bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel WGA and WTA for Comparative Genome and Transcriptome NGS Analysis Using Tiny Cell Numbers
Authors: Korfhage Christian , Fricke Evelyn , Meier Andreas 
Published: July 2015

AbstractGenomic DNA determines how and when the transcriptome is changed by a trigger or environmental change and how cellular metabolism is influenced. Comparative genome and transcriptome analysis of the same cell sample links a defined genome with all changes in the bases, structure, or numbers of the transcriptome. However, comparative genome and transcriptome analysis using next‐generation sequencing (NGS) or real‐time PCR is often limited by the small amount of sample available. In mammals, the amount of DNA and RNA in a single cell is ∼10 picograms, but deep analysis of the genome and transcriptome currently requires several hundred nanograms of nucleic acids for library preparation for NGS sequencing. Consequently, accurate whole‐genome amplification (WGA) and whole‐transcriptome amplification (WTA) is required for such quantitative analysis. This unit describes how the genome and the transcriptome of a tiny number of cells can be amplified in a highly parallel and comparable process. Protocols for quality control of amplified DNA and application of amplified DNA for NGS are included. © 2015 by John Wiley & Sons, Inc.
Gene Silencing by RNAi in Mammalian Cells
Authors: Ponthan Frida , Yusoff Narazah Mohd , Soria Natalia Martinez , Heidenreich Olaf , Coffey Kelly 
Published: July 2015

AbstractThis unit provides information how to use short interfering RNA (siRNA) for sequence‐specific gene silencing in mammalian cells. Several methods for siRNA generation and optimization, as well as recommendations for cell transfection and transduction, are presented. © 2015 by John Wiley & Sons, Inc.
CRISPR‐Cas9 Genome Editing in Drosophila
Authors: Gratz Scott J. , Rubinstein C. Dustin , Harrison Melissa M. , Wildonger Jill , O'Connor‐Giles Kate M. 
Published: July 2015

AbstractThe CRISPR‐Cas9 system has transformed genome engineering of model organisms from possible to practical. CRISPR‐Cas9 can be readily programmed to generate sequence‐specific double‐strand breaks that disrupt targeted loci when repaired by error‐prone non‐homologous end joining (NHEJ) or to catalyze precise genome modification through homology‐directed repair (HDR). Here we describe a streamlined approach for rapid and highly efficient engineering of the Drosophila genome via CRISPR‐Cas9‐mediated HDR. In this approach, transgenic flies expressing Cas9 are injected with plasmids to express guide RNAs (gRNAs) and positively marked donor templates. We detail target‐site selection; gRNA plasmid generation; donor template design and construction; and the generation, identification, and molecular confirmation of engineered lines. We also present alternative approaches and highlight key considerations for experimental design. The approach outlined here can be used to rapidly and reliably generate a variety of engineered modifications, including genomic deletions and replacements, precise sequence edits, and incorporation of protein tags. © 2015 by John Wiley & Sons, Inc.
Using the PhenX Toolkit to Add Standard Measures to a Study
Authors: Hendershot Tabitha , Pan Huaqin , Haines Jonathan , Harlan William R. , Marazita Mary L. , McCarty Catherine A. , Ramos Erin M. , Hamilton Carol M. 
Published: July 2015

AbstractThe PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) offers high‐quality, well‐established measures of phenotypes and exposures for use by the scientific community. The goal is to promote the use of standard measures, enhance data interoperability, and help investigators identify opportunities for collaborative and translational research. The Toolkit contains 395 measures drawn from 22 research domains (fields of research), along with additional collections of measures for Substance Abuse and Addiction (SAA) research, Mental Health Research (MHR), and Tobacco Regulatory Research (TRR). Additional measures for TRR that are expected to be released in 2015 include Obesity, Eating Disorders, and Sickle Cell Disease. Measures are selected by working groups of domain experts using a consensus process that includes input from the scientific community. The Toolkit provides a description of each PhenX measure, the rationale for including it in the Toolkit, protocol(s) for collecting the measure, and supporting documentation. Users can browse measures in the Toolkit or can search the Toolkit using the Smart Query Tool or a full text search. PhenX Toolkit users select measures of interest to add to their Toolkit. Registered Toolkit users can save their Toolkit and return to it later to revise or complete. They then have options to download a customized Data Collection Worksheet that specifies the data to be collected, and a Data Dictionary that describes each variable included in the Data Collection Worksheet. The Toolkit also has a Register Your Study feature that facilitates cross‐study collaboration by allowing users to find other investigators using the same PhenX measures. © 2015 by John Wiley & Sons, Inc.
Visualization of Telomere Integrity and Function In Vitro and In Vivo Using Immunofluorescence Techniques
Authors: Cesare Anthony J. , Heaphy Christopher M. , O'Sullivan Roderick J. 
Published: July 2015

AbstractIn cancer cells, telomere length maintenance occurs largely via the direct synthesis of TTAGGG repeats at chromosome ends by telomerase, or less frequently by the recombination‐dependent alternative lengthening of telomeres (ALT) pathway. The latter is characterized by the atypical clustering of telomeres within promyelocytic leukemia (PML) nuclear bodies, which harbor proteins that are linked with DNA repair and recombination activity. For this reason, it is speculated that these associated PML bodies represent the sites of the recombination that maintains telomere length. The protocols described here can be employed for the routine investigation of the structural integrity of telomeres and the association of proteins at telomeres in normal cells, challenged cells, and archived formalin‐fixed paraffin‐embedded clinical tissue specimens that may have activated the ALT pathway. © 2015 by John Wiley & Sons, Inc.
Influence of local ionization on ionospheric densities in Titan's upper atmosphere
Authors: Sagnières Luc B. M. , Galand Marina , Cui Jun , Lavvas Panayotis P. , Vigren Erik , Vuitton Véronique , Yelle Roger V. , Wellbrock Anne , Coates Andrew J. 
Published: July 2015

AbstractTitan has the most chemically complex ionosphere of the solar system. The main sources of ions on the dayside are ionization by EUV solar radiation and on the nightside include ionization by precipitated electrons from Saturn's magnetosphere and transport of ions from the dayside, but many questions remain open. How well do models predict local ionization rates? How strongly do the ionization processes drive the ionospheric densities locally? To address these questions, we have carried out an analysis of ion densities from the Ion and Neutral Mass Spectrometer (INMS) from 16 close flybys of Titan's upper atmosphere. Using a simple chemical model applied to the INMS data set, we have calculated the ion production rates and local ionization frequencies associated with primary ions
and
. We find that on the dayside the solar energy deposition model overestimates the INMS‐derived
production rates by a factor of 2. On the nightside, however, the model driven by suprathermal electron intensities from the Cassini Plasma Spectrometer Electron Spectrometer sometimes agrees and other times underestimates the INMS‐derived
production rates by a factor of up to 2–3. We find that below 1200 km, all ion number densities correlate with the local ionization frequency, although the correlation is significantly stronger for short‐lived ions than long‐lived ions. Furthermore, we find that, for a given N2 local ionization frequency,
has higher densities on the dayside than on the nightside. We explain that this is due to CH4 being more efficiently ionized by solar photons than by magnetospheric electrons for a given amount of N2 ionization.
From products to processes: Academic events to foster interdisciplinary and iterative dialogue in a changing climate
Authors: Addor Nans , Ewen Tracy , Johnson Leigh , Çöltekin Arzu , Derungs Curdin , Muccione Veruska 
Published: July 2015

AbstractIn the context of climate change, both climate researchers and decision makers deal with uncertainties, but these uncertainties differ in fundamental ways. They stem from different sources, cover different temporal and spatial scales, might or might not be reducible or quantifiable, and are generally difficult to characterize and communicate. Hence, a mutual understanding between current and future climate researchers and decision makers must evolve for adaptation strategies and planning to progress. Iterative two‐way dialogue can help to improve the decision making process by bridging current top‐down and bottom‐up approaches. One way to cultivate such interactions is by providing venues for these actors to interact and exchange on the uncertainties they face. We use a workshop‐seminar series involving academic researchers, students, and decision makers as an opportunity to put this idea into practice and evaluate it. Seminars, case studies, and a round table allowed participants to reflect upon and experiment with uncertainties. An opinion survey conducted before and after the workshop‐seminar series allowed us to qualitatively evaluate its influence on the participants. We find that the event stimulated new perspectives on research products and communication processes, and we suggest that similar events may ultimately contribute to the midterm goal of improving support for decision making in a changing climate. Therefore, we recommend integrating bridging events into university curriculum to foster interdisciplinary and iterative dialogue among researchers, decision makers, and students.
Appreciation of peer reviewers for 2014
Authors: Becker Thorsten W. , Bass Jay , Blichert‐Toft Janne , Derry Lou , Lee Cin‐Ty , Tyburczy James , Vance Derek , Yokoyama Yusuke 
Published: July 2015

AbstractThe editorial and scientific publishing process relies on the sustained work of volunteer reviewers, and evaluating the interdisciplinary and broad interest papers published in G‐Cubed can be a particular challenge. As Editors and Associated Editors, we are therefore hugely appreciative of the efforts of our reviewers, and would like to thank and acknowledge them in this editorial. G‐Cubed published 257 manuscripts out of 431 submissions in 2014, and for this, we were able to rely on the efforts of 710 dedicated reviewers. Their names are listed below; in italics are those 27 who provided three or more reviews. A big thank you from the G‐Cubed team!
Space geodetic observation of the deformation cycle across the Ballenas Transform, Gulf of California
Authors: Plattner Christina , Malservisi Rocco , Amelung Falk , Dixon Timothy H. , Hackl Matthias , Verdecchia Alessandro , Lonsdale Peter , Suarez‐Vidal Francisco , Gonzalez‐Garcia Javier 
Published: July 2015

AbstractThe Gulf of California, Mexico, accommodates ~90% of North America‐Pacific plate relative motion. While most of this motion occurs on marine transform faults and spreading centers, several fault segments in the central Gulf come close to peninsular Baja California. Here we present Global Positioning System and interferometric synthetic aperture radar data near the Ballenas transform fault, separating the peninsula from Angel de la Guarda Island. We observe interseismic motion between June 2004 and May 2009 and displacements associated with the 3 August 2009Mw6.9 earthquake. From the interseismic data we estimate a locking depth of 9–12.5 km and a slip rate of 44.9–48.1 mm/yr, indicating that faults east of Angel de la Guarda deform at negligible rates and that the Ballenas Transform accommodates virtually all of the relative motion between the North American plate and the Baja California microplate. Our preferred model for coseismic slip on a finite rectangular fault plane suggests 1.3 m of strike‐slip displacement along a vertical rupture plane that is 60 km long and extends from the surface to a depth of 13 km in the eastern Ballenas Channel, striking parallel to Baja California‐North America relative plate motion. These estimates agree with the seismic moment tensor and the location of the major foreshock and aftershocks and are compatible with the fault location identified from high‐resolution bathymetric mapping. The geodetic moment is 33% higher than the seismic moment in part because some afterslip and viscous flow in the first month after the earthquake are included in the geodetic estimate. Coulomb stress changes for adjacent faults in the Gulf are consistent with the location of smaller aftershocks following the 2009 main shock and suggest potential triggering of the 12 April 2012Mw6.9 Guaymas earthquake.
Retrieving of atmospheric parameters from multi‐GNSS in real time: Validation with water vapor radiometer and numerical weather model
Authors: Li Xingxing , Zus Florian , Lu Cuixian , Dick Galina , Ning Tong , Ge Maorong , Wickert Jens , Schuh Harald 
Published: July 2015

AbstractThe multiconstellation Global Navigation Satellite Systems (GNSS) (e.g., GPS, GLObal NAvigation Satellite System (GLONASS), Galileo, and BeiDou) offers great opportunities for real‐time retrieval of atmospheric parameters for supporting numerical weather prediction nowcasting or severe weather event monitoring. In this study, the observations from different GNSS are combined to retrieve atmospheric parameters based on the real‐time precise point positioning technique. The atmospheric parameters, retrieved from multi‐GNSS observations of a 180 day period from about 100 globally distributed stations, including zenith total delay, integrated water vapor, horizontal gradient, and slant total delay (STD), are analyzed and evaluated. The water vapor radiometer data and a numerical weather model, the operational analysis of the European Centre for Medium‐Range Weather Forecasts (ECMWF), are used to independently validate the performance of individual GNSS and also demonstrate the benefits of multiconstellation GNSS for real‐time atmospheric monitoring. Our results show that the GLONASS and BeiDou have the potential capability for real‐time atmospheric parameter retrieval for time‐critical meteorological applications as GPS does, and the combination of multi‐GNSS observations can improve the performance of a single‐system solution in meteorological applications with higher accuracy and robustness. The multi‐GNSS processing greatly increases the number of STDs. The mean and standard deviation of STDs between each GNSS and ECMWF exhibit a good stability as function of the elevation angle, the azimuth angle, and time, in general. An obvious latitude dependence is confirmed by a map of station specific mean and standard deviations. Such real‐time atmospheric products, provided by multi‐GNSS processing with higher accuracy, stronger reliability, and better distribution, might be highly valuable for atmospheric sounding systems, especially for nowcasting of extreme weather.
A new ice cloud parameterization for infrared radiative transfer simulation of cloudy radiances: Evaluation and optimization with IIR observations and ice cloud profile retrieval products
Authors: Vidot Jérôme , Baran Anthony J. , Brunel Pascal 
Published: July 2015

AbstractA new ice cloud optical property database in the thermal infrared has been parameterized for the RTTOV radiative transfer model. The Self‐Consistent Scattering Model (SCSM) database is based on an ensemble model of ice crystals and a parameterization of the particle size distribution. This convolution can predict the radiative properties of cirrus without the need of a priori information on the ice particle shape and an estimate of the ice crystal effective dimension. The ice cloud optical properties are estimated through linear parameterizations of ambient temperature and ice water content. We evaluate the new parameterization against existing parameterizations used in RTTOV. We compare infrared observations from Imaging Infrared Radiometer, on board CALIPSO, against RTTOV simulations of the observations. The simulations are performed using two different products of ice cloud profiles, retrieved from the synergy between space‐based radar and lidar observations. These are the 2C‐ICE and DARDAR products. We optimized the parameterization by testing different SCSM databases, derived from different shapes of the particle size distribution, and weighting the volume extinction coefficient of the ensemble model. By selecting a large global data set of ice cloud profiles of visible optical depths between 0.03 and 4, we found that the simulations, based on the optimized SCSM database parameterization, reproduces the observations with a mean bias of only 0.43 K and a standard deviation of 6.85 K. The optimized SCSM database parameterization can also be applied to any other radiative transfer model.
Identifying robust transport features of the upper tropical troposphere
Authors: Bergman J. W. , Pfister L. , Yang Q. 
Published: July 2015

AbstractMultimodel ensembles of back trajectories calculated from four different analysis data sets and two different trajectory formulations (“diabatic” and “kinematic”) are analyzed to investigate seasonal mean boundary layer‐to‐“tropopause” (100 hPa) transport in the tropics. Transport paths are separated into two legs: “convective uplift” (boundary layer to detrainment) and “radiative ascent” (detrainment to tropopause). The following three diagnostic measures are used: source location, source‐to‐tropopause transport time, and the source “influence” (i.e., the fraction of air with short transport times) at 100 hPa. Ensemble means and standard deviations identify “robust features” (i.e., common to all ensemble members) while experimental hybrid calculations explain model‐to‐model discrepancies. Convective uplift is a major contributor to uncertainties in boundary layer‐to‐tropopause transport times and source locations. Spatial patterns of boundary layer influence at 100 hPa are nevertheless robust. Detrainment‐to‐tropopause transport times are robust despite substantial model‐to‐model variations of convective detrainment height because ascent rates are faster at low altitudes than at high altitudes. Detrainment‐to‐tropopause transport also has robust horizontal spatial patterns for both convective sources and convective influence, particularly during boreal winter. Most model‐to‐model discrepancies occur at small spatial scales and are associated with differing distributions of convection. The location of maximum convective influence associated with the Asian summer monsoon is a notable exception. This exceptionally large discrepancy is associated primarily with radiative ascent. The fact that the observed maxima of important tropospheric constituents are collocated with the maximum convective influence for the diabatic calculations but not for the kinematic calculations suggests that diabatic trajectories could be more reliable in this region.
Schaltung und Fixierung der Konformation von Amiden durch nahegelegene positive Ladungen
Authors: Bartuschat Amelie L. , Wicht Karina , Heinrich Markus R. 
Published: July 2015

AbstractTertiäre Amide, die üblicherweise als cis‐trans‐Gemische auftreten, können wirkungsvoll in die cis‐Konformation überführt werden, indem man eine positive Ladung in der Nähe der Amidcarbonylgruppe platziert. Dieser Effekt ermöglichte die Herstellung eines cis‐Prolylamids und die Verbesserung einer stark Rotamer‐abhängigen radikalischen Cyclisierung.
Anellierte Thiophen‐Pyrrol‐haltige Ringsysteme bis zu einem Heterodecacen
Authors: Wetzel Christoph , Brier Eduard , Vogt Astrid , Mishra Amaresh , Mena‐Osteritz Elena , Bäuerle Peter 
Published: July 2015

AbstractEine neue Klasse von π‐konjugierten polycyclischen Kohlenwasserstoffen, die interessante elektronische Eigenschaften verspricht, wird vorgestellt. Die Synthese und Erweiterung der nur aus Fünfring‐Heterocyclen bestehenden S,N‐Heteroacenreihe bis zu einem sehr langen, stabilen und noch gut löslichen Decacen SN10 gelingt über mehrfache Pd‐katalysierte Aminierungen von halogenierten Thiophenvorstufen als zentrale Reaktionen. Die neuartigen Heteroacene wurden über optische Spektroskopie und Elektrochemie charakterisiert und liefern interessante Struktur‐Eigenschafts‐Beziehungen. Ein fast vollständiger Bindungslängenausgleich im “Inneren” des konjugierten π‐Systems und eine ungewöhnliche Fischgräten‐Packung im Festkörper sind strukturelle Besonderheiten der neuen Systeme.
Post‐Assembly Stabilization of Rationally Designed DNA Crystals
Authors: Zhao Jiemin , Chandrasekaran Arun Richard , Li Qian , Li Xiang , Sha Ruojie , Seeman Nadrian C. , Mao Chengde 
Published: July 2015

AbstractThis manuscript reports an effort to stabilize self‐assembled DNA crystals. Owing to their weak inter‐unit cohesion, self‐assembled DNA crystals are fragile, which limits the potential applications of such crystals. To overcome this problem, another molecule was introduced, which binds to the cohesive sites and stabilizes the inter‐unit interactions. The extra interactions greatly improve the stability of the DNA crystals. The original DNA crystals are only stable in solutions of high ionic strength (e.g., ≥1.2 M (NH4)2SO4); in contrast, the stabilized crystals can be stable at ionic strengths as low as that of a 0.02 M solution of (NH4)2SO4. The current strategy is expected to represent a general approach for increasing the stability of self‐assembled DNA nanostructures for potential applications, for example, as structural scaffolds and molecular sieves.
Chemical Evolution of a Bacterial Proteome
Authors: Hoesl Michael Georg , Oehm Stefan , Durkin Patrick , Darmon Elise , Peil Lauri , Aerni Hans‐Rudolf , Rappsilber Juri , Rinehart Jesse , Leach David , Söll Dieter , Budisa Nediljko 
Published: July 2015

AbstractWe have changed the amino acid set of the genetic code of Escherichia coli by evolving cultures capable of growing on the synthetic noncanonical amino acid L‐β‐(thieno[3,2‐b]pyrrolyl)alanine ([3,2]Tpa) as a sole surrogate for the canonical amino acid L‐tryptophan (Trp). A long‐term cultivation experiment in defined synthetic media resulted in the evolution of cells capable of surviving Trp→[3,2]Tpa substitutions in their proteomes in response to the 20 899 TGG codons of the E. coli W3110 genome. These evolved bacteria with new‐to‐nature amino acid composition showed robust growth in the complete absence of Trp. Our experimental results illustrate an approach for the evolution of synthetic cells with alternative biochemical building blocks.
Self‐Healing Materials from V‐ and H‐Shaped Supramolecular Architectures
Authors: Chen Senbin , Mahmood Nasir , Beiner Mario , Binder Wolfgang H. 
Published: July 2015

AbstractIntegrating self‐healing capability into supramolecular architectures is an interesting strategy, and can considerably enhance the performance and broaden the scope of applications for this important class of polymers. Herein we report the rational design of novel V‐shaped barbiturate (Ba) functionalized soft–hard–soft triblock copolymers with a reversible supramolecular healing motif (Ba) in the central part of the hard block, which undergoes autonomic repair at 30 °C. The designed synthesis also offers a suitable macromolecular building block to further self‐assemble with heterocomplementary α,ω‐Hamilton wedge (HW) functionalized polyisoprene (PI; HW‐PI‐HW), resulting in an H‐shaped supramolecular architecture with efficient self‐healing capabilities that can recover up to around 95 % of the original mechanical performance at 30 °C within 24 h.