bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface Trapping and STM Observation of Conformational Isomers of a Bis(Terpyridine) Ligand from Metallosupramolecular Grids
Authors: Karan Sujoy , Hamann Christian , Tang Hao , Stefankiewicz Artur R. , Lehn Jean‐Marie , Berndt Richard 
Published: February 2015

AbstractTetranuclear Co‐grid complexes incorporating bis‐tridentate ligands, namely 4,6‐bis(2,2′‐bipyrid‐6‐yl)‐2‐phenylpyrimidine, were electrosprayed onto a Au(111) substrate under an ultrahigh vacuum. Fragmentation occurs leaving the ligands in four different conformations. Most ligands are found to form H‐bonded dimers. The most abundant conformer of the ligand on the Au surface is an asymmetric form, which has not been observed before. The present results indicate that the fragmentation of coordination compounds during the deposition process, in principle, allows for surface trapping, identification, and investigation of high energy, out‐of‐equilibrium conformations of the ligand molecules at low temperatures, which otherwise would not be observable.
Xylose Isomerization with Zeolites in a Two‐Step Alcohol–Water Process
Authors: Paniagua Marta , Saravanamurugan Shunmugavel , Melian‐Rodriguez Mayra , Melero Juan A. , Riisager Anders 
Published: February 2015

AbstractIsomerization of xylose to xylulose was efficiently catalyzed by large‐pore zeolites in a two‐step methanol–water process that enhanced the product yield significantly. The reaction pathway involves xylose isomerization to xylulose, which, in part, subsequently reacts with methanol to form methyl xyluloside (step 1) followed by hydrolysis after water addition to form additional xylulose (step 2). NMR spectroscopy studies performed with 13C‐labeled xylose confirmed the proposed reaction pathway. The most active catalyst examined was zeolite Y, which proved more active than zeolite beta, ZSM‐5, and mordenite. The yield of xylulose obtained over H‐USY (Si/Al=6) after 1 h of reaction at 100 °C was 39 %. After water hydrolysis in the second reaction step, the yield increased to 47 %. Results obtained from pyridine adsorption studies confirm that H‐USY (6) is a catalyst that combines Brønsted and Lewis acid sites, and isomerizes xylose in alcohol media to form xylulose at low temperature. The applied zeolites are commercially available; do not contain any auxiliary tetravalent metals, for example, tin, titanium, or zirconium; isomerize xylose efficiently; are easy to regenerate; and are prone to recycling.
Electrifying White Biotechnology: Engineering and Economic Potential of Electricity‐Driven Bio‐Production
Authors: Harnisch Falk , Rosa Luis F. M. , Kracke Frauke , Virdis Bernardino , Krömer Jens O. 
Published: February 2015

AbstractInvited for the cover of this issue are the groups of Falk Harnisch at the Helmholtz Centre for Environmental Research (Germany) and his collaboration partners at The University of Queensland (Australia). The image depicts their vision of the world, if “electrification” of white biotechnology comes true. The Concept itself is available at 10.1002/cssc.201402736.
Potential for adaptive evolution at species range margins: contrasting interactions between red coral populations and their environment in a changing ocean
Authors: Ledoux Jean‐Baptiste , Aurelle Didier , Bensoussan Nathaniel , Marschal Christian , Féral Jean‐Pierre , Garrabou Joaquim 
Published: February 2015

AbstractStudying population‐by‐environment interactions (PEIs) at species range margins offers the opportunity to characterize the responses of populations facing an extreme regime of selection, as expected due to global change. Nevertheless, the importance of these marginal populations as putative reservoirs of adaptive genetic variation has scarcely been considered in conservation biology. This is particularly true in marine ecosystems for which the deep refugia hypothesis proposes that disturbed shallow and marginal populations of a given species can be replenished by mesophotic ones. This hypothesis therefore assumes that identical PEIs exist between populations, neglecting the potential for adaptation at species range margins. Here, we combine reciprocal transplant and common garden experiments with population genetics analyses to decipher the PEIs in the red coral, Corallium rubrum. Our analyses reveal partially contrasting PEIs between shallow and mesophotic populations separated by approximately one hundred meters, suggesting that red coral populations may potentially be locally adapted to their environment. Based on the effective population size and connectivity analyses, we posit that genetic drift may be more important than gene flow in the adaptation of the red coral. We further investigate how adaptive divergence could impact population viability in the context of warming and demonstrate differential phenotypic buffering capacities against thermal stress. Our study questions the relevance of the deep refugia hypothesis and highlights the conservation value of marginal populations as a putative reservoir of adaptive genetic polymorphism.
Nanopipet‐Based Resistive Pulse Sensing to Follow Alterations in the Size and Concentration of Nanoparticles During Membrane Filtration
Authors: Terejánszky Péter , Makra István , Lukács Alda , Gyurcsányi Róbert E. 
Published: February 2015

AbstractWe propose a calibration‐free resistive pulse sensing (RPS) methodology based on nanopipets to follow the size and concentration changes of nanoparticles during size‐selective separation processes. The study was performed with monodisperse latex nanoparticles and their mixtures that were subjected to separation procedures such as filtration through track‐etch membranes of various pore diameters as well as centrifugal filtration. The RPS measurements were found to be suitable to determine both the recovery of the nanoparticles after filtration as well as subtle changes in their size distribution. Filtration through track‐etch membranes preserved the mean size of the nanoparticles while their recovery was affected by the size of the pore and coexistence of larger nanoparticle fractions in the sample. Centrifugal filtration resulted in the appearance of aggregates.
Enhanced Production of Cellulase from Bacillus licheniformis K‐3 with Potential for Saccharification of Rice Straw
Authors: Gupta Mahak , Sharma Mukul , Singh Satbir , Gupta Puneet , Bajaj Bijender Kumar 
Published: February 2015

AbstractThe unavailability of process‐suitable cellulases and expensive cost prompted research on the economic production of proficient enzymes. Bacillus licheniformis K‐3, an isolate from degrading lignocellulosic biomass, can produce cellulose, possessing activity and stability over broad pH range (4.0–10) and at elevated temperature (40–90 °C). B. licheniformis K‐3 can be used to successfully utilize agricultural residues (such as wheat bran, corn waste, wheat straw, almond hulls, soybean meal, and mustard cake) as substrates for growth and cellulase production. The most effective fermentation variables (wheat bran, incubation time, and medium pH) have been earmarked on the basis of Plackett–Burman designed experiments and they were optimized by using response surface methodology to achieve a 7‐fold enhancement in the cellulase yield. Partially purified cellulase showed efficient saccharification potential for single‐phase sulphuric‐acid‐pretreated rice straw.
Transcriptional profiling of the soil invertebrate Folsomia candida in pentachlorophenol-contaminated soil
Authors: Qiao Min , Wang Guang-Peng , Zhang Cai , Roelofs Dick , van Straalen Nico M. , Zhu Yong-Guan 
Published: February 2015

Abstract

Pentachlorophenol (PCP), a widely used pesticide, is considered to be an endocrine disruptor. The molecular effects of chemicals with endocrine-disrupting potential on soil invertebrates are largely unknown. In the present study, the authors explored the transcriptional expression changes of collembola (Folsomia candida) in response to PCP contamination. A total of 92 genes were significantly differentially expressed at all exposure times, and the majority of them were found to be downregulated. In addition to the transcripts encoding cytochrome P450s and transferase enzymes, chitin-binding protein was also identified in the list of common differentially expressed genes. Analyses of gene ontology annotation and enrichment revealed that cell cycle-related transcripts were significantly induced by PCP, indicating that PCP can stimulate cell proliferation in springtail, as has been reported in human breast cancer cells. Enrichment of functional terms related to steroid receptors was observed, particularly in 20 significant differentially expressed genes involved in chitin metabolism in response to PCP exposure. Combined with confirmation by quantitative polymerase chain reaction, the results indicate that the adverse effects on reproduction of springtails after exposure to PCP can be attributed to a chemical-induced delay in the molting cycle and that molting-associated genes may serve as possible biomarkers for assessing toxicological effects. Environ Toxicol Chem 2015;34:1362–1368. © 2015 SETAC
Banana leaf and glucose mineralization and soil organic matter in microhabitats of banana plantations under long-term pesticide use
Authors: Blume Elena , Reichert José Miguel 
Published: February 2015

Abstract

Soil organic matter (SOM) and microbial activity are key components of soil quality and sustainability. In the humid tropics of Costa Rica 3 pesticide regimes were studied—fungicide (low input); fungicide and herbicide (medium input); and fungicide, herbicide, and nematicide (high input)—under continuous banana cultivation for 5 yr (young) or 20 yr (old) in 3 microhabitats—nematicide ring around plants, litter pile of harvested banana, and bare area between litter pile and nematicide ring. Soil samples were incubated sequentially in the laboratory: unamended, amended with glucose, and amended with ground banana leaves. Soil organic matter varied with microhabitat, being greatest in the litter pile, where microbes had the greatest basal respiration with ground banana leaf, whereas microbes in the nematicide ring had the greatest respiration with glucose. These results suggest that soil microbes adapt to specific microhabitats. Young banana plantations had similar SOM compared with old plantations, but the former had greater basal microbial respiration in unamended and in glucose-amended soil and greater first-order mineralization rates in glucose-amended soil, thus indicating soil biological quality decline over time. High pesticide input did not decrease microbial activity or mineralization rate in surface soil. In conclusion, microbial activity in tropical volcanic soil is highly adaptable to organic and inorganic inputs. Environ Toxicol Chem 2015;34:1232–1238. © 2015 SETAC
Direct Toll‐Like Receptor 8 signaling increases the functional avidity of human CD8+ T lymphocytes generated for adoptive T cell therapy strategies
Authors: Chatillon Jean‐François , Hamieh Mohamad , Bayeux Florence , Abasq Claire , Fauquembergue Emilie , Drouet Aurélie , Guisier Florian , Latouche Jean‐Baptiste , Musette Philippe 
Published: February 2015

AbstractAdoptive transfer of in vitro activated and expanded antigen‐specific cytotoxic T lymphocytes (CTLs) is a promising therapeutic strategy for infectious diseases and cancers. Obtaining in vitro a sufficient amount of highly specific cytotoxic cells and capable of retaining cytotoxic activity in vivo remains problematic. We studied the role of Toll‐Like Receptor‐8 (TLR8) engagement on peripheral CTLs activated with melanoma antigen MART‐1‐expressing artificial antigen‐presenting cells (AAPCs). After a 3‐week co‐culture, 3–27% of specific CTLs were consistently obtained. CTLs expressed TLR8 in the intracellular compartment and at the cell surface. Specific CTLs activated with a TLR8 agonist (CL075) 24 h before the end of the culture displayed neither any change in their production levels of molecules involved in cytotoxicity (IFN‐γ, Granzyme B, and TNF‐α) nor major significant change in their cell surface phenotype. However, these TLR8‐stimulated lymphocytes displayed increased cytotoxic activity against specific peptide‐pulsed target cells related to an increase in specific anti‐melanoma CTL functional avidity. TLR8 engagement on CTLs could, therefore, be useful in different immunotherapy strategies.
Electron Transport Mediated by Peptides Immobilized on Surfaces
Authors: Juhaniewicz Joanna , Pawlowski Jan , Sek Slawomir 
Published: February 2015

AbstractElectron transfer reactions in proteins and peptides are crucial for biological energy conversion. Therefore, an important goal of fundamental research is to provide scientific insight into the mechanisms determining the bridge‐mediated electron transport. One of the main tasks is to understand how the efficiency of this process is affected by the particular structure of a peptide, as well as the surrounding environment, and eventually, how we can control it by means of external chemical and physical factors. The latter could be of crucial importance for the design and development of biosensors and other functional devices, which may benefit from the unique electron transfer properties of peptides. Monolayers immobilized on solid surfaces seem to be particularly useful for that purpose. In this paper, we present the progress of fundamental research related to electron transport through peptides adsorbed onto metal surfaces. Specifically, we have focused on electrochemical studies and nanoscale molecular junction approaches. We have critically reviewed existing data and discussed the discrepancies in the measured efficiencies of electron transport. Some suggestions for future fundamental research in this area are provided. In particular, the need to combine the electrochemical and molecular junction approaches to explore the conductance behavior of peptides under full electrochemical control is emphasized. Some potential applications of peptide monolayers, which take advantage of the unique electrical properties of these compounds, are also discussed.
Understanding What Students Know
Authors: Castek Jill , Coiro Julie 
Published: February 2015

AbstractThis piece is framed by questions we are often asked when we talk about online reading assessments and instruction with teachers. We begin with some of the lessons we have learned in our own experiences with designing measures of online reading comprehension. Then we share our thoughts about key design considerations as well as some of the biggest challenges of trying to capture online research and reading skills when online texts and authentic tasks are constantly changing. By sharing these perspectives, we hope to inspire new ways of tracking students’ progress that can help teachers design powerful literacy instruction that integrates digital texts and new technologies.
Identification of Spatial Durbin Panel Models
Authors: Lee Lung‐fei , Yu Jihai 
Published: February 2015

SummaryThis paper considers identification of spatial Durbin dynamic panel models under 2SLS and ML estimations. We show that the parameters are generally identified via 2SLS moment relations or expected log‐likelihood or quasi‐likelihood functions. Monte Carlo experiments suggest that omitting relevant Durbin terms can result in significant biases in regression estimates, while including an irrelevant Durbin term causes no obvious loss of efficiency. Empirical illustration of the international spillover of economic growth through bilateral trade shows that inclusion of Durbin terms can be important. Copyright © 2015 John Wiley & Sons, Ltd.
ER Stress During the Pubertal Growth Spurt Results in Impaired Long-Bone Growth in Chondrocyte-Specific ERp57 Knockout Mice
Authors: Linz Andrea , Knieper Yvonne , Gronau Tobias , Hansen Uwe , Aszodi Attila , Garbi Natalio , Hämmerling Günter J , Pap Thomas , Bruckner Peter , Dreier Rita 
Published: February 2015

ABSTRACT

Long-bone growth by endochondral ossification is cooperatively accomplished by chondrocyte proliferation, hypertrophic differentiation, and appropriate secretion of collagens, glycoproteins, and proteoglycans into the extracellular matrix (ECM). Before folding and entering the secretory pathway, ECM macromolecules in general are subject to extensive posttranslational modification, orchestrated by chaperone complexes in the endoplasmic reticulum (ER). ERp57 is a member of the protein disulfide isomerase (PDI) family and facilitates correct folding of newly synthesized glycoproteins by rearrangement of native disulfide bonds. Here, we show that ERp57-dependent PDI activity is essential for postnatal skeletal growth, especially during the pubertal growth spurt characterized by intensive matrix deposition. Loss of ERp57 in growth plates of cartilage-specific ERp57 knockout mice (ERp57 KO) results in ER stress, unfolded protein response (UPR), reduced proliferation, and accelerated apoptotic cell death of chondrocytes. Together this results in a delay of long-bone growth with the following characteristics: (1) enlarged growth plates; (2) expanded hypertrophic zones; (3) retarded osteoclast recruitment; (4) delayed remodeling of the proteoglycan-rich matrix; and (5) reduced numbers of bone trabeculae. All the growth plate and bone abnormalities, however, become attenuated after the pubertal growth spurt, when protein synthesis is decelerated and, hence, ERp57 function is less essential. © 2015 American Society for Bone and Mineral Research.
Frequency of recommendations for additional imaging in diagnostic ultrasound examinations: Evaluation of radiologist, technologist, and other examination‐related factors
Authors: Margolis Nathaniel E. , Rosenkrantz Andrew B. , Babb James S. , Macari Michael 
Published: February 2015

ABSTRACTObjectiveOur aim in this study was to evaluate the effect of the radiologist, technologist, and other examination‐related factors on the frequency of recommendations for additional imaging (RAI) during sonographic (US) interpretation.MethodsWe retrospectively reviewed 719 US reports from a single academic medical center for the presence of RAI. All studies had been interpreted by one of three abdominal radiologists. Examinations were performed at an outpatient radiology facility with no onsite radiologist (n = 299) or at an inpatient emergency department or hospital‐based outpatient setting that had an onsite radiologist (n = 420). Possible associations between the frequency of RAI and the presence of an onsite radiologist, location of the examination, body part or region imaged, patient age, technologist performing the exam, and radiologist reading the exam were evaluated.ResultsThere were significant differences between each pair of radiologists in terms of overall frequency of RAI (p < 0.001) (radiologist 1: 12.0% [22/184]; radiologist 2: 21.6% [78/361]; and radiologist 3: 45.5% [79/174]). In addition, there were statistically significant differences in the frequency of RAI among studies scanned by the 10 different US technologists (13.6%–40.0%, p = 0.03). However, other factors such as patient age, patient sex, US unit, patient location, and radiologist location were not associated with the frequency of RAI (p = 0.15–0.93).ConclusionsThe individual radiologist and technologist influenced the frequency of RAI for US examinations, whereas other examination‐related factors did not. The observed substantial variability in RAI between radiologists and technologists warrants further study, with consideration of strategies to optimize RAI within US reports. © 2015 Wiley Periodicals, Inc. J Clin Ultrasound 43:463–468 2015
Efficient tryptophan‐catabolizing activity is consistently conserved through evolution of TDO enzymes, but not IDO enzymes
Authors: Yuasa Hajime J. , Ball Helen J. 
Published: February 2015

ABSTRACTIndoleamine 2,3‐dioxygenase (IDO) and tryptophan 2,3‐dioxygenase (TDO) enzymes have independently evolved to catalyze the first step in the catabolism of tryptophan (L‐Trp) through the kynurenine pathway. TDO is found in almost all metazoan and many bacterial species, but not in fungi. We show that TDO enzymes have high catalytic‐efficiency for L‐Trp catabolism, regardless of their biological origin, suggesting that TDO has been an L‐Trp‐specific degrading enzyme throughout its evolution. Meanwhile, IDO was initially discovered in mammals, and subsequently has been found in lower vertebrates, several invertebrates, fungi and a number of bacterial species. Some lineages have independently generated multiple IDO paralogues through gene duplications. Interestingly, only mammalian IDO1s and fungal “typical” IDOs have high affinity and catalytic efficiency for L‐Trp catabolism, comparable to TDOs. We show that invertebrate IDO enzymes have low affinity and catalytic efficiency for L‐Trp catabolism. We suggest that the phylogenetic distribution of “low catalytic‐efficiency IDOs” indicates the ancestral IDO also had low affinity and catalytic efficiency for L‐Trp catabolism. IDOs with high catalytic‐efficiency for L‐Trp‐catabolism may have evolved in certain lineages to fulfill particular biological roles. The low catalytic‐efficiency IDOs have been well conserved in a number of lineages throughout their evolution, although it is not clear that the enzymes contribute significantly to L‐Trp catabolism in these species. Investigation of other substrates and functions of the ancestral IDO and low catalytic efficiency IDOs may identify additional biological roles for these enzymes. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 128–140, 2015. © 2015 Wiley Periodicals, Inc.
Oxygen and redox potential gradients in the rhizosphere of alfalfa grown on a loamy soil
Authors: Uteau Daniel , Hafner Silke , Pagenkemper Sebastian Kouso , Peth Stephan , Wiesenberg Guido L. B. , Kuzyakov Yakov , Horn Rainer 
Published: February 2015

AbstractOxygen (O2) supply and the related redox potential (EH) are important parameters for interactions between roots and microorganisms in the rhizosphere. Rhizosphere extension in terms of the spatial distribution of O2 concentration and EH is poorly documented under aerobic soil conditions. We investigated how far O2 consumption of roots and microorganisms in the rhizosphere is replenished by O2 diffusion as a function of water/air‐filled porosity. Oxygen concentration and EH in the rhizosphere were monitored at a mm‐scale by means of electroreductive Clark‐type sensors and miniaturized EH electrodes under various matric potential ranges. Respiratory activity of roots and microorganisms was calculated from O2 profiles and diffusion coefficients. pH profiles were determined in thin soil layers sliced near the root surface.Gradients of O2 concentration and the extent of anoxic zones depended on the respiratory activity near the root surface. Matric potential, reflecting air‐filled porosity, was found to be the most important factor affecting O2 transport in the rhizosphere. Under water‐saturated conditions and near field capacity up to –200 hPa, O2 transport was limited, causing a decline in oxygen partial pressures (pO2) to values between 0 and 3 kPa at the root surface. Aerobic respiration increased by a factor of 100 when comparing the saturated with the driest status. At an air‐filled porosity of 9% to 12%, diffusion of O2 increased considerably. This was confirmed by EH around 300 mV under aerated conditions, while EH decreased to 100 mV on the root surface under near water‐saturated conditions. Gradients of pO2 and pH from the root surface indicated an extent of the rhizosphere effect of 10–20 mm. In contrast, EH gradients were observed from 0 to 2 mm from the root surface. We conclude that the rhizosphere extent differs for various parameters (pH, Eh, pO2) and is strongly dependent on soil moisture.