bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid
Authors: Suarez-Ulloa Victoria , Fernandez-Tajes Juan , Aguiar-Pulido Vanessa , Prego-Faraldo M. Veronica , Florez-Barros Fernanda , Sexto-Iglesias Alexia , Mendez Josefina , Eirin-Lopez Jose M. 
Published: November 2015

Background.Harmful Algal Blooms (HABs) responsible for Diarrhetic Shellfish Poisoning (DSP) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the primary cause of acute DSP intoxications. Although several studies have described the molecular effects of high OA concentrations on sentinel organisms (e.g., bivalve molluscs), the effect of prolonged exposures to low (sublethal) OA concentrations is still unknown. In order to fill this gap, this work combines Next-Generation sequencing and custom-made microarray technologies to develop an unbiased characterization of the transcriptomic response of mussels during early stages of a DSP bloom.Methods.Mussel specimens were exposed to a HAB episode simulating an early stage DSP bloom (200 cells/L of the dinoflagellateProrocentrum limafor 24 h). The unbiased characterization of the transcriptomic responses triggered by OA was carried out using two complementary methods of cDNA library preparation: normalized and Suppression Subtractive Hybridization (SSH). Libraries were sequenced and read datasets were mapped to Gene Ontology and KEGG databases. A custom-made oligonucleotide microarray was developed based on these data, completing the expression analysis of digestive gland and gill tissues.Results.Our findings show that exposure to sublethal concentrations of OA is enough to induce gene expression modifications in the musselMytilus. Transcriptomic analyses revealed an increase in proteasomal activity, molecular transport, cell cycle regulation, energy production and immune activity in mussels. Oppositely, a number of transcripts hypothesized to be responsive to OA (notably the Serine/Threonine phosphatases PP1 and PP2A) failed to show substantial modifications. Both digestive gland and gill tissues responded similarly to OA, although expression modifications were more dramatic in the former, supporting the choice of this tissue for future biomonitoring studies.Discussion.Exposure to OA concentrations within legal limits for safe consumption of shellfish is enough to disrupt important cellular processes in mussels, eliciting sharp transcriptional changes as a result. By combining the study of cDNA libraries and a custom-made OA-specific microarray, our work provides a comprehensive characterization of the OA-specific transcriptome, improving the accuracy of the analysis of expresion profiles compared to single-replicated RNA-seq methods. The combination of our data with related studies helps understanding the molecular mechanisms underlying molecular responses to DSP episodes in marine organisms, providing useful information to develop a new generation of tools for the monitoring of OA pollution.
Contribution of alluvial groundwater to the outflow of mountainous catchments
Authors: Käser Daniel , Hunkeler Daniel 
Published: November 2015

AbstractAlluvial aquifers in mountainous regions cover typically a limited area. Their contribution to catchment storage and outflow is rarely isolated; alluvial groundwater discharge under gauging stations is generally assumed negligible; and hydrological models tend to lump alluvial storage with other units. The role of alluvial aquifers remains therefore unclear: can they contribute significantly to outflow when they cover a few percent of catchment area? Should they be considered a dynamic storage unit or merely a transmission zone? We address these issues based on the continuous monitoring of groundwater discharge, river discharge (one year), and aquifer storage (6 months) in the 6 km2 alluvial system of a 194 km2 catchment. River and groundwater outflow were measured jointly through “coupled gauging stations.” The contribution of alluvial groundwater to outflow was highest at the outlet of a subcatchment (52 km2), where subsurface discharge amounted to 15% of mean annual outflow, and 85% of outflow during the last week of a drought. In this period, alluvial‐aquifer depletion supported 75% of the subcatchment outflow and 35% of catchment outflow—thus 3% of the entire catchment supported a third of the outflow. Storage fluctuations occurred predominantly in the aquifer's upstream part, where heads varied over 6 m. Not only does this section act as a significant water source, but storage recovers also rapidly at the onset of precipitation. Storage dynamics were best conceptualized along the valley axis, rather than across the more conventional riparian‐channel transect. Overall the contribution of alluvial aquifers to catchment outflow deserves more attention.
A new application of conditional nonlinear optimal perturbation approach to boundary condition uncertainty
Authors: Wang Qiang , Mu Mu 
Published: November 2015

AbstractThe conditional nonlinear optimal perturbation (CNOP) approach was mainly used to investigate the effects of the uncertainties in initial condition and model parameters on model results. This study presents a new application of the CNOP approach to the investigation of the effects of boundary condition uncertainty. Specifically, we first give the general formulation of the CNOP approach for uncertainties of initial and boundary conditions and model parameters. The method is then applied to analyze the effects of nutrient perturbations at the bottom boundary of the water column on the modeled deep chlorophyll maximum (DCM) using an ocean ecosystem model. The results show that nutrient perturbations at the bottom boundary have significant impacts on the modeled DCM. Interestingly, the approach also reveals that nonlinear processes play important roles in the evolution of phytoplankton perturbations caused by nutrient perturbations at the bottom boundary. This implies that the CNOP approach is useful for investigating the effects of boundary condition uncertainty.
Seasonal variability of nutrient concentrations in the Mediterranean Sea: Contribution of Bio‐Argo floats
Authors: Pasqueron de Fommervault Orens , D'Ortenzio Fabrizio , Mangin Antoine , Serra Romain , Migon Christophe , Claustre Hervé , Lavigne Héloïse , Ribera d'Alcalà Maurizio , Prieur Louis , Taillandier Vincent , Schmechtig Catherine , Poteau Antoine , Leymarie Edouard , Dufour Aurélie , Besson Florent , Obolensky Grigor 
Published: November 2015

AbstractIn 2013, as part of the French NAOS (Novel Argo Oceanic observing System) program, five profiling floats equipped with nitrate sensors (SUNA‐V2) together with CTD and bio‐optical sensors were deployed in the Mediterranean Sea. At present day, more than 500 profiles of physical and biological parameters were acquired, and significantly increased the number of available nitrate data in the Mediterranean Sea. Results obtained from floats confirm the general view of the basin, and the well‐known west‐to‐east gradient of oligotrophy. At seasonal scale, the north western Mediterranean displays a clear temperate pattern sustained by both deep winter mixed layer and shallow nitracline. The other sampled areas follow a subtropical regime (nitracline depth and mixed layer depth are generally decoupled). Float data also permit to highlight the major contribution of high‐frequency processes in controlling the nitrate supply during winter in the north western Mediterranean Sea and in altering the nitrate stock in subsurface in the eastern basin.
A Mild Lewis‐Acid‐Catalyzed Method for Head‐to‐Tail Dimerization or Cyclization of tert‐Alcohols
Authors: Ramulu Bokka Venkat , Mahendar Lodi , Satyanarayana Gedu 
Published: November 2015

AbstractA mild and practical method is developed for the efficient synthesis of (1,1‐dimethyl‐3‐phenylbut‐3‐enyl)benzenes and indanes promoted by Lewis acid, starting from tert‐benzyl alcohols. The reaction is temperature dependent and furnished the products with excellent regioselectivity. In the case of simple dimerization, Markovnikov head‐to‐tail coupling took place. On the other hand, reaction at elevated temperatures gave indanes through subsequent Friedel–Crafts cycloalkylation. Significantly, even electron‐rich aromatic systems were compatible for the formation of indanes, which would not be feasible by earlier reports, thus, revealing the advantage of the mild nature of the present protocol.
Dyad of pain and depression in chronic rhinosinusitis
Authors: Cox Daniel R. , Ashby Shaelene , DeConde Adam S. , Mace Jess C. , Orlandi Richard R. , Smith Timothy L. , Alt Jeremiah A. 
Published: November 2015

BackgroundPain and depression often coexist as comorbidities in patients with chronic disease and exert a major impact on quality of life (QOL). Little is known about the relationship between pain and depression in chronic rhinosinusitis (CRS). Our objective was to investigate this relationship and to analyze the effect of pain and depression on QOL in CRS.MethodsPatients with CRS were prospectively recruited as part of an observational cohort study. A total of 70 participants provided pain scores using both the Brief Pain Inventory Short Form (BPI‐SF) and the Short Form McGill Pain Questionnaire (SF‐MPQ). Patients at risk for depression were identified using the Patient Health Questionnaire–2 (PHQ‐2). CRS‐specific QOL was determined using the 22‐item Sino‐Nasal Outcome Test (SNOT‐22).ResultsSignificant positive correlations were found between depression scores and all pain measures (R = 0.475 to 0.644, p < 0.001). Patients with a PHQ‐2 score ≥1 had significantly higher scores on all reported pain measures. Significant positive correlations were found between all pain measures, the total SNOT‐22 score, and 3 SNOT‐22 subdomains (sleep, psychological dysfunction, and ear/facial symptoms; R = 0.323 to 0.608, p < 0.05).ConclusionAdult patients with CRS at risk for depression experience more pain and have overall worse disease‐specific QOL. Further research investigating the complex interactions between depression and pain and the role it plays in CRS disease‐specific QOL is warranted.
Hierarchical Self‐Assembly of Supramolecular Muscle‐Like Fibers
Authors: Goujon Antoine , Du Guangyan , Moulin Emilie , Fuks Gad , Maaloum Mounir , Buhler Eric , Giuseppone Nicolas 
Published: November 2015

AbstractAn acid–base switchable [c2]daisy chain rotaxane terminated with two 2,6‐diacetylamino pyridine units has been self‐assembled with a bis(uracil) linker. The complementary hydrogen‐bond recognition patterns, together with lateral van der Waals aggregations, result in the hierarchical formation of unidimensional supramolecular polymers associated in bundles of muscle‐like fibers. Microscopic and scattering techniques reveal that the mesoscopic structure of these bundles depends on the extended or contracted states that the rotaxanes show within individual polymer chains. The observed local dynamics span over several length scales because of a combination of supramolecular and mechanical bonds. This work illustrates the possibility to modify the hierarchical mesoscopic structuring of large polymeric systems by the integrated actuation of individual molecular machines.
Synthesis of (±)‐Lasubine II Using N‐Methoxyamines
Authors: Yokoyama Takashi , Fukami Yutaro , Sato Takaaki , Chida Noritaka 
Published: November 2015

AbstractThe synthesis of (±)‐lasubine II has been achieved through a three‐component allylation capitalizing on the unique properties of N‐methoxyamines. This reaction enabled the installation of all the carbon atoms of lasubine II in a single operation. The N‐methoxy group was efficiently used for the subsequent nitrone formation. A single‐step cyclization of isoxazolidines or N‐methoxyamines to form functionalized piperidine rings was also developed.
Mesoscale modeling for the rapid movement of monsoonal isochrones
Authors: Kumar Vinay , Krishnamurti T. N. 
Published: November 2015

AbstractThe progresses of fast moving 2013 monsoonal isochrones were simulated with WRF model at 25 km and compared with slower moving isochrones of 2014. A large number of sensitivity experiments were performed by enhancing of soil moisture, stratiform rain up to 25%, their combination and reducing soil temperature by 12%, over 5 grid points to the north of the isochrones over a relatively dry soil layer. The modified soil parameters and startiform rain ahead of isochrones enhances the population of the buoyant elements, divergent flows of the local Hadley circulation normal to the isochrones; resulting in a fast movement of the isochrones.
Incorporation of FcRn‐mediated disposition model to describe the population pharmacokinetics of therapeutic monoclonal IgG antibody in clinical patients
Authors: Ng Chee M. 
Published: November 2015

AbstractPurpose. The two‐compartment linear model used to describe the population pharmacokinetics (PK) of many therapeutic monoclonal antibodies (TMAbs) offered little biological insight to antibody disposition in humans. The purpose of this study is to develop a semi‐mechanistic FcRn‐mediated IgG disposition model to describe the population PK of TMAbs in clinical patients. Methods. A standard two‐compartment linear PK model from a previously published population PK model of pertuzumab was used to simulate intensive PK data of 100 subjects for model development. Two different semi‐mechanistic FcRn‐mediated IgG disposition models were developed and First Order Conditional Estimation (FOCE) with the interaction method in NONMEM was used to obtain the final model estimates. The performances of these models were then compared with the two‐compartment linear PK model used to simulate the data for model development. Results. A semi‐mechanistic FcRn‐mediated IgG disposition model consisting of a peripheral tissue compartment and FcRn‐containing endosomes in the central compartment best describes the simulated pertuzumab population PK data. This developed semi‐mechanistic population PK model had the same number of model parameters, produced very similar concentration–time profiles but provided additional biological insight to the FcRn‐mediated IgG disposition in human subjects compared with the standard linear two‐compartment linear PK model. Conclusion. This first reported semi‐mechanistic model may serve as an important model framework for developing future population PK models of TMAbs in clinical patients. Copyright © 2015 John Wiley & Sons, Ltd.
Multimerized HIV‐gp41‐derived peptides as fusion inhibitors and vaccines
Authors: Nomura Wataru , Mizuguchi Takaaki , Tamamura Hirokazu 
Published: November 2015

ABSTRACTTo date, several antigens based on the amino‐terminal leucine/isoleucine heptad repeat (NHR) region of an HIV‐1 envelope protein gp41 and fusion inhibitors based on the carboxy‐terminal leucine/isoleucine heptad repeat (CHR) region of gp41 have been reported. We have developed a synthetic antigen targeting the membrane‐fusion mechanism of HIV‐1. This uses a template designed with C3‐symmetric linkers and mimics the trimeric form of the NHR‐derived peptide N36. The antiserum obtained by immunization of the N36 trimeric antigen binds preferentially to the N36 trimer and blocks HIV‐1 infection effectively, compared with the antiserum obtained by immunization of the N36 monomer. Using another template designed with different C3‐symmetric linkers, we have also developed a synthetic peptide mimicking the trimeric form of the CHR‐derived peptide C34, with ∼100 times the inhibitory activity against the HIV‐1 fusion mechanism than that of the monomer C34 peptide. A dimeric derivative of C34 has potent inhibitory activity at almost the same levels as this C34 trimer mimic, suggesting that presence of a dimeric form of C34 is structurally critical for fusion inhibitors. As examples of rising mid‐size drugs, this review describes an effective strategy for the design of HIV vaccines and fusion inhibitors based on a relationship with the native structure of proteins involved in HIV fusion mechanisms. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 622–628, 2016.
A New Na+‐Dependent RNA‐Cleaving DNAzyme with over 1000‐fold Rate Acceleration by Ethanol
Authors: Zhou Wenhu , Saran Runjhun , Chen Qingyun , Ding Jinsong , Liu Juewen 
Published: November 2015

AbstractEnzymes working in organic solvents are important for analytical chemistry, catalysis, and mechanistic studies. Although a few protein enzymes are highly active in organic solvents, little is known regarding nucleic acid‐based enzymes. Herein, we report the first RNA‐cleaving DNAzyme, named EtNa, that works optimally in concentrated organic solvents containing only monovalent Na+. The EtNa DNAzyme has a rate of 2.0 h−1 in 54 % ethanol (with 120 mm NaCl and no divalent metal ions), and a Kd of 21 mm Na+. It retains activity even in 72 % ethanol as well as in DMSO. With 4 mm Na+, the rate in 54 % ethanol is >1000‐fold higher than that in water. We also demonstrated the use of EtNa to measuring the ethanol content in alcoholic drinks. In total, this DNAzyme has three unique features: divalent metal independent activity, Na+ selectivity among monovalent metals, and acceleration by organic solvents.
Efficacy and safety of routine thrombus aspiration in patients with ST‐segment elevation myocardial infarction undergoing primary percutaneous coronary intervention: An updated systematic review and meta‐analysis of randomized controlled trials
Authors: Mastoris Ioannis , Giustino Gennaro , Sartori Samantha , Baber Usman , Mehran Roxana , Kini Annapoorna S. , Sharma Samin K. , Dangas George D. 
Published: November 2015

BackgroundRandomized clinical trials evaluating the role of thrombus aspiration (TA) in patients undergoing primary percutaneous coronary intervention (PPCI) for ST‐segment elevation myocardial infarction (STEMI) have yielded contrasting results. Therefore, the efficacy and safety of TA in STEMI is unclear.ObjectiveWe sought to evaluate the efficacy and safety of TA during PPCI for STEMI compared with conventional PPCI alone.MethodsWe included study‐level data from 25 randomized, controlled trials, involving 21,733 patients with STEMI and PPCI. The primary efficacy endpoint was major adverse cardiac events (MACE) according to study definitions; the primary safety endpoint was stroke.ResultsThe mean weighted follow‐up time across studies was 8.2 months. Compared with conventional PPCI, TA was associated with significant lower risk for MACE [relative risk (RR): 0.91; 95% confidence interval (CI): 0.83–1.00; P = 0.042). However, this benefit in MACE was counterbalanced by a significant increase in the risk for stroke (RR: 1.58; 95% CI: 1.11–2.25; P = 0.011). There were no differences in the risk of myocardial infarction (RR: 0.94; 95% CI: 0.78–1.12; P = 0.486), target vessel revascularization (RR: 0.93; 95% CI: 0.82–1.04; P = 0.2), and definite or probable stent thrombosis (RR: 0.84; 95% CI: 0.66–1.07; P = 0.148). TA was associated with an ostensible lower risk for all‐cause mortality, which did not reach statistical significance (RR: 0.88; 95% CI: 0.78–1.00; P = 0.059).ConclusionsCompared with conventional PPCI for STEMI, adjunctive TA reduces the risk of subsequent MACE. However, the benefit in MACE is counterbalanced by an increased risk in stroke. Considering the above potential risks and benefits, TA should be considered in selected patients lesions rather than routinely. © 2015 Wiley Periodicals, Inc.
Mitral valve‐in‐valve with the lotus mechanically expanding platform
Authors: Feldman Ted , Reardon Michael J. 
Published: November 2015

Key Points

Disadvantages of existing balloon expandable or self‐expanding transcatheter platforms for mitral valve‐in‐valve include the potential for malposition during deployment and for LV outflow tract obstruction
Controlled mechanical valve expansion, the option to reposition, and stable hemodynamics throughout the procedure make the LOTUS valve an attractive option for mitral valve‐in‐valve
Correct sizing remains a critical aspect of all trancatheter valve implant procedures, including valve‐in‐valve implants
Tuning the Electrochemistry of Free‐Base Porphyrins in Acidic Nonaqueous Media: Influence of Solvent, Supporting Electrolyte, and Ring Substituents
Authors: Cui Yan , Zeng Lihan , Fang Yuanyuan , Zhu Jialiang , Devillers Charles H. , Lucas Dominique , Desbois Nicolas , Gros Claude P. , Kadish Karl M. 
Published: November 2015

AbstractA detailed study of reduction potentials, electroreduction mechanisms, and acid–base chemistry was carried out on two series of free‐base porphyrins in nonaqueous media. The first series is represented by four β‐pyrrole‐substituted tetraphenylporphyrin (TPP) derivatives, two of which are planar and two of which are nonplanar in their nonprotonated form. The second comprises porphyrins with 0–4 meso‐phenyl groups on the macrocycle. Equilibrium constants for the conversion of each neutral porphyrin to its diprotic [H4P]2+ form were determined and the electrochemistry was then elucidated as a function of: 1) type of nonaqueous solvent, 2) anion of supporting electrolyte, 3) porphyrin ring substituents, and 4) concentration of acid added to solution. Spectroelectrochemistry was used to characterize absorption spectra of each electroreduced species and, when combined with results of the above studies, significantly improves our ability to tune redox reactivity of these types of compounds.
ChemInform Abstract: Synthesis and Structural/Physical Properties of U3Fe2Ge7: A Single‐Crystal Study.
Authors: Henriques Margarida S. , Gorbunov Denis I. , Waerenborgh Joao C. , Pasturel Mathieu , Andreev Alexander V. , Dusek Michal , Skourski Yurii , Havela Ladislav , Goncalves Antonio P. 
Published: November 2015

AbstractSingle crystals of U3Fe2Ge7 are grown from an equimolar mixture of the elements in a tin flux (graphite crucible in evacuated silica tubes, 1273 K, 2 d; cooling to 573 K with a rate of 5 K/h).
ChemInform Abstract: Experimental Investigation of Phase Equilibria in Cu—Ge—Ti System.
Authors: Xie Z. Y. , Lv K. L. , Liu H. S. , Cai G. M. , Jin Z. P. 
Published: November 2015

AbstractArc melting of the elements followed by annealing (923 K, 10 d or 1073 K, 60 d) is used in combination with electron probe microscopy and powder XRD to evaluate the phase relations in isothermal sections of the Cu—Ge—Ti ternary system (20 and 15 three‐phase regions at 923 and 1073 K, respectively).
ChemInform Abstract: Syntheses and Crystal Structures of the Rare‐Earth Metal(III) Bromide ortho‐Oxidotungstates(VI) with the Formula REBr[WO4] (RE: Y, Gd—Yb).
Authors: Schustereit Tanja , Schleid Thomas , Hartenbach Ingo 
Published: November 2015

AbstractSingle crystals of the title compounds are prepared by solid state reactions of Ln2O3 (Ln: Y, Gd, Dy, Ho, Er, Tm, Yb) or Tb and Tb4O7, LnBr3, and WO3 (silica ampules, 850—1030 °C, 7 d).
ChemInform Abstract: Titanocene(III) Chloride Mediated Radical‐Induced Opening of Monosubstituted Epoxy Acetates for the Synthesis of Primary Allylic Alcohols.
Authors: Chakraborty P. , Mandal S. K. , Roy S. C. 
Published: November 2015

AbstractPrimary allylic alcohols (II) are simply and efficiently synthesized from monosubstituted epoxy acetates (I) by title reaction via acetate elimination.
ChemInform Abstract: Robust Bifunctional Aluminium—Salen Catalysts for the Preparation of Cyclic Carbonates from Carbon Dioxide and Epoxides.
Authors: Rulev Yuri A , Gugkaeva Zalina , Maleev Victor I , North Michael , Belokon Yuri N 
Published: November 2015

AbstractThe title reaction applies only to terminal epoxides and the catalysts can be recovered and reused for 3 catalytic cycles without significant loss of the catalytic activity.
ChemInform Abstract: Effective Formylation of Amines with Carbon Dioxide and Diphenylsilane Catalyzed by Chelating bis(tzNHC) Rhodium Complexes.
Authors: Nguyen Thanh V. Q. , Yoo Woo‐Jin , Kobayashi Shu 
Published: November 2015

AbstractThe shown rhodium complex (TZNHC) is the best catalyst for the reductive formylation reaction of amines with CO2 and Ph2SiH2.