bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cancer as the Disintegration of Robustness: Population-Level Variance in Gene Expression Identifies Key Differences Between Tobacco- and HPV-Associated Oropharyngeal Carcinogenesis
Authors: Ben-Dayan Miriam M. , MacCarthy Thomas , Schlecht Nicolas F. , Belbin Thomas J. , Childs Geoffrey , Smith Richard V. , Prystowsky Michael B. , Bergman Aviv 
Published: July 2015

Context
Oropharyngeal squamous cell carcinoma is associated both with tobacco use and with human papillomavirus (HPV) infection. It is argued that carcinogen-driven tumorigenesis is a distinct disease from its virally driven counterpart. We hypothesized that tumorigenesis is the result of a loss of genotypic robustness resulting in an increase in phenotypic variation in tumors compared with adjacent histologically normal tissues, and that carcinogen-driven tumorigenesis results in greater variation than its virally driven counterpart.

Objectives
To examine the loss of robustness in carcinogen-driven and virally driven oropharyngeal squamous cell carcinoma samples, and to identify potential pathways involved.

Design
We used coefficients of variation for messenger RNA and microRNA expression to measure the loss of robustness in oropharyngeal squamous cell carcinoma samples. Tumors were compared with matched normal tissues, and were further categorized by HPV and patient smoking status. Weighted gene coexpression networks were constructed for genes with highly variable expression among the HPV− tumors from smokers.

Results
We observed more genes with variable messenger RNA expression in tumors compared with normal tissues, regardless of HPV and smoking status, and more microRNAs with variable expression in HPV− and HPV+ tumors from smoking patients than from nonsmokers. For both the messenger RNA and microRNA data, we observed more variance among HPV− tumors from smokers compared with HPV+ tumors from nonsmokers. The gene coexpression network construction highlighted pathways that have lost robustness in carcinogen-induced tumors but appear stable in virally induced tumors.

Conclusions
Using coefficients of variation and coexpression networks, we identified multiple altered pathways that may play a role in carcinogen-driven tumorigenesis.
Determining the average path length of amplified spontaneous emission in a four-level laser near the 1/3 mode-degeneracy cavity configurations
Authors: Chen Ching-Hsu , Lu Ming-Lun , Tai Po-Tse 
Published: July 2015

Abstract
We determine the average path length l
s of amplified spontaneous emission (ASE) by comparing the numerical slope of a straight line with the experimental slope in the graph of the square of relaxation oscillation frequency versus normalized pump ratio. The simple method is applied in an end-pumped Nd:YVO4 laser with the 1/3 mode-degeneracy cavity having the transverse mode spacing equal to 1/3 of the longitudinal mode spacing. We find that l
s is larger at the degeneracy than that far from the degeneracy. This result indicates the existence of stronger ASE at the degeneracy, which is confirmed below the threshold. This is because many spontaneous emission photons can undergo amplification not only before escaping from the gain medium but also after leaving the gain medium, owing to cavity reflection. Our method can be applied in the situations where the Auger upconversion effect is absent, weak, or well-known.
Direct preparation of Cu2ZnSnSe4 films by microwave irradiation and its dependence on the Sn/(Sn + Zn) ratio
Authors: Kaigawa Ryuji , Hashimoto Shintaro , Irago Tomoki , Klenk Reiner 
Published: July 2015

Abstract
Cu2ZnSnSe4 (CZTSe) films with various Sn/(Sn + Zn) ratios were directly prepared on metallic Ti foils by microwave irradiation and their properties were investigated. The Sn/(Sn + Zn) ratio and Cu/(Sn + Zn) ratio of the precursor could be preserved by using a sealed container filled with 0.15 atm of Ar. Single-phase CZTSe crystals with a kesterite (stannite) structure and without by-products were observed with Sn/(Sn + Zn) ratios between 0.4 and 0.6. The hole densities of the Cu–Zn–Sn–Se films are minimal (<1017/cm3) with Sn/(Sn + Zn) ratios ranging from 0.5 to 0.6.
Whole‐Transcriptome Amplification of Single Cells for Next‐Generation Sequencing
Authors: Korfhage Christian , Fricke Evelyn , Meier Andreas 
Published: July 2015

AbstractSingle‐cell transcriptome analysis gives insight into the heterogeneity of neighboring cells in tissues or cell cultures. It has been shown that the variability of cells is important for biological function. However, cell variability can be an indication of disease (e.g., cancer). In order to elucidate cell variability in health and disease, single‐cell transcriptomes can be analyzed by new next‐generation sequencing (NGS) platforms. NGS analysis currently requires a few hundred nanograms of RNA. Consequently, accurate whole‐transcriptome amplification is required to analyze the transcriptome of a single cell by NGS. This unit describes the entire workflow from cells to NGS, including cell quality testing, cell lysis, gDNA removal, whole‐transcriptome amplification, and NGS library preparation. Recommendations for WTA quality control are given and optional protocols for using purified RNA for WTA and WTA purification are described. © 2015 by John Wiley & Sons, Inc.
Assaying Cell Cycle Status Using Flow Cytometry
Authors: Kim Kang Ho , Sederstrom Joel M. 
Published: July 2015

AbstractIn this unit, two protocols are described for analyzing cell cycle status using flow cytometry. The first is based on the simultaneous analysis of proliferation‐specific marker (Ki‐67) and cellular DNA content, which discriminate resting/quiescent cell populations (G0 cell) and quantify cell cycle distribution (G1, S, or G2/M), respectively. The second is based on differential staining of DNA and RNA through co‐staining of Hoechst 33342 and Pyronin Y, which is also useful to identify G0 cells from G1 cells. Along with these methods for analyzing cell cycle status, two additional methods for cell proliferation assays with recent updates of newly developed fluorophores, which allow multiplex analysis of cell cycle status, cell proliferation, and a gene of interest using flow cytometry, are outlined. © 2015 by John Wiley & Sons, Inc.
Glycosylation Analysis for Congenital Disorders of Glycosylation
Authors: Li Xueli , Raihan Mohd A. , Reynoso Francis Jeshira , He Miao 
Published: July 2015

AbstractCongenital disorders of glycosylation (CDG) are a group of diseases with highly variable phenotypes and inconsistent clinical features. Since the first description of a CDG in 1980, approximately 100 disorders have been identified. Most of these are defects in protein glycosylation, although an increasing number are defects of glycolipid or proteoglycan biosynthesis. A group of biochemical markers has been used to characterize protein glycosylation abnormalities in CDG. This unit describes three protocols that can be used to measure plasma or serum carbohydrate deficient transferrin (CDT) profile, N‐glycan profile, and O‐glycan profile by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) or liquid chromatography‐electrospray ionization‐tandem mass spectrometry (LC‐ESI‐MS). The quantification of particular biomarkers, such as T antigens or sialylated T antigens, could also be achieved by liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). These techniques can be used to identify a majority of patients with defects in protein glycosylation, although different techniques, such as flow cytometry with immunostaining, are necessary to detect defects in glycolipid or proteoglycan biosynthesis which is not included in this unit. © 2015 by John Wiley & Sons, Inc.
Prediction of flash flood hazard impact from Himalayan river profiles
Authors: Devrani R. , Singh V. , Mudd S. M. , Sinclair H. D. 
Published: July 2015

AbstractTo what extent can we treat topographic metrics such as river long profiles as a long‐term record of multiple extreme geomorphic events and hence use them for hazard prediction? We demonstrate that in an area of rapid mountain erosion where the landscape is highly reactive to extreme events, channel steepness measured by integrating area over upstream distance (chi analysis) can be used as an indicator of geomorphic change during flash floods. We compare normalized channel steepness to the impact of devastating floods in the upper Ganga Basin in Uttarakhand, northern India, in June 2013. The pattern of sediment accumulation and erosion is broadly predictable from the distribution of normalized channel steepness; in reaches of high steepness, channel lowering up to 5 m undercut buildings causing collapse; in low steepness reaches, channels aggraded up to 30 m and widened causing flooding and burial by sediment. Normalized channel steepness provides a first‐order prediction of the signal of geomorphic change during extreme flood events. Sediment aggradation in lower gradient reaches is a predictable characteristic of floods with a proportion of discharge fed by point sources such as glacial lakes.
Antarctic bedrock topography uncertainty and ice sheet stability
Authors: Gasson E. , DeConto R. , Pollard D. 
Published: June 2015

AbstractAntarctic bedrock elevation estimates have uncertainties exceeding 1 km in certain regions. Bedrock elevation, particularly where the bedrock is below sea level and bordering the ocean, can have a large impact on ice sheet stability. We investigate how present‐day bedrock elevation uncertainty affects ice sheet model simulations for a generic past warm period based on the mid‐Pliocene, although these uncertainties are also relevant to present‐day and future ice sheet stability. We perform an ensemble of simulations with random topographic noise added with various length scales and with amplitudes tuned to the uncertainty of the Bedmap2 data set. Total Antarctic ice sheet retreat in these simulations varies between 12.6 and 17.9 m equivalent sea level rise after 3 kyrs of warm climate forcing. This study highlights the sensitivity of ice sheet models to existing uncertainties in bedrock elevation and the ongoing need for new data acquisition.
Cumulative ozone effect on canopy stomatal resistance and the impact on boundary layer dynamics and CO2 assimilation at the diurnal scale: A case study for grassland in the Netherlands
Authors: Super Ingrid , Vilà‐Guerau de Arellano Jordi , Krol Maarten C. 
Published: July 2015

AbstractBiological, chemical, and dynamical processes occurring at the surface strongly interact at diurnal scales. Therefore, this study examines the seasonal ozone impact on stomatal resistance, surface energy balance, boundary layer dynamics, and CO2 assimilation at this (sub)diurnal scale under changing conditions. We combine a seasonal canopy resistance module with a surface‐boundary layer model that solves the diurnal evolution of dynamical and chemical variables in a well‐mixed, convective boundary layer. The model is constrained with observations from Cabauw (Netherlands) for the dry year 2003, representing a well‐mixed boundary layer at midlatitudes over water‐stressed grassland. To quantify the ozone impact, the Cumulative Uptake of Ozone is calculated over a growing season, which gives an estimate of the reduction in stomatal aperture and photosynthesis. From a sensitivity analysis with mixed‐layer temperature and soil moisture content we conclude that drought is the dominant factor that determines the surface energy partitioning and limits CO2 assimilation. Although drought causes stomatal closure, the results indicate that ozone damage, nevertheless, occurs. A second sensitivity analysis with CO2 and ozone shows that ozone damage causes an increase in stomatal resistance of up to 40% under high ozone levels and that CO2‐induced stomatal closure limits ozone damage. The impact on boundary layer development through the effect of CO2 and ozone on the stomatal resistance is much smaller. At the diurnal scale soil moisture influences the surface energy partitioning, which affects the entrainment of ozone‐rich air. Due to ozone damage, the CO2 assimilation flux is reduced by about 15%.
Photoacoustic Tomography for Biomedical Applications
Authors: Yao Junjie , Xia Jun , Wang Lihong V. 
Published: June 2015

AbstractPhotoacoustic tomography (PAT) has quickly become one of the fastest growing biomedical imaging modalities, since its first demonstration of functional imaging in small animal about a decade ago. Combining optical excitation with acoustic detection, PAT can provide detailed color pictures of tissues deep into the body without the radiation hazard of X‐rays, the lack of soft‐tissue contrast in ultrasonography, or the superficial penetration limitation of optical microscopy. This article will present cutting‐edge PAT technologies, focusing on their preclinical and clinical applications in biomedicine.
Optical Contrast Agents for Imaging, Biosensing, and Therapy
Authors: Ho Chris Jun Hui , Dinish U. S. , Olivo Malini 
Published: June 2015

Abstract
Over the past few decades, there has been a wide variety of optical contrast agents developed for various imaging, biosensing, and therapeutic applications. In the move toward clinical translation, research efforts have been heavily focused on improving various aspects of such contrast agents, such as sensitivity, specificity, toxicity, water solubility, and targeting efficacy. In this review, we focus on some of the notable optical contrast agents typically employed for imaging, biosensing, and therapy. The first section provides a brief discussion on the typical organic dyes used in fluorescence imaging, with a specific focus on indocyanine green, which is an important near‐infrared dye widely used for clinical applications. The second section focuses on specially designed nanotags used in surface‐enhanced Raman spectroscopy, a highly sensitive molecular biosensing technique with multiplexing capabilities. Multifunctional theranostic nanosensitizers concurrently used in imaging and therapy are covered in the subsequent sections. In the conclusion section, perspectives on future directions for the development of novel optical contrast agents are briefly discussed.
Singular Optics
Authors: Gbur Greg 
Published: June 2015

AbstractAt positions where the intensity of a wavefield vanishes, the phase is undefined and hence “singular.” Traditionally thought of as mere mathematical curiosities, thesephase singularitieshave been shown to have a well‐defined and non‐trivial mathematical structure and their existence has implications for a number of optical applications. This article summarizes the field ofsingular optics. It begins with examples of singularities that appear in optical wavefields, looks at analogies between the typical structures of singularities (optical vortices) and dislocations in crystal structures, and then considers general properties of optical vortices. The generation and detection of vortex‐carrying beams is discussed, and the angular momentum properties of such beams are analyzed. Finally, other types of singularities in wavefields are considered, and possible applications of singularities are surveyed.
Isoprenoidbiosynthese in pathogenen Bakterien: Nukleare inelastische Streuung ermöglicht Einblicke in den ungewöhnlichen [4Fe‐4S]‐Cluster vom E.‐coli‐Protein LytB/IspH
Authors: Faus Isabelle , Reinhard Annegret , Rackwitz Sergej , Wolny Juliusz A. , Schlage Kai , Wille Hans‐Christian , Chumakov Aleksandr , Krasutsky Sergiy , Chaignon Philippe , Poulter C. Dale , Seemann Myriam , Schünemann Volker 
Published: June 2015

AbstractDas Protein LytB/ISPH katalysiert den letzten Schritt des Methylerythritolphosphat(MEP)‐Wegs, der zur Terpenoidbiosynthese in vielen pathogenen Bakterien dient. Deswegen gilt der MEP‐Weg als Angriffspunkt für neue potentielle Antibiotika, da er essenziell für Mikroorganismen ist, beim Menschen jedoch nicht vorkommt. Substratfreies LytB hat einen besonderen [4Fe‐4S]2+‐Cluster mit einer bisher unbekannten Struktur. Experimente mit nuklearer inelastischer Streuung (NIS, oder “nuclear resonance vibrational spectroscopy”, NRVS) in Kombination mit quantenchemischen‐molekülmechanischen (QM/MM) Rechnungen zeigen, dass das apikale Eisen des Clusters eindeutig mit drei Wassermolekülen koordiniert ist. Zusätzlich präsentieren wir NIS‐Experimente von LytB gebunden mit dem natürlichen Substrat (E)‐4‐Hydroxy‐3‐methylbut‐2‐en‐1‐yl‐diphosphat (HMBPP) sowie mit den Inhibitoren (E)‐4‐Amino‐3‐methylbut‐2‐en‐1‐yl‐diphosphat und (E)‐4‐Mercapto‐3‐methylbut‐2‐en‐1‐yl‐diphosphat.
Versatile Design Principles for Facile Access to Unstrained Conjugated Organoborane Macrocycles
Authors: Chen Pangkuan , Yin Xiaodong , Baser‐Kirazli Nurcan , Jäkle Frieder 
Published: June 2015

AbstractA facile and versatile approach was developed to access ambipolar boron‐containing macrocycles. Two examples of new conjugated cyclic motifs are presented with carbazole moieties as donors and borane moieties as acceptors embedded into the ring system. They were first predicted using computational methods. Possible targets with appropriately shaped π‐conjugated bridges that minimize the overall ring strain were identified and their geometry was optimized by DFT methods. The synthetic demonstration was then accomplished using organometallic condensation reactions under high dilution conditions. The resulting monodisperse macrocycles provide important insights into the design principles necessary for the preparation of new unstrained macrocycles with interesting optical and electronic characteristics. The current research also offers a more general approach to conjugated ambipolar B/N macrocycles as a promising new family of (opto)electronic materials.
Precipitating Sodium Dodecyl Sulfate to Create Ultrastable and Stimulable Foams
Authors: Zhang Li , Mikhailovskaya Alesya , Yazhgur Pavel , Muller François , Cousin Fabrice , Langevin Dominique , Wang Nan , Salonen Anniina 
Published: June 2015

AbstractUltrastable foams are made very simply by adding salt (NaCl or KCl) to sodium dodecyl sulfate. The addition of high concentrations of salt leads to the precipitation of the surfactant on the bubble surfaces and as crystals in the interstices between the bubbles. As a consequence, the ageing of the foams is stopped to make them stable indefinitely, or until they are heated above the melting temperature of the crystals. The use of KCl is shown to be much more effective than that of NaCl because potassium dodecyl sulfate has a higher melting temperature and faster rates of crystallization. The crystalline structures have been investigated inside the foam using small angle neutron scattering. The larger lattice spacing of the crystals formed with NaCl in comparison with KCl has been evidenced. These simple temperature stimulable foams could have many potential applications.
The MoMo Quintuple Bond as a Ligand to Stabilize Transition‐Metal Complexes
Authors: Lu Duan‐Yen , Chen Peter P.‐Y. , Kuo Ting‐Shen , Tsai Yi‐Chou 
Published: June 2015

AbstractHerein, we report the employment of the MoMo quintuple bonded amidinate complex to stabilize Group 10 metal fragments {(Et3P)2M} (M=Pd, Pt) and give rise to the isolation of the unprecedented δ complexes. X‐ray analysis unambiguously revealed short contacts between Pd or Pt and two Mo atoms and a slight elongation of the MoMo quintuple bond in these two compounds. Computational studies show donation of the MoMo quintuple‐bond δ electrons to an empty σ orbital on Pd or Pt, and back‐donation from a filled Pd or Pt dπ orbital into the MoMo δ* level (LUMO), consistent with the Dewar–Chatt–Duncanson model.
A Cell‐Permeable ATP Analogue for Kinase‐Catalyzed Biotinylation
Authors: Fouda Ahmed E. , Pflum Mary Kay H. 
Published: June 2015

AbstractATP analogues have been powerful compounds for the study of kinase‐catalyzed phosphorylation. However, the cell impermeability of ATP analogues has largely limited their use to in vitro lysate‐based experiments. Herein, we report the first cell‐permeable ATP analogue, ATP–polyamine–biotin (APB). APB is shown to promote biotin labeling of kinase substrates in live cells and has future applications in phosphoprotein purification and analysis. More generally, these studies provide a foundation for the development of additional cell‐permeable ATP analogues for cell‐signaling research.
Pyridylidene‐Mediated Dihydrogen Activation Coupled with Catalytic Imine Reduction
Authors: Auth Johanna , Padevet Jaroslav , Mauleón Pablo , Pfaltz Andreas 
Published: June 2015

AbstractIn recent years, dihydrogen activation at non‐metallic centers has received increasing attention. A system in which dihydrogen is trapped by a pyridylidene intermediate that is generated from a pyridinium salt and a base is now reported. The dihydropyridine formed in this process can act as reducing agent towards organic electrophiles. By coupling the hydrogen‐activation step with subsequent hydride transfer from the dihydropyridine to an imine, a catalytic process was established. Treatment of the N‐phenylimine of phenyl trifluoromethyl ketone with 5–20 mol % of N‐mesityl‐3,5‐bis(2,6‐dimethylphenyl)pyridinium triflate and 0.3–1.0 equivalents of LiN(SiMe3)2 under 50 bar of hydrogen gas resulted in high conversion into the corresponding amine.
Four‐ and Sixfold Tandem‐Domino Reactions Leading to Dimeric Tetrasubstituted Alkenes Suitable as Molecular Switches
Authors: Tietze Lutz F. , Waldecker Bernd , Ganapathy Dhandapani , Eichhorst Christoph , Lenzer Thomas , Oum Kawon , Reichmann Sven O. , Stalke Dietmar 
Published: June 2015

AbstractA highly efficient palladium‐catalyzed fourfold tandem‐domino reaction consisting of two carbopalladation and two CH‐activation steps was developed for the synthesis of two types of tetrasubstituted alkenes 3 and 6 with intrinsic helical chirality starting from substrates 1 and 4, respectively. A sixfold tandem‐domino reaction was also developed by including a Sonogashira reaction. 20 compounds with different substitution patterns were prepared with yields of up to 97 %. Structure elucidation by X‐ray crystallography confirmed helical chirality of the two alkene moieties. Photophysical investigations of some of the compounds showed pronounced switching properties through light‐controlled changes of their stereochemical configuration.
Synthesis of Fluorophores that Target Small Molecules to the Endoplasmic Reticulum of Living Mammalian Cells
Authors: Meinig J. Matthew , Fu Liqiang , Peterson Blake R. 
Published: June 2015

AbstractThe endoplasmic reticulum (ER) plays critical roles in the processing of secreted and transmembrane proteins. To deliver small molecules to this organelle, we synthesized fluorinated hydrophobic analogues of the fluorophore rhodol. These cell‐permeable fluorophores are exceptionally bright, with quantum yields of around 0.8, and they were found to specifically accumulate in the ER of living HeLa cells, as imaged by confocal laser scanning microscopy. To target a biological pathway controlled by the ER, we linked a fluorinated hydrophobic rhodol to 5‐nitrofuran‐2‐acrylaldehyde. In contrast to an untargeted nitrofuran warhead, delivery of this electrophilic nitrofuran to the ER by the rhodol resulted in cytotoxicity comparable to the ER‐targeted cytotoxin eeyarestatin I, and specifically inhibited protein processing by the ubiquitin–proteasome system. Fluorinated hydrophobic rhodols are outstanding fluorophores that enable the delivery of small molecules for targeting ER‐associated proteins and pathways.