bluuebunny/crossref_metadata_2025 huggingface dataset:
The influences of mass loading and rapid dilution of secondary organic aerosol on particle volatility
Authors: Kolesar K. R. , Chen C. , Johnson D. , Cappa C. D.
Published: April 2015

Abstract. The thermally-induced evaporation of secondary organic aerosol (SOA) has been characterized for SOA formed from the dark ozonolysis of α-pinene + O3 at initial mass concentrations ranging from 1 to 800 μg m−3. Temperature-dependent particle size distributions were measured using a thermodenuder and the resulting mass thermograms were compared between the SOA formed at the various SOA mass concentrations. Negligible differences were observed between the mass thermograms for SOA concentrations < 300 μg m−3. At higher SOA concentrations, the observed mass thermograms indicated the SOA was actually slightly less volatile than the SOA at lower concentrations; this is likely an artifact due to either saturation of the gas-phase or to re-condensation during cooling. The thermograms observed when the SOA was formed at high concentrations (> 380 μg m−3) and then rapidly isothermally diluted to low concentrations (1–20 μg m−3) were identical to those for the SOA that was initially formed at low concentrations. The experimental results were compared to a kinetic model that simulates particle evaporation upon heating in a thermodenuder for a given input volatility distribution and particle composition. Three cases were considered: (1) the SOA was composed of semi-volatile monomer species with a volatility distribution based on that derived previously from consideration of SOA growth experiments, (2) the initial SOA was composed almost entirely of non-volatile dimers that decompose upon heating into their semi-volatile monomer units, which can then evaporate; and (3) where a volatility distribution was derived by fitting the model to the observed mass thermograms. It was found that good agreement is obtained between model predictions and the observations when the particle composition is either dominated by compounds of low volatility or by dimers. These same models were used to simulate isothermal evaporation of the SOA and were found to be broadly consistent with literature observations that indicate that SOA evaporation occurs with multiple timescales. The use of the semi-volatile monomer volatility distribution fails to reproduce the observed evaporation. The presence of dimers and larger oligomers in secondary organic aerosol formed from products of the reaction of α-pinene and O3 has been well-established in laboratory studies. However, the timescale and relative importance of the formation of oligomers or low volatility compounds in the growth and evaporation of SOA has been debated. This study provides further support that low volatility compounds and oligomers are formed in α-pinene + O3 in high abundances and suggests that their formation occurs rapidly upon particle formation.
The dayside magnetopause location during radial interplanetary magnetic field periods: Cluster observation and model comparison
Authors: Huang T. , Wang H. , Shue J.-H. , Cai L. , Pi G.
Published: April 2015

Abstract. The present work has investigated the midlatitudinal magnetopause locations under radial interplanetary field (RIMF) conditions. Among 262 (256) earthward (sunward) RIMF events from years of 2001 to 2009, Cluster satellites have crossed the magnetopause 22(12) times, with 10 (7) events occurring at midlatitudes. The observed midlatitudinal magnetopause positions are compared with two empirical magnetopause models (Shue et al., 1998; Boardsen et al., 2000) (hereafter referred to as the Shue98 model and the Boardsen00 model). The observation–model differences exhibit local time asymmetry. For earthward RIMF cases, the Shue98 model underestimates the magnetopause positions in the postnoon sector, while it overestimates the magnetopause positions in the dawn and dusk sectors. The Boardsen00 model generally underestimates the magnetopause after 6 MLT (magnetic local time), with larger deviations in the postnoon sector as compared to those in the prenoon. For sunward RIMF cases, the selected events are mainly clustered around the dawn and dusk sectors. The comparison with the Shue98 model indicates contractions in the dawn and expansions in the dusk sector, while the comparison with Boardsen00 indicates general expansions, with larger expansions in the later local time sectors. The local time variations in the differences between observations and the Shue98 and the Boardsen00 models indicate that the real magnetopause could be asymmetrically shaped during radial IMF periods, which should be considered by magnetopause models. The observation–model differences in the magnetopause positions (Δ RMP) during RIMF periods correlate well with the solar wind dynamic pressure, with larger Δ RMP for larger Pd. The southern magnetopause expands further outward relative to the model prediction when the dipole tilt angle is more negative (local summer in the Southern Hemisphere). For earthward RIMF cases, the generally good correlations between Δ RMP and the IMF cone angle are consistent with the previous hypothesis (Dušík et al., 2010) that, with more radial IMF, the subsolar magnetopause will expand further outward, owever, this is not the case for the comparison with Boardsen00 during sunward IMF periods, as it shows less dependence on the IMF cone angle.
The verification of seasonal precipitation forecasts for early warning in Zambia and Malawi
Authors: Hyvärinen O. , Mtilatila L. , Pilli-Sihvola K. , Venäläinen A. , Gregow H.
Published: April 2015

Abstract. We assess the probabilistic seasonal precipitation forecasts issued by Regional Climate Outlook Forum (RCOF) for the area of two southern African countries, Malawi and Zambia from 2002 to 2013. The forecasts, issued in August, are of rainy season rainfall accumulations in three categories (above normal, normal, and below normal), for early season (October–December) and late season (January–March). As observations we used in-situ observations and interpolated precipitation products from Global Precipitation Climatology Project (GPCP), Global Precipitation Climatology Centre (GPCC), and Climate Prediction Centre (CPC) Merged Analysis of Precipitation (CMAP). Differences between results from different data products are smaller than confidence intervals calculated by bootstrap. We focus on below normal forecasts as they were deemed to be the most important for society. The well-known decomposition of Brier score into three terms (Reliability, Resolution, and Uncertainty) shows that the forecasts are rather reliable or well-calibrated, but have a very low resolution; that is, they are not able to discriminate different events. The forecasts also lack sharpness as forecasts for one category are rarely higher than 40 % or less than 25 %. However, these results might be unnecessarily pessimistic, because seasonal forecasts have gone through much development during the period when the forecasts verified in this paper were issued, and forecasts using current methodology might have performed better.
Evidence for biological shaping of hair ice
Authors: Hofmann D. , Preuss G. , Mätzler C.
Published: April 2015

Abstract. An unusual ice type, called hair ice, grows on the surface of dead wood of broad-leaf trees at temperatures slightly below 0 °C. We describe this phenomenon and present physical, chemical, and biological investigations to gain insight in the properties and processes related to hair ice. Tests revealed that the biological activity of a winter-active fungus is required in the wood for enabling the growth of hair ice. We confirmed the fungus hypothesis originally suggested by Wegener (1918) by reproducing hair ice on wood samples. Treatment by heat and fungicide, respectively, suppresses the formation of hair ice. Fruiting bodies of Asco- and Basidiomycota are identified on hair-ice carrying wood. One species, Exidiopsis effusa (Ee), has been present on all investigated samples. Both hair-ice producing wood samples and those with killed fungus show essentially the same temperature variation, indicating that the heat produced by fungal metabolism is very small, that the freezing rate is not influenced by the fungus activity and that ice segregation is the common mechanism of ice growth at the wood surface. The fungus plays the role of shaping the ice hairs and to prevent them from recrystallisation. Melted hair ice indicates the presence of organic matter. Chemical analyses show a complex mixture of several thousand CHO(N,S)-compounds similar to fulvic acids in dissolved organic matter (DOM). The evaluation reveals decomposed lignin as the main constituent. Further work is needed to clarify its role in hair-ice growth and to identify the recrystallisation inhibitor.
Parallelisms between sea surface temperature changes in the western tropical Atlantic (Guiana basin) and high latitude climate signals over the last 140 000 years
Authors: Rama-Corredor O. , Martrat B. , Grimalt J. O. , López-Otalvaro G. E. , Flores J. A. , Sierro F.
Published: April 2015

Abstract. Sea surface temperatures (SST) in the Guiana basin over the last 140 ka were obtained by measuring the C37 alkenone unsaturation index U37'k in sediment core MD03-2616 (7° N, 53° W). The resulting dataset is unique for this period in the western tropical Atlantic region. SSTs range from 25.1 to 28.9 °C, i.e. glacial-to-interglacial amplitude of 3.8 °C, which is common in tropical areas. During the last two interglacials (MIS1 and MIS5e) and warm long interstadials (MIS5d-a), the sediments studied trace rapid transmission of the climate variability from arctic-to-tropical latitudes and vice-versa. During these periods, MD03-2616 SSTs showed a remarkable parallelism with temperature changes observed in Greenland and SST records of North Atlantic cores. The last deglaciation in Guiana is particularly revealing. MIS2 stands out as the coldest period of the interval analysed, with SSTs reaching as low as 25.1 °C. It contains reminders of northern latitude events such as the Bølling-Allerød warming and the Younger Dryas cooling which ensued. These oscillations were previously documented in the δ18O of the Sajama tropical ice core and are present in Guiana with rates of ca. 6 °C ka−1 and changes of over 2 °C. During the glacial interval, significant abrupt variability is observed; e.g. oscillations of 0.5–1.2 °C during MIS3, i.e. about 30% of the maximum glacial–interglacial SST change. Nevertheless, in the MD03-2616 record it is hard to identify unambiguously either the Dansgaard–Oeschger type of oscillations described in northern latitudes or the SST drops associated with the Heinrich events characterising North Atlantic records. Although these specific events form the background of the climate variability observed, what truly shapes SSTs in Guiana is a long-term tropical response to precessional changes, which is modulated in the opposite way to polar variability. This lack of synchrony is consistent with other tropical records in locations to the north or south of Guiana and evidences an arctic-to-tropical decoupling when a substantial reduction in the Atlantic meridional overturning circulation (AMOC) takes place.
Decadal regime shift linkage between global marine fish landings and atmospheric planetary wave forcing
Authors: Powell A. M. , Xu J.
Published: April 2015

Abstract. This investigation focuses on a global forcing mechanism for decadal regime shifts and their subsequent impacts. The proposed global forcing mechanism is that the global atmospheric planetary waves can lead to changes in the global surface air–sea conditions and subsequently fishery changes. In this study, the five decadal regime shifts (1956–1957, 1964–1965, 1977–1978, 1988–1989, and 1998–1999) in the most recent 59-year period (1950–2008) have been identified based on Student t tests and their association with global marine ecosystem change has been discussed. Changes in the three major oceanic (Pacific, Atlantic, and Indian) ecosystems will be explored with the goal of demonstrating the linkage between stratospheric planetary waves and the ocean surface forcing that leads to fisheries impacts. The global forcing mechanism is described with a top-down approach to help the multidisciplinary audience follow the analysis. Following previous work, this analysis addresses how changes in the atmospheric planetary waves may influence the vertical wind structure, surface wind stress, and their connection with the global ocean ecosystems based on a coupling of the atmospheric regime shifts with the decadal regime shifts determined from marine life changes. The multiple decadal regime shifts related to changes in marine life are discussed using the United Nations Food and Agriculture Organization's (FAO) global fish capture data (catch/stock). Analyses are performed to demonstrate that examining the interactions between the atmosphere, ocean, and fisheries is a plausible approach to explaining decadal climate change in the global marine ecosystems and its impacts. The results show a consistent mechanism, ocean wind stress, responsible for marine shifts in the three major ocean basins. Changes in the planetary wave pattern affect the ocean wind stress patterns. A change in the ocean surface wind pattern from longwave (relatively smooth and less complex) to shorter-wave (more convoluted and more complex) ocean surface wind stress creates changes in global marine fisheries.
OESbathy version 1.0: a method for reconstructing ocean bathymetry with realistic continental shelf-slope-rise structures
Authors: Goswami A. , Olson P. L. , Hinnov L. A. , Gnanadesikan A.
Published: April 2015

Abstract. We present a method for reconstructing global ocean bathymetry that uses a plate cooling model for the oceanic lithosphere, the age distribution of the oceanic crust, global oceanic sediment thicknesses, plus shelf-slope-rise structures calibrated at modern active and passive continental margins. Our motivation is to reconstruct realistic ocean bathymetry based on parameterized relationships of present-day variables that can be applied to global oceans in the geologic past, and to isolate locations where anomalous processes such as mantle convection may affect bathymetry. Parameters of the plate cooling model are combined with ocean crustal age to calculate depth-to-basement. To the depth-to-basement we add an isostatically adjusted, multicomponent sediment layer, constrained by sediment thickness in the modern oceans and marginal seas. A continental shelf-slope-rise structure completes the bathymetry reconstruction, extending from the ocean crust to the coastlines. Shelf-slope-rise structures at active and passive margins are parameterized using modern ocean bathymetry at locations where a complete history of seafloor spreading is preserved. This includes the coastal regions of the North, South, and Central Atlantic Ocean, the Southern Ocean between Australia and Antarctica, and the Pacific Ocean off the west coast of South America. The final products are global maps at 0.1° × 0.1° resolution of depth-to-basement, ocean bathymetry with an isostatically adjusted, multicomponent sediment layer, and ocean bathymetry with reconstructed continental shelf-slope-rise structures. Our reconstructed bathymetry agrees with the measured ETOPO1 bathymetry at most passive margins, including the east coast of North America, north coast of the Arabian Sea, and northeast and southeast coasts of South America. There is disagreement at margins with anomalous continental shelf-slope-rise structures, such as around the Arctic Ocean, the Falkland Islands, and Indonesia.
High-resolution analysis of 1 day extreme precipitation in Sicily
Authors: Maugeri M. , Brunetti M. , Garzoglio M. , Simolo C.
Published: April 2015

Abstract. Sicily, the major Mediterranean island, experienced several exceptional precipitation episodes and floods during the last century, with dramatic consequences on human life and environment. A long term, rational planning of urban development is mandatory for protecting population and avoiding huge economic losses in the future. This requires a deep knowledge of the distributional features of extreme precipitation over the complex territory of Sicily. In the present study, we address this issue, and attempt a detailed investigation of observed 1-day precipitation extremes and their frequency distribution, based on a dense data-set of high-quality, homogenized station records in 1921–2005. We extrapolate very high quantiles (return levels) corresponding to 10-, 50- and 100-year return periods, as predicted by a generalized extreme value distribution. Return level estimates are produced on a regular high-resolution grid (30 arcsec) using a variant of regional frequency analysis combined with regression techniques. Results clearly reflect the complexity of this region, and make evident the high vulnerability of its eastern and northeastern parts as those prone to the most intense and potentially damaging events. This analysis thus provides an operational tool for extreme precipitation risk assessment and, at the same time, is an useful basis for validation and downscaling of regional climate models.
Business Development Services Provided by Islamic Microfinance Institutions and Customer Satisfaction: The Mediation Role of Perceived Benefits. A Study on SMEs in Yemen
Authors: Fararah Fahmi Shaaban , Swidi Abdullah Kaid Al- , Yusoff Wan Sulaiman B. Wan
Published: April 2015

This study seeks to determine the effect of Business Development Services (BDS) on the comfort level of the Islamic Microfinance System and SMEs owners in Yemen. Based on the importance of SMEs in Yemen which consists of 99.6% of all businesses in Yemen and their important role on the overall economic development by reducing poverty and creating new job. The paper made it easy to see what effectiveness the Islamic microfinance system is bringing in SMEs sector in the country.532 questionnaire were distributed amongst the SMEs owners in Yemen to collect data, 346 were returned and further 320 were selected for Data analysis. It was found in the study that there was a remarkable effect of BDS on the satisfaction and the perceived benefits that SMEs owners got through dealing with Islamic microfinance system. The additional findings were to confirmed the role of perceived benefits mediating the relationship between satisfaction and BDS but the moderating effects of perceived benefits on the two were not confirmed.
Global Broadband Benchmarking 2013: Best Practice Lessons for Governments
Authors: Roetter Martyn F.
Published: April 2015

Is there a “one size fits all” set of international best practices for broadband policy? No, argues Martyn Roetter, because local circumstances are far too diverse. However, he says that there are many useful lessons to be drawn from experiences in different parts of the world. He reviews successful broadband projects in fifteen countries from five regions: Latin America, Africa, Asia, Europe, and North America. Based on these examples, and acknowledging their differences, Mr. Roetter distills common characteristics of successful (and unsuccessful) broadband policies in the areas of public-private partnerships, public funding of broadband, effectively competitive markets, spectrum management, and the role of government intervention. Ultimately, he concludes that the roles of government and the private sector must be complementary.
Human Pluripotent Stem Cell-Derived Radial Glia Recapitulate Developmental Events and Provide Real-Time Access to Cortical Neurons and Astrocytes
Authors: Duan Lishu , Peng Chian-Yu , Pan Liuliu , Kessler John A.
Published: April 2015

Studies of human cerebral cortex development are limited by difficulties in accessing and manipulating human neural tissue at specific development stages. We have derived human radial glia (hRG), which are responsible for most cerebral cortex neurogenesis, from human pluripotent stem cells. These hRG display the hallmark morphological, cellular, and molecular features of radial glia in vitro. They can be passaged and generate layer-specific subtypes of cortical neurons in a temporal and passage-dependent fashion. In later passages, they adopt a distinct progenitor phenotype that gives rise to cortical astrocytes and GABAergic interneurons. These hRG are also capable of following developmental cues to engraft, differentiate, migrate, and integrate into the embryonic mouse cortex when injected into E14 lateral ventricles. Moreover, hRG-derived cells can be cryopreserved at specific stages and retain their stage-specific phenotypes and competence when revived. Our study demonstrates that cultured hRG maintain a cell-intrinsic clock that regulates the progressive generation of stage-specific neuronal and glial subtypes. It also describes an easily accessible cell source for studying hRG lineage specification and progression and an on-demand supply of specific cortical neuron subtypes and astrocytes.

Significance

This study describes a protocol that uses human pluripotent stem cells to differentiate into radial glia and, in turn, generate a large number of cortical pyramidal neurons, interneurons, and astrocytes that are important for both mechanistic studies and use in cellular replacement therapy.
Inhibition of an NAD+ Salvage Pathway Provides Efficient and Selective Toxicity to Human Pluripotent Stem Cells
Authors: Kropp Erin M. , Oleson Bryndon J. , Broniowska Katarzyna A. , Bhattacharya Subarna , Chadwick Alexandra C. , Diers Anne R. , Hu Qinghui , Sahoo Daisy , Hogg Neil , Boheler Kenneth R. , Corbett John A. , Gundry Rebekah L.
Published: April 2015

The tumorigenic potential of human pluripotent stem cells (hPSCs) is a major limitation to the widespread use of hPSC derivatives in the clinic. Here, we demonstrate that the small molecule STF-31 is effective at eliminating undifferentiated hPSCs across a broad range of cell culture conditions with important advantages over previously described methods that target metabolic processes. Although STF-31 was originally described as an inhibitor of glucose transporter 1, these data support the reclassification of STF-31 as a specific NAD+ salvage pathway inhibitor through the inhibition of nicotinamide phosphoribosyltransferase (NAMPT). These findings demonstrate the importance of an NAD+ salvage pathway in hPSC biology and describe how inhibition of NAMPT can effectively eliminate hPSCs from culture. These results will advance and accelerate the development of safe, clinically relevant hPSC-derived cell-based therapies.

Significance

The tumorigenic potential of human pluripotent stem cells (hPSCs) is a major limitation to the widespread use of hPSC derivatives in the clinic. This study provides detailed analyses of cellular metabolic flux to define an efficient strategy for selective hPSC elimination that is effective across many culture conditions and does not have cytotoxic effects on hPSC-derived progeny. Of broad significance to the stem cell and regenerative medicine fields, this study also highlights the importance of examining the effect of in vitro culturing parameters when evaluating the efficacy of hPSC-elimination strategies, especially those that target metabolic processes.
Study of the Mobile Phone Technology in Creating Awareness among Small Farmers of Sindh Province
Authors: Har Bakhsh Makhijani  , Muhammad Ismail Kumbhar  , Shuhabuddin Mughal  , Hameeda Masood Shah  , Naseer Ahmed Abbasi
Published: April 2015

Information and communication knowledge have played a positive role in different segments of the society such as in agriculture education and community development. Now a days most of the farmers are using these technologies especially mobile phones which have given a fruitful result to community. This study was conducted in Sindh Pakistan and survey was conducted in district Jamshoro Taulka Manjhand. Total two hundred respondents were randomly selected for data collection. The study indicated that 90% of the respondents possessed their personal mobile phones and 70% of the respondents utilized mobile for communication with their friends. While 75% of the were of the opinion asked that mobile phones have made their lives easy. However, the results showed that 72% did not contact with any agriculture officer and similarly not contacted with customers to sell their product. Furthermore, study revealed that 74.5% of the respondents replied that they utilize internet on mobile phones. Overall result indicated that farmers are not getting any benefit or increase their income, save time and energy by using the mobile phones in their places.
Effect of rbST on Serum Biochemical Values During Various Physiological and Weather Conditions in Kundhi Buffaloes
Authors: Kachiwal A.B. , Sheikh B.A. , Sheikh S.A. , Qureshi T.A. , Memon K.H.
Published: April 2015

This study was performed to investigate the effect of rbST treatment on some biochemical parameters in addition to values of thyroid hormones in Kundhi buffaloes. Sixteen Kundhi buffaloes were divided into two groups. Group-A (N=8) served as control and Group-B (N=8) was treated with 250 mg of rbST fortnightly for 1st lactation. Blood samples were collected weekly during lactation period from day one to 60 as pre-treatment values and then from day 61 to completion of 1st lactation in Kundhi buffaloes as post-treatment values. The findings revealed overall non significant variation in the serum biochemical and thyroid hormone values between control and rbST treated buffaloes, whereas, significant differences were observed during various physiological and weather conditions in both groups. Glucose and uric acid values were observed higher during parturition and winter season in Kundhi buffaloes. Protein level was higher in rbST treated buffaloes during open days.
In Vito Fertilization in Buffaloes: A Review
Authors: Abd-Allah Saber Mohamed
Published: April 2015

This is the review of original data concerning the effect of some factors on oocyte development in vitro of buffaloes. In vitro fertilization is a multi – step process: oocytes maturation, fertilization and embryo culture.
In vitro fertilization is strongly influenced by events occurring during oocyte maturation, fertilization and the subsequent development of the fertilized oocytes. With the advancement of IVF procedures, variability in developmental rate and viability of in vitro produced buffalo embryos so, improving the efficiency and identifying the sources of variations between IVF systems are more important when routinely producing blastocysts from individuals of high genetic merits. Also, the development of specific culture regimes capable of supporting in vitro maturation (IVM), in vitro fertilization (IVF) and in vitro culture (IVC) to the blastocyst stage is highly desirable in breeding systems. This paper discusses the technical aspects of the procedures involved in in vitro fertilization of buffaloes.
Hvordan indsætter redaktøren/tidsskriftschefen referencer i overensstemmelse med CrossRef's krav?
Authors: Frederiksen Niels Erik , Thestrup Jesper Boserup
Published: April 2015

Artiklen viser, hvor man skal indsætte referencer i OJS for at leve op til de krav CrossRef stiller i forbindelse med tildeling af DOI’er. Først vises hvordan det foregår, hvis man anvender OJS’s standard-workflow, dernæst hvis man vælger den såkaldte QuickSubmit Plugin.
Re-visiting the trans insertion model for complexin clamping
Authors: Krishnakumar Shyam S , Li Feng , Coleman Jeff , Schauder Curtis M , Kümmel Daniel , Pincet Frederic , Rothman James E , Reinisch Karin M
Published: April 2015

We have previously proposed that complexin cross-links multiple pre-fusion SNARE complexes via a trans interaction to function as a clamp on SNARE-mediated neurotransmitter release. A recent NMR study was unable to detect the trans clamping interaction of complexin and therefore questioned the previous interpretation of the fluorescence resonance energy transfer and isothermal titration calorimetry data on which the trans clamping model was originally based. Here we present new biochemical data that underscore the validity of our previous interpretation and the continued relevancy of the trans insertion model for complexin clamping.
Spreading good news
Authors: Fawcett Jeffrey A , Innan Hideki
Published: April 2015

Gene conversion has a central role in the evolutionary fine-tuning of regulatory elements in the fruit fly Drosophila miranda.
Selective Proteomic Proximity Labeling Assay Using Tyramide (SPPLAT): A Quantitative Method for the Proteomic Analysis of Localized Membrane‐Bound Protein Clusters
Authors: Rees Johanna Susan , Li Xue‐Wen , Perrett Sarah , Lilley Kathryn Susan , Jackson Antony Philip
Published: April 2015

This manuscript describes a new and general method to identify proteins localized into spatially restricted membrane microenvironments. Horseradish peroxidase (HRP) is brought into contact with a target protein by being covalently linked to a primary or secondary antibody, an antigen or substrate, a drug, or a toxin. A biotinylated tyramide‐based reagent is then added. In the presence of HRP and hydrogen peroxide, the reagent is converted into a free radical that only diffuses a short distance before covalently labeling proteins within a few tens to hundreds of nanometers from the target. The biotinylated proteins can then be isolated by standard affinity chromatography and identified by liquid chromatography (LC) and mass spectrometry (MS). The assay can be made quantitative by using stable isotope labeling with amino acids in cell culture (SILAC) or isobaric tagging at the peptide level. © 2015 by John Wiley & Sons, Inc.
Mapping 3′ mRNA Isoforms on a Genomic Scale
Authors: Jin Yi , Geisberg Joseph V. , Moqtaderi Zarmik , Ji Zhe , Hoque Mainul , Tian Bin , Struhl Kevin
Published: April 2015

Most eukaryotic genes are transcribed into mRNAs with alternative poly(A) sites. Emerging evidence suggests that mRNA isoforms with alternative poly(A) sites can perform critical regulatory functions in numerous biological processes. In recent years, a number of strategies utilizing high‐throughput sequencing technologies have been developed to aid in the identification of genome‐wide poly(A) sites. This unit describes a modified protocol for a recently published 3′READS (3′ region extraction and deep sequencing) method that accurately identifies genome‐wide poly(A) sites and that can be used to quantify the relative abundance of the resulting 3′ mRNA isoforms. This approach minimizes nonspecific sequence reads due to internal priming and typically yields a high percentage of sequence reads that are ideally suited for accurate poly(A) identification. © 2015 by John Wiley & Sons, Inc.
Tools and Procedures for Visualization of Proteins and Other Biomolecules
Authors: Pan Lurong , Aller Stephen G.
Published: April 2015

Protein, peptides, and nucleic acids are biomolecules that drive biological processes in living organisms. An enormous amount of structural data for a large number of these biomolecules has been described with atomic precision in the form of structural “snapshots” that are freely available in public repositories. These snapshots can help explain how the biomolecules function, the nature of interactions between multi‐molecular complexes, and even how small‐molecule drugs can modulate the biomolecules for clinical benefits. Furthermore, these structural snapshots serve as inputs for sophisticated computer simulations to turn the biomolecules into moving, “breathing” molecular machines for understanding their dynamic properties in real‐time computer simulations. In order for the researcher to take advantage of such a wealth of structural data, it is necessary to gain competency in the use of computer molecular visualization tools for exploring the structures and visualizing three‐dimensional spatial representations. Here, we present protocols for using two common visualization tools—the Web‐based Jmol and the stand‐alone PyMOL package—as well as a few examples of other popular tools. © 2015 by John Wiley & Sons, Inc.
Heymann Nephritis in Lewis Rats
Authors: Wang Yuan Min , Lee Vincent W.S. , Wu Huiling , Harris David C.H. , Alexander Stephen I.
Published: April 2015

Human membranous nephritis is a major cause of end‐stage kidney disease. Active Heymann nephritis (HN) is an auto‐immune model of membranous nephritis induced in Lewis rats by immunization with a crude renal tubular antigen (Fx1A) or megalin (gp330). The pathogenesis of HN is through the binding of anti‐Fx1A autoantibodies to the auto‐antigen expressed on glomerular epithelial cells, resulting in severe glomerular injury and proteinuria. The pathological features of HN include immune deposits in glomeruli and infiltration of glomeruli and the tubulointerstitium by macrophages and T cells. This unit describes the method of the preparation of Fx1A and the induction of HN in Lewis rats by immunization with Fx1A. © 2015 by John Wiley & Sons, Inc.
Neural Stem Cell‐Mediated Delivery of Oncolytic Adenovirus
Authors: Kim Julius W. , Kane J. Robert , Young Jacob S. , Chang Alan L. , Kanojia Deepak , Qian Shuo , Spencer Drew A. , Ahmed Atique U. , Lesniak Maciej S.
Published: April 2015

The use of stem cells (SCs) as carriers for therapeutic agents has now progressed to early clinical trials. These clinical trials exploring SC‐mediated delivery of oncolytic adenoviruses will commence in the near future, hopefully yielding meritorious results that can provoke further scientific inquiry. Preclinical animal studies have demonstrated that SCs can be successfully loaded with conditionally‐replicative adenoviruses and delivered to the tumor, whereupon they may evoke pronounced therapeutic efficacy. In this protocol, we describe the maintenance of SCs, provide an analysis of optimal adenoviral titers for SC loading, and evaluate the optimized viral loading on SCs. © 2015 by John Wiley & Sons, Inc.
Uncompensated Polychromatic Analysis of Mitochondrial Membrane Potential Using JC‐1 and Multilaser Excitation
Authors: De Biasi Sara , Gibellini Lara , Cossarizza Andrea
Published: April 2015

The lipophilic cation JC‐1 (5,5′,6,6′‐tetrachloro‐1,1′,3,3′‐tetraethyl‐benzimidazolyl carbocyanine iodide) has been used for more than 20 years as a specific dye for measuring mitochondrial membrane potential (ΔΨm). In this unit, we revise our original protocol (that made use of a single 488 nm laser for the detection of monomers and aggregates, and where compensation was an important step) to use dual‐laser excitation. Moreover, thanks to recently developed multilaser instruments and novel probes for surface and intracellular markers, JC‐1 can be utilized by polychromatic flow cytometry to simultaneously detect, without any compensation between fluorescences, ΔΨm along with other biological parameters, such as apoptosis and the production of reactive oxygen species. © 2015 by John Wiley & Sons, Inc.
Measurement of Intracellular Ions by Flow Cytometry
Authors: Posey, Avery D. , Kawalekar Omkar U. , June Carl H.
Published: April 2015

Using flow cytometry, single‐cell measurements of calcium can be made on isolated populations identified by one or more phenotypic characteristics. Most earlier techniques for measuring cellular activation parameters determined the mean value for a population of cells, which did not permit optimal resolution of the responses. The flow cytometer is particularly useful for this purpose because it can measure ion concentrations in large numbers of single cells and thereby allows ion concentration to be correlated with other parameters such as immunophenotype and cell cycle stage. A limitation of flow cytometry, however, is that it does not permit resolution of certain complex kinetic responses such as cellular oscillatory responses. This unit describes the preparation of cells, including labeling with antibodies and with calcium probes, and discusses the principles of data analysis and interpretation. © 2015 by John Wiley & Sons, Inc.
An analytic model of toroidal half‐wave oscillations: Implication on plasma density estimates
Authors: Bulusu Jayashree , Sinha A. K. , Vichare Geeta
Published: April 2015

The developed analytic model for toroidal oscillations under infinitely conducting ionosphere (“Rigid‐end”) has been extended to “Free‐end” case when the conjugate ionospheres are infinitely resistive. The present direct analytic model (DAM) is the only analytic model that provides the field line structures of electric and magnetic field oscillations associated with the “Free‐end” toroidal wave for generalized plasma distribution characterized by the power law ρ = ρo(ro/r)m, where m is the density index and r is the geocentric distance to the position of interest on the field line. This is important because different regions in the magnetosphere are characterized by different m. Significant improvement over standard WKB solution and an excellent agreement with the numerical exact solution (NES) affirms validity and advancement of DAM. In addition, we estimate the equatorial ion number density (assuming H+ atom as the only species) using DAM, NES, and standard WKB for Rigid‐end as well as Free‐end case and illustrate their respective implications in computing ion number density. It is seen that WKB method overestimates the equatorial ion density under Rigid‐end condition and underestimates the same under Free‐end condition. The density estimates through DAM are far more accurate than those computed through WKB. The earlier analytic estimates of ion number density were restricted to m = 6, whereas DAM can account for generalized m while reproducing the density for m = 6 as envisaged by earlier models.
Determining crustal structure beneath seismic stations overlying a low‐velocity sedimentary layer using receiver functions
Authors: Yu Youqiang , Song Jianguo , Liu Kelly H. , Gao Stephen S.
Published: April 2015

The receiver function (RF) technique has been widely applied to investigate crustal and mantle layered structures using P‐to‐S converted (Ps) phases from velocity discontinuities. However, the presence of low‐velocity (relative to that of the bedrock) sediments can give rise to strong reverberations in the resulting RFs, frequently masking the Ps phases from crustal and mantle boundaries. Such reverberations are caused by P‐to‐S conversions and their multiples associated with the strong impedance contrast across the bottom of the low‐velocity sedimentary layer. Here we propose and test an approach to effectively remove the near‐surface reverberations and decipher the Ps phases associated with the Moho discontinuity. Autocorrelation is first applied on the observed RFs to determine the strength and two‐way traveltime of the reverberations, which are then used to construct a resonance removal filter in the frequency domain to remove or significantly reduce the reverberations. The filtered RFs are time corrected to eliminate the delay effects of the sedimentary layer and applied to estimate the subsediment crustal thickness and VP/VSusing a H‐k stacking procedure. The resulting subsediment crustal parameters (thickness and VP/VS) are subsequently used to determine the thickness and VP/VS of the sedimentary layer, using a revised version of the H‐k stacking procedure. Testing using both synthetic and real data suggests that this computationally inexpensive technique is efficient in resolving subsediment crustal properties beneath stations sitting on a low‐velocity sedimentary layer and can also satisfactorily determine the thickness and VP/VS of the sedimentary layer.
Budget of shallow magma plumbing system at Asama Volcano, Japan, revealed by ground deformation and volcanic gas studies
Authors: Kazahaya Ryunosuke , Aoki Yosuke , Shinohara Hiroshi
Published: April 2015

Multiple cycles of the intensive volcanic gas discharge and ground deformation (inflation and deflation) were observed at Asama Volcano, Japan, from 2000 to 2011. Magma budget of the shallow magma plumbing system was estimated on the basis of the volcanic gas emission rates and ground deformation data. Recent inflations observed in 2004 and 2008 were modeled as a dike intrusion to 2–3 km west of Asama Volcano. Previous studies proposed that magma ascends from a midcrustal magma reservoir to the dike and reaches the surface via a sinuous conduit which connects the dike to the summit. The intensive volcanic sulfur dioxide discharge of up to 4600 t/d at the volcano was modeled by magma convective degassing through this magma pathway. The volcano deflates as shrinkage of the magma in a reservoir by volcanic gas discharge. We estimated the volume change of the dike modeled based on the GPS observations, the volume decrease of the magma by the volcanic gas discharge, and the amount of degassed magma produced to calculate the magma budget. The results show that the volume decrease of the magma by the volcanic gas discharge was larger than the volume change of the dike during the inflation periods. This indicates that a significant volume of magma at least more than 2 times larger than the volume change of the dike was supplied from the midcrustal magma reservoir to the dike. The volume decrease of the dike was comparable with the volume decrease of the magma by the volcanic gas discharge during the deflation periods. The long‐term deflation trend of the dike and the volume of degassed magma (108–9 m3) suggest that the degassed magma produced is not stored in the dike and the magma is mainly supplied from the midcrustal magma reservoir. In both periods, the volume of degassed magma produced was 1 order of magnitude larger than the volume change of the dike. This indicates that the actual volume of the magma supplied from the midcrustal magma reservoir is up to 1 order of magnitude larger than the volume change of the dike. These results strongly suggest that an amount of magma moved through a magma reservoir is possible to be significantly larger than volume change of the magma reservoir estimated by the geodetic observations.
Understanding coastal morphodynamic patterns from depth‐averaged sediment concentration
Authors: Ribas F. , Falqués A. , de Swart H. E. , Dodd N. , Garnier R. , Calvete D.
Published: April 2015

This review highlights the important role of the depth‐averaged sediment concentration (DASC) to understand the formation of a number of coastal morphodynamic features that have an alongshore rhythmic pattern: beach cusps, surf zone transverse and crescentic bars, and shoreface‐connected sand ridges. We present a formulation and methodology, based on the knowledge of the DASC (which equals the sediment load divided by the water depth), that has been successfully used to understand the characteristics of these features. These sand bodies, relevant for coastal engineering and other disciplines, are located in different parts of the coastal zone and are characterized by different spatial and temporal scales, but the same technique can be used to understand them. Since the sand bodies occur in the presence of depth‐averaged currents, the sediment transport approximately equals a sediment load times the current. Moreover, it is assumed that waves essentially mobilize the sediment, and the current increases this mobilization and advects the sediment. In such conditions, knowing the spatial distribution of the DASC and the depth‐averaged currents induced by the forcing (waves, wind, and pressure gradients) over the patterns allows inferring the convergence/divergence of sediment transport. Deposition (erosion) occurs where the current flows from areas of high to low (low to high) values of DASC. The formulation and methodology are especially useful to understand the positive feedback mechanisms between flow and morphology leading to the formation of those morphological features, but the physical mechanisms for their migration, their finite‐amplitude behavior and their decay can also be explored.
Electrical conductivity of the Earth's mantle from the first Swarm magnetic field measurements
Authors: Civet F. , Thébault E. , Verhoeven O. , Langlais B. , Saturnino D.
Published: April 2015

We present a 1‐D electrical conductivity profile of the Earth's mantle down to 2000 km derived from L1b Swarm satellite magnetic field measurements from November 2013 to September 2014. We first derive a model for the main magnetic field, correct the data for a lithospheric field model, and additionally select the data to reduce the contributions of the ionospheric field. We then model the primary and induced magnetospheric fields for periods between 2 and 256 days and perform a Bayesian inversion to obtain the probability density function for the electrical conductivity as function of depth. The conductivity increases by 3 orders of magnitude in the 400–900 km depth range. Assuming a pyrolitic mantle composition, this profile is interpreted in terms of temperature variations leading to a temperature gradient in the lower mantle that is close to adiabatic.
Feldspathic rocks on Mars: Compositional constraints from infrared spectroscopy and possible formation mechanisms
Authors: Rogers A. Deanne , Nekvasil Hanna
Published: April 2015

Rare feldspar‐dominated surfaces on Mars were previously reported based on near‐infrared (NIR) spectral data and were interpreted to consist of anorthosite or felsic rocks. Using thermal infrared (TIR) data over the feldspar detections with the largest areal extent in Nili Patera and Noachis Terra, we rule out felsic interpretations. Basaltic or anorthositic compositions are consistent with TIR measurements, but the geologic contexts for these regions do not support a plutonic origin. Laboratory NIR spectral measurements demonstrate that large plagioclase crystals (>~840 µm) can be detected in mixtures with as much as 50 vol % mafics, which is higher than the previously stated requirement of no more than 15% mafics. Thus, anorthositic or felsic interpretations need not be invoked for all NIR‐based feldspar detections. Plagioclase‐enriched basaltic eruptive products can be formed from Martian basalts through partial crystallization at the base of a thick crust, followed by low‐pressure crystallization of the residual liquids.
Particle mobilization in porous media: Temperature effects on competing electrostatic and drag forces
Authors: You Zhenjiang , Bedrikovetsky Pavel , Badalyan Alexander , Hand Martin
Published: April 2015

The fluid flow in natural reservoirs mobilizes fine particles. Subsequent migration and straining of the mobilized particles in rocks greatly reduce reservoir permeability and well productivity. This chain of events typically occurs over the temperature ranges of 20–40°C for aquifers and 120–300°C for geothermal reservoirs. However, the present study might be the first to present a quantitative analysis of temperature effects on the forces exerted on particles and of the resultant fines migration. Based on torque balance between electrostatic and drag forces acting on attached fine particles, we derived a model for the maximum retention concentration and used it to characterize the detachment of multisized particles from rock surfaces. Results showed that electrostatic force is far more affected than water viscosity by temperature variation. An analytical model for flow toward wellbore that is subject to fines migration was derived. The experiment‐based predictive modeling of the well impedance for a field case showed high agreement with field historical data (coefficient of determination R2 = 0.99). It was found that the geothermal reservoirs are more susceptible to fine particle migration than are conventional oilfields and aquifers.
Drivetrain Noise, Vibration, and Harshness
Authors: Rahnejat H. , Theodossiades S. , Kelly P. , Menday M.T.
Published: April 2015

This chapter describes the plethora of noise, vibration, and harshness (NVH) concerns in vehicular drivetrain systems. With a trend toward compact lightweight lightly damped drivetrain systems, such phenomena are likely to exacerbate. SignificantNVHconcerns such as transmission rattle, driveline clonk, and clutch in‐cycle whoop are described and methods of measurement and modeling are described. TheseNVHphenomena are regarded as refinement quality issues by vehicle customers, thus a concern to the automobile industry. Various methods of palliation are also discussed.