bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co‐immobilization of Laccase and TEMPO in the Compartments of Mesoporous Silica for a Green and One‐Pot Cascade Synthesis of Coumarins by Knoevenagel Condensation
Authors: Mogharabi‐Manzari Mehdi , Amini Mohsen , Abdollahi Mohammad , Khoobi Mehdi , Bagherzadeh Ghodsieh , Faramarzi Mohammad Ali 
Published: January 2018

AbstractCo‐immobilization of bio‐ and chemocatalysts produces sustainable, recyclable hybrid systems that open new horizons for green cascade approaches in organic synthesis. Here, the co‐immobilization of laccase and 2,2,6,6‐tetramethylpiperidin‐1‐oxyl (TEMPO) in mesoporous silica was used for the one‐pot aqueous synthesis of 30 coumarin‐3‐carboxylate derivatives under mild conditions through the condensation of in situ oxidized 2‐hydroxybenzyl alcohols and malonate derivatives. A maximum yield was obtained after incubating at pH 6.0 and 45 °C for 24 h. An efficient organic synthesis was catalyzed by the hybrid catalyst in 10 % organic solvent. More than 95 % of the initial activity of the enzyme was preserved after 10 cycles, and no significant catalyst deactivation occurred after 10 runs. This new system efficiently catalyzed the in situ aerobic oxidation of salicyl alcohols, followed by Knoevenagel condensation, which confirmed the possibility of producing efficient hybrid catalysts by co‐immobilization of catalytic species in mesoporous materials.
The Role of Copper in the Upgrading of Bioalcohols
Authors: Zaccheria Federica , Scotti Nicola , Ravasio Nicoletta 
Published: January 2018

AbstractSome recent results on Guerbet reactions are reported and a short review on dehydrogenative coupling of alcohols (DHC) is presented. The focus of this Minireview is on the role of acidic and basic sites and, in particular, on the role of Cu if it is present in the catalyst, taking into account that the two processes share the first step, namely alcohol dehydrogenation, whereas the second one is determining in driving selectivity towards self‐coupling or symmetrical ester formation. The main type of catalysts for the Guerbet reaction are based on hydrotalcites, hydroxyapatite and supported metal systems, whereas the catalysts for DHC are copper catalysts on different supports. The role of acidic and basic sites in determining activity and selectivity to Guerbet alcohols has been investigated and quite stringent requirements for the selectivity of the reaction have been highlighted. For DHC, we have focused on the role of the interaction of copper with the support, which in turn influences the distribution of acidic and basic sites. The morphology of the metallic phase has been suggested as a distinctive factor in promoting C−C coupling or C−O coupling in the second step for Cu‐containing catalysts.
New Stretching Method for Aligning Gels: Its Application to the Measurement Residual Chemical Shift Anisotropies (RCSAs) without the Need for Isotropic Shift Correction
Authors: Hellemann Erich , Gil Roberto R. 
Published: January 2018

AbstractAn existing gel stretching device is modified, permitting the use of organic solvents for the study of small molecules. Different from the original device, gels are stretched into 4 mm open‐ended NMR tubes and then inserted into regular 5 mm NMR tubes. No open‐ended tubes are inserted in the NMR probe avoiding the risk of sample leaking. It is also shown that residual chemical shift anisotropies (RCSAs) measured with the device are free of isotropic shift interferences and corrections for them are not needed during the post‐acquisition data analysis. Three internal references for chemical shift were evaluated (CCl4, CBr4 and TMS), being CCl4 the most convenient one to measure RCSAs in CDCl3. RCSAs measured with the modified stretching device using CCl4 as the internal chemical shift reference were enough to determine the relative configuration of three small molecules with an excellent degree of configuration discrimination.
Specific Noncovalent Interactions Determine Optimal Structure of a Buried Ligand Moiety: QM/MM and Pure QM Modeling of Complexes of the Small‐Molecule CD4 Mimetics and HIV‐1 gp120
Authors: Moraca Francesca , Rinaldo David , Smith Amos B. , Abrams Cameron F. 
Published: January 2018

AbstractThe small‐molecule CD4 mimetics (smCD4mcs) are a class of highly potent HIV‐1 entry inhibitors characterized by a unique structure–activity relationship (SAR). They share a halogenated phenyl ring (region 1) that deeply inserts into an otherwise water‐filled cavity at the CD4 binding site on the gp120 surface, the so‐called F43 cavity. Conservative modifications to region 1 away from this halogenated phenyl motif have all led to loss of activity, despite the fact that they are predicted by standard empirical computational approaches to bind equally well, making it difficult to further optimize this region of the compounds to increase binding to gp120. In this study we used quantum mechanical methods to understand the roots of the interactions between region 1 and the F43 cavity. We clearly demonstrate the presence of halogen bond/σ‐hole and dispersion interactions between region 1 and the F43 cavity residues F376–N377, which are not captured by standard molecular mechanics approaches and the role played by the smCD4mc in the F43 cavity desolvation. These findings rationalize why the halogenated region 1 has proven so difficult to move beyond in smCD4mc optimization, in agreement with experimental evidence.
3D‐e‐Chem: Structural Cheminformatics Workflows for Computer‐Aided Drug Discovery
Authors: Kooistra Albert J. , Vass Márton , McGuire Ross , Leurs Rob , de Esch Iwan J. P. , Vriend Gert , Verhoeven Stefan , de Graaf Chris 
Published: January 2018

AbstracteScience technologies are needed to process the information available in many heterogeneous types of protein–ligand interaction data and to capture these data into models that enable the design of efficacious and safe medicines. Here we present scientific KNIME tools and workflows that enable the integration of chemical, pharmacological, and structural information for: i) structure‐based bioactivity data mapping, ii) structure‐based identification of scaffold replacement strategies for ligand design, iii) ligand‐based target prediction, iv) protein sequence‐based binding site identification and ligand repurposing, and v) structure‐based pharmacophore comparison for ligand repurposing across protein families. The modular setup of the workflows and the use of well‐established standards allows the re‐use of these protocols and facilitates the design of customized computer‐aided drug discovery workflows.
Influence of provider factors and race on uptake of breast cancer gene expression profiling
Authors: Reeder‐Hayes Katherine E. , Wheeler Stephanie B. , Baggett Christopher D. , Zhou Xi , Meng Ke , Roberts Megan C. , Carey Lisa A. , Meyer Anne‐Marie 
Published: January 2018

BACKGROUNDGene expression profiling (GEP) has been rapidly adopted for early breast cancer and can aid in chemotherapy decision making. Study results regarding racial disparities in testing are conflicting, and may reflect different care settings. To the authors' knowledge, data regarding the influence of provider factors on testing are scarce.METHODSThe authors used a statewide, multipayer, insurance claims database linked to cancer registry records to examine the impact of race and provider characteristics on GEP uptake in a cohort of patients newly diagnosed with breast cancer between 2005 and 2012. Incidence proportion models were used to examine the adjusted likelihood of testing. Models were stratified by lymph node status (N0 vs N1).RESULTSAmong 11,958 eligible patients, 23% of black and 26% of non‐Hispanic white patients received GEP. Among patients with N0 disease, black individuals were 16% less likely to receive testing after adjustment for clinical factors and the provider's specialty and volume of patients with breast cancer (95% confidence interval, 0.77‐0.93). Adjustment for provider characteristics did not attenuate the effect of race on testing. Patients of middle‐volume providers were more likely to be tested compared with those with either high‐volume or low‐volume providers, whereas patients seeing a medical oncologist were more likely to be tested compared with those whose only providers were from surgical specialties.CONCLUSIONSProvider volume and specialty were found to be significant predictors of GEP use, but did not explain racial disparities in testing. Further research concerning the key contributors to lagging test use among black women is needed to optimize the equitable use of GEPs and support personalized treatment decision making for all patients. Cancer 2018;124:1743‐51. © 2018 American Cancer Society
Making Use of Cancer Genomic Databases
Authors: Creighton Chad J. 
Published: January 2018

AbstractThe vast amounts of genomic data now deposited in public repositories represent rich resources for cancer researchers. Large‐scale genomics initiatives such as The Cancer Genome Atlas have made available data from multiple molecular profiling platforms (e.g., somatic mutation, RNA and protein expression, and DNA methylation) for the same set of over 10,000 human tumors. There has been much collective effort toward providing user‐friendly software tools for biologists lacking computational skills to ask questions of large‐scale genomic datasets. At the same time, there remains a clear need for skilled bioinformatics analysts to answer the types of questions that cannot easily be addressed using the public user‐friendly software tools. This overview introduces the reader to the many resources available for working with cancer genomic databases. © 2018 by John Wiley & Sons, Inc.
CRISPR/Cas9‐Mediated Genome Editing in Epstein‐Barr Virus‐Transformed Lymphoblastoid B‐Cell Lines
Authors: Jiang Sizun , Wang Liang Wei , Walsh Michael J. , Trudeau Stephen J. , Gerdt Catherine , Zhao Bo , Gewurz Benjamin E. 
Published: January 2018

AbstractEpstein‐Barr virus (EBV) efficiently transforms primary human B cells into immortalized lymphoblastoid cell lines (LCLs), which are extensively used in human genetic, immunological and virological studies. LCLs provide unlimited sources of DNA for genetic investigation, but can be difficult to manipulate, for instance because low retroviral or lentiviral transduction frequencies hinder experiments that require co‐expression of multiple components. This unit details Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 engineering for robust LCL genome editing. We describe the generation and delivery of single‐guide RNAs (sgRNAs), or dual‐targeting sgRNAs, via lentiviral transduction of LCLs that stably express Cas9 protein. CRISPR/Cas9 editing allows LCL loss‐of‐function studies, including knock‐out of protein‐coding genes or deletion of DNA regulatory elements, and can be adapted for large‐scale screening approaches. Low transfection efficiencies are a second barrier to performing CRISPR editing in LCLs, which are not typically lipid‐transfectable. To circumvent this barrier, we provide an optimized protocol for LCL nucleofection of Cas9/sgRNA ribonucleoprotein complexes (RNPs) as an alternative route to achieve genome editing in LCLs. These editing approaches can also be employed in other B‐cell lines, including Burkitt lymphoma and diffuse large B‐cell lymphoma cells, and are highly reproducible. © 2018 by John Wiley & Sons, Inc.
Pooled Lentiviral‐Delivery Genetic Screens
Authors: Piccioni Federica , Younger Scott T. , Root David E. 
Published: January 2018

AbstractPooled cell‐based screens of mammalian genetic perturbations enable systematic large‐scale, even genome‐scale, evaluation of gene function. Pooled screens introduce genetic perturbations into a cell population through viral transduction such that each cell integrates into its DNA a single or small number of library perturbations with barcodes identifying the perturbations. One then selects and physically isolates the subset of cells that exhibit the phenotype of interest. Sequencing the barcodes in the hit cells reveals which genes favored or inhibited the hit phenotype. Various genetic perturbations are possible, including CRISPR gene knockout, ectopic gene expression, and RNA interference. Regardless of the type of library being screened or the type of cell model being tested, such screens involve many common steps and procedures. This unit describes detailed experimental protocols for the key steps, and also highlights some of the key factors to achieving a well‐powered, reproducible screen result. © 2018 by John Wiley & Sons, Inc.
CRISPR‐Cas9‐Edited Site Sequencing (CRES‐Seq): An Efficient and High‐Throughput Method for the Selection of CRISPR‐Cas9‐Edited Clones
Authors: Veeranagouda Yaligara , Debono‐Lagneaux Delphine , Fournet Hamida , Thill Gilbert , Didier Michel 
Published: January 2018

AbstractThe emergence of clustered regularly interspaced short palindromic repeats–Cas9 (CRISPR‐Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR‐Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells). Here we described a next‐generation sequencing method called CRISPR‐Cas9 Edited Site Sequencing (CRES‐Seq) for the efficient and high‐throughput screening of CRISPR‐Cas9‐edited clones. CRES‐Seq facilitates the precise genotyping up to 96 CRISPR‐Cas9‐edited sites (CRES) in a single MiniSeq (Illumina) run with an approximate sequencing cost of $6/clone. CRES‐Seq is particularly useful when multiple genes are simultaneously targeted by CRISPR‐Cas9, and also for screening of clones generated from multiallelic genes/polyploid cells. © 2018 by John Wiley & Sons, Inc.
Method for Determining Crystal Grain Size by X‐Ray Diffraction
Authors: He Kai , Chen Nuofu , Wang Congjie , Wei Lishuai , Chen Jikun 
Published: January 2018

AbstractThe crystal grain size can be quantitatively calculated by Scherrer equation according to the diffraction peak broadening in the XRD curves. Actually, the results calculated by the Scherrer equation are the thickness that perpendicular to the crystal planes. However, in the actual XRD measurements, the broadening of the diffraction peaks is not only because of the Micro‐level changes of crystal such as grain size and lattice distortion, but also due to the instrumental broadening. Thus, the Scherrer equation is less reliable if the full width at half maximum caused by the physical broadening is smaller than that caused by the instrumental broadening. In this paper, it is concluded that the applicable range of the Scherrer equation will increases with the increasing diffraction angle. As an example of Scherrer equation's application, the calculation result for the maximum applicable scope of Si(100) films is 137 nm.
Unravelling the Effects of the Environmental Technology Portfolio on Corporate Sustainable Development
Authors: Wang Derek D. 
Published: January 2018

AbstractA firm's environmental technology portfolio comprises of a heterogeneous class of technologies, each with distinct economic and environmental implications. Having a portfolio with a proper mix of different technologies is critical in achieving economic and environmental goals. Using data on major United States’ corporates, I identify five types of environmental technologies: pollution control, eco‐efficiency, green design, low‐carbon energy, and management systems. I find that the composition of the environmental technology portfolio affects a firm's performance. Most notably, raising the share of low‐carbon energy and pollution control technologies in the portfolio can negatively affect economic performance. But both low‐carbon energy and pollution control are effective in improving carbon productivity. The other technologies do not display significant impacts on firm performance. The results highlight that firms should take the differential effects of environmental technologies into consideration when designing an adequate technology portfolio to attain desired economic and environmental objectives. Copyright © 2018 John Wiley & Sons, Ltd and ERP Environment
Using field data to quantify chemical impacts on wildlife population viability
Authors: Hilbers Jelle P. , Hoondert Renske P. J. , Schipper Aafke M. , Huijbregts Mark A. J. 
Published: January 2018

AbstractEnvironmental pollution is an important driver of biodiversity loss. Yet, to date, the effects of chemical exposure on wildlife populations have been quantified for only a few species, mainly due to a lack of appropriate laboratory data to quantify chemical impacts on vital rates. In this study, we developed a method to quantify the effects of toxicant exposure on wildlife population persistence based on field monitoring data. We established field‐based vital‐rate‐response functions for toxicants, using quantile regression to correct for the influences of confounding factors on the vital rates observed, and combined the response curves with population viability modelling. We then applied the method to quantify the impact of DDE on three bird species: the White‐tailed Eagle, Bald Eagle, and Osprey. Population viability was expressed via five population extinction vulnerability metrics: population growth rate (r1), critical patch size (CPS), minimum viable population size (MVP), probability of population extirpation (PE), and median time to population extirpation (MTE). We found that past DDE exposure concentrations increased population extirpation vulnerabilities of all three bird species. For example, at DDE concentrations of 25 mg/kg wet mass of egg (the maximum historic exposure concentration reported in literature for the Osprey), r1 became small (White‐tailed Eagle and Osprey) or close to zero (Bald Eagle), the CPS increased up to almost the size of Connecticut (White‐tailed Eagle and Osprey) or West Virginia (Bald Eagle), the MVP increased up to approximately 90 (White‐tailed Eagle and Osprey) or 180 breeding pairs (Bald Eagle), the PE increased up to almost certain extirpation (Bald Eagle) or only slightly elevated levels (White‐tailed Eagle and Osprey) and the MTE became within decades (Bald Eagle) or remained longer than a millennium (White‐tailed Eagle and Osprey). Our study provides a method to derive species‐specific field‐based response curves of toxicant exposure, which can be used to assess population extinction vulnerabilities and obtain critical levels of toxicant exposure based on maximum permissible effect levels. This may help conservation managers to better design appropriate habitat restoration and population recovery measures, such as reducing toxicant levels, increasing the area of suitable habitat or reintroducing individuals.
The primacy of bears as seed dispersers in salmon‐bearing ecosystems
Authors: Harrer Laurie E. F. , Levi Taal 
Published: January 2018

AbstractSalmon–bear ecosystems that historically existed throughout most of the northern temperate and boreal regions of planet earth now persist only in the North Pacific. Extensive research on salmon–bear interactions has focused on the role that bears (Ursus arctosandU. americanus) play in provisioning terrestrial systems with marine‐derived nutrients, but little attention has been paid to how the much higher bear population densities in salmon‐bearing ecosystems then affect ecological communities. Salmon‐supported brown bears secondarily consume large quantities of fruit and may thus serve as important seed dispersers, but the relative seed dispersal services provided by bears and birds are unknown. We sought to (1) quantify the number of seeds dispersed by bears relative to birds, and (2) by brown bears relative to black bears, and to (3) assess whether the two sympatric bears temporally partition berry resources as a result of competitively dominant brown bears switching to feed on salmon, thus opening niche space for black bears. We used a combination of motion‐triggered camera traps and environmentalDNA(eDNA) from residual saliva to quantify the roles of birds, black bears, and brown bears as seed dispersers of devil's club (Oplopanax horridus), the dominant understory shrub at our field site in northern southeast Alaska. Brown bears were the numerically dominant seed dispersers, particularly before salmon became widely available, after which black bears became common seed dispersers, likely due to alleviation of interference competition. Birds accounted for only a small fraction of seed dispersal. This is the first demonstration of a temperate plant being primarily dispersed by mammalian gut passage. Our results suggest that bears are uniquely important seed dispersers, which may influence plant community composition in salmon‐bearing ecosystems.
Drivers and demographic consequences of seasonal mass changes in an alpine ungulate
Authors: Douhard Mathieu , Guillemette Simon , Festa‐Bianchet Marco , Pelletier Fanie 
Published: January 2018

AbstractWe know little about the determinants and demographic consequences of the marked seasonal mass changes exhibited by many northern and alpine mammals. We analysed 43 years of data on individual winter mass loss (the difference between mass in early June and mass in mid‐September the previous year) and summer mass gain (the difference between mass in mid‐September and in early June of the same year) in adult bighorn sheep (Ovis canadensis). We calculated relative seasonal mass change as a proportion of individual body mass at the start of each season. We first examined the effects of weather and population density on relative changes in body mass. We then assessed the consequences of relative seasonal mass changes on reproduction. Mean April–May temperature was the main driver of relative seasonal mass changes: warm springs reduced both relative winter mass loss and summer mass gain of both sexes, likely partially due to a trade‐off between growth rate of plants and duration of access to high‐quality forage. Because these effects cancelled each other, spring temperature did not influence mass in mid‐September. Mothers that lost relatively more mass during the winter had lambs that gained less mass during summer, likely because these females allocated fewer resources to lactation. Winter survival of lambs increased with their summer mass gain. In males, relative mass loss during winter, which includes the rut, did not influence the probability of siring at least one lamb, possibly indicating that greater mating effort did not necessarily translate into greater reproductive success. Our findings improve our understanding of how weather influences recruitment and underline the importance of cryptic mechanisms behind the effects of climate change on demographic traits.