysage et la biodiversité saisis par le droit
Authors: Breton Jean-Marie
Published: October 2012

Le droit français s’est intéressé tardivement à la protection de la nature et à la conservation de l’environnement, à travers une démarche juridique qui ne s’est que progressivement distinguée des disciplines juridiques classiques, pour finir par s’en démarquer nettement, tout en demeurant largement « en commerce » avec celles-ci.La saisie par le droit des questions environnementales et la formulation normative des réponses à y apporter a fait écho au souci de concevoir et de mettre en œuvre des instruments aptes à satisfaire à des objectifs de protection à la fois compris et interprétés par référence à une vision sociétale du patrimoine naturel, et adéquats aux données socio-culturelles (à connotation largement identitaire dans le cadre caraïbo-guyanais) de son appréhension par les populations comme par les aménageurs et les gestionnaires.La construction diachronique d’une protection juridique pertinente, en termes de durabilité notamment, a dépassé la seule démarche normative au profit de la reconnaissance d’un véritable droit à l’environnement, à travers ses déclinaisons législatives et constitutionnelles. Aujourd’hui, le droit positif prend en compte, au-delà du seul « environnement » envisagé in globo, aussi bien les paysages, ès-qualité, qui font l’objet d’un traitement et d’une protection juridiques spécifiques, que la biodiversité, dont la conservation et la gestion, du fait de sa reconnaissance conventionnelle en tant que patrimoine commun de l’Humanité, dans une perspective intergénérationnelle, ont suscité des dispositifs juridiques ad hoc, sur le plan national aussi bien que régional et international.
Pays, mouvements et sons dans la vallée de Grande-Rivière : pour une approche phénoménologique des paysages de Guadeloupe
Authors: Benoît Catherine
Published: October 2012

Si la perception de la nature antillaise comme faisant paysage ne fait pas l'ombre d'un doute aujourd'hui pour un Européen, en est-il de même pour la population guadeloupéenne? Si l'on définit le paysage comme l’expression culturelle motivée par la vue de la relation qu’un individu ou un groupe social entretient avec le milieu qui l’environne, alors cette notion ne rend pas compte des relations premières que les Guadeloupéens ont avec leur environnement. L’analyse de la perception et du vécu que la population de la vallée de Grande-Rivière a de son environnement montre en fait l’existence d’une esthétique polysensorielle de l’environnement qui privilégie d'abord l'ouïe, le sens du mouvement et le bien-être dans l'appréciation des lieux. Cet article propose une phénoménologie des paysages dans les années mille neuf cent quatre-vingt-dix avant le développement des politiques publiques d’aménagement du territoire et de gestion du paysage qui ont peut-être modifié ce vécu de l’environnement.
La forêt guyanaise, entre valorisation et protection des ressources écosystémiques
Authors: Calmont André
Published: October 2012

La forêt guyanaise est un écosystème extrêmement complexe, au patrimoine floristique et faunistique d’une grande diversité. Pendant longtemps, l’exploitation des ressources de et dans l’écosystème était insignifiante et n’avait jamais été pensée dans un cadre de développement durable. Toutefois, la population ayant triplée en une trentaine d’années, passant de 73 000 habitants en 1982 à plus de 220 000 aujourd’hui, la pression des activités humaines sur le milieu forestier est devenue significative, par la production de bois, la chasse, la cueillette, l’agriculture, l’utilisation de la biomasse à des fins énergétiques ou encore l’exploitation aurifère. Les risques environnementaux menacent donc la biodiversité de ce milieu. La prise de conscience de cette situation potentielle a conduit les pouvoirs publics à prendre, dans un contexte international favorable, un certain nombre de mesures en matière de réglementation et de gestion durable et surtout de mise en place d’un réseau d’espaces naturels protégés, dont un récent parc national, le Parc amazonien de Guyane.
Du bleu au vert, quand l’île tente de tourner le dos à la mer
Authors: Germanaz Christian , Sicre Michel
Published: October 2012

L’objectif de cette communication est d’analyser les modalités de l’introduction du paysage végétal dans les images de destination à l’usage des espaces insulaires tropicaux. À partir des exemples de communications et d’aménagements réalisés aux Seychelles, à Maurice et à La Réunion, nous proposons une réflexion sur l‘intérêt et les conséquences qu’implique l’investissement du paysage « vert » pour les économies insulaires dont le développement fait une part importante à l’activité touristique. Quels enseignements, les expériences india-océaniques peuvent-elles apporter au contexte de la Caraïbe et des Guyanes et réciproquement?
Le paysage façonné par le droit, entre la rationalité du droit positif et l’empirisme culturel juridique
Authors: Barrière Olivier
Published: October 2012

Le paysage en tant que produit d’une représentation sociale est le résultat d’actions naturelles et humaines, une sorte d’alchimie socio-physico-biologique dans laquelle la régulation juridique intervient fortement. Ainsi peut-on voir le paysage formé par le droit, particulièrement celui, transversal, de l’environnement, avec celui de l’aménagement du territoire et de l’urbanisme. Le droit positif français façonne le paysage dans un contexte d’appropriation, d’actions publiques d’aménagement et de projets collectifs, favorisant le passage d’un droit du paysage à un droit au paysage par le biais de l’intérêt paysager. Cependant, les normes codifiées et les instruments juridiques issus de politiques publiques sont adoptés et pris au sein d’un contexte paradigmatique suffisamment évolutif pour atteindre une patrimonialisation du paysage, quoiqu’imparfaite.En intégrant dans l’analyse en guise d’illustration l’exemple des Amérindiens Wayana, situés dans le contexte du département d’outre-mer de la Guyane, une autre dimension s’ouvre et des interrogations se posent. La cartographie participative de la territorialisation réalisée auprès des acteurs locaux sur support de photographies satellitaires permet une mise en parallèle de l’endogène au national. On touche là au point sensible de l’apposition de paradigmes juridiques différents, d’un côté celui du droit commun (positif), de l’autre celui d’un droit plus endogène, issu de spécificités sociaux culturelles et éco-géographiques.
Habitabilité et nature urbaines : vers un outil d’évaluation des projets urbains
Authors: Delabarre Muriel , Marry Solène
Published: October 2012

L’objet de cet article — dont le terrain d’analyse s’inscrit dans la métropole lyonnaise en se focalisant plus spécifiquement sur les jardins aquatiques du projet urbain de La Confluence — a trait à la question d’habitabilité urbaine. Nous apportons un questionnement sur les indicateurs évaluatifs de nature en ville et tentons de déterminer une grille d’évaluation des projets urbains. Toute la complexité d’une démarche évaluative réside dans les critères de choix des indicateurs, notamment lorsque l’objet d’étude se révèle mouvant spatialement et temporellement.
Pulmonary Embolization with Tunneled Hemodialysis Catheter-Associated Blood Stream Infection: The Perils of Systemic Anticoagulation
Authors: Gharaibeh Kamel A. , Csongrádi Éva , Shoemaker-Moyle Michael , Lerant Anna , Tapolyai Mihály , Fülöp Tibor
Published: October 2012

A 35-year old African-American male with end-stage renal disease on hemodialysis through a tunneled dialysis catheter (TDC) presented with fever, diffuse aches and generalized distress. Blood cultures (BC) were obtained and empirical broad-spectrum antibiotic therapy started. After urgent renal dialysis, TDC was pulled at the bedside. Chest computed tomography (CT) diagnosed pulmonary embolism and systemic i.v. heparin was initiated. BC grew Gram positive cocci (methicillin-sensitive S. aureus) and cardiac echocardiogram confirmed acute bacterial endocarditis. Due to declined mental status, CT imaging was obtained revealing massive intracranial hemorrhage leading to the patient's death. Further chest CT review revealed only hemodynamically non-significant pulmonary emboli in some segmental and subsegmental arteries. Pulmonary embolization may be an expected occurrence with removal of infected TDC; systemic anticoagulation may not be warranted in such cases and may lead to catastrophic intracranial hemorrhage. This case draws our attention to the perils of rigid adherence to protocol and the failure of considering the needs of special patient cohorts and individualized care.
Modeling the irradiance dependency of the quantum efficiency of photosynthesis
Authors: Silsbe Greg M. , Kromkamp Jacco C.
Published: October 2012

Measures of the quantum efficiency of photosynthesis (ϕPSII) across an irradiance (E) gradient are an increasingly common physiological assay and alternative to traditional photosynthetic‐irradiance (PE) assays. Routinely, the analysis and interpretation of these data are analogous to PE measurements. Relative electron transport rates (rETR = E × ϕPSII) are computed and fit to a PE curve to retrieve physiologically meaningful PE parameters. This widespread approach is statistically flawed as the response variable (rETR) is explicitly dependent on the predictor variable (E). Alternatively the E‐dependency of ϕPSII can be modeled directly while retaining the desired PE parameters by normalizing a given PE model to E. This manuscript presents a robust analysis in support of this alternative procedure. First, we demonstrate that scaling ϕPSII to rETR unnecessarily amplifies the measurement error of ϕPSII and using a Monte‐Carlo analysis on synthetic data induces significantly higher uncertainty in computed PE parameters relative to modeling the E‐dependency of ϕPSII directly. Next a large dataset is simultaneously fitted to four PE models implemented in their original and E‐normalized forms. Four statistical criteria used to evaluate the efficacy of nonlinear models demonstrate improved model fits and more precise PE parameters when data are modeled as E‐dependent changes in ϕPSII. The analysis presented in this manuscript clearly demonstrates that modeling the E‐dependency of ϕPSII directly should be the norm for interpreting active fluorescence measures.
CH4 and CO distributions over tropical fires as observed by the Aura TES satellite instrument and modeled by GEOS-Chem
Authors: Worden J. , Wecht K. , Frankenberg C. , Alvarado M. , Bowman K. , Kort E. , Kulawik S. , Lee M. , Payne V. , Worden H.
Published: October 2012

Abstract. Tropical fires represent a highly uncertain source of atmospheric methane (CH4) because of the variability of fire emissions and the dependency of the fire CH4 emission factors (g kg−1 dry matter burned) on fuel type and combustion phase. In this paper we use new observations of CH4 and CO in the free troposphere from the Aura Tropospheric Emission Sounder (TES) satellite instrument to place constraints on the role of tropical fire emissions versus microbial production (e.g. in wetlands and livestock) during the (October) 2006 El Nino, a time of significant peat fire emissions from Indonesia We first evaluate the global CH4 distributions from TES using the GEOS-Chem model. We find a mean bias between the observations and model of 26.3 ppb CH4 that is independent of latitude between 50° S and 80° N consistent with previous validation studies of TES CH4 retrievals using aircraft measurements. The slope of the distribution of CH4 versus CO as observed by TES and modeled by GEOS-Chem is consistent (within the TES observation error) for air parcels over the Indonesian peat fires, South America, and Africa. The CH4 and CO distributions are correlated between R = 0.42 and R = 0.46, with these correlations primarily limited by the TES random error. Over Indonesia, the observed slope of 0.13 (ppb ppb−1) ± 0.01, as compared to a modeled slop of 0.153 (ppb ppb−1) ± 0.005 and an emission ratio used within the GEOS-Chem model of approximately 0.11 (ppb ppb−1) indicates that most of the observed methane enhancement originated from the fire. Slopes of 0.47 (ppb ppb−1) ± 0.04 and 0.44 (ppb ppb−1) ± 0.03 over South America and Africa show that the methane in the observed air parcels primarily came from microbial generated emissions. Sensitivity studies using GEOS-Chem show that part of the observed correlation for the Indonesian observations and most of the observed correlations over South America and Africa are a result of transport and mixing of the fire and nearby microbial generated emissions into the observed air parcels. Differences between observed and modeled CH4 distributions over South America and Southern Africa indicate that the magnitude of the methane emissions for this time period are inconsistent with observations even if the relative distribution of fire versus biotic emissions are consistent. This study shows the potential for estimation of CH4 emissions over tropical regions using joint satellite observations of CH4 and CO.
Effects of internal mixing and aggregate morphology on optical properties of black carbon using a discrete dipole approximation model
Authors: Scarnato B. , Vahidinia S. , Richard D. T. , Kirchstetter T. W.
Published: October 2012

Abstract. According to recent studies, internal mixing of black carbon (BC) with other aerosol materials in the atmosphere alters its aggregate shape, absorption of solar radiation, and radiative forcing. These mixing state effects are not yet fully understood. In this study, we characterize the morphology and mixing state of bare BC and BC internally mixed with sodium chloride (NaCl) using electron microscopy and examine the sensitivity of optical properties to BC mixing state and aggregate morphology using a discrete dipole approximation model (DDSCAT). DDSCAT predicts a higher mass absorption coefficient, lower single scattering albedo (SSA), and higher absorption Angstrom exponent (AAE) for bare BC aggregates that are lacy rather than compact. Predicted values of SSA at 550 nm range between 0.18 and 0.27 for lacy and compact aggregates, respectively, in agreement with reported experimental values of 0.25 ± 0.05. The variation in absorption with wavelength does not adhere precisely to a power law relationship over the 200 to 1000 nm range. Consequently, AAE values depend on the wavelength region over which they are computed. In the 300 to 550 nm range, AAE values ranged in this study from 0.70 for compact to 0.95 for lacy aggregates. The SSA of BC internally mixed with NaCl (100–300 nm in radius) is higher than for bare BC and increases with the embedding in the NaCl. Internally mixed BC SSA values decrease in the 200–400 nm wavelength range, a feature also common to the optical properties of dust and organics. Linear polarization features are also predicted in DDSCAT and are dependent on particle morphology. The bare BC (with a radius of 80 nm) presents in the linear polarization a bell shape feature, which is a characteristic of the Rayleigh regime (for particles smaller than the wavelength of incident radiation). When BC is internally mixed with NaCl (100–300 nm in radius), strong depolarization features for near-VIS incident radiation are evident, such as a decrease in the intensity and multiple modes at different angles corresponding to different mixing states. DDSCAT, being flexible on the geometry and refractive index of the particle, can be used to study the effect of mixing state and complex morphology on optical properties of realistic BC aggregates. This study shows that DDSCAT predicts morphology and mixing state dependent optical properties that have been reported previously and are relevant to radiative transfer and climate modeling and interpretation of remote sensing measurements.
Marine bacteria in deep Arctic and Antarctic ice cores: a proxy for evolution in oceans over 300 million generations
Authors: Price P. B. , Bay R. C.
Published: October 2012

Abstract. Using fluorescence spectrometry to map autofluorescence of chlorophyll (Chl) and tryptophan (Trp) versus depth in polar ice cores in the US National Ice Core Laboratory, we found that the Chl and Trp concentrations often showed an annual modulation of up to 25%, with peaks at depths corresponding to local summers. Using epifluorescence microscopy (EFM) and flow cytometry (FCM) triggered on red fluorescence at 670 nm to study microbes from unstained melts of the polar ice, we inferred that picocyanobacteria may have been responsible for the red fluorescence in the cores. Micron-size bacteria in all ice melts from Arctic and Antarctic sites showed FCM patterns of scattering and of red vs. orange fluorescence (interpreted as due to Chl vs. phycoerythrin (PE)) that bore similarities to patterns of cultures of unstained picocyanobacteria Prochlorococcus and Synechococcus. Concentrations in ice from all sites were low, but measurable at ~ 1 to ~ 103 cells cm−3. Calibrations showed that FCM patterns of mineral grains and volcanic ash could be distinguished from microbes with high efficiency by triggering on scattering instead of by red fluorescence. Average Chl and PE autofluorescence intensities showed no decrease per cell with time during up to 150 000 yr of storage in glacial ice. Taking into account the annual modulation of ~ 25% and seasonal changes of ocean temperatures and winds, we suggest that picocyanobacteria are wind-transported year-round from warmer ocean waters onto polar ice. Ice cores offer the opportunity to study evolution of marine microbes over ~ 300 million generations by analysing their genomes vs. depth in glacial ice over the last 700 000 yr as frozen proxies for changes in their genomes in oceans.
Analysis of long-term terrestrial water storage variations in Yangtze River basin
Authors: Huang Y. , Salama M. S. , Krol M. S. , van der Velde R. , Hoekstra A. Y. , Zhou Y. , Su Z.
Published: October 2012

Abstract. In this study, we analyze 32 yr of TWS data obtained from Interim Reanalysis Data (ERA-Interim) and Noah model from Global Land Data Assimilation System (GLDAS-Noah) for the period between 1979 and 2010. The accuracy of these datasets is validated against 26 yr (1979–2004) of runoff dataset from Yichang gauging station and compared to 32 yr of independent precipitation data obtained from Global Precipitation Climatology Centre Full Data Reanalysis Version 6 (GPCC) and NOAA's PRECipitation REConstruction over Land (PREC/L). Spatial and temporal analysis of the TWS data shows that TWS in the Yangtze River basin is decreasing significantly since the year 1998. The driest period of the basin is noted from 2005 to 2010, especially in the middle and lower Yangtze reaches. The TWS changed abruptly into persistently high negative anomalies in the middle and lower Yangtze reaches in 2004. From both basin and annual perspectives, 2006 is detected as the major inflection point at which the system exhibits a persistent decrease in TWS. Comparing these TWS trends to independent precipitation datasets shows that the recent decrease in TWS can mainly be attributed to a decrease in precipitation amount. Our finding is based on observation and modeling data sets and confirms previous results based on gauging station datasets.
Deep-sea nematodes (Comesomatidae) from the Southwest Pacific Ocean: five new species and three new species records
Authors: Leduc Daniel
Published: October 2012

The present study describes five new free-living nematode species and provides three new species records of the family Comesomatidae (genera Cervonema Wieser, 1954, Dorylaimopsis Ditlevsen, 1918, Hopperia Vitiello, 1969, and Kenyanema Muthumbi et al., 1997) from the continental margin of New Zealand, Southwest Pacific. Dichotomous identification keys are provided for all known species of Dorylaimopsis and Hopperia. Cervonema shiae Chen & Vincx, 2000 is recorded for the first time outside the type locality (Beagle Channel, Chile). C. kaikouraensis sp. nov. is characterised by amphideal fovea with 5.5 turns situated at 1.7 head diameter from anterior end, jointed outer labial setae, equal in length to cephalic setae, sperm dimorphism, and 5-6 small pre-cloacal supplements. C. multispira sp. nov. is characterised by amphideal fovea with 8.0-8.5 turns situated at 2.6-4.0 head diameter from anterior end, cephalic setae 2-3 μm long, slightly shorter than outer labial setae, presence of six uninucleated cells in males (potentially pseudocoelomocytes or supplementary excretory cells), 5 small pre-cloacal supplements, and strongly cuticularised, arcuate spicules with capitulum. C. proberti sp. nov. is characterised by amphideal fovea with 5 turns and located at < 1 head diameter from anterior end, cephalic setae 1.6-2.0 times longer than outer labial setae, and 8 small pre-cloacal supplements. Dorylaimopsis nodderi sp. nov. is characterised by cuticle with lateral differentiation consisting of three longitudinal rows of larger dots in the pharyngeal and caudal regions, two rows of larger dots in middle region of body, and spicules with rounded ventral projection at one third of spicule length from distal end, giving appearance of a joint. Hopperia ancora sp. nov. is characterised by short conical cephalic setae, spicules with hook-like projection at distal end, gubernaculum with bent apophyses, and 11-13 pre-cloacal supplements. H. beaglense Chen & Vincx, 1998 is recorded from Kaikoura Canyon, the first record of this species outside the type locality (Beagle Channel, Chile). Kenyanema monorchis Muthumbi et al., 1997 is also recorded for the first time outside the type locality (Indian Ocean).
Study of Arabian Seawater Temperature Fluctuations
Authors: M. Arif Hussain  , Shaheen Abbas  , M. Rashid Kamal Ansari  , Asma Zaffar
Published: October 2012

It is well known that the ocean has an important role in climate variability and change. To study the variations in sea-surface temperature (SST) of Arabian sea near Karachi coastal region, we apply the probability distributions theory as it gives more insights of SST fluctuating behavior. In this regard the adequacy of Normal. Gamma, and Lognormal probability distributions is tested with the help of Kolmogorov-Smirnov D-test. It is found that most of the months of the year follow Normal probability distribution, whereas April, August, October, and November follow Lognormal probability distribution. Further, using the distribution parameters mean and standard deviations of monthly SST are also calculated, which come out to be (23.33 ± 0.316), (23.19 ± 0.300), (24.36 ± 0.312), (26.27 ± 0.360), (28.31 ± 0.325), (29.19 ± 0.347), (28.64 ± 0.346), (27.38 ± 0.364), (27.34 ± 0.322), (27.61 ± 0.311), (26.43 ± 0.352), (24.65 ±0.380).
Performance Measures in Binary Classification
Authors: Kohl Matthias
Published: October 2012

We give a brief overview over common performance measures for binary classification. We cover sensitivity, specificity, positive and negative predictive value, positive and negative likelihood ratio as well as ROC curve and AUC.
Exploitation of a Laccase/Meldola’s Blue System for NAD+ Regeneration in Preparative Scale Hydroxysteroid Dehydrogenase‐Catalyzed Oxidations
Authors: Ferrandi Erica Elisa , Monti Daniela , Patel Ilabahen , Kittl Roman , Haltrich Dietmar , Riva Sergio , Ludwig Roland
Published: October 2012

An enzymatic regeneration system consisting of laccase and the 2H+/2e− redox mediator Meldola’s blue (MB) was developed for the efficient oxidation of reduced nicotinamide adenine dinucleotide (NADH) cofactor and employed in the gram‐scale oxidation of cholic acid (1) to its 7‐keto derivative (1a) by 7α‐hydroxysteroid dehydrogenase (7α‐HSDH) in an aqueous, buffered reaction system. The regenerating enzyme, laccase, reduces molecular oxygen as terminal 4H+/4e− acceptor to water and concomitantly reoxidizes NADH via MB at high turnover rates. The regeneration system was successfully applied to quantitatively convert 1 (50 mM, 20.4 g) into 1a with a space‐time yield of 5.8 mmol L−1 h−1. High total turnover numbers were achieved for 7α‐HSDH (4.2×105) and laccase (1.1×106). Alternatively, the regeneration system was employed on the conversion of the methyl ester derivative of cholic acid (2, 200 mM, 5.9 g) dissolved in isopropyl acetate as organic solvent in a biphasic system. Due to the high concentration of 2 and the excellent performance of the enzymatic cascade reaction even under the harsh process conditions, space‐time yields of up to 20 mmol L−1 h−1 (8.5 g L−1 h−1) of the produced 7‐keto derivative 2a were obtained. The irreversibility and high driving force of the regenerating reaction allowed quantitative conversions and easy product recovery.
Feed distribution in distillation: Assessing benefits and limits with column profile maps and rigorous process simulation
Authors: Beneke Daniel , Hildebrandt Diane , Glasser David
Published: October 2012

This contribution describes the column profile map (CPM) methodology for designing distributed feed distillation columns. For non‐sharp product distributions, a case study shows that energy savings of approximately 35% can be obtained if the feed stage(s) are designed optimally. Feed distribution allows capital cost savings, expands operating leaves, and can obtain greater separation feasibility. However, this column only has benefits in ternary and higer‐order systems and when product distributions are non‐sharp. To validate these counter‐intuitive claims, a real Benzene, p‐Xylene, Toluene system is modeled using CPMs, and the resulting design parameters are transported to Aspen Plus®. Using a sum of squared errors objective function to quantify savings, a cost saving trend very similar to the one predicted by the CPM method is obtained. This article therefore describes a complete design methodology for distributed feed systems and provides convincing evidence of benefits of such a system. © 2012 American Institute of Chemical Engineers AIChE J, 59: 1668–1683, 2013
Cognitive and behavioral aspects of Smith–Lemli–Opitz syndrome
Authors: Diaz‐Stransky Andrea , Tierney Elaine
Published: October 2012

The brain's high concentrations of cholesterol make it especially vulnerable to the cholesterol biosynthetic defect that characterizes Smith–Lemli–Opitz syndrome (SLOS). An attempt to characterize the cognitive and behavioral phenotype of SLOS has identified increased rates of intellectual disability, language and motor developmental delay, repeated self‐injury behaviors, sensory hyperreactivity, hyperactivity, affect dysregulation, and sleep disturbances. Some research has suggested that carriers of the gene mutation that results in SLOS display increased risk of suicidal behavior. Cholesterol dysregulation impairs neuroplasticity, which may be a mechanism underlying some of the mentioned abnormalities. Discrete positive effects have been reported with the use of cholesterol supplementation in the treatment of SLOS. Research has been limited by the small number of subjects available, and a limited understanding of lipid metabolism in the brain. Hopefully future research will help clarify the role that cholesterol plays in cognitive and behavioral abnormalities like the ones associated with SLOS. This would accelerate the development of treatments for SLOS, and perhaps also further understanding of non‐syndromic psychiatric disorders such as autism and attention deficit hyperactivity disorder. © 2012 Wiley Periodicals, Inc.
Reconstruction of periodicity of repetitive linear enamel hypoplasia from perikymata counts on imbricational enamel among dry‐adapted chimpanzees (Pan troglodytes verus) from Fongoli, Senegal
Authors: Skinner Mark F. , Pruetz Jill D.
Published: October 2012

Periodicity of repetitive linear enamel hypoplasia (rLEH) in apes from high latitudes with single wet and dry seasons annually has not been described. We reconstruct periodicity and duration of rLEH in canine teeth from three recently deceased chimpanzees from Fongoli, Senegal with a marked seven‐month dry season. High‐resolution dental molds were taken in the field for magnified imaging with digital microscopy. Photomontages allowed counting of perikymata between episodes of rLEH for reconstruction of periodicity and duration of physiological stress. Where rLEH spans the imbricational enamel, the number of events is consistent with years required to form canine imbricational enamel; i.e., periodicity of rLEH seems circannual. We predicted perikymata counts between rLEH events ranging from 52 to 61 based on reported “long counts” of 7–6 days. Counts ranged from 29.5 to 44, individual mean of 36.7. This discrepancy could be explained by recurrent stress with a periodicity of 7.2–8.4 months, or by long counts of 10 days per stria. Neither is supported in the literature. Since we find evidence of rLEH with circannual periodicity, we postulate the existence of non‐emergent imbricational striae. Based on evidence that stress at Fongoli recurs annually, we reconstruct stress duration of 2–3 months, longer than reported for chimpanzees living in other habitats, which we attribute to heat stress and food shortage near shrinking waterholes. We conclude that canine teeth from a small mortality cohort of chimpanzees at Fongoli preserve a faithful record of dry season stress in an extreme environment. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.
Revisiting the Gain–Loss Separability Assumption in Prospect Theory
Authors: Por Han‐Hui , Budescu David V.
Published: October 2012

A fundamental assumption of prospect theory is gain–loss separability (GLS)—the assertion that the overall utility of a prospect can be expressed as a function of the utilities of its positive and negative components. Violations of GLS may potentially limit the generalization of results from studies of single‐domain prospects to mixed prospects and systematically distort the predictions of the theory. Violations also have implications for how choices with positive and negative components should be presented to decision makers. Previous studies, using different elicitation methods, have documented different rates, and types, of systematic violations of GLS. We discuss the differences between two specific elicitation methods—binary choice and certainty equivalents—and report results of a new study of GLS using both methods and randomly generated prospects. We compare the extent and nature of GLS violations under the two elicitation methods using between‐subject and within‐subject analyses. We find (i) systematic violations of GLS under both methods, (ii) higher rates of violations under choice, (iii) higher sensitivity to the outcomes for the certainty equivalents, which is consistent with the predictions of the scale‐compatibility hypothesis, and (iv) different patterns of violations under the two methods, which are explained by method‐specific preferences. We discuss the psychological mechanisms underlying the findings and the implications for presenting information with gain and loss components. Copyright © 2012 John Wiley & Sons, Ltd.
In vitro selection of sialic acid specific RNA aptamer and its application to the rapid sensing of sialic acid modified sugars
Authors: Cho Suhyung , Lee Bo‐Rahm , Cho Byung‐Kwan , Kim June‐Hyung , Kim Byung‐Gee
Published: October 2012

Sialic acids (SAs) are located on the terminal positions of glycan on a cell surface, which play important role in the spread and metastasis of cancer cells and infection of pathogen. For their detection and diagnosis, the finding of SA specific ligand is an essential prerequisite. Here, RNA aptamer for N‐acetylneuraminic acid (Neu5Ac), a representative of SAs, with the high affinity of 1.35 nM and the selectivity was screened by in vitro selection method. The strong binding of the screened aptamer was enough to protect the hydrolysis of Neu5Ac by neuraminidase with the stoichiometry of 1:1 molar ratio. For the rapid detection of SAs, the RNA aptamer was further engineered to the aptazyme sensor by conjugating with a ribozyme following the characterization of selected aptamer by RNase footprinting assay. Without additional desialylation, modification, or/and purification processes, the aptazyme indicated high catalytic activities in the presence of Neu5Ac over 20 µM in several minutes. Also, we observed that the aptazyme sensor shows high sensitivities to Neu5Ac‐conjugated sugars as well as Neu5Ac monomer, but not in non‐Neu5Ac modified sugars. The aptamer for Neu5Ac can support valuable tools in a wide range of bioanalytical applications as well as biosensors. Biotechnol. Bioeng. 2013; 110: 905–913. © 2012 Wiley Periodicals, Inc.
Reconstitution of cellulose and lignin after [C2mim][OAc] pretreatment and its relation to enzymatic hydrolysis
Authors: Yuan Tong‐Qi , Wang Wei , Zhang Li‐Ming , Xu Feng , Sun Run‐Cang
Published: October 2012

Although the effects of cellulose crystallinity and lignin content as two major structural features on enzymatic hydrolysis have been extensively studied, debates regarding their effects still exist. In this study, reconstitution of cellulose and lignin after 1‐ethyl‐3‐methylimidazolium acetate ([C2mim][OAc]) pretreatment was proposed as a new method to study their effects on enzymatic digestibility. Different mechanisms of lignin content for reduction of cellulose hydrolysis were found between the proposed method and the traditional method (mixing of cellulose and lignin). The results indicated that a slight change of the crystallinity of the reconstituted materials may play a minor role in the change of enzyme efficiency. In addition, the present study suggested that the lignin content does not significantly affect the digestibility of cellulose, whereas the conversion of cellulose fibers from the cellulose I to the cellulose II crystal phase plays an important role when an ionic liquid pretreatment of biomass was conducted. Biotechnol. Bioeng. 2013; 110: 729–736. © 2012 Wiley Periodicals, Inc.
Ruthenium‐Catalyzed Allylation–Cyclization Reactions of Cyclic 1,3‐Dicarbonyl Compounds with 1‐Vinyl Propargyl Alcohols
Authors: Jonek Anita , Berger Stefanie , Haak Edgar
Published: October 2012

Ruthenium‐catalyzed allylation–cyclization reactions of cyclic 1,3‐dicarbonyl compounds with 1‐vinyl propargyl alcohols that lead to diverse carbo‐ or heterocyclic products in a one‐pot cascade process are reported. These mechanistically distinct reactions are catalyzed by a single ruthenium(0) complex that contains a redox‐coupled dienone ligand. The reaction pathway strongly depends on the substrate substitution pattern, which determines the mode of activation of the 1‐vinyl propargyl alcohol. The environmentally benign process, which generates water as the only waste product, is of wide scope and allows the atom‐economic synthesis of highly functionalized furans, pyrans, and spirocarbocycles.
Synthesis and Self‐Organization of Zinc β‐(Dialkoxyphosphoryl)porphyrins in the Solid State and in Solution
Authors: Vinogradova Ekaterina V. , Enakieva Yulia Y. , Nefedov Sergey E. , Birin Kirill P. , Tsivadze Aslan Y. , Gorbunova Yulia G. , Bessmertnykh Lemeune Alla G. , Stern Christine , Guilard Roger
Published: October 2012

The first synthesis and self‐organization of zinc β‐phosphorylporphyrins in the solid state and in solution are reported. β‐Dialkoxyphosphoryl‐5,10,15,20‐tetraphenylporphyrins and their ZnII complexes have been synthesized in good yields by using Pd‐ and Cu‐mediated carbon–phosphorous bond‐forming reactions. The Cu‐mediated reaction allowed to prepare the mono‐β‐(dialkoxyphosphoryl)porphyrins 1 Zn–3 Zn starting from the β‐bromo‐substituted zinc porphyrinate ZnTPPBr (TPP=tetraphenylporphyrin) and dialkyl phosphites HP(O)(OR)2 (R=Et, iPr, nBu). The derivatives 1 Zn–3 Zn were obtained in good yields by using one to three equivalents of CuI. When the reaction was carried out in the presence of catalytic amounts of palladium complexes in toluene, the desired zinc derivative 1 Zn was obtained in up to 72 % yield. The use of a Pd‐catalyzed CP bond‐forming reaction was further extended to the synthesis of β‐poly(dialkoxyphosphoryl)porphyrins. An unprecedented one‐pot sequence involving consecutive reduction and phosphorylation of H2TPPBr4 led to the formation of a mixture of the 2,12‐ and 2,13‐bis(dialkoxy)phosphorylporphyrins 5 H2 and 6 H2 in 81 % total yield. According to the X‐ray diffraction studies, 1 Zn and 3 Zn are partially overlapped cofacial dimers formed through the coordination of two Zn centers by two phosphoryl groups belonging to the adjacent molecules. The equilibrium between the monomeric and the dimeric species exists in solutions of 1 Zn and 3 Zn in weakly polar solvents according to spectroscopic data (UV/Vis absorption and NMR spectroscopy). The ratio of each form is dependent on the concentration, temperature, and traces of water or methanol. These features demonstrated that zinc β‐phosphorylporphyrins can be regarded as new model compounds for the weakly coupled chlorophyll pair in the photosynthesis process.
(110)‐Oriented ZIF‐8 Thin Films on ITO with Controllable Thickness
Authors: Hou Chuantao , Xu Qin , Peng Jinyun , Ji Zhengping , Hu Xiaoya
Published: October 2012

(110)‐oriented zeolitic imidazolate framework (ZIF)‐8 thin films with controllable thickness are successfully deposited on indium tin oxide (ITO) electrodes at room temperature. The method applied uses 3‐aminopropyltriethoxysilane (APTES) in the form of self‐assembled monolayers (SAMs), followed by a subsequent adoption of the layer‐by‐layer (LBL) method. The crystallographic preferential orientation (CPO) index shows that the ZIF‐8 thin films are (110)‐oriented. A possible mechanism for the growth of the (110)‐oriented ZIF‐8 thin films on 3‐aminopropyltriethoxysilane modified ITO is proposed. The observed cross‐sectional scanning electron microscopy (SEM) images and photoluminescent (PL) spectra of the ZIF‐8 thin films indicate that the thickness of the ZIF‐8 layers is proportional to the number of growth cycles. The extension of such a SAM method for the fabrication of ZIF‐8 thin films as described herein should be applicable in other ZIF materials, and the as‐prepared ZIF‐8 thin films on ITO may be explored for photoelectrochemical applications.
Prognostic impact of human papillomavirus status, survivin, and epidermal growth factor receptor expression on survival in patients treated with radiochemotherapy for very advanced nonresectable oropharyngeal cancer
Authors: Semrau Robert , Duerbaum Helena , Temming Susanne , Huebbers Christian , Stenner Markus , Drebber Uta , Klussmann Jens Peter , Müller Rolf‐Peter , Preuss Simon F.
Published: October 2012

Background

The influence of human papillomavirus (HPV) status on survival for patients with very advanced inoperable oropharyngeal SCC treated with radiochemotherapy (RCT) was studied.

Methods

Patients received either 69.2 Gy with concomitant boost (ccb) or 70 Gy conventionally fractionated (cf), weekly paclitaxel 40 mg/m2, and carboplatin area under the concentration–time curve (AUC) 1. Tumor was analyzed for the presence of high‐risk HPV‐DNA using polymerase chain reaction (PCR) and direct DNA sequencing. p16‐expression, survivin, and epidermal growth factor receptor (EGFR) expression were evaluated by immunohistochemistry and influence on survival was calculated.

Results

Of 52 patients, 25.0% were HPV positive and 75.0% HPV negative. The 2‐year progression‐free survival (PFS) was 70.1% for p16‐positive patients and 37.1% for p16‐negative patients (p = .005). The 3‐year overall survival (OS) rate was 43.9% for all patients and did not significantly differ between the groups. Neither survivin nor EGFR expression influenced PFS or OS significantly.

Conclusions

HPV status influences PFS in patients with advanced, nonresectable tumor stages but not OS. Additional risk factors seem to have a stronger influence on survival than HPV status. © 2012 Wiley Periodicals, Inc. Head Neck, 2013
Patterns of musculoskeletal pain in the population: A latent class analysis using a nationally representative interviewer‐based survey of 4817 Danes
Authors: Hartvigsen J. , Davidsen M. , Hestbaek L. , Sogaard K. , Roos E.M.
Published: October 2012

Background

Pain from the musculoskeletal system often occurs in more than one site. This appears to affect prognosis negatively. Knowledge about specific pain patterns is lacking.

Objectives

To define specific patterns of musculoskeletal co‐complaints occurring alongside a primary musculoskeletal complaint.

Methods

Using data from an interview‐based health survey of a nationally representative sample of the adult Danish population in 1991 (n = 4817), we describe the co‐occurrence of musculoskeletal complaints. Using latent class analysis, we identify clusters of musculoskeletal complaints.

Results

Forty percent reported a complaint during a 2‐week period; the most common being the low back, neck, shoulder, and knee, and 40% reported more than one complaint. Two latent classes were found for each of the nine primary pain sites except for the low back where three were found. For all primary pain areas, the largest class had site‐specific pain only, whereas the smallest class had diffuse pain covering large parts of the body. For participants with a primary musculoskeletal complaint in the spine, the highest probabilities for co‐complaints were at other sites in the spine. For primary complaints in the extremities, co‐complaints occurred most commonly at adjacent areas. One noticeable exception was a primary complaint of knee pain where co‐complaints were found in more remote areas as the neck and low back.

Conclusions

Unique clusters of musculoskeletal co‐complaints can be determined based on primary pain site. These patterns are different for persons with a primary complaint in the spine compared with persons with a primary complaint in the extremities.
Reaction energetics on long‐range corrected density functional theory: Diels–Alder reactions
Authors: Singh Raman K. , Tsuneda Takao
Published: October 2012

The possibility of quantitative reaction analysis on the orbital energies of long‐range corrected density functional theory (LC‐DFT) is presented. First, we calculated the Diels–Alder reaction enthalpies that have been poorly given by conventional functionals including B3LYP functional. As a result, it is found that the long‐range correction drastically improves the reaction enthalpies. The barrier height energies were also computed for these reactions. Consequently, we found that dispersion correlation correction is also crucial to give accurate barrier height energies. It is, therefore, concluded that both long‐range exchange interactions and dispersion correlations are essentially required in conventional functionals to investigate Diels–Alder reactions quantitatively. After confirming that LC‐DFT accurately reproduces the orbital energies of the reactant and product molecules of the Diels–Alder reactions, the global hardness responses, the halves of highest occupied molecular orbital (HOMO)‐lowest unoccupied molecular orbital (LUMO) energy gaps, along the intrinsic reaction coordinates of two Diels–Alder reactions were computed. We noticed that LC‐DFT results satisfy the maximum hardness rule for overall reaction paths while conventional functionals violate this rule on the reaction pathways. Furthermore, our results also show that the HOMO‐LUMO gap variations are close to the reaction enthalpies for these Diels–Alder reactions. Based on these results, we foresee quantitative reaction analysis on the orbital energies. © 2012 Wiley Periodicals, Inc.