bluuebunny/crossref_metadata_2025 huggingface dataset:
Schubversuche an Stahlbetonbalken unterschiedlicher M/V‐Kombinationen
Authors: Tue Nguyen Viet , Ehmann Rainer , Tung Nguyen Duc
Published: July 2015

Der vorliegende Aufsatz berichtet über experimentelle Untersuchungen zum Einfluss des statischen Systems und der Belastungsart auf das Querkraftverhalten von Biegebauteilen ohne Querkraftbewehrung. Zehn rechteckige Stahlbetonbalken mit drei statischen Systemen und zwei Belastungsarten wurden hierbei getestet, wodurch nahezu alle in der Praxis möglichen M/V‐Kombinationen erfasst werden konnten. Die Ergebnisse zeigen erhebliche Unterschiede in der Querkrafttragfähigkeit von Schubfeldern unterschiedlicher M/V‐Kombinationen. Die Querkrafttragfähigkeit von Einfeldbalken unter Gleichlast ist höher als jene von vergleichbaren Balken unter Einzellast. Ferner ist die Querkrafttragfähigkeit von Krag‐ und Mittelstützen von Durchlaufbalken unter Gleichlast deutlich höher als die Querkrafttragfähigkeit von Einfeldbalken. Im Allgemeinen kann mit den Versuchsergebnissen festgestellt werden, dass die zugehörige Biegebeanspruchung die Querkrafttragfähigkeit eines Bauteils positiv beeinflusst. Weiterhin spielt das Rissbild infolge Biegung eine entscheidende Rolle für die Querkrafttragfähigkeit bei schubschlanken Stahlbetonbauteilen.

Shear tests on reinforced concrete beams with different M/V‐combinations

This paper presents an experimental investigation on the effect of structural system and load configuration on the shear behavior of flexural reinforced concrete (RC) members without shear reinforcement. A total of ten rectangular beams with three structural systems and two load configurations were tested. With the chosen test set‐up, almost all M/V‐combinations commonly encountered in practice can be investigated. The test results indicate significant differences of the shear capacity of members with different M/V‐combinations. The shear capacity of the simply supported beam under a uniform load is higher than that of similar beams under a concentrated load. Moreover, the shear capacity of the cantilever and continuous beams under uniform load is significantly higher than that of simply supported beams. Generally, it can be concluded that the co‐existing flexural action has a positive influence on the shear resistance of a RC member without shear reinforcement. Furthermore, the flexural crack pattern plays an important role in the shear resistance of slender RC members.
qPCR for second year undergraduates: A short, structured inquiry to illustrate differential gene expression
Authors: McCauslin Christine Seitz , Gunn Kathryn Elaine , Pirone Dana , Staiger Jennifer
Published: July 2015

We describe a structured inquiry laboratory exercise that examines transcriptional regulation of the NOS2 gene under conditions that simulate the inflammatory response in macrophages. Using quantitative PCR and the comparative CT method, students are able determine whether transcriptional activation of NOS2 occurs and to what degree. The exercise is aimed at second year undergraduates who possess basic knowledge of gene expression events. It requires only 4–5 hr of dedicated laboratory time and focuses on use of the primary literature, data analysis, and interpretation. Importantly, this exercise provides a mechanism to introduce the concept of differential gene expression and provides a starting point for development of more complex guided or open inquiry projects for students moving into upper level molecular biology, immunology, and biochemistry course work. © 2015 by the International Union of Biochemistry and Molecular Biology, 43(4):273–282, 2015.
Microautophagy involves programmed cell semi‐death of sieve elements in developing caryopsis of Triticum aestivum L.
Authors: Yang Wenli , Cai Jingtong , Zhou Zhuqing , Zhou Guangsheng , Mei Fangzhu , Wang Likai
Published: July 2015

Differentiation of sieve elements (SEs) involves programmed cell semi‐death, in which a small amount of organelles is retained. However, the mechanisms by which a large amount of SE cytoplasm is degraded and the specific proteases involved are not clear. In this study, we confirmed that the degradation of cytoplasm outside of the vacuole was mediated by microautophagy of the vacuole, and that the tonoplast selectively fused with the plasma membrane after most of the cytoplasm in the vacuoles was degraded. The integration of space enclosed a small amount of cytoplasm. Therefore, that fraction of the cytoplasm was preserved. At the same time, the cytosol was weakly acidic during membrane fusion because part of the tonoplast was ruptured. We also demonstrated that wheat aspartic protease (WAP1) and proteases including cathepsin B activity (PICA) were involved in programmed cell semi‐death of SEs. PICA showed strongest activity before mass of the cytoplasm was degraded, which might contribute toward SE stability. We found that WAP1 mainly degraded the cytoplasm. Therefore, programmed cell semi‐death of SEs might result from the joint action of vacuoles and multiple proteases.
Computational Investigation on the Mechanism of Amide Bond Formation by using Phosphine‐Based Redox Catalysis
Authors: Di Santo Emanuela , Alberto Marta E. , Russo Nino , Toscano Marirosa
Published: July 2015

A density functional theory investigation of the PPh3‐catalyzed formation of amides from benzoic acid was explored. The results confirm the involvement of a phosphonium intermediate that is crucial to activate the carboxylate for nucleophilic acyl substitution.
Influence of Tortuous Geometry on the Hydrodynamic Characteristics of Laminar Flow in Microchannels
Authors: Dai Zhenhui , Fletcher David F. , Haynes Brian S.
Published: July 2015

Flow visualizations are performed to study the hydrodynamic characteristics of laminar flow in tortuous microchannels for a wide range of Reynolds numbers. The detailed flow patterns in wavy channels are identified and found to be greatly affected by geometrical parameters. In wavy channels, steady flow exists at low Reynolds numbers, but above a critical number unsteady flow develops. The critical Reynolds number is found to depend on the characteristics of the channel path. Recirculation zones form immediately after the inner corners of the sharp bends, with their size and magnitude of the recirculation velocity increasing with higher Reynolds numbers. Large fluctuations in recirculation zone locations highlight the importance of these flow features in the development of transient flow. The flow behaviors play very important roles in determining the pressure drop in wavy channels relative to straight channels.
Measuring Cumulative Exposure to Oxygen with a Diphenylphosphine–Alkyl Naphthaleneimide Luminescence Turn‐On Dyad
Authors: Shritz Rozalia , Shapira Reut , Borzin Elena , Tumanskii Boris , Reichstein Werner , Meichner Christoph , Schwaiger Florian , Reichstein Paul M. , Kreyenschmidt Judith , Haarer Dietrich , Kador Lothar , Eichen Yoav
Published: July 2015

2‐(2‐Diphenylphosphanylethyl)benzo[de]isoquinoline‐1,3‐dione is a poorly luminescent, photoinduced‐electron‐transfer (PET) dyad, NI‐(Ph)2P:, in which the luminescence of its naphthaleneimide (NI) part is quenched by the lone‐pair electrons of the phosphorus atom of the (Ph)2P: group. Photoinduced oxidation of (Ph)2P: to (Ph)2PO by molecular oxygen regenerates the luminescence of the NI group, because the oxidized form (Ph)2PO does not serve as a quencher to the NI system. The oxidation of (Ph)2P: is thermally inaccessible. The NI‐(Ph)2P: system was applied to monitoring the cumulative exposure of oxidation‐sensitive goods to molecular oxygen. The major advantage of this new PET system is that it reacts with oxygen only via the photoinduced channel, which offers the flexibility of monitoring the cumulative exposure to oxygen in different time periods, simply by varying the sampling frequency. Electronic‐energy calculations and optical spectroscopic data revealed that the luminescence turn‐on upon reaction with molecular oxygen relies on a PET mechanism.
How Does Substitutional Doping Affect Visible Light Absorption in a Series of Homodisperse Ti11 Polyoxotitanate Nanoparticles?
Authors: Chen Yang , Jarzembska Katarzyna N. , Trzop Elżbieta , Zhang Lei , Coppens Philip
Published: July 2015

Homodisperse doped polyoxotitanate nanoclusters with formulae Ti11(MX)O14(OiPr)17 (M=Mn, Fe or Co; X=Cl, Br or I, OiPr=isopropoxide) display strongly dopant‐dependent properties. Spectroscopic solution and reflectance measurements backed up by density of states and time‐dependent DFT calculations based on the determined structures, show the prominent effect of FeX substitution by decreasing the HOMO–LUMO gap of the particles. The effect is attributed to the presence of an occupied Fe β orbital halfway up the bandgap, leading to long‐wavelength absorption with electron transfer to the titanium atoms of the cluster. Whereas the light absorption varies significantly with variation of the transition metal dopant, its dependency on the nature of the halogen atom or the change in dipole moment across the series is minor.
A Step‐by‐Step Assembly of a 3D Coordination Polymer in the Solid‐State by Desolvation and [2+2] Cycloaddition Reactions
Authors: Medishetty Raghavender , Tandiana Rika , Wu Jien , Bai Zhaozhi , Du Yonghua , Vittal Jagadese J.
Published: July 2015

Two solid‐state structural transformations that occur in a stepwise and a controlled manner are described. A combination of desolvation and cycloaddition reactions has been employed to synthesise a 3D coordination polymer (CP) from 1D CP [Cd(bdc)(4‐spy)2(H2O)]⋅2 H2O⋅2 DMF (bdc=1,4‐benzenedicarboxylate, 4‐spy=4‐styrylpyridine) presumably via a 2D layered structure, [Cd2(bdc)2(4‐spy)4]. In the absence of single crystals to follow the course of the photocycloaddition reaction, thermogravimetry, XAFS and NOESY NMR experiments were used to propose the formation of layered and pillared layered structures. Further, the present strategy enables us to synthesise new multidimensional architectures that are otherwise inaccessible by the self‐assembly process.
Catalytic Asymmetric Bromination of Unfunctionalized Olefins with H2O as a Nucleophile
Authors: Zhang Xun , Li Jing , Tian Hua , Shi Yian
Published: July 2015

The dimeric cinchona alkaloid (DHQD)2PHAL is used to catalyze an effective asymmetric bromohydroxylation of unfunctionalized olefins with H2O as nucleophile an N‐bromobenzamide as a bromine source. A variety of optically active bromohydrins are formed with up to 88 % ee.
Rückgewinnung Seltener Erden aus quecksilberbelasteten Leuchtstoffen mittels Feststoffchlorierung
Authors: Lorenz Tom , Golon Katja , Fröhlich Peter , Bertau Martin
Published: July 2015

Durch die Entsorgung quecksilberhaltiger Leuchtstoffe werden dem Wertstoffkreislauf jedes Jahr große Mengen an Seltenen Erden entzogen. Zur Rückgewinnung dieser Wertstoffe wurde die Feststoffchlorierung mit NH4Cl untersucht. Dies ist eine Aufschlussmethode abseits nasschemischer oder pyrometallurgischer Verfahren. Die betrachteten, teils Hg‐haltigen Leuchtstoffmischungen enthielten neben La, Ce, Gd und Tb mit geringeren Elementgehalten vor allem Y und Eu. Durch NH4Cl‐Zugabe und Erhitzen bis zur Zersetzungstemperatur des NH4Cl wurden Y und Eu in einer Sublimationsapparatur mit hohen Ausbeuten selektiv aufgeschlossen. Die Abhängigkeit des Aufschlussgrades und der Selektivität vom NH4Cl/Leuchtstoffmischung‐Verhältnis und der Temperatur wurden systematisch untersucht.
Applying precision medicine to the active surveillance of prostate cancer
Authors: Reichard Chad A. , Stephenson Andrew J. , Klein Eric A.
Published: July 2015

The recent introduction of a variety of molecular tests will potentially reshape the care of patients with prostate cancer. These tests may make more accurate management decisions possible for those patients who have been “overdiagnosed” with biologically indolent disease, which represents an exceptionally small mortality risk. There is a wide range of possible applications of these tests to different clinical scenarios in patient populations managed with active surveillance. Cancer 2015;121:3435–43. © 2015 American Cancer Society.
Race‐specific features and outcomes of nodular lymphocyte‐predominant Hodgkin lymphoma: Analysis of the National Cancer Data Base
Authors: Olszewski Adam J. , Shrestha Rajesh , Cook Nathaniel M.
Published: July 2015

BACKGROUND

The incidence of nodular lymphocyte‐predominant Hodgkin lymphoma (NLPHL) is higher among African Americans than among other races, but to the authors' knowledge, the characteristics of NLPHL in this population have not been evaluated. The authors compared clinical features, treatments, and survival of black and white patients with NLPHL using the National Cancer Data Base.

METHODS

The authors extracted the records of 602 black and 1950 white patients with NLPHL who were diagnosed between 1998 and 2011. Overall survival (OS) was compared using the log‐rank test.

RESULTS

Black patients were on average younger than white patients (median age, 42 years vs 45 years; P =.0001), more often female (49% vs 29%; P<.0001), and more likely to have the axillary lymph nodes as the primary disease site (25% vs 17%; P =.0002). They also had unfavorable socioeconomic characteristics, a higher rate of no treatment in patients with early‐stage disease, and a longer time to therapy initiation (median, 53.5 days vs 47 days; P<.0001). Despite this, the authors found no significant difference between the races with regard to stage distribution or survival (P =.39). OS at 7 years was 90.1% in patients with early‐stage (American Joint Committee on Cancer stage IA/B, IIA) and 79.4% in patients with advanced stage (American Joint Committee on Cancer stage IIB, III/IV) NLPHL. Survival in the early stage of disease was not found to be significantly different after various treatment strategies (stratified log‐rank P = .18), except that the administration of chemotherapy was associated with a better outcome in black patients (log‐rank P =.011 vs P =.81 for white patients).

CONCLUSIONS

Differences in clinical presentation suggest the interaction of race‐specific and sex‐specific susceptibility factors for NLPHL. Further research is needed to elucidate these factors, and to investigate possible heterogeneous effects of treatments by race. Clinical trials comparing standard treatment strategies are unlikely to detect differences in OS among patients with early‐stage NLPHL. Cancer 2015;121:3435–43. © 2015 American Cancer Society.
The relative bioavailability of 2 prototype fixed‐dose combination formulations for amlodipine and rosuvastatin in healthy white and Chinese subjects
Authors: Nwe Htar H. , Bullman Jonathan N. , Joshi Shashidhar M. , Stylianou Annie , Kapsi Shiva G.
Published: July 2015

A fixed‐dose combination (FDC) may improve patient compliance and clinical outcomes in the management of cardiovascular risk in hypertensive and dyslipidemic patients. The study (NCT02075619) evaluated the bioavailability of 2 prototype FDC tablet formulations (FDC1 and FDC2) of amlodipine/rosuvastatin (10 mg/20 mg) compared with coadministered reference tablets. It was a randomized, single‐dose, 3‐way crossover pilot study in healthy white (n = 12) and Chinese (n = 12) adults. Three treatments (FDC1, FDC2, and reference) were administered after fasting with a washout period of 12–17 days. The pharmacokinetics of amlodipine and rosuvastatin were studied for all subjects (pooled) and by ethnicity. Safety and tolerability were also evaluated. Both FDCs met the bioequivalence criteria (90% confidence intervals falling within the range of 0.80–1.25) for AUC0–t and Cmax for amlodipine and rosuvastatin. Intrasubject variability (AUC0–t and Cmax) was in the region of 23%–25% for rosuvastatin and 7%–10% for amlodipine. The FDC formulations demonstrated similar bioavailability to coadministered commercially available amlodipine and rosuvastatin. All treatments were generally well tolerated.
Relative bioavailability of diclofenac potassium from softgel capsule versus powder for oral solution and immediate‐release tablet formulation
Authors: Bende Girish , Biswal Shibadas , Bhad Prafulla , Chen Yuming , Salunke Atish , Winter Serge , Wagner Robert , Sunkara Gangadhar
Published: July 2015

The oral bioavailability of diclofenac potassium 50 mg administered as a soft gelatin capsule (softgel capsule), powder for oral solution (oral solution), and tablet was evaluated in a randomized, open‐label, 3‐period, 6‐sequence crossover study in healthy adults. Plasma diclofenac concentrations were measured using a validated liquid chromatography–mass spectrometry/mass spectrometry method, and pharmacokinetic analysis was performed by noncompartmental methods. The median time to achieve peak plasma concentrations of diclofenac was 0.5, 0.25, and 0.75 hours with the softgel capsule, oral solution, and tablet formulations, respectively. The geometric mean ratio and associated 90%CI for AUCinf, and Cmax of the softgel capsule formulation relative to the oral solution formulation were 0.97 (0.95–1.00) and 0.85 (0.76–0.95), respectively. The geometric mean ratio and associated 90%CI for AUCinf and Cmax of the softgel capsule formulation relative to the tablet formulation were 1.04 (1.00–1.08) and 1.67 (1.43–1.96), respectively. In conclusion, the exposure (AUC) of diclofenac with the new diclofenac potassium softgel capsule formulation was comparable to that of the existing oral solution and tablet formulations. The peak plasma concentration of diclofenac from the new softgel capsule was 67% higher than the existing tablet formulation, whereas it was 15% lower in comparison with the oral solution formulation.
Organic Semiconductor/Gold Interface Interactions: From Physisorption on Planar Surfaces to Chemical Reactions with Metal Nanoparticles
Authors: Ligorio Giovanni , Nardi Marco Vittorio , Christodoulou Christos , Koch Norbert
Published: July 2015

The interaction of gold nanoparticles (AuNPs) with prototypical organic semiconductors used in optoelectronics, namely, tris(8‐hydroxyquinoline)aluminium (Alq3) and 4,4‐bis[N‐(1‐naphthyl)‐N‐phenylamino]diphenyl (α‐NPD), is investigated in situ by X‐ray photoelectron spectroscopy (XPS). These AuNPs‐on‐molecule experiments are compared with the reversed molecule‐on‐Au cases. The molecules‐on‐Au systems show only weak interactions, and the evolution of the XP spectra is dominated by final‐state effects. In contrast, in the AuNPs‐on‐molecules cases, both initial‐state effects and final‐state effects occur. Spectral features arising for both molecules and metal indicate charge transfer and the formation of organometallic complexes (initial‐state effects). The energy shift in the metal emission underlines the size‐induced nanometric nature of the molecule/Au interaction (final‐state effects). Consequently, the chemical interaction between metals and organic semiconductors likely depends strongly on the deposition sequence in general.
Self‐Assembly Mechanism of Nanoparticles of Ni‐Based Prussian Blue Analogues at the Air/Liquid Interface: A Synchrotron X‐ray Reflectivity Study
Authors: Giner‐Casares Juan J. , Clemente‐León Miguel , Coronado Eugenio , Brezesinski Gerald
Published: July 2015

Prussian Blue analogue (PBA) nanoparticles can be self‐assembled at air/liquid interfaces to build novel materials with interesting magnetic features. Herein, we study the influence of the size of PBA Cs0.4Ni[Cr(CN)6]0.9 and K0.25Ni[Fe(CN)6]0.75 nanoparticles on the self‐assembly behavior by synchrotron X‐ray reflectivity. Both nanoparticles show similar Z‐potential values. The phospholipid dipalmitoylphosphatidylcholine and the amino surfactant dimethyldioctadecylammonium have been used as Langmuir monolayers to anchor the PBA nanoparticles and study the interplay of forces directing the self‐assembly of the nanoparticles at the surfactant/liquid interface. Whereas Cs0.4Ni[Cr(CN)6]0.9 nanoparticles with a diameter of 8 nm form an incomplete layer at the surfactant/water interface, the larger K0.25Ni[Fe(CN)6]0.75 nanoparticles with a diameter of 20 nm generate complete layers that can be stacked to one another. The size of the PBA nanoparticles is the main parameter determining the final arrangement at the air/liquid interface, due to the different extent of interparticle interaction. This study aims at the rationale design of PBA nanoparticles for an effective interfacial self‐assembly, ultimately leading to functional materials.
Synthesis, Structures, and Single‐Molecule Magnet Behaviour of High‐Nuclearity Nickel(II) Dicubane‐Type Complexes with Pyridyl–Alcohol Ligands
Authors: Hameury Sophie , Kayser Laure , Pattacini Roberto , Rosa Patrick , Barra Anne‐Laure , Braunstein Pierre
Published: July 2015

The condensation reaction between two chemically different tetranuclear cubane‐like clusters [Ni(μ3‐Cl)(Cl)(HL)]4 (1; HL=2‐methyl‐1‐(pyridin‐2‐yl)propan‐2‐ol) and [Ni(μ3‐OH)(Cl)(HL)]4 (2) provides new access to higher nuclearity complexes, as shown with the synthesis of the octanuclear complex [Ni8(μ3‐Cl)3(μ3‐OH)5(μ‐Cl)2Cl6(HL)7] (3). In one instance, we also isolated the heptanuclear complex [Ni7(μ3‐Cl)2(μ3‐OH)6Cl4(H2O)2(HL)6]Cl2 (4). Magnetic properties measured by superconducting quantum interference device (SQUID) susceptometry evidenced S=8 and S=5 ground states for complexes 3 and 4, respectively. In particular, alternating current (ac) susceptometry evidenced slow relaxation of the magnetisation for complex 3, and suggests a similar behaviour at sub‐kelvin temperatures for complex 4.
Nickel Hexacyanoferrate as Suitable Alternative to Ag for Electrochemical Lithium Recovery
Authors: Trócoli R. , Battistel A. , La Mantia F.
Published: July 2015

Currently, Li is mainly produced through evaporation of Li‐rich brines obtained from South American countries such as Bolivia, Chile, and Argentina. The most commonly used process, the lime–soda evaporation, requires a long time and several purification steps, which produces a considerable amount of chemical waste. Various electrochemical methods have been proposed as alternatives, but they use expensive metals such as Ag or Pt, thus rendering these methods economically unacceptable. In this work, we present KNiFe(CN)6, an abundant and environmentally friendly material, as alternative to these expensive components. The Prussian blue derivate has a higher affinity toward cations (Na+ or K+) than for Li+. Additionally, the use of KNiFe(CN)6 permits the utilization of seawater or brine water as recovery solution, thus reducing the consumption of fresh water, which is typically a scarce element in Li production sites.
Cytologic findings of NUT midline carcinoma in the hilum of the lung
Authors: Policarpio‐Nicolas Maria Luisa C. , de Leon Essel Marie B. , Jagirdar Jaishree
Published: July 2015

Nuclear protein in testis (NUT) midline carcinoma (NMC) is a clinically lethal malignancy affecting all age group often located in the midline structures such as mediastinum, larynx and nasopharynx. It is characterized by chromosomal translocation between chromosomes 15 and 19 with the formation of chimeric gene BRD‐NUT. We present the cytologic findings of NMC including the immunohistochemical stains performed. The patient is a 34‐year‐old man who presented with 1 month history of dyspnea and interscapular pain followed by nonproductive cough a week before consultation. He was initially diagnosed with pneumonia. Due to progression of symptoms, a chest CT scan was performed revealing a large hilar mass and mediastinal adenopathy. A core biopsy with touch preparations of the hilar mass was performed which revealed cohesive malignant cells with ovoid to elongated nuclei, fine to coarse chromatin pattern, irregular nuclear contour, prominent nucleoli, and scant ill‐defined cytoplasm arranged in sheets and focally pseudoglandular pattern. Although focal nuclear overlapping and crush artifact were identified, karyorrhectic debris and mitotic figures were rare. Squamous differentiation was absent. The core biopsy showed discohesive malignant cells with tumor necrosis. No nuclear molding, glandular or squamous differentiation was identified. The tumor was immunoreactive for p63 and NUT with high Ki‐67 (>80%). The tumor was negative for keratin, lymphoid, myeloid, neuroendocrine markers and S‐100. This case emphasizes that cytologic features of NMC can mimic poorly differentiated, undifferentiated and neuroendocrine carcinomas and the importance of immunohistochemical stains especially NUT monoclonal antibody in arriving at the diagnosis. Diagn. Cytopathol. 2015;43:739–742. © 2015 Wiley Periodicals, Inc.
Fine‐needle‐aspiration cytology of a proximal type epithelioid sarcoma: A case report
Authors: Pendse Avani A. , Dodd Leslie G.
Published: July 2015

Epithelioid sarcoma is a rare mesenchymal neoplasm, with an as yet unidentified cell of origin. Two subtypes of epithelioid sarcoma, distal/classic and proximal/large cell type, are recognized in the literature; with the proximal‐type having a lower incidence amongst the two. Here, we present a case of proximal‐type epithelioid sarcoma in a previously healthy young man. Fine‐needle‐aspiration of a large axillary mass was performed for diagnosis. The cytologic findings included a dispersed population of large epithelioid to polyhedral cells with abundant cytoplasm. Immunohistochemical staining showed coexpression of keratin and vimentin, as well as loss of INI1 staining, consistent with an epithelioid sarcoma, proximal subtype. Diagn. Cytopathol. 2015;43:859–862. © 2015 Wiley Periodicals, Inc.
rBEFdata: documenting data exchange and analysis for a collaborative data management platform
Authors: Pfaff Claas‐Thido , König‐Ries Birgitta , Lang Anne C. , Ratcliffe Sophia , Wirth Christian , Man Xingxing , Nadrowski Karin
Published: July 2015

We are witnessing a growing gap separating primary research data from derived data products presented as knowledge in publications. Although journals today more often require the underlying data products used to derive the results as a prerequisite for a publication, the important link to the primary data is lost. However, documenting the postprocessing steps of data linking, the primary data with derived data products has the potential to increase the accuracy and the reproducibility of scientific findings significantly. Here, we introduce the rBEFdata R package as companion to the collaborative data management platform BEFdata. The R package provides programmatic access to features of the platform. It allows to search for data and integrates the search with external thesauri to improve the data discovery. It allows to download and import data and metadata into R for analysis. A batched download is available as well which works along a paper proposal mechanism implemented by BEFdata. This feature of BEFdata allows to group primary data and metadata and streamlines discussions and collaborations revolving around a certain research idea. The upload functionality of the R package in combination with the paper proposal mechanism of the portal allows to attach derived data products and scripts directly from R, thus addressing major aspects of documenting data postprocessing. We present the core features of the rBEFdata R package along an ecological analysis example and further discuss the potential of postprocessing documentation for data, linking primary data with derived data products and knowledge.
Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree–herbivore networks
Authors: Robinson Kathryn M. , Hauzy Céline , Loeuille Nicolas , Albrectsen Benedicte R.
Published: July 2015

Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait‐matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra‐floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom‐up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen–herbivore bipartite networks, the role of environmental variations is a dominant constraint.
A constant threat for HIV: Fc‐engineering to enhance broadly neutralizing antibody activity for immunotherapy of the acquired immunodeficiency syndrome
Authors: Nimmerjahn Falk
Published: July 2015

Passive immunotherapy with polyclonal or hyperimmune serum immunoglobulin G (IgG) preparations provides an efficient means of protecting immunocompromised patients from microbial infections. More recently, the use of passive immunotherapy to prevent or to treat established infections with the human immunodeficiency virus (HIV) has gained much attention, due to promising preclinical data obtained in monkey and humanized mouse in vivo model systems, demonstrating that the transfer of HIV‐specific antibodies can not only prevent HIV infection, but also diminish virus load during chronic infection. Furthermore, an array of broadly neutralizing HIV‐specific antibodies has become available and the importance of the IgG constant region as a critical modulator of broadly neutralizing activity has been demonstrated. The aim of this review is to summarize the most recent findings with regard to the molecular and cellular mechanisms responsible for antibody‐mediated clearance of HIV infection, and to discuss how this may help to improve HIV therapy via optimizing Fcγ‐receptor‐dependent activities of HIV‐specific antibodies.
Litomosoides sigmodontis induces TGF‐β receptor responsive, IL‐10‐producing T cells that suppress bystander T‐cell proliferation in mice
Authors: Hartmann Wiebke , Schramm Christoph , Breloer Minka
Published: July 2015

Helminth parasites suppress immune responses to prolong their survival within the mammalian host. Thereby not only helminth‐specific but also nonhelminth‐specific bystander immune responses are suppressed. Here, we use the murine model of Litomosoides sigmodontis infection to elucidate the underlying mechanisms leading to this bystander T‐cell suppression. When OT‐II T cells specific for the third‐party antigen ovalbumin are transferred into helminth‐infected mice, these cells respond to antigen‐specific stimulation with reduced proliferation compared to activation within non‐infected mice. Thus, the presence of parasitic worms in the thoracic cavity translates to suppression of T cells with a different specificity at a different site. By eliminating regulatory receptors, cytokines, and cell populations from this system, we provide evidence for a two‐staged process. Parasite products first engage the TGF‐β receptor on host‐derived T cells that are central to suppression. In a second step, host‐derived T cells produce IL‐10 and subsequently suppress the adoptively transferred OT‐II T cells. Terminal suppression was IL‐10‐dependant but independent of intrinsic TGF‐β receptor‐ or PD‐1‐mediated signaling in the suppressed OT‐II T cells. Blockade of the same key suppression mediators, i.e. TGF‐β‐ and IL‐10 receptor, also ameliorated the suppression of IgG response to bystander antigen vaccination in L. sigmodontis‐infected mice.
Fonsecaea pedrosoi‐induced Th17‐cell differentiation in mice is fostered by Dectin‐2 and suppressed by Mincle recognition
Authors: Wüthrich Marcel , Wang Huafeng , Li Mengyi , Lerksuthirat Tassanee , Hardison Sarah E. , Brown Gordon D. , Klein Bruce
Published: July 2015

Chromoblastomycosis is a chronic skin infection caused by the pigmented saprophytic mould Fonsecaea pedrosoi. Chronicity of infection can be broken by a coordinated innate recognition of the spores by pattern recognition receptors. While Mincle signaling via the Syk/Card9 pathway is required for fungal recognition by host cells, it is not sufficient for host control. Exogenously applied TLR agonists are necessary to promote the induction of proinflammatory cytokines and clearance of infection in vivo. Here, we investigated whether costimulation by TLR agonists fosters the development of adaptive immune responses, by examining the development of fungus‐specific T cells. Subcutaneous infection of mice with F. pedrosoi spores induced the activation, expansion, and differentiation of Ag‐specific CD4+ T cells but TLR costimulation did not further augment these T‐cell responses. The Dectin‐2/FcRγ/Card9 signaling pathway promoted the differentiation of fungus‐specific CD4+ T cells into Th17 cells, whereas Mincle inhibited the development of this T‐helper subset in infected mice. These results indicate differential roles for Dectin‐2 and Mincle in the generation of adaptive immune responses to F. pedrosoi infection.
Sensory abnormalities and pain in Parkinson disease and its modulation by treatment of motor symptoms
Authors: Cury R.G. , Galhardoni R. , Fonoff E.T. , Perez Lloret S. , dos Santos Ghilardi M.G. , Barbosa E.R. , Teixeira M.J. , Ciampi de Andrade D.
Published: July 2015

Pain and sensory abnormalities are present in a large proportion of Parkinson disease (PD) patients and have a significant negative impact in quality of life. It remains undetermined whether pain occurs secondary to motor impairment and to which extent it can be relieved by improvement of motor symptoms. The aim of this review was to examine the current knowledge on the mechanisms behind sensory changes and pain in PD and to assess the modulatory effects of motor treatment on these sensory abnormalities. A comprehensive literature search was performed. We selected studies investigating sensory changes and pain in PD and the effects of levodopa administration and deep brain stimulation (DBS) on these symptoms. PD patients have altered sensory and pain thresholds in the off‐medication state. Both levodopa and DBS improve motor symptoms (i.e.: bradykinesia, tremor) and change sensory abnormalities towards normal levels. However, there is no direct correlation between sensory/pain changes and motor improvement, suggesting that motor and non‐motor symptoms do not necessarily share the same mechanisms. Whether dopamine and DBS have a real antinociceptive effect or simply a modulatory effect in pain perception remain uncertain. These data may provide useful insights into a mechanism‐based approach to pain in PD, pointing out the role of the dopaminergic system in pain perception and the importance of the characterization of different pain syndromes related to PD before specific treatment can be instituted.
Near‐bed shear stress, turbulence production and dissipation in a shallow and narrow tidal channel
Authors: Pieterse Aline , Puleo Jack A. , McKenna Thomas E. , Aiken Rebecca A.
Published: July 2015

Near‐bed, highly resolved velocity profiles were measured in the lower 0.03 m of the water column using acoustic Doppler profiling velocimeters in narrow tidal channels in a salt marsh. The bed shear stress was estimated from the velocity profiles using three methods: the log‐law, Reynolds stress, and shear stress derived from the turbulent kinetic energy (TKE). Bed shear stresses were largest during ebbing tide, while near‐bed velocities were larger during flooding tide. The Reynolds stress and TKE method gave similar results, while the log‐law method resulted in smaller bed shear stress values during ebbing tide. Shear stresses and turbulent kinetic energy followed a similar trend with the largest peaks during ebbing tide. The maximum turbulent kinetic energy was on the order of 1 × 10− 2 m2/s2. The fluid shear stress during flooding tide was approximately 30% of the fluid shear stress during ebbing tide. The maximum TKE‐derived shear stress was 0.7 N/m2 and 2.7 N/m2 during flooding and ebbing tide, respectively, and occurred around 0.02 m above the bed. Turbulence dissipation was estimated using the frequency spectrum and structure function methods. Turbulence dissipation estimates from both methods were maximum near the bed (~0.01 m). Both the structure function and the frequency spectrum methods resulted in maximum dissipation estimates on the order of 4 × 10− 3 m2/s3. Turbulence production exceeded turbulence dissipation at every phase of the tide, suggesting that advection and vertical diffusion are not negligible. However, turbulence production and dissipation were within a factor of 2 for 77% of the estimates. The turbulence production and dissipation decreased quickly away from the bed, suggesting that measurements higher in the water column cannot be translated directly to turbulence production and dissipation estimates near the bed. Copyright © 2015 John Wiley & Sons, Ltd.
Peroxide levels along the fragrance value chain comply with IFRA standards
Authors: Api A. M. , Boyd J. , Renskers K.
Published: July 2015

Autoxidation of certain perfume ingredients can result in the formation of sensitizing chemicals although the parent compounds are non‐sensitizing. Peroxide values were determined for 875 freshly manufactured fragrance compounds, 34 hydroalcoholic fragrance products retrieved from retail establishments, 80 hydroalcoholic fragrance products retrieved from end‐use consumers and in natural oils containing linalool stored either under Good Manufacturing Practice (GMP) or non‐GMP conditions. Only 2/875 freshly manufactured fragrance compounds had peroxide values in excess of 10 mmol/l. There was no apparent correlation between the peroxide values and the concentrations of either linalool or limonene or the sum of their concentrations. None of the hydroalcoholic fragrance products retrieved from either retail establishments or consumers had peroxide values exceeding 10 mmol/l. Under typical storage and use conditions, there was very little peroxide formation. Utilization of GMPs that comply with IFRA standards results in products that comply with IFRA standards for preventing induction of sensitization owing to autoxidation of fragrance ingredients. Copyright © 2015 John Wiley & Sons, Ltd.
A refined r‐factor algorithm for TVD schemes on arbitrary unstructured meshes
Authors: Zhang Di , Jiang Chunbo , Cheng Liang , Liang Dongfang
Published: July 2015

A refined r‐factor algorithm for implementing total variation diminishing (TVD) schemes on arbitrary unstructured meshes, referred to henceforth as a face‐perpendicular far‐upwind interpolation scheme for arbitrary meshes (FFISAM), is proposed based on an extensive review of the existing r‐factor algorithms available in the literature. The design principles, as well as the respective advantages and disadvantages, of the existing algorithms are first systematically analyzed before presenting the FFISAM. The FFISAM is designed to combine the merits of various existing r‐factor algorithms. The performance of the FFISAM, implemented in 10 classical TVD schemes, is evaluated against four two‐dimensional pure‐advection benchmark test cases where analytical solutions are available. The numerical results clearly show that the FFISAM leads to a better overall performance than the existing algorithms in terms of accuracy and convergence on arbitrary unstructured meshes for the 10 classical TVD schemes. Copyright © 2015 John Wiley & Sons, Ltd.
An innovative open boundary treatment for incompressible SPH
Authors: Khorasanizade Sh. , Sousa J. M. M.
Published: July 2015

An innovative inflow/outflow boundary treatment has been proposed to be used in smoothed particle hydrodynamics (SPH). Among other strategies, it involves the use of extended regions at open boundary sections and a procedure to enforce the mass continuity constraint, as well as to minimize outflow reflections. This methodology has been coupled with a modified ‘particle shifting’ algorithm, so that the robustness of the method could be ensured at high Reynolds number regimes. Confined flow around a square cylinder with an open outflow has been selected as the flow problem to analyze the performance of the new method. Detailed comparisons with data available in the literature for a variety of mesh‐based methods have been made for two different values of the blockage ratio β, namely for β = 1/4 and 1/8, and a range of supercritical Reynolds numbers. The results obtained with the present implementation of truly incompressible SPH have demonstrated numerical accuracy comparable with that of other methods, as well as the success of the open boundary treatment. A direct comparison with previously published SPH results for a distinct blockage ratio, namely for β = 1/5, has also revealed that a major improvement has been achieved by the use of the method described in this paper. Copyright © 2015 John Wiley & Sons, Ltd.
A Fast Multiple‐Kernel Method With Applications to Detect Gene‐Environment Interaction
Authors: Marceau Rachel , Lu Wenbin , Holloway Shannon , Sale Michèle M. , Worrall Bradford B. , Williams Stephen R. , Hsu Fang‐Chi , Tzeng Jung‐Ying
Published: July 2015

Kernel machine (KM) models are a powerful tool for exploring associations between sets of genetic variants and complex traits. Although most KM methods use a single kernel function to assess the marginal effect of a variable set, KM analyses involving multiple kernels have become increasingly popular. Multikernel analysis allows researchers to study more complex problems, such as assessing gene‐gene or gene‐environment interactions, incorporating variance‐component based methods for population substructure into rare‐variant association testing, and assessing the conditional effects of a variable set adjusting for other variable sets. The KM framework is robust, powerful, and provides efficient dimension reduction for multifactor analyses, but requires the estimation of high dimensional nuisance parameters. Traditional estimation techniques, including regularization and the “expectation‐maximization (EM)” algorithm, have a large computational cost and are not scalable to large sample sizes needed for rare variant analysis. Therefore, under the context of gene‐environment interaction, we propose a computationally efficient and statistically rigorous “fastKM” algorithm for multikernel analysis that is based on a low‐rank approximation to the nuisance effect kernel matrices. Our algorithm is applicable to various trait types (e.g., continuous, binary, and survival traits) and can be implemented using any existing single‐kernel analysis software. Through extensive simulation studies, we show that our algorithm has similar performance to an EM‐based KM approach for quantitative traits while running much faster. We also apply our method to the Vitamin Intervention for Stroke Prevention (VISP) clinical trial, examining gene‐by‐vitamin effects on recurrent stroke risk and gene‐by‐age effects on change in homocysteine level.
A Bayesian analysis of Generalized Pareto Distribution of runoff minima
Authors: Liu Youcun , Lu Miaojie , Huo Xueli , Hao Yonghong , Gao Hongkai , Liu Yan , Fan Yonghui , Cui Yuhuan , Metivier Francois
Published: July 2015

Global climate change models have predicted the intensification of extreme events, and these predictions are already occurring. For disaster management and adaptation of extreme events, it is essential to improve the accuracy of extreme value statistical models. In this study, Bayes' Theorem is introduced to estimate parameters in Generalized Pareto Distribution (GPD), and then the GPD is applied to simulate the distribution of minimum monthly runoff during dry periods in mountain areas of the Ürümqi River, Northwest China. Bayes' Theorem treats parameters as random variables and provides a robust way to convert the prior distribution of parameters into a posterior distribution. Statistical inferences based on posterior distribution can provide a more comprehensive representation of the parameters. An improved Markov Chain Monte Carlo (MCMC) method, which can solve high‐dimensional integral computation in the Bayes equation, is used to generate parameter simulations from the posterior distribution. Model diagnosis plots are made to guarantee the fitted GPD is appropriate. Then based on the GPD with Bayesian parameter estimates, monthly runoff minima corresponding to different return periods can be calculated. The results show that the improved MCMC method is able to make Markov chains converge faster. The monthly runoff minima corresponding to 10a, 25a, 50a and 100a return periods are 0.60 m3/s, 0.44 m3/s, 0.32 m3/s and 0.20 m3/s respectively. The lower boundary of 95% confidence interval of 100a return level is below zero, which implies that the Ürümqi River is likely to cease to flow when 100a return level appears in dry periods. Copyright © 2015 John Wiley & Sons, Ltd.
Fish, n − 3 polyunsaturated fatty acids and n − 6 polyunsaturated fatty acids intake and breast cancer risk: The Japan Public Health Center‐based prospective study
Authors: Kiyabu Grace Y. , Inoue Manami , Saito Eiko , Abe Sarah K. , Sawada Norie , Ishihara Junko , Iwasaki Motoki , Yamaji Taiki , Shimazu Taichi , Sasazuki Shizuka , Shibuya Kenji , Tsugane Shoichiro ,   for the JPHC Study Group
Published: July 2015

Limited and inconsistent studies exist on the association between the intake of fish, n − 3 polyunsaturated fatty acids (PUFA) and n − 6 PUFA and breast cancer. Fish and n − 3 PUFA support various body functions and are thought to reduce the carcinogenesis risk while n − 6 PUFA may have a positive association with cancer risk. We examined the association between intake of fish, n − 3 PUFA [including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), docosapentaenoic acid (DPA) and alpha‐linolenic acid (ALA)] and n − 6 PUFA and breast cancer with subanalyses on estrogen (ER) and progesterone receptor (PR) status. We investigated 38,234 Japanese women aged 45–74 years from the Japan Public Health Center‐based prospective study (JPHC study), and during 14.1 years of follow‐up time, 556 breast cancer cases were newly diagnosed. Breast cancer risk was not associated with the intake of total fish, n − 3 PUFA and n − 6 PUFA when analyzed in totality through multivariable Cox proportional hazards regression models with age as the time scale. Intake of total n − 6 was positively associated with the development of ER+PR+ tumors [multivariable‐adjusted HR Q4 vs. Q1 = 2.94 (95% CI: 1.26–6.89; ptrend = 0.02)]. Intake of EPA was associated with a decreased breast cancer risk for ER+PR+ tumors [multivariable‐adjusted HR Q2 vs. Q1 = 0.47 (95% CI: 0.25–0.89; ptrend =0.47)]. While the overall association between the intake of total fish, n − 3 PUFA and n − 6 PUFA and breast cancer risk is null, for ER+PR+ tumors, a positive association was seen between n − 6 intake and breast cancer, and a marginally significant inverse association was observed for EPA intake.