bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation of Human Melanoma Stem Cells Using ALDH as a Marker
Authors: Luo Yuchun , Nguyen Nicholas , Fujita Mayumi 
Published: October 2013

ABSTRACTThis unit describes a protocol for establishing a patient‐derived tumor xenograft model (PDTX model) of human melanoma and isolating human melanoma stem cells from human melanoma specimens using aldehyde dehydrogenase (ALDH) as a marker. One major limitation of analyzing a small fraction of cancer stem cells from patient tumor samples is that substantial quantities of fresh tumor tissues are not available. To overcome this challenge, we have established a PDTX model of human melanoma. In this model, human tumor tissues obtained from melanoma patients are dissected into small pieces and subsequently implanted into immunocompromised mice. The PDTX tumors retain fundamental genotypic and phenotypic features of the original tumors and are suitable for further biological analyses. Using the PDTX model, we have analyzed ALDH‐labeled human melanoma stem cells. This unit will describe how to establish a PDTX model using human tumor samples. We will also describe how to isolate and analyze ALDH‐labeled human melanoma stem cells using this model. Curr. Protoc. Stem Cell Biol. 26:3.8.1‐3.8.10. © 2013 by John Wiley & Sons, Inc.
Laboratory Growth and Maintenance of Streptococcus pyogenes (The Group A Streptococcus, GAS)
Authors: Gera Kanika , McIver Kevin S. 
Published: October 2013

AbstractStreptococcus pyogenes is a Gram‐positive bacterium that strictly infects humans. It is the causative agent of a broad spectrum of diseases accounting for millions of infections and at least 517,000 deaths each year worldwide. It is a nutritionally fastidious organism that ferments sugars to produce lactic acid and has strict requirements for growth. To aid in the study of this organism, this unit describes the growth and maintenance of S. pyogenes. Curr. Protoc. Microbiol. 30:9D.2.1‐9D.2.13. © 2013 by John Wiley & Sons, Inc.
Toward an integrated software platform for systems pharmacology
Authors: Ghosh Samik , Matsuoka Yukiko , Asai Yoshiyuki , Hsin Kun‐Yi , Kitano Hiroaki 
Published: October 2013

ABSTRACTUnderstanding complex biological systems requires the extensive support of computational tools. This is particularly true for systems pharmacology, which aims to understand the action of drugs and their interactions in a systems context. Computational models play an important role as they can be viewed as an explicit representation of biological hypotheses to be tested. A series of software and data resources are used for model development, verification and exploration of the possible behaviors of biological systems using the model that may not be possible or not cost effective by experiments. Software platforms play a dominant role in creativity and productivity support and have transformed many industries, techniques that can be applied to biology as well. Establishing an integrated software platform will be the next important step in the field. © 2013 The Authors. Biopharmaceutics & Drug Disposition published by John Wiley & Sons, Ltd.
A p‐Quinodimethane‐Bridged Porphyrin Dimer
Authors: Zeng Wangdong , Ishida Masatoshi , Lee Sangsu , Sung Young Mo , Zeng Zebing , Ni Yong , Chi Chunyan , Kim Dongho , Wu Jishan 
Published: October 2013

AbstractA p‐quinodimethane (p‐QDM)‐bridged porphyrin dimer 1 has been prepared for the first time. An unexpected Michael addition reaction took place when we attempted to synthesize compound 1 by reaction of the cross‐conjugated keto‐linked porphyrin dimers 8 a and 8 b with alkynyl/aryl Grignard reagents. Alternatively, compound 1 could be successfully prepared by intramolecular Friedel–Crafts alkylation of the diol‐linked porphyrin dimer 14 with concomitant oxidation in air. Compound 1 shows intense one‐photon absorption (OPA, λmax=955 nm, ε=45400 M−1 cm−1) and a large two‐photon absorption (TPA) cross‐section (σ(2)max=2080 GM at 1800 nm) in the near‐infrared (NIR) region due to its extended π‐conjugation and quinoidal character. It also exhibits a short singlet excited‐state lifetime of 25 ps. The cyclic voltammogram of 1 displays multiple redox waves with a small electrochemical energy gap of 0.86 eV. The ground‐state geometry, electronic structure, and optical properties of 1 have been further studied by density functional theory (DFT) calculations and compared with those of the keto‐linked dimer 8 b. This research has revealed that incorporation of a p‐QDM unit into the porphyrin framework had a significant impact on its optical and electronic properties, leading to a novel NIR OPA and TPA chromophore.
Fullerene‐sp2‐Iminosugar Balls as Multimodal Ligands for Lectins and Glycosidases: A Mechanistic Hypothesis for the Inhibitory Multivalent Effect
Authors: Rísquez‐Cuadro Rocío , García Fernández José M. , Nierengarten Jean‐François , Ortiz Mellet Carmen 
Published: October 2013

AbstractConcerted functioning of lectins and carbohydrate‐processing enzymes, mainly glycosidases, is essential in maintaining life. It was commonly assumed that the mechanisms by which each class of protein recognizes their cognate sugar partners are intrinsically different: multivalency is a characteristic feature of carbohydrate–lectin interactions, whereas glycosidases bind to their substrates or substrate‐analogue inhibitors in monovalent form. Recent observations on the glycosidase inhibitory potential of multivalent glycomimetics have questioned this paradigm and led to postulate an inhibitory multivalent effect. Here the mechanisms at the origin of this phenomenon have been investigated. A D‐gluco‐configured sp2‐iminosugar glycomimetic motif, namely 1‐amino‐5N,6O‐oxomethylydenenojirimycin (1N‐ONJ), behaving, simultaneously, as a ligand of peanut agglutinin (PNA) lectin and as an inhibitor of several glycosidases, has been identified. Both the 1N‐ONJ–lectin‐ and 1N‐ONJ–glycosidase‐recognition processes have been found to be sensitive to multivalency, which has been exploited in the design of a lectin–glycosidase competitive assay to explore the implication of catalytic and non‐glycone sites in enzyme binding. A set of isotropic dodecavalent C60‐fullerene–sp2‐iminosugar balls incorporating matching or mismatching motifs towards several glycosidases (inhitopes) was synthesized for that purpose, thereby preventing differences in binding modes arising from orientational preferences. The data supports that: 1) multivalency allows modulating the affinity and selectivity of a given inhitope towards glycosidases; 2) multivalent presentation can switch on the inhibitory capacity for some inhitope–glycosidase pairs, and 3) interactions of the multivalent inhibitors with non‐glycone sites is critical for glycosidase recognition. The ensemble of results point to a shift in the binding mode on going from monovalent to multivalent systems: in the first case a typical ′′key–lock′′ model involving, essentially, the high‐affinity active site can be assumed, whereas in the second, a lectin‐like behavior implying low‐affinity non‐glycone sites probably operates. The differences in responsiveness to multivalency for different glycosidases can then be rationalized in terms of the structure and accessibility of the corresponding carbohydrate‐binding regions.
Vibrational Circular Dichroism Discrimination of Diastereomeric Cedranol Acetates
Authors: Gordillo‐Román Bárbara , Camacho‐Ruiz Jorge , Bucio María A. , Joseph‐Nathan Pedro 
Published: October 2013

ABSTRACTThe reliability of vibrational circular dichroism (VCD) spectroscopy to discriminate four diastereomeric cedranol acetates 1, 2, 3, 4 by means of their absolute configuration is examined. The usage of CompareVOA software to quantify comparisons of the measured infrared (IR) and VCD spectra with the corresponding simulated spectra at the B3LYP/DGDZVP and B3PW91/DGDZVP levels of theory for each diastereomer enabled the B3PW91 functional to be qualified as superior to the B3LYP functional for vibrational calculations of 1, 2, 3, 4. Analogously, a set of quantitative VCD spectra cross‐comparisons of 1, 2, 3, 4 unambiguously distinguished the diastereomers using B3PW91 and failed using B3LYP. Remarkably, quantitative IR spectra cross‐comparisons of 1, 2, 3, 4 using B3PW91 or B3LYP functionals demonstrated that the achiral spectroscopic IR technique is not able to distinguish cedranol acetate diastereomers. VCD comparisons using anisotropy g‐factor values of bands in the 1550–950 cm‐1 region of the spectra were of aid to facilitate visual spectra matching for each diastereomer. Chirality 25:939‐951, 2013. © 2013 Wiley Periodicals, Inc.
Neurogenesis in the lamprey central nervous system following spinal cord transection
Authors: Zhang Guixin , Pizarro Ivonne Vidal , Swain Gary P. , Kang Shin H. , Selzer Michael E. 
Published: October 2013

ABSTRACTAfter spinal cord transection, lampreys recover functionally and axons regenerate. It is not known whether this is accompanied by neurogenesis. Previous studies suggested a baseline level of nonneuronal cell proliferation in the spinal cord and rhombencephalon (where most supraspinal projecting neurons are located). To determine whether cell proliferation increases after injury and whether this includes neurogenesis, larval lampreys were spinally transected and injected with 5‐bromo‐2&prime‐deoxyuridine (BrdU) at 0–3 weeks posttransection. Labeled cells were counted in the lesion site, within 0.5 mm rostral and caudal to the lesion, and in the rhombencephalon. One group of animals was processed in the winter and a second group was processed in the summer. The number of labeled cells was greater in winter than in summer. The lesion site had the most BrdU labeling at all times, correlating with an increase in the number of cells. In the adjacent spinal cord, the percentage of BrdU labeling was higher in the ependymal than in nonependymal regions. This was also true in the rhombencephalon but only in summer. In winter, BrdU labeling was seen primarily in the subventricular and peripheral zones. Some BrdU‐labeled cells were also double labeled by antibodies to glial‐specific (antikeratin) as well as neuron‐specific (anti‐Hu) antigens, indicating that both gliogenesis and neurogenesis occurred after spinal cord transection. However, the new neurons were restricted to the ependymal zone, were never labeled by antineurofilament antibodies, and never migrated away from the ependyma even at 5 weeks after BrdU injection. They would appear to be cerebrospinal fluid‐contacting neurons. J. Comp. Neurol. 522:1316–1332, 2014. © 2013 Wiley Periodicals, Inc.
SPICE modeling of nonlinear memristive behavior
Authors: Vourkas Ioannis , Batsos Athanasios , Sirakoulis Georgios Ch. 
Published: October 2013

SummaryThe recent discovery of the ‘modern’ memristor has drawn great attention of both academia and industry. Given their favorable performance merits, memristors are expected to play a fundamental role in electronic industry. Modeling of memristive devices is essential for circuit design, and a number of Simulation Program with Integrated Circuit Emphasis (SPICE) models have already been introduced. The common problem in most models is that there is no threshold consideration; hence, only a few address the nonlinear nature of the device. This paper aims to present a SPICE implementation of a threshold‐type switching model of a voltage‐controlled memristive device that attributes the switching effect to a tunneling distance modulation. Threshold‐type switching is closer to the actual behavior of most experimentally realizable memristive systems, and our modeling approach addresses the issue of programming thresholds. Both the netlist and the simple schematic are provided, thus making it easy to comprehend and ready to be used. Compared with other modeling solutions, it involves significantly low‐complexity operation under an unlimited set of frequencies, and its simulation results are in good qualitative and quantitative agreement with the theoretical formulation. The proposed model is used to simulate an antiserial memristive switch, proving that it can be efficiently introduced in complex memristive circuits. Copyright © 2013 John Wiley & Sons, Ltd.
The importance of selection at the level of the pair over 25 years in a natural population of birds
Authors: Björklund Mats , Gustafsson Lars 
Published: October 2013

AbstractKnowledge of the pattern of selection in natural populations is fundamental for our understanding of the evolutionary process. Selection at higher levels has gained considerable theoretical support in recent years, and one possible level of selection is the breeding pair where fitness is a function of the pair and cannot be reduced to single individuals. We analyzed the importance of pair‐level selection over 25 years in a natural population of the collared flycatcher. Pair‐level selection was significant in five and probably in another 9 years. The relative importance of pair‐level selection varied over years and can have stronger or the same strength as directional selection. This means that selection can act on the combination of the breeding pair in addition to selection on each individual separately. Overall, the conservative estimates obtained here show that this is a potentially important form of selection.
One‐Pot Synthesis of Benzimidazo[1,2‐f]phenanthridines by Cascade Palladium‐Catalyzed N‐Arylation and Intramolecular C–H Coupling
Authors: Liu Jianming , Zhang Ningfei , Yue Yuanyuan , Liu Guihua , Liu Ren , Zhang Yuanli , Zhuo Kelei 
Published: October 2013

AbstractAn efficient protocol has been developed that uses sequential N‐arylation and intramolecular C–H coupling for the construction of azole‐fused phenanthridine heterocycle derivatives in good yields. This new method allows the one‐pot synthesis of polysubstituted complex molecules from readily available benzo[d]imidazoles and 1,2‐dibromobenzenes.
Design and validation of a thermoreversible material for percutaneous tissue hydrodissection
Authors: Johnson Alexander , Sprangers Anthony , Cassidy Patrick , Heyrman Sean , Hinshaw J. Louis , Lubner Meghan , Puccinelli John , Brace Chris 
Published: October 2013

AbstractInterventional oncology procedures such as thermal ablation are becoming routine for many cancers. Hydrodissection—separating tissues with fluids—protects tissues near the treatment zone to improve ablation's safety and facilitate more aggressive treatments. However, currently used fluids such as normal saline and 5% dextrose in water (D5W) migrate in the peritoneum, reducing their protective efficacy. As a hydrodissection alternative, we investigated a thermoreversible poloxamer 407 (P407) solution. Such a material can be injected as a liquid which then forms a semi‐solid gel at body temperature without syneresis. The desired gelation temperature of 32°C was achieved with 15.4 wt/wt % P407. Viscosity analysis revealed the lowest viscosity and ideal injection point was at 14°C. Solution viscosity increased during gelation, to a peak of 65 kPa*s at 40°C. The electrical impedance of P407 was significantly greater than isotonic saline, but lower than D5W, indicating its potential for electrical protection. The P407 gel was similar to other hydrodissection fluids at ultrasound and CT imaging. Ex vivo liver ablations showed that P407 protects neighboring tissues, but may require a thicker barrier for comparable protection to D5W. Overall, we found that the P407 solution is a feasible alternative to traditional hydrodissection fluids and warrants additional study. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 101B: 1400–1409, 2013.
Laser fabrication of porous silicon‐based platforms for cell culturing
Authors: Peláez Ramón‐J. , Afonso Carmen‐N. , Vega Fidel , Recio‐Sánchez Gonzalo , Torres‐Costa Vicente , Manso‐Silván Miguel , García‐Ruiz Josefa‐P. , Martín‐Palma Raúl‐J. 
Published: October 2013

AbstractIn this study, we explore the selective culturing of human mesenchymal stem cells (hMSCs) on Si‐based diffractive platforms. We demonstrate a single‐step and flexible method for producing platforms on nanostructured porous silicon (nanoPS) based on the use of single pulses of an excimer laser to expose phase masks. The resulting patterns are typically 1D patterns formed by fringes or 2D patterns formed by circles. They are formed by alternate regions of almost unmodified nanoPS and regions where the nanoPS surface has melted and transformed into Si nanoparticles. The patterns are produced in relatively large areas (a few square millimeters) and can have a wide range of periodicities and aspect ratios. Direct binding, that is, with no previous functionalization of the pattern, alignment, and active polarization of hMSCs are explored. The results show the preferential direct binding of the hMSCs along the transformed regions whenever their width compares with the dimensions of the cells and they escape from patterns for smaller widths suggesting that the selectivity can be tailored through the pattern period. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 101B: 1463–1468, 2013.
Exploring Quality in Gradient Copolymers
Authors: Elsen Andrea M. , Li Yuanchao , Li Qiaoxi , Sheiko Sergei S. , Matyjaszewski Krzysztof 
Published: October 2013

Quality of gradient copolymers is evaluated by atomic force microscopy (AFM) and correlated with molecular weight distribution (MWD) values. ARGET ATRP is employed with decreasing levels of catalyst concentrations to generate copolymers with increasing / values. The copolymers are transformed into molecular bottlebrushes to enable imaging and analysis of individual molecules by AFM. The average height (cross‐sectional) profile of all bottlebrushes agrees with the instantaneous composition (ICHEMA‐TMS) of the analogous copolymer backbone, as determined by 1H NMR. The copolymer synthesized with 500 ppm of catalyst exhibits more narrow distributions of both brush height and backbone length when analyzed as a bottlebrush by AFM. Correspondingly, the copolymers synthesized with lower catalyst concentrations yield bottlebrushes with broader height and length distribution. These results establish MWD values as an excellent trait to assess quality within gradient copolymers.
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Readiness redefined: A behavioral task during screening predicted 1‐year weight loss in the look AHEAD study
Authors: Tsai Adam G. , Fabricatore Anthony N. , Wadden Thomas A. , Higginbotham Allison J. , Anderson Andrea , Foreyt John , Hill James O. , Jeffery Robert W. , Gluck Marci E. , Lipkin Edward W. , Reeves Rebecca S. , Van Dorsten Brent 
Published: October 2013

ObjectivePredicting outcome in weight loss trials from baseline characteristics has proved difficult. Readiness to change is typically measured by self‐report.MethodsPerformance of a behavioral task, completion of food records, from the screening period in the Look AHEAD study (n = 549 at four clinical centers) was assessed. Completeness of records was measured by the number of words and Arabic numerals (numbers) recorded per day, the number of eating episodes per day, and days per week where physical activity was noted. The primary outcome was weight loss at one year.ResultsIn univariable analysis, both the number of words recorded and the number of numbers recorded were associated with greater weight loss. In multivariable analysis, individuals who recorded 20‐26, 27‐33, and ≥34 words per day lost 9.12%, 11.40%, and 12.08% of initial weight, compared to 8.98% for individuals who recorded less than 20 words per day (P values of 0.87, 0.008, and <0.001, respectively, compared to <20 words per day).ConclusionsParticipants who kept more detailed food records at screening lost more weight after 1 year than individuals who kept sparser records. The use of objective behavioral screening tools may improve the assessment of weight loss readiness.
How to Prepare a Good Cu/ZnO Catalyst or the Role of Solid State Chemistry for the Synthesis of Nanostructured Catalysts
Authors: Behrens Malte , Schlögl Robert 
Published: October 2013

Abstract In this research report we summarize recent progress that has been made in the field of Cu/ZnO catalyst synthesis. We briefly introduce the fields of application of this catalyst: methanol synthesis, the water gas shift reaction, and methanol steam reforming. The review is focused on the well‐documented industrial synthesis protocol and on the early stages of catalyst synthesis. The setting of the most critical synthesis parameters during co‐precipitation and ageing, like pH and temperature, is discussed in detail. We show how these parameters effect the phase formation and identify zincian malachite, (Cu, Zn)2(OH)2CO3, as the relevant precursor phase for high‐performance catalysts. A special emphasis is placed on the solid state chemistry of this precursor phase, in particular on the structural effects of Cu, Zn substitution. Based on the structural analysis, it is shown that the industrial synthesis recipe was empirically optimized to maximize the zinc incorporation into zincian malachite. From this insight a simple and generic geometric concept for the synthesis of nanostructured composite catalysts based on de‐mixing of solid solution precursors is derived. With this concept, the complex multi‐step industrial synthesis can be rationalized and the so‐called “chemical memory” of this catalyst synthesis can be understood. We also demonstrate how application of this concept can lead to new interesting catalytic materials, which help to address fundamental questions of this catalyst system like to role of the Al2O3 promoter or the so‐called Cu‐Zn synergy.
Shock reflection in the presence of an upstream expansion wave and a downstream shock wave
Authors: Yao Y. , Li S. G. , Wu Z. N. 
Published: October 2013

AbstractIn this paper, we consider shock reflection problems, occurring in supersonic and hypersonic intake flow under off-design conditions, in which the incident shock wave is disturbed by the lip-generated upstream expansion wave and the reflected shock wave intersects with a downstream cowl-turning deflected shock wave. The expansion wave and deflected shock wave are here generated with the same magnitude of flow deflection angle or turning angle. With the help of shock interaction theory and numerical simulation, the influence of the turning angle of the lip and cowl on the flow structure and the critical conditions for transition between regular reflection and Mach reflection are analysed. It is found that the dual-solution domain is significantly altered by the interference between the expansion wave and shock waves. The flow structure in the condition of Mach reflection is then analysed with a model updated from a previous study. It is shown that the Mach stem height is an increasing function of the turning angle, while the horizontal position of the Mach stem is shifted in the downstream direction for small turning angle and in the upstream direction for large turning angle.
Anterior rhinoscopy and middle meatal culture in acute rhinosinusitis
Authors: Thunberg U , Engström K , Olaison S , Hugosson S 
Published: October 2013

AbstractObjective:To assess the use of bacterial culture findings for middle meatal samples obtained via anterior rhinoscopy, in the diagnosis of adults with acute rhinosinusitis.Materials and methods:Microbial cultures were prepared for 30 adult patients with acute rhinosinusitis and suspected bacterial involvement, using samples from the nasopharynx, and from the nasal middle meatus obtained via anterior rhinoscopy. Findings for the ipsilateral maxillary antrum were used as a reference.Results:Seventeen patients had a bacterial infection as verified by a positive culture from the maxillary antrum. Middle meatal samples had a similar sensitivity but a better specificity, positive predictive value and negative predictive value, compared with nasopharyngeal samples, although predictive values were not statistically significant at a 95 per cent confidence level.Conclusion:Anterior rhinoscopy with culture of middle meatal samples can be recommended as a diagnostic procedure for acute rhinosinusitis. The results can also guide the decision on antibiotic treatment.