bluuebunny/crossref_metadata_2025 huggingface dataset:
Process to generate a synthetic diagnostic for microwave imaging reflectometry with the full-wave code FWR2D
Authors: Ren X. , Domier C. W. , Kramer G. , Luhmann N. C. , Muscatello C. M. , Shi L. , Tobias B. J. , Valeo E.
Published: October 2014

A synthetic microwave imaging reflectometer (MIR) diagnostic employing the full-wave reflectometer code (FWR2D) has been developed and is currently being used to guide the design of real systems, such as the one recently installed on DIII-D. The FWR2D code utilizes real plasma profiles as input, and it is combined with optical simulation tools for synthetic diagnostic signal generation. A detailed discussion of FWR2D and the process to generate the synthetic signal are presented in this paper. The synthetic signal is also compared to a prescribed density fluctuation spectrum to quantify the imaging quality. An example is presented with H-mode-like plasma profiles derived from a DIII-D discharge, where the MIR focal is located in the pedestal region. It is shown that MIR is suitable for diagnosing fluctuations with poloidal wavenumber up to 2.0 cm−1 and fluctuation amplitudes less than 5%.
Dynamic properties and local order in liquid Al-Ni alloys
Authors: Jakse N. , Pasturel A.
Published: October 2014

Ab initio molecular dynamics simulations are used to describe the connection between dynamic and structural properties in liquid Al90Ni10 and Al80Ni20 alloys at various temperatures. We find that self-diffusion coefficients and viscosity are strongly composition-dependent while their temperature dependence follows an Arrhenius-type behavior, in close agreement with experiment. Through comparisons between both alloys and the corresponding pure elements, we demonstrate that the composition and temperature dependence of these transport properties can be related to the detailed description of the short-range order and more particularly to the interplay between icosahedral short-range order and chemical short-range order. Finally, all our results are used to discuss the known correlation between transport properties and the two-body excess entropy.
Theoretical study of time-resolved luminescence in semiconductors. II. Pulsed excitation
Authors: Maiberg Matthias , Scheer Roland
Published: October 2014

In the second part of this series, we studied TRL decay on semiconductor layers and thin film homostructures after a pulsed excitation by simulation with Synopsys TCAD® and by mathematical approximation. Again, our working example is Cu(In,Ga)Se2. We investigate the influence of the excitation pulse length, axial diffusion, bulk-defects, and defects at the contacts, as well as space charge on the TRL-decay separately by quasi one-dimensional simulations of semiconductor layers and semiconductor homostructures. Material parameters like defect density, carrier mobility, and surface recombination velocity are varied in a wide range, such that the calculations are applicable to other semiconductors. We further study the influence of multi-pulse excitation. We show how material parameters such as carrier lifetime and carrier mobility can be extracted from the TRL transients and how the samples can be characterized by excitation dependent measurements in the open circuit case. We can explain some effects found in luminescence experiments, like an increased decay in semiconductor junctions due to the electric field in the space charge region. However, we also discuss the effect of charge storage which may lead to decreased decay. It is revealed that under high injection conditions single layers within a semiconductor stack can be characterized in terms of carrier lifetime.
Atomic intermixing and interface roughness in short-period InAs/GaSb superlattices for infrared photodetectors
Authors: Ashuach Y. , Lakin E. , Saguy C. , Kaufmann Y. , Zolotoyabko E.
Published: October 2014

A set of advanced characterization methods, including high-resolution X-ray diffraction (measurements and simulations), cross-sectional scanning tunneling microscopy, and high-angle annular dark-field scanning transmission electron microscopy is applied to quantify the interface roughness and atomic intermixing (in both cation and anion sub-lattices) in short period (6–7 nm) InAs/GaSb superlattices intended for mid-wavelength (M) and long-wavelength (L) infrared detectors. The undesired atomic intermixing and interface roughness in the L-samples were found to be considerably lower than in the M-samples. In all specimens, anion intermixing is much higher than that in the cation sub-lattice. Possible origins of these findings are discussed.
Complete characterization by Raman spectroscopy of the structural properties of thin hydrogenated diamond-like carbon films exposed to rapid thermal annealing
Authors: Rose Franck , Wang Na , Smith Robert , Xiao Qi-Fan , Inaba Hiroshi , Matsumura Toru , Saito Yoko , Matsumoto Hiroyuki , Dai Qing , Marchon Bruno , Mangolini Filippo , Carpick Robert W.
Published: October 2014

We have demonstrated that multi-wavelength Raman and photoluminescence spectroscopies are sufficient to completely characterize the structural properties of ultra-thin hydrogenated diamond-like carbon (DLC:H) films subjected to rapid thermal annealing (RTA, 1 s up to 659 °C) and to resolve the structural differences between films grown by plasma-enhanced chemical vapor deposition, facing target sputtering and filtered cathodic vacuum arc with minute variations in values of mass density, hydrogen content, and sp3 fraction. In order to distinguish unequivocally between films prepared with different density, thickness, and RTA treatment, a new method for analysis of Raman spectra was invented. This newly developed analysis method consisted of plotting the position of the Raman G band of carbon versus its full width at half maximum. Moreover, we studied the passivation of non-radiative recombination centers during RTA by performing measurements of the increase in photoluminescence in conjunction with the analysis of DLC:H networks simulated by molecular dynamics. The results show that dangling bond passivation is primarily a consequence of thermally-induced sp2 clustering rather than hydrogen diffusion in the film.
Examination of the ambient effects on the stability of amorphous indium-gallium-zinc oxide thin film transistors using a laser-glass-sealing technology
Authors: Yamada Kazuo , Nomura Kenji , Abe Katsumi , Takeda Satoshi , Hosono Hideo
Published: October 2014

The effect of an ambient atmosphere with a positive bias constant current stress (CCS) and a negative bias illumination stress (NBIS) on the stability of amorphous In-Ga-Zn-O thin film transistors (TFTs) is examined by utilizing a glass-hermetic-sealant with a moisture permeability of less than 10−6 g/m2 · day. In the CCS test, the threshold voltage shift (ΔVth) was remarkably suppressed in the glass-sealed TFTs. The unsealed and resin-sealed TFTs exhibited large ΔVth values. During the NBIS tests, the glass-sealed TFTs had almost the same negative ΔVth as the unsealed and resin sealed TFTs. Among the different TFTs, no significant differences were observed in the threshold voltage, the subthreshold swing and the saturation mobility as a function of the photon energy. It is concluded that ambient molecules were the primary origin of the instability of the ΔVth, induced by a CCS, but they were not related to the NBIS instability. The major role of the effective passivation layers in the NBIS test was not to simply block out the ambient effects, but to reduce the extra density of states at/near the surface of the back channel.
Effect of Zn doping on the magneto-caloric effect and critical constants of Mott insulator MnV2O4
Authors: Shahi Prashant , Singh Harishchandra , Kumar A. , Shukla K. K. , Ghosh A. K. , Yadav A. K. , Nigam A. K. , Chatterjee Sandip
Published: October 2014

X-ray absorption near edge spectra (XANES) and magnetization of Zn doped MnV2O4 have been measured and from the magnetic measurement the critical exponents and magnetocaloric effect have been estimated. The XANES study indicates that Zn doping does not change the valence states in Mn and V. It has been shown that the obtained values of critical exponents β, γ and δ do not belong to universal class and the values are in between the 3D Heisenberg model and the mean field interaction model. The magnetization data follow the scaling equation and collapse into two branches indicating that the calculated critical exponents and critical temperature are unambiguous and intrinsic to the system. All the samples show large magneto-caloric effect. The second peak in magneto-caloric curve of Mn0.95Zn0.05V2O4 is due to the strong coupling between orbital and spin degrees of freedom. But 10% Zn doping reduces the residual spins on the V-V pairs resulting the decrease of coupling between orbital and spin degrees of freedom.
DOE acquiring new supercomputers and climate models
Authors: Kramer David
Published: October 2014

Researchers say they are preparing the way for scientific exascale computing.
Atom-like crystal defects: From quantum computers to biological sensors
Authors: Childress Lilian , Walsworth Ronald , Lukin Mikhail
Published: October 2014

Impurities in a crystal lattice are the key ingredient in recent efforts to control and apply the coherence and entanglement of spins in condensed-matter systems.
Quantum Darwinism, classical reality, and the randomness of quantum jumps
Authors: Zurek Wojciech H.
Published: October 2014

The core principles that underlie quantum weirdness also explain why only selected quantum states survive monitoring by the environment and, as a result, why we experience our world as classical.
The development of standard negation in Quechua
Authors: Pineda-Bernuy Edith
Published: October 2014

This paper provides a discussion on the development of standard negation in Quechua languages. The analysis of the current variation leads to the detection of at least three main standard patterns across Quechua varieties. The diversification of the standard pattern is assumed to be due to the introduction of the non-factual clitic -chu in the negative sentence. I suggest that this was the beginning of a cycle of negation in the Quechua language family. The negative cycle, called the Jespersen Cycle, then followed the next phases with the grammaticalization of the new incomer allowing first bipartite negation and finally single negation again. Notably, this negative cycle involved no weakening of the sort assumed by Jespersen to have played an important role in such changes. Keywords: single negation; bipartite negation; Jespersen Cyclel standard negation
Prestigious fruit trees in ancient Israel: first palynological evidence for growing Juglans regia and Citrus medica
Authors: Langgut Dafna
Published: October 2014

This article describes the earliest evidence for the growing of two prestigious fruit trees:Juglans regia(Persian walnut) andCitrus medica(citron) in ancient Israel. The study also tries to identify the origin of these trees as well as their influence on Jewish tradition and culture. The palynological information from the Southern Levant supports the hypothesis of the survival ofJ. regiaduring the Last Glacial period in some areas of Eurasia. Accumulating palynological information as well as archeobotanical evidence ofJ. regiaplant remains from northern Israel from ∼1800 years BCE suggests the beginning of horticulture of walnut in the Southern Levant. The growing of walnut within Israel probably started in the north, and nearly one millennium later, palynological evidence indicates thatJ. regiacultivation had spread also to the Judean Mountains. Walnut is mentioned only once in the Bible, in Song of Solomon (6:11). From the interpretation of this text as well other Jewish texts and the available palynological diagrams, it is clear that since the Persian period (fifth to fourth centuries BCE),J. regiawas well established in ancient Israel. Citron, although being one of the four species of the Jewish feast of Tabernacles (Sukkot), is not native to the flora of the Near East. The earliest archeobotanical evidence of the growing ofC. medicain Israel was recently discovered in a Royal Persian garden in Ramat Rahel near Jerusalem, dated to the fifth to fourth centuries BCE.C. medicaseems to have made its way to Ramat Rahel from India via Persia. From that point on, citron gradually penetrated the Jewish culture and tradition. The citron is not mentioned in the Bible, and the association between the citron and thePürî `ëc hädär(Leviticus 23:40), translated “fruit of the goodly tree,” was only made during the first century AD.
Rudolph’s two step coding theorem and Alpern’s lemma for ℝ^{𝕕} actions
Authors: Kra Bryna , Quas Anthony , Şahi̇n Ayşe
Published: October 2014

Rudolph showed that the orbits of any measurable, measure preserving

R

d

\mathbb {R}^d

action can be measurably tiled by

2
d

2^d

rectangles and asked if this number of tiles is optimal for

d
>
1

d>1

. In this paper, using a tiling of

R

d

\mathbb {R}^d

by notched cubes, we show that

d
+
1

d+1

tiles suffice. Furthermore, using a detailed analysis of the set of invariant measures on tilings of

R

2

\mathbb {R}^2

by two rectangles, we show that while for

R

2

\mathbb {R}^2

actions with completely positive entropy this bound is optimal, there exist mixing

R

2

\mathbb {R}^2

actions whose orbits can be tiled by 2 tiles.
Can permanent closures of nearshore areas reduce the proportions of undersized fish in the Icelandic longline fishery?
Authors: Björnsson Björn , Sólmundsson Jón , Pálsson Ólafur K.
Published: October 2014

In recent years, about one-third of the cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) catches in Icelandic waters have been obtained with longline. Although longlining has been regarded as a conservation-oriented fishing method, a serious drawback of this fishing gear is the high catches of undersized fish. Our purpose was to locate areas where catches of undersized fish are high and consider if it may be feasible to close them permanently for longlining. Extensive length measurements used in the analysis were made by official inspectors on-board longliners during 2005–2013 in the main fishing area around Iceland. We found that the percentage of undersized cod (<55 cm total length) and haddock (<45 cm) in those samples decreased in relation to both depth and distance from shore. Our results suggest that permanent closures of large nearshore areas for longlining is a feasible option to reduce catch of undersized cod and haddock.
Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination
Authors: Ignarski Michael , Singh Aditi , Swart Estienne C. , Arambasic Miroslav , Sandoval Pamela Y. , Nowacki Mariusz
Published: October 2014

Genome-wide DNA remodelling in the ciliate Paramecium is ensured by RNA-mediated trans-nuclear crosstalk between the germline and the somatic genomes during sexual development. The rearrangements include elimination of transposable elements, minisatellites and tens of thousands non-coding elements called internally eliminated sequences (IESs). The trans-nuclear genome comparison process employs a distinct class of germline small RNAs (scnRNAs) that are compared against the parental somatic genome to select the germline-specific subset of scnRNAs that subsequently target DNA elimination in the progeny genome. Only a handful of proteins involved in this process have been identified so far and the mechanism of DNA targeting is unknown. Here we describe chromatin assembly factor-1-like protein (PtCAF-1), which we show is required for the survival of sexual progeny and localizes first in the parental and later in the newly developing macronucleus. Gene silencing shows that PtCAF-1 is required for the elimination of transposable elements and a subset of IESs. PTCAF-1 depletion also impairs the selection of germline-specific scnRNAs during development. We identify specific histone modifications appearing during Paramecium development which are strongly reduced in PTCAF-1 depleted cells. Our results demonstrate the importance of PtCAF-1 for the epigenetic trans-nuclear cross-talk mechanism.
Evaluation of the NonpathogenicAgrobacterium vitisStrain ARK-1 for Crown Gall Control in Diverse Plant Species
Authors: Kawaguchi Akira , Inoue Koji , Tanina Koji
Published: October 2014

The nonpathogenic strain of Agrobacterium (=Rhizobium) vitis ARK-1 is a biological agent able to effectively control grapevine crown gall. In this study, treating apple, Japanese pear, peach, rose, and tomato by soaking the roots in a cell suspension of ARK-1 before planting into soil infected with tumorigenic Agrobacterium spp. reduced the number of plants developing crown gall tumors. Meta-analyses of the results from six field trials of apple, four field trials of Japanese pear, and four field trials of peach, from 2010 to 2013, showed integrated risk ratio (IRR) after treatment with ARK-1 to be 0.38 for apple crown gall, 0.16 for Japanese pear crown gall, and 0.20 for peach crown gall, indicating that the disease incidence was significantly reduced by ARK-1 treatment. Meta-analyses of the results from three greenhouse trials of rose and three greenhouse trials of tomato showed IRR after treatment with ARK-1 to be 0.29 for rose crown gall and 0.16 for tomato crown gall, indicating that the disease incidence was significantly reduced by ARK-1 treatment. These results indicated that control by ARK-1 covers five different species of host plants and tumorigenic (Ti) strains of Agrobacterium species.
Mitochondrial Haplotype-Based Identification of Ethanol-Preserved Root-Knot Nematodes from Africa
Authors: Pagan Chris , Coyne Danny , Carneiro Regina , Kariuki George , Luambano Nessie , Affokpon Antoine , Williamson Valerie M.
Published: October 2014

The asexual root-knot nematodes (RKNs) (Meloidogyne spp.) exemplified by Meloidogyne incognita are widespread and damaging pests in tropical and subtropical regions worldwide. Comparison of amplification products of two adjacent polymorphic regions of the mitochondrial genome using DNA extracts of characterized RKN strains, including 15 different species, indicate that several species are derived from the same or closely related female lineages. Nevertheless, M. javanica, M. enterolobii, M. incognita, and other key species could each be assigned unique mitochondrial haplotypes based on polymerase chain reaction fragment size and restriction cleavage patterns. M. arenaria isolates did not group as a single haplotype, consistent with other reports of diversity within this species. To test the utility of this assay, we characterized ethanol-preserved samples from 103 single-species isolates from four countries in sub-Saharan Africa (Benin, Nigeria, Kenya, and Tanzania). Mitochondrial haplotypes corresponding to M. javanica and M. incognita were the most prevalent. Samples from western Africa included several instances of M. enterolobii but this species was not detected in samples from East Africa. This protocol provides progress toward a standardized strategy for identification of RKN species from small, preserved samples and a rational starting point for classifying species present in regions where previous knowledge has been limited.
Accuracy of Malignant Hyperthermia Diagnoses in Hospital Discharge Records
Authors: Pinyavat Teeda , Rosenberg Henry , Lang Barbara H. , Wong Cynthia A. , Riazi Sheila , Brady Joanne E. , Sun Lena S. , Li Guohua
Published: October 2014

Background:

In 1997, the International Classification of Diseases (ICD), 9th Revision Clinical Modification (ICD-9) coding system introduced the code for malignant hyperthermia (MH) (995.86). The aim of this study was to estimate the accuracy of coding for MH in hospital discharge records.

Methods:

An expert panel of anesthesiologists reviewed medical records for patients with a discharge diagnosis of MH based on ICD-9 or ICD-10 codes from January 1, 2006 to December 31, 2008 at six tertiary care medical centers in North America. All cases were categorized as possible, probable, or fulminant MH, history of MH (family or personal) or other.

Results:

A total of 47 medical records with MH diagnoses were reviewed; 68.1% had a documented surgical procedure and general anesthesia, and 23.4% (95% CI, 12.3–38.0%) had a possible, probable, or fulminant MH event. Dantrolene was given in 81% of the MH events. All patients judged to have an incident MH event survived to discharge. Family and personal history of MH accounted for 46.8% of cases. High fever without evidence of MH during admission accounted for 23.4%, and the reason for MH coding was unclear in 6.4% of cases.

Conclusions:

Approximately one quarter of ICD-9 or ICD-10 coded MH diagnoses in hospital discharge records refer to incident MH episodes and an additional 47% to MH susceptibility (including personal history or family history). Information such as surgical procedure, anesthesia billing data, and dantrolene administration may aid in identifying incident MH cases among those with an ICD-9 or ICD-10 coded MH diagnosis in their hospital discharge records.
Data smashing: uncovering lurking order in data
Authors: Chattopadhyay Ishanu , Lipson Hod
Published: October 2014

From automatic speech recognition to discovering unusual stars, underlying almost all automated discovery tasks is the ability to compare and contrast data streams with each other, to identify connections and spot outliers. Despite the prevalence of data, however, automated methods are not keeping pace. A key bottleneck is that most data comparison algorithms today rely on a human expert to specify what ‘features' of the data are relevant for comparison. Here, we propose a new principle for estimating the similarity between the sources of arbitrary data streams, using neither domain knowledge nor learning. We demonstrate the application of this principle to the analysis of data from a number of real-world challenging problems, including the disambiguation of electro-encephalograph patterns pertaining to epileptic seizures, detection of anomalous cardiac activity from heart sound recordings and classification of astronomical objects from raw photometry. In all these cases and without access to any domain knowledge, we demonstrate performance on a par with the accuracy achieved by specialized algorithms and heuristics devised by domain experts. We suggest that data smashing principles may open the door to understanding increasingly complex observations, especially when experts do not know what to look for.
Guaranteed resonance enclosures and exclosures for atoms and molecules
Authors: Bögli Sabine , Brown B. Malcolm , Marletta Marco , Tretter Christiane , Wagenhofer Markus
Published: October 2014

In this paper, we confirm, with absolute certainty, a conjecture on a certain oscillatory behaviour of higher auto-ionizing resonances of atoms and molecules beyond a threshold. These results not only definitely settle a more than 30 year old controversy in Rittby
et al.
(1981
Phys. Rev. A
24
, 1636–1639 (
doi:10.1103/PhysRevA.24.1636
)) and Korsch
et al.
(1982
Phys. Rev. A
26
, 1802–1803 (
doi:10.1103/PhysRevA.26.1802
)), but also provide new and reliable information on the threshold. Our interval-arithmetic-based method allows one, for the first time, to
en
close and to
ex
clude resonances with guaranteed certainty. The efficiency of our approach is demonstrated by the fact that we are able to show that the approximations in Rittby
et al.
(1981
Phys. Rev. A
24
, 1636–1639 (
doi:10.1103/PhysRevA.24.1636
))
do
lie near true resonances, whereas the approximations of higher resonances in Korsch
et al.
(1982
Phys. Rev. A
26
, 1802–1803 (
doi:10.1103/PhysRevA.26.1802
)) do
not
, and further that there exist two new pairs of resonances as suggested in Abramov
et al.
(2001
J. Phys. A
34
, 57–72 (
doi:10.1088/0305-4470/34/1/304
)).
Microbial community dynamics in the forefield of glaciers
Authors: Bradley James A. , Singarayer Joy S. , Anesio Alexandre M.
Published: October 2014

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.
The Prox1–Vegfr3 feedback loop maintains the identity and the number of lymphatic endothelial cell progenitors
Authors: Srinivasan R. Sathish , Escobedo Noelia , Yang Ying , Interiano Ashley , Dillard Miriam E. , Finkelstein David , Mukatira Suraj , Gil Hyea Jin , Nurmi Harri , Alitalo Kari , Oliver Guillermo
Published: October 2014

The mammalian lymphatic vasculature is important for returning fluids from the extracellular tissue milieu back to the blood circulation. We showed previously that Prox1 dosage is important for the development of the mammalian lymphatic vasculature. The lack of Prox1 activity results in the complete absence of lymphatic endothelial cells (LECs). In Prox1 heterozygous embryos, the number of LECs is reduced because of a decrease in the progenitor pool in the cardinal vein. This reduction is caused by some progenitor cells being unable to maintain Prox1 expression. In this study, we identified Vegfr3, the cognate receptor of the lymphangiogenic growth factor Vegfc, as a dosage-dependent, direct in vivo target of Prox1. Using various mouse models, we also determined that Vegfr3 regulates Prox1 by establishing a feedback loop necessary to maintain the identity of LEC progenitors and that Vegfc-mediated activation of Vegfr3 signaling is necessary to maintain Prox1 expression in LEC progenitors. We propose that this feedback loop is the main sensing mechanism controlling the number of LEC progenitors and, as a consequence, the number of budding LECs that will form the embryonic lymphatic vasculature.
Network dynamics determine the autocrine and paracrine signaling functions of TNF
Authors: Caldwell Andrew B. , Cheng Zhang , Vargas Jesse D. , Birnbaum Harry A. , Hoffmann Alexander
Published: October 2014

A hallmark of the inflammatory response to pathogen exposure is the production of tumor necrosis factor (TNF) that coordinates innate and adaptive immune responses by functioning in an autocrine or paracrine manner. Numerous molecular mechanisms contributing to TNF production have been identified, but how they function together in macrophages remains unclear. Here, we pursued an iterative systems biology approach to develop a quantitative understanding of the regulatory modules that control TNF mRNA synthesis and processing, mRNA half-life and translation, and protein processing and secretion. By linking the resulting model of TNF production to models of the TLR-, the TNFR-, and the NFκB signaling modules, we were able to study TNF’s functions during the inflammatory response to diverse TLR agonists. Contrary to expectation, we predicted and then experimentally confirmed that in response to lipopolysaccaride, TNF does not have an autocrine function in amplifying the NFκB response, although it plays a potent paracrine role in neighboring cells. However, in response to CpG DNA, autocrine TNF extends the duration of NFκB activity and shapes CpG-induced gene expression programs. Our systems biology approach revealed that network dynamics of MyD88 and TRIF signaling and of cytokine production and response govern the stimulus-specific autocrine and paracrine functions of TNF.
Distinct functions of macrophage-derived and cancer cell-derived cathepsin Z combine to promote tumor malignancy via interactions with the extracellular matrix
Authors: Akkari Leila , Gocheva Vasilena , Kester Jemila C. , Hunter Karen E. , Quick Marsha L. , Sevenich Lisa , Wang Hao-Wei , Peters Christoph , Tang Laura H. , Klimstra David S. , Reinheckel Thomas , Joyce Johanna A.
Published: October 2014

During the process of tumor progression, cancer cells can produce the requisite growth- and invasion-promoting factors and can also rely on noncancerous cells in the tumor microenvironment as an alternative, cell-extrinsic source. However, whether the cellular source influences the function of such tumor-promoting factors remains an open question. Here, we examined the roles of the cathepsin Z (CtsZ) protease, which is provided by both cancer cells and macrophages in pancreatic neuroendocrine tumors in humans and mice. We found that tumor proliferation was exclusively regulated by cancer cell-intrinsic functions of CtsZ, whereas tumor invasion required contributions from both macrophages and cancer cells. Interestingly, several of the tumor-promoting functions of CtsZ were not dependent on its described catalytic activity but instead were mediated via the Arg–Gly–Asp (RGD) motif in the enzyme prodomain, which regulated interactions with integrins and the extracellular matrix. Together, these results underscore the complexity of interactions within the tumor microenvironment and indicate that cellular source can indeed impact molecular function.
Synthesis of Caged NAADP
Authors: Galione Antony , Chuang Kai-Ting , Funnell Tim M. , Davis Lianne C. , Morgan Anthony J. , Ruas Margarida , Parrington John , Churchill Grant C.
Published: October 2014

Caged derivatives of Ca2+-mobilizing messengers, such as nicotinic acid adenine dinucleotide phosphate (NAADP), are particularly useful for establishing the effects of these messengers on Ca2+ signaling. Caged NAADP is no longer commercially available but can be synthesized in house, as described here. In brief, a stable precursor of the caging reagent is made and converted to an unstable reactive reagent immediately before addition to the compound to be caged.
Basic Quantitative Polymerase Chain Reaction Using Real-Time Fluorescence Measurements
Authors: Ares Manuel
Published: October 2014

This protocol uses quantitative polymerase chain reaction (qPCR) to measure the number of DNA molecules containing a specific contiguous sequence in a sample of interest (e.g., genomic DNA or cDNA generated by reverse transcription). The sample is subjected to fluorescence-based PCR amplification and, theoretically, during each cycle, two new duplex DNA molecules are produced for each duplex DNA molecule present in the sample. The progress of the reaction during PCR is evaluated by measuring the fluorescence of dsDNA–dye complexes in real time. In the early cycles, DNA duplication is not detected because inadequate amounts of DNA are made. At a certain threshold cycle, DNA–dye complexes double each cycle for 8–10 cycles, until the DNA concentration becomes so high and the primer concentration so low that the reassociation of the product strands blocks efficient synthesis of new DNA and the reaction plateaus. There are two types of measurements: (1) the relative change of the target sequence compared to a reference sequence and (2) the determination of molecule number in the starting sample. The first requires a reference sequence, and the second requires a sample of the target sequence with known numbers of the molecules of sequence to generate a standard curve. By identifying the threshold cycle at which a sample first begins to accumulate DNA–dye complexes exponentially, an estimation of the numbers of starting molecules in the sample can be extrapolated.
Isolation of Mitochondria from Cells and Tissues
Authors: Clayton David A. , Shadel Gerald S.
Published: October 2014

Mitochondria are complex organelles at the center of cellular metabolism, apoptosis, and signaling. They continue to be the subject of intense basic investigation to understand their composition and function, but they have also captivated the attention of clinical researchers because of the growing knowledge of the (sometimes unexpected) roles of mitochondria in human diseases and aging. A full understanding of these intriguing organelles often requires their purification from cells or tissues under specific physiological or pathological conditions. Here we provide some introductory considerations for those interested in purifying mitochondria for subsequent downstream biophysical, structural, and functional analysis.
Revisit to diffraction anomalous fine structure
Authors: Kawaguchi T. , Fukuda K. , Tokuda K. , Shimada K. , Ichitsubo T. , Oishi M. , Mizuki J. , Matsubara E.
Published: October 2014

The diffraction anomalous fine structure (DAFS) method that is a spectroscopic analysis combined with resonant X-ray diffraction enables the determination of the valence state and local structure of a selected element at a specific crystalline site and/or phase. This method has been improved by using a polycrystalline sample, channel-cut monochromator optics with an undulator synchrotron radiation source, an area detector and direct determination of resonant terms with a logarithmic dispersion relation. This study makes the DAFS method more convenient and saves a large amount of measurement time in comparison with the conventional DAFS method with a single crystal. The improved DAFS method has been applied to some model samples, Ni foil and Fe3O4powder, to demonstrate the validity of the measurement and the analysis of the present DAFS method.
A high-precision instrument for mapping of rotational errors in rotary stages
Authors: Xu Weihe , Lauer Kenneth , Chu Yong , Nazaretski Evgeny
Published: October 2014

A rotational stage is a key component of every X-ray instrument capable of providing tomographic or diffraction measurements. To perform accurate three-dimensional reconstructions, runout errors due to imperfect rotation (e.g.circle of confusion) must be quantified and corrected. A dedicated instrument capable of full characterization and circle of confusion mapping in rotary stages down to the sub-10 nm level has been developed. A high-stability design, with an array of five capacitive sensors, allows simultaneous measurements of wobble, radial and axial displacements. The developed instrument has been used for characterization of two mechanical stages which are part of an X-ray microscope.
Finite noncrystallographic groups, 11-vertex equi-edged triangulated clusters and polymorphic transformations in metals
Authors: Talis Alexander , Kraposhin Valentin
Published: October 2014

The one-to-one correspondence has been revealed between a set of cosets of the Mathieu groupM11, a set of blocks of the Steiner systemS(4, 5, 11) and 11-vertex equi-edged triangulated clusters. The revealed correspondence provides the structure interpretation of theS(4, 5, 11) system: mapping of the biplane 2-(11, 5, 2) onto the Steiner systemS(4, 5, 11) determines uniquely the 11-vertex tetrahedral cluster, and the automorphisms of theS(4, 5, 11) system determine uniquely transformations of the said 11-vertex tetrahedral cluster. The said transformations correspond to local reconstructions during polymorphic transformations in metals. The proposed symmetry description of polymorphic transformation in metals is consistent with experimental data.
The scholarship of application in the context of academic entrepreneurialism
Authors: Hayes Tang Hei-hang
Published: October 2014

Purpose

– The purpose of this paper is to undertake an inquiry into the way academic entrepreneurialism manifests itself in the changing discourses of the notion of “scholarship”. It particularly examines the contexts, rationales, definitions and implications of the discursive field of the “scholarship of application”. The global trend of academic entrepreneurialism profoundly affects the organisation of higher education institutions and academic life. Particularly, the form of scholarship has been undergoing subtle but constant transformation. The emergence of knowledge economies worldwide influences the practices and goals of traditional academy and illustrates commitment for fundamental knowledge and the new economies emphasise the results and impacts brought by applied knowledge. Alongside the “scholarship of discovery”, the “scholarship of application” is given attention.

Design/methodology/approach

– By reviewing the related literature, this paper articulates the definitions and dimensions of the “scholarship of application”. In addition, the impacts brought about by the concerned academic and policy discourses will be discussed.

Findings

– This paper finds that the emergence of the discursive field of the “scholarship of application” – as well as the discussions and actions in response to it – coincide with the intense neoliberal changes that affected traditional academia in the 1990s. It is argued that the emergence of and subsequent responses to the discursive field of the “scholarship of application” resulted in transforming purposes and practices of academic life. The discursive field of the “scholarship of application” also impacts on the concerned academic and policy discourses.

Originality/value

– To sustain the advancement of the scholarship of application, this paper implies the need to develop practices, cultivate culture as well as formulate prestige and reward mechanisms inherent to the existing higher education systems.
Radical innovation, market forces, political and business relationships
Authors: Chen Haowen , Liu Heng , Cheung Han
Published: October 2014

Purpose

– This study aims to investigate the relationships between radical innovation, market forces and political/business relationships in China by combining social capital theory and contingent theory. The paper focuses on how two types of managerial ties (i.e. business and political ties) impact firms’ capacity for radical innovation. It also examines the different moderating effects of market forces (i.e. demand uncertainty, technological turbulence and competitive intensity) on the linkage of managerial ties with radical innovation in the Chinese transitional context.

Design/methodology/approach

– A systematic literature review on managerial ties, radical innovation and market forces in emerging markets provides the theoretical foundation of our conceptual model and hypothesis. Using a survey sample of 119 Chinese firms, the authors conduct a regression analysis on the theoretical model and hypotheses.

Findings

– The results show that business ties have an inverted U-shape effect on radical innovation, while political ties have a positive impact on radical innovation. Furthermore, the market forces in transitional economies (i.e. demand uncertainty, technological turbulence and competitive intensity) have different moderating effects on the relationships between two types of managerial ties and Chinese firms’ radical innovation.

Research limitations/implications

– This study adopts its data set from the Chinese context. It would be necessary to replicate this research in other transitional economies because of specific differences between China and other transitional economies.

Practical implications

– Findings from our study indicate that firms which wish to succeed in radical innovation may need to adapt their tie-based strategies according to different market settings.

Originality/value

– The paper is original in its comparative investigation of the effect of business ties and political ties on radical innovation in contingent transitional market environments using a combination of social capital and contingent theories.
A dilemma of terracotta professional – the case of implementing information systems in a terracotta unit
Authors: Mohapatra Sanjay , Nayak Amit , Bhangadiya Ankita , Bagchi Ipshit , Sharma Pradeep Kumar , Behera Sukanya
Published: October 2014

Subject area

The case concerns strategy.

Study level/applicability

This study is applicable to information system, development sector and application of technology in development sector.

Case overview

Krutika Terracotta Unit is a small unit located in Bhubaneswar, Odisha (India), owned by Mr Tarun Tapan Sahoo. The organization product portfolio varies from decorative statues, pots and vessel to customized products demanded by customers. Organization is also involved in training and renting the products for traditional fairs, marriages and religious ceremony in Bhubaneswar along with order sales. The case attempts to get a close picture of the industry. The exercise of developing the vision, mission, and goals for the organization was carried out and an attempt was made to align the information system with the business objectives even though the organization does not have a very structured organogram. Using BIS will surely reduce manual work and will give qualitative output. There will be lesser hassles in management. The defined and integrated approach will also help in taking strategic decisions well. The objective is to develop and apply well-structured BIS which can be integrated with the existing system so as to develop the terracotta organization in terms of reachability and profit-making with better decision-making capacity.

Expected learning outcomes

To learn about the business model of a handicraft marketing organization; to learn about the processes involved in traditional art form of Terracotta; to go through the exercise of creating vision, mission, goals of the organization through mutual discussion and expectation of owner; to determine how BIS helps in achieving higher productivity in Krutika Terracotta Unit; and to get an idea about how NPV calculation and social ROI should be measured for finding feasibility of technology investment.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes. Defence statement has been uploaded. Consent form to publish has been uploaded.
The financial viability of the Yamuna Expressway
Authors: Singhania Monica , Kumar Kamal
Published: October 2014

Subject area

The case focuses on issues concerning infrastructure development by Jaypee Infratech Ltd. (JIL) in the context of emerging market of India. This is undertaken by employing the usage of strength weakness opportunity and threat analysis (SWOT) analysis, political, economical, sociological and technological analysis (PEST) analysis and Porter's Five Forces Model and competitor analysis. It also outlines the importance of financing model adopted with respect to Concessionaire Agreement drafted and executed towards making an infrastructure project financially viable so as to reduce the risk associated with infrastructure projects which requires huge investments and long gestation period. Further, it also highlights the importance of how future projects can be undertaken on the basis of public private partnership (PPP) model.

Study level/applicability

This case can be used as a teaching tool in the following courses: MBA/Post Graduate Program in Management in Management Accounting, Management Control Systems and Strategic Cost Management. It can be used to explain concepts of SWOT analysis and Porter's Five Forces Model analysis. Students are also introduced to the technique of financial analysis. Executive training programs for Middle- and Senior-level employees to explain the Infrastructure Financing and Concessionaire Agreement for infrastructure projects. Under-graduate/Post-graduate programs in Entrepreneurship.

Case overview

JIL was established as a Special Purpose Vehicle in 2007 to execute the Yamuna Expressway project. Originally the contract was awarded to parent company Jai Prakash Associates Ltd. in 2003. The project entails financing, construction, operation, maintenance and collection of toll for 36 years and then transferring it back to Government of Uttar Pradesh of 165.5 km Yamuna Expressway, and subsequently development of 530-million square feet of area from five parcels of land earmarked along the expressway. The project highlights how a PPP infrastructure project can be made financially viable.

Expected learning outcomes

SWOT analysis was used to identify the strengths, weaknesses, opportunities and threats to a company. Also, application of Porter's Five Forces Model was done to analyze an industry. Determining quantitative terms like Long-Term Return on equity, Return on Capital Employed, Book Value vs Market value, Net Margins, Income Tax benefits enjoyed under section 80-IA and Minimum Alternative Tax (MAT); determining financial viability of an infrastructure project over its entire life cycle.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes
Locating the real William Colenso: reviewing a thirty year research journey
Authors: Morris Matthews Kay
Published: October 2014

Purpose

– The purpose of this paper is to demonstrate the importance of ongoing conversations between researchers and librarians. Without such conversations followed by the active purchasing of manuscripts, the important contributions of individual first settlers would likely remain untold. The research review that unfolds here is of one of New Zealand's significant first settlers, William Colenso (1811-1899). Yet, 30 years ago William Colenso was mostly regarded as a local rather than a national figure, renowned and ridiculed for his being dismissed from the Church Missionary Society for moral impropriety in 1852. By 2011, however, a conference dedicated to his life and work attracted both national and international scholars raising awareness and contributing unique knowledge about Colenso as missionary, printer, linguist, explorer, botanist, politician, author and inspector of schools. It is argued that such scholarship was enabled through the purposeful collecting of Colenso's papers over 30 years.

Design/methodology/approach

– The historical analysis draws from original documents and published papers chronicling the role and the views of one of New Zealand's first inspector of schools. A self-reflective review approach will show how new knowledge can enhance earlier published works and provide opportunities for further analysis.

Findings

– It will be demonstrated that as a result of ongoing conversations between librarians and researchers purposeful buying of archives and manuscripts have added fresh perspectives to the contributions William Colenso made to education in provincial New Zealand.

Originality/value

– This work is perhaps the first critical re-reading and review of one's own scholarship undertaken across 30 years within New Zealand history of education. It offers unique self-reflections on the subject focus and analyses of it over time.