bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioID: A Screen for Protein‐Protein Interactions
Authors: Roux Kyle J. , Kim Dae In , Burke Brian 
Published: November 2013

AbstractBioID is a unique method to screen for physiologically relevant protein interactions that occur in living cells. This technique harnesses a promiscuous biotin ligase to biotinylate proteins based on proximity. The ligase is fused to a protein of interest and expressed in cells, where it biotinylates proximal endogenous proteins. Because it is a rare protein modification in nature, biotinylation of these endogenous proteins by BioID fusion proteins enables their selective isolation and identification with standard biotin‐affinity capture. Proteins identified by BioID are candidate interactors for the protein of interest. BioID can be applied to insoluble proteins, can identify weak and/or transient interactions, and is amenable to temporal regulation. Initially applied to mammalian cells, BioID has potential application in a variety of cell types from diverse species. Curr. Protoc. Protein Sci. 74:19.23.1‐19.23.14. © 2013 by John Wiley & Sons, Inc.
High‐Throughput Cloning and Expression of Integral Membrane Proteins in Escherichia coli
Authors: Bruni Renato , Kloss Brian 
Published: November 2013

AbstractRecently, several structural genomics centers have been established and a remarkable number of three‐dimensional structures of soluble proteins have been solved. For membrane proteins, the number of structures solved has been significantly trailing those for their soluble counterparts, not least because over‐expression and purification of membrane proteins is a much more arduous process. By using high‐throughput technologies, a large number of membrane protein targets can be screened simultaneously and a greater number of expression and purification conditions can be employed, leading to a higher probability of successfully determining the structure of membrane proteins. This unit describes the cloning, expression, and screening of membrane proteins using high‐throughput methodologies developed in the laboratory. Basic Protocol 1 describes cloning of inserts into expression vectors by ligation‐independent cloning. Basic Protocol 2 describes the expression and purification of the target proteins on a miniscale. Lastly, for the targets that do express on the miniscale, Basic Protocols 3 and 4 outline the methods employed for the expression and purification of targets on a midi‐scale, as well as a procedure for detergent screening and identification of detergent(s) in which the target protein is stable. Curr. Protoc. Protein Sci. 74:29.6.1‐29.6.34. © 2013 by John Wiley & Sons, Inc.
The nitrogen cycle of tropical montane forest in Ecuador turns inorganic under environmental change
Authors: Wilcke Wolfgang , Leimer Sophia , Peters Thorsten , Emck Paul , Rollenbeck Rütger , Trachte Katja , Valarezo Carlos , Bendix Jörg 
Published: November 2013

AbstractWater‐bound nitrogen (N) cycling in temperate terrestrial ecosystems of the Northern Hemisphere is today mainly inorganic because of anthropogenic release of reactive N to the environment. In little‐industrialized and remote areas, in contrast, a larger part of N cycling occurs as dissolved organic N (DON). In a north Andean tropical montane forest in Ecuador, the N cycle changed markedly during 1998–2010 along with increasing N deposition and reduced soil moisture. The DON concentrations and the fractional contribution of DON to total N significantly decreased in rainfall, throughfall, and soil solutions. This inorganic turn of the N cycle was most pronounced in rainfall and became weaker along the flow path of water through the system until it disappeared in stream water. Decreasing organic contributions to N cycling were caused not only by increasing inorganic N input but also by reduced DON production and/or enhanced DON decomposition. Accelerated DON decomposition might be attributable to less waterlogging and higher nutrient availability. Significantly increasing NO3‐N concentrations and NO3‐N/NH4‐N concentration ratios in throughfall and litter leachate below the thick organic layers indicated increasing nitrification. In mineral soil solutions, in contrast, NH4‐N concentrations increased and NO3‐N/NH4‐N concentration ratios decreased significantly, suggesting increasing net ammonification. Our results demonstrate that the remote tropical montane forests on the rim of the Amazon basin experienced a pronounced change of the N cycle in only one decade. This change likely parallels a similar change which followed industrialization in the temperate zone of the Northern Hemisphere more than a century ago.
Listeria monocytogenes: Cultivation and Laboratory Maintenance
Authors: Jones Grant S. , D'Orazio Sarah E.F. 
Published: November 2013

AbstractThis unit describes general procedures for the lab cultivation and storage of the Gram‐positive facultative intracellular bacterium Listeria monocytogenes. The basic protocols are relevant for a wide scope of applications including microbial genetics and both in vitro and in vivo infection studies. Commonly used L. monocytogenes strains, serotypes, and growth parameters are also discussed. Curr. Protoc. Microbiol. 31:9B.2.1‐9B.2.7. ©2013 by John Wiley & Sons, Inc.
A Mouse Model of Foodborne Listeria monocytogenes Infection
Authors: Bou Ghanem Elsa N. , Myers‐Morales Tanya , D'Orazio Sarah E.F. 
Published: November 2013

AbstractListeria monocytogenes causes foodborne disease in humans that ranges in severity from mild, self‐limiting gastroenteritis to life‐threatening systemic infections of the blood, brain, or placenta. The most commonly used animal model of listeriosis is intravenous infection of mice. This systemic model is highly reproducible, and thus, useful for studying cell‐mediated immune responses against an intracellular bacterial pathogen, but it completely bypasses the gastrointestinal phase of L. monocytogenes infection. Intragastric inoculation of L. monocytogenes produces more variable results and may cause direct bloodstream invasion in some animals. The foodborne transmission model described here does not require specialized skills to perform and results in infections that more closely mimic human disease. This natural feeding model can be used to study both the host‐ and pathogen‐derived factors that govern susceptibility or resistance to orally acquired L. monocytogenes. Curr. Protoc. Microbiol. 31:9B.3.1‐9B.3.16. © 2013 by John Wiley & Sons, Inc.
Propagation, Quantification, Detection, and Storage of West Nile Virus
Authors: Brien James D. , Lazear Helen M. , Diamond Michael S. 
Published: November 2013

AbstractWest Nile virus (WNV) is a member of the Flaviviridae family of enveloped, single‐stranded, positive‐sense RNA viruses. WNV, an emerging viral pathogen, is transmitted by mosquitoes to birds and mammals and is responsible for an increasing incidence of human disease in North America and Europe. Due to its ease of use in the laboratory and the availability of robust mouse models of disease, WNV provides an excellent experimental system for studying molecular virology and pathogenesis of infection by flaviviruses. Here, we describe common laboratory techniques used to propagate, quantify, detect, and store WNV. We also briefly describe appropriate safety precautions required for the laboratory use of WNV, which is classified as a Biosafety Level 3 pathogen by the United States Centers for Disease Control and Prevention. Curr. Protoc. Microbiol. 31:15D.3.1‐15D.3.18. ©2013 by John Wiley & Sons, Inc.
Human Norovirus Detection and Production, Quantification, and Storage of Virus‐Like Particles
Authors: Debbink Kari , Costantini Veronica , Swanstrom Jesica , Agnihothram Sudhakar , Vinjé Jan , Baric Ralph , Lindesmith Lisa 
Published: November 2013

AbstractHuman noroviruses constitute a significant worldwide disease burden. Each year, noroviruses cause over 267 million infections, deaths in over 200,000 children under the age of five, and over 50% of U.S. food‐borne illness. Due to the absence of a tissue culture model or small animal model to study human norovirus, virus‐like particles (VLPs) and ELISA‐based biological assays have been used to answer questions about norovirus evolution and immunity as well to provide a potential vaccine platform. This chapter outlines the protocols for norovirus detection in stool, as well as norovirus VLP design, production, purification, and storage using a Venezuelan equine encephalitis virus (VEE)–based virus replicon particle (VRP) expression system. Curr. Protoc. Microbiol. 31:15K.1.1‐15K.1.45. © 2013 by John Wiley & Sons, Inc.
DNA Immunization
Authors: Wang Shixia , Lu Shan 
Published: November 2013

AbstractDNA immunization was discovered in early 1990s, and its use has been expanded from vaccine studies to a broader range of biomedical research areas, such as the generation of high‐quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation, and gene gun. In addition, several common considerations related to DNA immunization are discussed. Curr. Protoc. Microbiol. 31:18.3.1‐18.3.24. ©2013 by John Wiley & Sons, Inc.
Bayes in biological anthropology
Authors: Konigsberg Lyle W. , Frankenberg Susan R. 
Published: November 2013

ABSTRACTIn this article, we both contend and illustrate that biological anthropologists, particularly in the Americas, often think like Bayesians but act like frequentists when it comes to analyzing a wide variety of data. In other words, while our research goals and perspectives are rooted in probabilistic thinking and rest on prior knowledge, we often proceed to use statistical hypothesis tests and confidence interval methods unrelated (or tenuously related) to the research questions of interest. We advocate for applying Bayesian analyses to a number of different bioanthropological questions, especially since many of the programming and computational challenges to doing so have been overcome in the past two decades. To facilitate such applications, this article explains Bayesian principles and concepts, and provides concrete examples of Bayesian computer simulations and statistics that address questions relevant to biological anthropology, focusing particularly on bioarchaeology and forensic anthropology. It also simultaneously reviews the use of Bayesian methods and inference within the discipline to date. This article is intended to act as primer to Bayesian methods and inference in biological anthropology, explaining the relationships of various methods to likelihoods or probabilities and to classical statistical models. Our contention is not that traditional frequentist statistics should be rejected outright, but that there are many situations where biological anthropology is better served by taking a Bayesian approach. To this end it is hoped that the examples provided in this article will assist researchers in choosing from among the broad array of statistical methods currently available. Am J Phys Anthropol 57:153–184, 2013. © 2013 Wiley Periodicals, Inc.
Density Functional Theory and Reaction Kinetics Studies of the Water–Gas Shift Reaction on Pt–Re Catalysts
Authors: Carrasquillo‐Flores Ronald , Gallo Jean Marcel R. , Hahn Konstanze , Dumesic James A. , Mavrikakis Manos 
Published: November 2013

AbstractPeriodic, self‐consistent density functional theory calculations (DFT‐GGA‐PW91) on Pt(1 1 1) and Pt3Re(1 1 1) surfaces, reaction kinetics measurements, and microkinetic modeling are employed to study the mechanism of the water–gas shift (WGS) reaction over Pt and Pt–Re catalysts. The values of the reaction rates and reaction orders predicted by the model are in agreement with the ones experimentally determined; the calculated apparent activation energies are matched to within 6 % of the experimental values. The primary reaction pathway is predicted to take place through adsorbed carboxyl (COOH) species, whereas formate (HCOO) is predicted to be a spectator species. We conclude that the clean Pt(1 1 1) is a good representation of the active site for the WGS reaction on Pt catalysts, whereas the active sites on the Pt–Re alloy catalyst likely contain partially oxidized metal ensembles.
Niobium: Activator and Stabilizer for a Copper‐Based Deacon Catalyst
Authors: Hammes Markus , Soerijanto Hary , Schomäcker Reinhard , Valtchev Martin , Stöwe Klaus , Maier Wilhelm F. 
Published: November 2013

AbstractA highly active Cu‐based Deacon catalyst with an enhanced lifetime was developed by combining two corrosion‐resistant high‐throughput reactor setups in this combinatorial study. Catalyst activities were studied in a sequential 10‐fold reactor equipped with online MS. For accelerated catalyst ageing studies, a parallel 10‐fold reactor was used. The starting point was a CuTi mixed‐metal oxide found in former discovery investigations. As development criteria, catalyst stability and HCl conversion were selected. The amount of Cu in the CuTi catalysts were analyzed before and after the ageing process by X‐ray fluorescence spectroscopy. Dopant elements were selected that are reported to form oxides with a high corrosion resistance against gaseous HCl. Our study revealed that doping with 1 mol % Nb reduced the Cu leaching during the reaction. Furthermore, the activation energy was decreased by Nb, which enhanced the chlorine production.
Axial Equilibrium Distance and Positioning of Particles in a Laminar Tube Flow
Authors: Matulka P. , Fischer M. , Ehrhard P. , Walzel P. 
Published: November 2013

AbstractParticle transport in a laminar tube flow at low Reynolds numbers leads to accumulation of particles at specific equilibrium radii. The equilibrium radius depends on the particle size. Small particles find their equilibrium radius near the wall and large particles near the tube axis. During their radial migration to the equilibrium position, the particles move in axial direction with the flow. In an experimental setup, the axial equilibrium distance is measurement for several tube Reynolds numbers. The axial equilibrium distance is the distance a particle migrates in the flow direction, until it reaches its radial equilibrium position. The results are compared with CFD‐simulations of single particle movement in a laminar tube flow.
Identification of Intermediates in Zeolite‐Catalyzed Reactions by In Situ UV/Vis Microspectroscopy and a Complementary Set of Molecular Simulations
Authors: Hemelsoet Karen , Qian Qingyun , De Meyer Thierry , De Wispelaere Kristof , De Sterck Bart , Weckhuysen Bert M. , Waroquier Michel , Van Speybroeck Veronique 
Published: November 2013

AbstractThe optical absorption properties of (poly)aromatic hydrocarbons occluded in a nanoporous environment were investigated by theoretical and experimental methods. The carbonaceous species are an essential part of a working catalyst for the methanol‐to‐olefins (MTO) process. In situ UV/Vis microscopy measurements on methanol conversion over the acidic solid catalysts H‐SAPO‐34 and H‐SSZ‐13 revealed the growth of various broad absorption bands around 400, 480, and 580 nm. The cationic nature of the involved species was determined by interaction of ammonia with the methanol‐treated samples. To determine which organic species contribute to the various bands, a systematic series of aromatics was analyzed by means of time‐dependent density functional theory (TDDFT) calculations. Static gas‐phase simulations revealed the influence of structurally different hydrocarbons on the absorption spectra, whereas the influence of the zeolitic framework was examined by using supramolecular models within a quantum mechanics/molecular mechanics framework. To fully understand the origin of the main absorption peaks, a molecular dynamics (MD) study on the organic species trapped in the inorganic host was essential. During such simulation the flexibility is fully taken into account and the effect on the UV/Vis spectra is determined by performing TDDFT calculations on various snapshots of the MD run. This procedure allows an energy absorption scale to be provided and the various absorption bands determined from in situ UV/Vis spectra to be assigned to structurally different species.
Binding Cofactors with Triplex‐Based DNA Motifs
Authors: Kröner Christoph , Göckel Anja , Liu Wenjing , Richert Clemens 
Published: November 2013

AbstractCofactors are pivotal compounds for the cell and many biotechnological processes. It is therefore interesting to ask how well cofactors can be bound by oligonucleotides designed not to convert but to store and release these biomolecules. Here we show that triplex‐based DNA binding motifs can be used to bind nucleotides and cofactors, including NADH, FAD, SAM, acetyl CoA, and tetrahydrofolate (THF). Dissociation constants between 0.1 μM for SAM and 35 μM for THF were measured. A two‐nucleotide gap still binds NADH. The selectivity for one ligand over the others can be changed by changing the sequence of the binding pocket. For example, a mismatch placed in one of the two triplets adjacent to the base‐pairing site changes the selectivity, favoring the binding of FAD over that of ATP. Further, changing one of the two thymines of an A‐binding motif to cytosine gives significant affinity for G, whereas changing the other does not. Immobilization of DNA motifs gives beads that store NADH. Exploratory experiments show that the beads release the cofactor upon warming to body temperature.
Familial Hypercholesterolemia: An Under‐recognized but Significant Concern in Cardiology Practice
Authors: Foody JoAnne M. 
Published: November 2013

ABSTRACTFamilial hypercholesterolemia (FH) is a common disorder in which genetic mutations in at least 1 of several genes lead to significantly increased levels of lipoproteins, in particular, low‐density lipoprotein cholesterol. Most commonly, mutations in the low‐density lipoprotein receptor gene result in high plasma levels of apolipoprotein B‐containing lipoproteins (eg, low‐density lipoprotein and lipoprotein(a)). High plasma levels of lipoproteins increase the risk of cardiovascular events by as much as 20‐fold if left untreated. A 2011 survey of cardiologists performed by the American College of Cardiology (ACC) suggests that there is a need for greater awareness of FH among cardiologists with regard to its prevalence and heritability, and of the risk of cardiovascular (CV) disease associated with the disorder, such as premature coronary heart disease. Given that many patients with FH may first present to CV specialists at the time of a major coronary event, it is critical that cardiologists have strategies to manage this high‐risk subset of patients. This brief review responds to areas of need identified in the ACC survey and is intended to provide current information about FH and increase awareness about this disorder among cardiologists.
Prevalence and characteristics of moderate to severe fatigue: A multicenter study in cancer patients and survivors
Authors: Wang Xin Shelley , Zhao Fengmin , Fisch Michael J. , O'Mara Ann M. , Cella David , Mendoza Tito R. , Cleeland Charles S. 
Published: November 2013

BACKGROUNDThe effective management of fatigue in patients with cancer requires a clear delineation of what constitutes nontrivial fatigue. The authors defined numeric cutpoints for fatigue severity based on functional interference and described the prevalence and characteristics of fatigue in patients with cancer and survivors.METHODSIn a multicenter study, outpatients with breast, prostate, colorectal, or lung cancer rated their fatigue severity and symptom interference with functioning on the M. D. Anderson Symptom Inventory numeric scale of 0 to 10. Ratings of symptom interference guided the selection of numeric rating cutpoints between mild, moderate, and severe fatigue levels. Regression analysis identified significant factors related to reporting moderate/severe fatigue.RESULTSThe statistically optimal cutpoints were ≥ 4 for moderate fatigue and ≥ 7 for severe fatigue. Moderate/severe fatigue was reported by 983 of 2177 patients (45%) undergoing active treatment and was more likely to occur in patients receiving treatment with strong opioids (odds ratio [OR], 3.00), those with a poor Eastern Cooperative Oncology Group performance status (OR, 2.00), those who had > 5% weight loss within 6 months (OR, 1.60), those who were receiving > 10 medications (OR, 1.58), those with lung cancer (OR, 1.55), and those with a history of depression (OR, 1.42). Among survivors (patients with complete remission or no evidence of disease, and not currently receiving cancer treatment), 29% of patients (150 of 515 patients) had moderate/severe fatigue that was associated with poor performance status (OR, 3.48) and a history of depression (OR, 2.21).CONCLUSIONSThe current study statistically defined fatigue severity categories related to significantly increased symptom interference. The high prevalence of moderate/severe fatigue in both actively treated patients with cancer and survivors warrants the promoting of the routine assessment and management of patient‐reported fatigue. Cancer 2014;120:425–432. © 2013 American Cancer Society.
Tolvaptan in hospitalized cancer patients with hyponatremia: A double‐blind, randomized, placebo‐controlled clinical trial on efficacy and safety
Authors: Salahudeen Abdulla K. , Ali Najeeba , George Marina , Lahoti Amit , Palla Shana 
Published: November 2013

BACKGROUNDThe rate of hyponatremia is higher in hospitalized cancer patients than in hospitalized patients without cancer and is associated with poor clinical outcomes. The availability of V2 receptor antagonists has been a major breakthrough in the management of hyponatremia, but its efficacy and safety in treating hyponatremia in patients with cancer is not known.METHODSAdult patients with cancer who were admitted to The University of Texas MD Anderson Cancer Center with nonhypovolemic hyponatremia (125‐130 mmol/L) were randomized to receive either tolvaptan or placebo in a double‐blind, placebo‐controlled, adaptive, randomized trial. Both groups received the standard of care for hyponatremia, except that patients were allowed to drink to thirst.RESULTSA preplanned Data Safety Monitoring Board analysis of 30 of 48 randomized patients who completed the study revealed that the primary endpoint of hyponatremia correction was met by 16 of 17 patients who received tolvaptan and by 1 of 13 patients who received placebo (94% vs 8%; P < .001), which met the study stopping rule for superiority. The secondary endpoints between the tolvaptan and placebo groups (mean ± standard deviation) for length of stay (21 ± 15 days vs 26 ± 15 days, respectively) and change in the Mini‐Mental State Examination score (−0.35 ± 1.66 vs 0.31 ± 2.42, respectively) were not significantly different. No overcorrection of serum sodium (>12 mmol/L per day) was noted in the tolvaptan group, and the main adverse events noted were dry mouth, polydipsia, and polyuria, leading to 13% study withdrawal.CONCLUSIONSAlthough tolvaptan was effective for correcting hyponatremia in patients with cancer, studies with a larger sample size will be required to confirm the current findings, including the outcomes of secondary endpoints. Cancer 2014;120:744–751. © 2013 American Cancer Society.