bluuebunny/crossref_metadata_2025 huggingface dataset:
The crystal-form transition behaviours and morphology changes in a polyamide 6 cyclic dimer
Authors: Peng Lu , Li Jie , Peng Shumin , Yi Chunwang , Jiang Feng
Published: November 2018

The characteristics of pure
α
- and
β
-form of the cyclic dimer (1,8-diazacyclotetradecane-2,9-dione) were systematically and integrally investigated during this study. The results showed that the
α
-form could dissolve and rapidly transform into the
β
-form in methanol, and in caprolactam solution at a lower temperature, an interesting transition occurred and formed co-precipitates, which refract colourful light under PLM. However, these dimers can aggregate in water, and they are then transformed into multi-slice layers and compact structures. The detailed transition behaviours between the two forms were further measured by FT-IR, XRD and DSC by varying the temperature from 25°C to 360°C, respectively, which showed that there are two endothermic transitions over the course of the heating programme. At a temperature of approximately 242°C, the
β
crystals were initially converted into
α
crystals, and then they melted when the temperature reached over 345°C. A video recorded under a light microscope also showed that the sublimation of the
β
cyclic dimer occurred after the transition. However, the
α
-form might sublimate at temperatures lower than 150°C when mixed with volatile matter.
Value of species and the evolution of conservation ethics
Authors: Hare Darragh , Blossey Bernd , Reeve H. Kern
Published: November 2018

The theory of evolution by natural selection can help explain why people care about other species. Building upon recent insights that morality evolves to secure fitness advantages of cooperation, we propose that conservation ethics (moral beliefs, attitudes, intuitions and norms regarding other species) could be adaptations that support cooperation between humans and non-humans. We present eco-evolutionary cost–benefit models of conservation behaviours as interspecific cooperation (altruism towards members of other species). We find that an evolutionary rule identical in structure to Hamilton's rule (which explains altruistic behaviour towards related conspecifics) can explain altruistic behaviour towards members of other species. Natural selection will favour traits for selectively altering the success of members of other species (e.g. conserving them) in ways that maximize inclusive fitness return benefits. Conservation behaviours and the ethics that evolve to reinforce them will be sensitive to local ecological and socio-cultural conditions, so will assume different contours in different places. Difficulties accurately assessing costs and benefits provided by other species, time required to adapt to ecological and socio-cultural change and barriers to collective action could explain the apparent contradiction between the widespread existence of conservation ethics and patterns of biodiversity decline globally.
Bioavailability and leaching of Cd and Pb from contaminated soil amended with different sizes of biochar
Authors: Fahmi Alaa Hasan , Samsuri Abd Wahid , Jol Hamdan , Singh Daljit
Published: November 2018

Biochars have been successfully used to reduce bioavailability and leaching of heavy metals in contaminated soils. The efficiency of biochar to immobilize heavy metals can be increased by reducing the particle size, which can increase the surface area and the cation exchange capacity (CEC). In this study, the empty fruit bunch biochar (EFBB) of oil palm was separated into two particle sizes, namely, fine (F-EFBB < 50 µm) and coarse (C-EFBB > 2 mm), to treat the contaminated soil with Cd and Pb. Results revealed that the addition of C-EFBB and F-EFBB increased the pH, electrical conductivity and CEC of the contaminated soil. The amounts of synthetic rainwater extractable and leachable Cd and Pb significantly decreased with the EFBB application. The lowest extractable and leachable Cd and Pb were observed from 1% F-EFBB-treated soil. The amount of extractable and leachable Cd and Pb decreased with increasing incubation times and leaching cycles. The application of F-EFBB to Cd and Pb-contaminated soil can immobilize the heavy metals more than that of C-EFBB. Therefore, the EFBB can be recommended for the remediation of heavy metal-contaminated soils, and a finer particle size can be applied at a lower application rate than the coarser biochar to achieve these goals.
Effect of arsenate substitution on phosphate repository of cell: a computational study
Authors: Singh Amit , Giri Kousik
Published: November 2018

The structural analogy with phosphate derives arsenate into various metabolic processes associated with phosphate inside the organisms. But it is difficult to evaluate the effect of arsenate substitution on the stability of individual biological phosphate species, which span from a simpler monoester form like pyrophosphate to a more complex phosphodiester variant like DNA. In this study, we have classified the physiological phosphate esters into three different classes on the basis of their structural differences. This classification has helped us to present a concise theoretical study on the kinetic stability of phosphate analogue species of arsenate against hydrolysis. All the calculations have been carried out using QM/MM methods of our Own N-layer Integrated molecular Orbital molecular Mechanics (ONIOM). For quantum mechanical region, we have used M06-2X density functional with 6-31+G(2d,2p) basis set and for molecular mechanics we have used the AMBER force field. The calculated rate constants for hydrolysis show that none of the phosphate analogue species of arsenate has a reasonable stability against hydrolysis.
Fluid flow lifting a body from a solid surface
Authors: Balta Samire , Smith Frank T.
Published: November 2018

If a body is at rest on horizontal ground and a sudden horizontal flow of fluid is applied, the body either remains on the ground (rocking, rolling, sliding or spinning) or is lifted off impulsively. This lift-off is followed by a return to the ground or by a fly-away in the sense of continued departure from the ground. Related phenomena arise in the lift-off of an air vehicle from, effectively, moving ground. The present investigation seeks fairly precise mechanistic conditions under which lift-off and subsequent return or fly-away occur for a thin body or more generally for any thin gap of fluid between a body and the ground. Nonlinear fluid–solid interaction takes place in which the motion of the body and the surrounding fluid affect each other. Small-time analysis on lift-off and a numerical study are presented, followed by large-time analysis showing a critical flow speed for fly-away for any shape of the body. The changes in ground effect, from being dominant during lift-off to diminishing in fly-away, are explored together with relevant applications.
Generalized quasilinear approximation of the interaction of convection and mean flows in a thermal annulus
Authors: Tobias S. M. , Oishi J. S. , Marston J. B.
Published: November 2018

In this paper, we examine the interaction of convection, rotation and mean flows in a thermal annulus. In this system, mean flows are driven by correlations induced by rotation leading to non-trivial Reynolds stresses. The mean flows act back on the convective turbulence acting as a barrier to transport. For this system, we demonstrate that the generalized quasilinear approximation (Marston
et al
. 2016
Phys. Rev. Lett.
116
, 214501. (
doi:10.1103/PhysRevLett.116.214501
)) may provide a much better approximation to the complicated full nonlinear dynamics than the widely used quasilinear approximation. This result will enable the construction of more accurate statistical theories for the description of geophysical and astrophysical flows.
A degenerate polar lattice for cloaking in full two-dimensional elastodynamics and statics
Authors: Nassar H. , Chen Y. Y. , Huang G. L.
Published: November 2018

A lattice design of a cloak for full two-dimensional elasticity is suggested when the background continuum is isotropic with Lamé parameters (λ, 
μ
) satisfying
μ
 ≤ λ. The lattice is
polar
in the sense that it elastically resists rotations; and is
degenerate
meaning it admits a stressless collapse mechanism. These characteristics are attained through the use of appropriately distributed restoring torques in conjunction with hinge-like spring-mass contacts. Thus, the lattice is proven to exhibit a rank-3 elasticity tensor lacking the minor symmetries. Accordingly, it rigorously adheres to the form-invariance requirements of the transformation method under the Brun–Guenneau–Movchan gauge. The cloak is numerically tested in statics and in dynamics under pressure and shear incident waves and shows satisfactory performance. Finally, a theoretical generalization extends the design to three dimensions and to arbitrarily anisotropic backgrounds so as to enable cloaking as well as other transformation-based static and dynamic field manipulation techniques in these cases.
Optimizing information transmission rates drives brain gyrification
Authors: Heyden S. , Ortiz M.
Published: November 2018

We investigate the functional optimality of the cerebral cortex of an adult human brain geometry. Unlike most competing models, we postulate that the cerebral cortex formation is driven by the objective of maximizing the total information transmission rate. Starting from a random path model, we show that this optimization problem is related to the Steklov eigenvalue problem. Combining realistic brain geometries with the finite-element method, we calculate the underlying Steklov eigenvalues and eigenfunctions. By comparison to a convex hull approximation, we show that the adult human brain geometry indeed reduces the Steklov eigenvalue spectrum and thus increases the rate at which information is exchanged between points on the cerebral cortex. With a view to possible clinical applications, the leading Steklov eigenfunctions and the resulting induced magnetic fields are computed and reported.
Reproductive control via the threat of eviction in the clown anemonefish
Authors: Rueger T. , Barbasch T. A. , Wong M. Y. L. , Srinivasan M. , Jones G. P. , Buston P. M.
Published: November 2018

In social groups, high reproductive skew is predicted to arise when the reproductive output of a group is limited, and dominant individuals can suppress subordinate reproductive efforts. Reproductive suppression is often assumed to occur via overt aggression or the threat of eviction. It is unclear, however, whether the threat of eviction alone is sufficient to induce reproductive restraint by subordinates. Here, we test two assumptions of the restraint model of reproductive skew by investigating whether resource limitation generates reproductive competition and whether the threat of eviction leads to reproductive restraint in the clown anemonefishAmphiprion percula. First, we use a feeding experiment to test whether reproduction is resource limited, which would create an incentive for the dominant pair to suppress subordinate reproduction. We show that the number of eggs laid increased in the population over the study period, but the per cent increase in fed groups was more than twice that in unfed groups (205% and 78%, respectively). Second, we use an eviction experiment to test whether the dominant pair evicts mature subordinates, which would create an incentive for the subordinates to forgo reproduction. We show that mature subordinates are seven times more likely to be evicted than immature subordinates of the same size. In summary, we provide experimental support for the assumptions of the restraint model by showing that resource limitation creates reproductive competition and a credible threat of eviction helps explain why subordinates forego reproduction. Transactional models of reproductive skew may apply well to this and other simple systems.
Discovery and exploitation of a natural ecological trap for a mosquito disease vector
Authors: Gardner Allison M. , Muturi Ephantus J. , Allan Brian F.
Published: November 2018

Ecological traps occur due to a mismatch between a habitat's attractiveness and quality, wherein organisms show preference for low-quality habitats over other available high-quality habitats. Our previous research identified leaf litter from common blackberry (Rubus allegheniensis) as a natural ecological trap for an important vector for West Nile virus (Culex pipiens), attracting mosquitoes to oviposit in habitats deleterious to the survival of their larvae. Here we demonstrate that manipulation of leaf litter in stormwater catch basins, an important source of disease vector mosquitoes in urban environments, can increaseCx. pipiensoviposition but reduce survival. In a series of experiments designed to elucidate the mechanisms that explain the attractive and lethal properties of this native plant, behavioural bioassays suggest that oviposition site selection byCx. pipiensis mediated primarily by chemical cues as leaves decompose. However, we also show that juvenile mosquito survival is mainly related to the suitability of the bacterial community in the aquatic habitat for mosquito nutritional needs, which does not appear to create a cue that influences oviposition choice. This mismatch between oviposition cues and drivers of larval habitat quality may account for the ecological trap phenomenon detected in this study. Our findings provide new insights into potential mechanistic pathways by which ecological traps may occur in nature and proof-of-concept for a new ‘attract-and-kill’ tool for mosquito control.
Cultural revolutions reduce complexity in the songs of humpback whales
Authors: Allen Jenny A. , Garland Ellen C. , Dunlop Rebecca A. , Noad Michael J.
Published: November 2018

Much evidence for non-human culture comes from vocally learned displays, such as the vocal dialects and song displays of birds and cetaceans. While many oscine birds use song complexity to assess male fitness, the role of complexity in humpback whale (Megaptera novaeangliae) song is uncertain owing to population-wide conformity to one song pattern. Although songs change gradually each year, the eastern Australian population also completely replaces their song every few years in cultural ‘revolutions’. Revolutions involve learning large amounts of novel material introduced from the Western Australian population. We examined two measures of song structure, complexity and entropy, in the eastern Australian population over 13 consecutive years. These measures aimed to identify the role of complexity and information content in the vocal learning processes of humpback whales. Complexity was quantified at two hierarchical levels: the entire sequence of individual sound ‘units’ and the stereotyped arrangements of units which comprise a ‘theme’. Complexity increased as songs evolved over time but decreased when revolutions occurred. No correlation between complexity and entropy estimates suggests that changes to complexity may represent embellishment to the song which could allow males to stand out amidst population-wide conformity. The consistent reduction in complexity during song revolutions suggests a potential limit to the social learning capacity of novel material in humpback whales.
The resistomes of six carbapenem-resistant pathogens – a critical genotype–phenotype analysis
Authors: Johnning Anna , Karami Nahid , Tång Hallbäck Erika , Müller Vilhelm , Nyberg Lena , Buongermino Pereira Mariana , Stewart Callum , Ambjörnsson Tobias , Westerlund Fredrik , Adlerberth Ingegerd , Kristiansson Erik
Published: November 2018

Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species – Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa – were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7–18 different genes per isolate), including the following encoding carbapenemases: bla
KPC-2, bla
OXA-48, bla
OXA-72, bla
NDM-1, bla
NDM-7 and bla
VIM-1. In addition, a novel version of bla
SHV was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance – based on acquired resistance determinants – was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.
Effects of Fermented Idesia Polycarpa Residues supplementation on laying performance of Laying Quails
Authors: Liu Xinanbei , Li Na , Shu Yueyue , Sun Yiran , Li Yu , Hua Wang , Ye Yang , Chen Fang , Tang Lin
Published: November 2018

Although Idesia polycarpa oil has been wildly explored as a raw material for biodiesel, the reports studying the by-product Idesia polycarpa fruit residues (IPR) are few. This study aimed to evaluate the effect of the Idesia polycarpa fruit residues fermented feed additive (IPFF) on the egg production of laying quails. The egg production and related performances include egg quality, yolk cholesterol, yolk fatty acid, quails’ jejunum morphology, and relative gene expression were determined in this study. Compared to the standard diet group, birds fed the 1% IPFF showed a higher egg production (87.7% on average, 11.5% above the control; P<0.01). The yolk fatty acid composition and n6/n3 ratio were affected by IPFF or IPR. Compared to the standard diet group, the egg cholesterol content was lower in both IPFF and IPR groups, and the yolk n6/n3 ratio in the 5% IPFF group (10.3; P<0.01) was more reasonable. Meanwhile, birds under IPFF dietary supplement showed a thicker jejunum wall, higher villus, and deeper crypt than the standard diet group. In addition, the altered mRNA expression of four genes involved in cholesterol and fatty acids metabolism (SREBP-1, SREBP-2, ADGL, APOVLDL-II) in the 1% IPFF group and 5% IPR group indicated that the lipids metabolism and transportation were enhanced in the interclavicular fat pad and liver, relative to the standard diet group.

HIGHLIGHTS

Egg production was higher in IPFF groups

Egg cholesterol was lower in IPFF groups

Lipid metabolism and transportation was enhanced in IPFF groups

Intestine wall was thicker in IPFF groups
‘Fishing’ for Mitochondrial DNA in The Egyptian Sacred Ibis Mummies
Authors: Wasef Sally , Huynen Leon , Millar Craig Donald , Subramanian Sankar , Ikram Salima , Holland Barbra , Willerslev Eske , Lambert David Martin
Published: November 2018

The long-term preservation of DNA requires a number of optimal conditions, including consistent exposure to cool, dry, and dark environments. As a result, the successful recovery of ancient DNA from material from warmer climates such as those in Egypt has often been met with scepticism. Egypt has an abundance of ancient mummified animals and humans, whose genetic analyses would offer important insights into ancient cultural practices. To date, the retrieval of complete genomes from ancient Egyptian remains of humans or other animals has been largely unsuccessful. To test for the presence of even short DNA sequences in Egyptian material, we performed second-generation shotgun sequencing of DNA libraries constructed from ancient Sacred Ibis mummies. Since most of the resulting Illumina libraries were shown to contain extremely low levels (less than 0.06%) of endogenous mitochondrial DNA, we aimed to enrich these samples using targeted in-solution hybridisation methods. Using biotinylated RNA baits designed to Sacred Ibis complete mitochondrial sequences, we trialled a number of conditions and parameters and achieved up to 4705-fold enrichment. We also found that a combination of hybridisation temperature and the use of the polymerase KAPA HiFi significantly increased both the efficiency of targeted hybridisation and post-hybridisation amplification respectively. Furthermore, improved enrichment was accompanied with only minor increases in clonality. Our method enabled us to reconstruct the first complete mitochondrial genomes from ancient Egyptian sub-fossil material.
Structural and biochemical studies define Nudt12 as a new class of RNA deNADding enzyme in mammalian cells
Authors: Grudzien-Nogalska Ewa , Wu Yixuan , Jiao Xinfu , Cui Huijuan , Hart Ronald P. , Tong Liang , Kiledjian Megerditch
Published: November 2018

We recently demonstrated mammalian cells harbor NAD-capped mRNAs that are hydrolyzed by the DXO deNADding enzyme. Here we report the Nudix protein Nudt12 is a second mammalian deNADding enzyme structurally and mechanistically distinct from DXO and targets different RNAs. Crystal structure of mouse Nudt12 in complex with the deNADding product AMP and three Mg2+ ions at 1.6 Å resolution provides exquisite insights into the molecular basis of the deNADding activity within the NAD pyrophosphate. Disruption of the Nudt12 gene stabilizes transfected NAD-capped RNA in cells and its endogenous NAD-capped mRNA targets are enriched in those encoding proteins involved in cellular energetics. Furthermore, exposure of cells to metabolic stress manifests changes in NAD-capped RNA levels indicating an association between NAD-capped RNAs and cellular metabolism. Lastly, we show that the bacterial RppH protein also possesses deNADding activity toward NAD-capped RNA but not free NAD, revealing a third class of deNADding enzymes.
aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq
Authors: Liu Wenbin , Yue Sibiao , Zheng Xiaobin , Cao Jia , Zheng Yixian
Published: November 2018

Much effort has been devoted to understand how chromatin modification regulates development and disease. Despite recent progress, however, it remains difficult to achieve high sensitivity and reliability of chromatin-immunoprecipitation-coupled deep sequencing (ChIP-seq) to map the epigenome and global transcription factor binding sites in cell populations of low cell abundance. We present a new Atlantis dsDNase-based technology, aFARP-ChIP-seq, that provides accurate profiling of genome-wide histone modifications in as few as 100 cells. By mapping histone lysine trimethylation (H3K4me3) and H3K27Ac in group I innate lymphoid cells from different tissues, aFARP-ChIP-seq uncovers potentially distinct active promoter and enhancer landscapes of several tissue-specific NK and ILC1. aFARP-ChIP-seq is also highly effective in mapping transcription factor binding sites in small number of cells. Since aFARP-ChIP-seq offers reproducible DNA fragmentation, it should allow multiplexing ChIP-seq of both histone modifications and transcription factor binding sites for low cell samples.
Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates
Authors: Eres Ittai E. , Luo Kaixuan , Hsiao Chiaowen Joyce , Blake Lauren E. , Gilad Yoav
Published: November 2018

A growing body of evidence supports the notion that variation in gene regulation plays a crucial role in both speciation and adaptation. However, a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive. In primates, one of the crucial missing pieces of information towards a better understanding of regulatory evolution is a comparative annotation of interactions between distal regulatory elements and promoters. Chromatin conformation capture technologies have enabled genome-wide quantifications of such distal 3D interactions. However, relatively little comparative research in primates has been done using such technologies. To address this gap, we used Hi-C to characterize 3D chromatin interactions in induced pluripotent stem cells (iPSCs) from humans and chimpanzees. We also used RNA-sequencing to collect gene expression data from the same lines. We generally observed that lower-order, pairwise 3D genomic interactions are conserved in humans and chimpanzees, but higher order genomic structures, such as TADs, are not as conserved. Inter-species differences in 3D genomic interactions are often associated with gene expression differences between the species. To provide additional functional context to our observations, we considered previously published chromatin data from human iPSCs. We found that inter-species differences in 3D genomic interactions, which are also associated with gene expression differences between the species, are enriched for both active and repressive marks. Overall, our data demonstrates that, as expected, an understanding of 3D genome reorganization is key to explaining regulatory evolution.
Mathematical Modeling Reveals the Factors Involved in the Phenomena of Cancer Stem Cells Stabilization
Authors: Bessonov N. , Pinna G. , Minarsky A. , Harel-Bellan A. , Morozova N.
Published: November 2018

Cancer Stem Cells (CSC), a subset of cancer cells resembling normal stem cells with self-renewal and asymmetric division capabilities, are present at various but low proportions in many tumors and are thought to be responsible for tumor relapses following conventional cancer therapies. In vitro, most intriguingly, when isolated, CSCs return to their original proportion level as shown by various investigators. This phenomenon still remains to be explained.

We suggest a mathematical model of cancer cell population dynamics, based on the main parameters of cell population dynamics, including the proliferation rates, the rates of cell death and the frequency of symmetric and asymmetric cell divisions both in CSCs and in non-CSCs. This model should help elucidating some important factors underlying the dynamics of the two populations, first of all, the phenomena of cancer stem cell population stabilization.

Author Summary

Cancer Stem Cells (CSC) present a subset of cancer cells which is thought to be responsible for tumor growth. That is why CSC are also named “tumor initiation cells”. Additionally, it was shown that CSC are resistant to chemo- and radio-therapies which suggests that these cells can be responsible for tumor relapses after these treatments. Experimental data in cancer cell lines have shown the intriguing phenomena of CSC population stability, which means that isolated CSC population rapidly stabilizes at its characteristic level (the relative proportion of CSC in a whole cancer population). We suggest a mathematical model of cancer cell population dynamics, based on experimentally measured dynamics of CSC population stabilization and including main parameters of cell population growth.

We have computationally predicted probability of different scenarios of cancer cell behavior for each experimental case with measurable growth parameters. Moreover, we provide an analytical tool for elucidating important biochemical factors responsible for a particular dynamics of CSC population.

The results may have important implications in therapeutic, because the destroying of a set of factors underlying CSC stability may help to avoid tumor relapses.
RUPEE: A fast and accurate purely geometric protein structure search
Authors: Ayoub Ronald , Lee Yugyung
Published: November 2018

Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. We have developed RUPEE, a fast, scalable, and purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles.

Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results.

The RUPEE protein structure search is available athttp://www.ayoubresearch.com. Code and data are available athttps://github.com/rayoub/rupee.
Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia: A report from the TARGET initiative
Authors: McNeer Nicole A. , Philip John , Geiger Heather , Ries Rhonda E. , Lavallée Vincent-Philippe , Walsh Michael , Shah Minita , Arora Kanika , Emde Anne-Katrin , Robine Nicolas , Alonzo Todd A , Kolb E. Anders , Gamis Alan S , Smith Malcolm , Gerhard Daniela Se , Guidry-Auvil Jaime , Meshinchi Soheil , Kentsis Alex
Published: November 2018

Acute myeloid leukemias (AML) are characterized by mutations of tumor suppressor and oncogenes, involving distinct genes in adults and children. While certain mutations have been associated with the increased risk of AML relapse, the genomic landscape of primary chemotherapy resistant AML is not well defined. As part of the TARGET initiative, we performed whole-genome DNA and transcriptome (RNA and miRNA) sequencing analysis of pediatric AML with failure of induction chemotherapy. We identified at least three genetic groups of patients with induction failure, including those withNUP98rearrangements, somatic mutations ofWT1in the absence ofNUP98mutations, and additional recurrent variants including those inKMT2CandMLLT10.Comparison of specimens before and after chemotherapy revealed distinct and invariant gene expression programs. While exhibiting overt therapy resistance, these leukemias nonetheless showed diverse forms of clonal evolution upon chemotherapy exposure. This included selection for mutant alleles ofFRMD8,DHX32,PIK3R1,SHANK3,MKLN1, as well as persistence ofWT1andTP53mutant clones, and elimination or contraction ofFLT3,PTPN11, andNRASmutant clones. These findings delineate genetic mechanisms of primary chemotherapy resistance in pediatric AML, which should inform improved approaches for its diagnosis and therapy.
Population genomics and demographic sampling of the ant-plantVachellia drepanolobiumand its symbiotic ants from sites across its range in East Africa
Authors: Boyle John H. , Martins Dino , Musili Paul M. , Pierce Naomi E.
Published: November 2018

The association between the African ant plant,Vachellia drepanolobium, and the ants that inhabit it has provided insight into the boundaries between mutualism and parasitism, the response of symbioses to environmental perturbations, and the ecology of species coexistence. We use a landscape genomics approach at sites sampled throughout the range of this system in Kenya to investigate the demographics and genetic structure of the different partners in the association. We find that different species of ant associates ofV. drepanolobiumshow striking differences in their spatial distribution throughout Kenya, and these differences are only partly correlated with abiotic factors. A comparison of the population structure of the host plant and its three obligately arboreal ant symbionts,Crematogaster mimosae,Crematogaster nigriceps, andTetraponera penzigi, shows that the ants exhibit somewhat similar patterns of structure throughout each of their respective ranges, but that this does not correlate in any clear way with the respective genetic structure of the populations of their host plants. A lack of evidence for local coadaptation in this system suggests that all partners have evolved to cope with a wide variety of biotic and abiotic conditions.
Stably expressed genes in single-cell RNA-sequencing
Authors: Deeke Julie M. , Gagnon-Bartsch Johann A.
Published: November 2018

Motivation

In single-cell RNA-sequencing (scRNA-seq) experiments, RNA transcripts are extracted and measured from isolated cells to understand gene expression at the cellular level. Measurements from this technology are affected by many technical artifacts, including batch effects. In analogous bulk gene expression experiments, external references, e.g., synthetic gene spike-ins often from the External RNA Controls Consortium (ERCC), may be incorporated to the experimental protocol for use in adjusting measurements for technical artifacts. In scRNA-seq experiments, the use of external spike-ins is controversial due to dissimilarities with endogenous genes and uncertainty about sufficient precision of their introduction. Instead, endogenous genes with highly stable expression could be used as references within scRNA-seq to help normalize the data. First, however, a specific notion of stable expression at the single cell level needs to be formulated; genes could be stable in absolute expression, in proportion to cell volume, or in proportion to total gene expression. Different types of stable genes will be useful for different normalizations and will need different methods for discovery.

Results

We compile gene sets whose products are associated with cellular structures and record these gene sets for future reuse and analysis. We find that genes whose final product are associated with the cytosolic ribosome have expressions that are highly stable with respect to the total RNA content. Notably, these genes appear to be stable in bulk measurements as well.

Supplementary information

The Supplement is available on bioRxiv, and the gene set database is available through GitHub.

Contact

johanngb@umich.edu
Deriving Cardiomyocytes from Human Amniocytes
Authors: Maguire Colin T. , Sunderland Ryan , Demarest Bradley , Gorsi Bushra , Jackson Josh , Lopez-Izquierdo Angelica , Tristani-Firouzi Martin , Yost H. Joseph , Condic Maureen L.
Published: November 2018

Many forms of congenital heart disease (CHD) have high morbidity-mortality rates and require challenging surgeries. Human amniocytes have important stem cell characteristics and could potentially provide patient-specific tissue for repairs of some types of CHDs. We report that amniocytes express features of poised cardiomyocytes. However, a variety of direct reprogramming approaches failed to convert their fetal and transcriptionally repressed state into bona fide cardiomyocytes. Induced-pluripotent stem cell (iPSC) reprogramming removes repression and converts amniocytes to a baseline pluripotent state. Based on molecular and electrophysiological signatures, iPSC reprogrammed amniocytes can be induced to differentiate into functionally immature, predominantly ventricular cardiomyocytes and a heterogeneous mixture of vascular and unspecified epithelial cells. Developmental time course analyses and pattern clustering of amniocyte-derived cardiomyocytes identifies numerous temporal co-regulators of cardiac induction and maturation as well as distinct sarcomeric and ion channel gene signatures. Normal fetal cardiomyocytes are derived by overcoming complex forms of transcriptional repression that suppress direct transdifferentiation of human amniocytes. These results suggest the possibility of using amniocytes as a source of patient-specific ventricular cardiomyocytes for cell therapies.

SUMMARY STATEMENT

Amniocytes are a possible source of patient-specific cardiomyocytes for newborns with congenital heart disease. Genome-wide DNA methylation patterns and transcriptional repressors preclude direct differentiation, but pluripotent reprogramming provides cardiomyocytes for dissecting genetic pathways contributing to this disease.
Chloro–formyl steroids as precursors for hybrid heterosteroids: synthesis, spectroscopic characterization, and molecular and supramolecular structures
Authors: Almagro Luis , Nogueras Manuel , Suárez Margarita , Cobo Justo , Glidewell Christopher
Published: November 2018

Two new functionalized steroids containing both chloro and formyl substituents in ring A, and intended as precursors for the synthesis of hybrid systems, have been synthesized from ketosteroid precursors. 3-Chloro-2-formyl-17,17-dimethyl-18-nor-5α-androstane-2,13-diene, (I), and methyl 3-chloro-4-formyl-12-oxo-5β-cholan-3-ene-24-oate, C26H37ClO4, (IV), have been synthesized using Vilsmeier reactions with 17β-hydroxy-17α-methyl-5α-androstan-3-one and methyl 3,13-dioxo-5β-cholan-24-oate, respectively. These products have been fully characterized using IR spectroscopy, 1H and 13C NMR spectroscopy, and high-resolution mass spectrometry, and in the case of (IV), a single-crystal X-ray diffraction study. Crystal structures have also been determined for the known analogues 3-chloro-2-formyl-17-oxo-5α-androst-2-ene, C20H27ClO2, (II), 3-chloro-2-formyl-5α-cholest-2-ene, C28H45ClO, (III), and the absolute and relative configurations are assigned for all four compounds (I)–(IV): when the fusion between rings A and B is trans, 3-chloro-2-formyl products are formed, but when this ring fusion is cis, a 3-chloro-4-formyl product results. The formation of (I) involves not only chloroformylation at ring A, but also dehydration and the 1,2 migration of a methyl group at ring D. In each of (II), (III) and (IV), rings B and C adopt almost perfect chair conformations, while ring A adopts a half-chair conformation. Ring D adopts an envelope conformation in each of (II) and (III), albeit differently folded in the two compounds, while in (IV), it adopts a half-chair conformation. A single C—H...O hydrogen bond links the molecules of (II) into C(6) chains which are linked into sheets by means of carbonyl–carbonyl interactions. The molecules of (IV) are linked into simple C(7) chains, again by a single C—H...O hydrogen bond, but there are no direction-specific interactions in (III) that are structurally significant.
Das Kapital and political economy in the broad sense: a review on Wang Yanan’s research
Authors: Jiang Lu , Ge Yang
Published: November 2018

Purpose

Wang has focused on the relationship between Das Kapital and the political economy in the broad sense. Numerous ideas covering the political economy in the broad sense are involved in the overall structure of Das Kapital, methodology of historical materialism and analyses of the historical fate of capitalist system. The paper aims to discuss these issues.

Design/methodology/approach

In broad outline, the Asiatic, ancient, feudal and modern bourgeois modes of production may be designated as epochs, marking progress in the economic development of society (Wang, 2007b). Historical materialism provides a new, scientific and objective explanation for understanding the dialectical development laws of society. It is crucial for constructing the theoretical system of a political economy in the broad sense. It could be said that it is the key to solving the puzzle of the historical course of social development.

Findings

Today, economic relations between the world’s top two economies have merged with each other. How can two countries with different systems trade with each other so well? These questions can no longer be answered with traditionally narrow political economic theory. The authors have to seek these answers from the perspective of a political economy in the broad sense.

Originality/value

Numerous ideas covering the political economy in the broad sense are involved in the overall structure of Das Kapital, methodology of historical materialism, and analyses of the historical fate of capitalist system.
“Sites of control and resistance”: outlaw emotions in an out-of-school book club
Authors: Neville Mary L.
Published: November 2018

Purpose

The purpose of this paper is to explore how three young women of color responded with “outlaw emotions” to the novelAristotle and Dante Discover the Secrets of the Universeby Benjamin Alire Sáenz in a literature discussion group. This paper considers how readers respond with outlaw emotions and how responses showed emotions as sites of control and resistance. The aim of this paper is to help English language arts (ELA) teachers construct culturally sustaining literature classrooms through an encouragement of outlaw emotions.

Design/methodology/approach

To examine how youth responded with emotion toAristotle and Dante, the author used humanizing and ethnographic research methodologies and conducted a thematic analysis of meeting transcripts, journal entries from youth and researcher memos.

Findings

Analyses indicated that youth responded with outlaw emotions toAristotle and Dante, and these responses showed how youth have both resisted and been controlled by structures of power. Youth responses of supposed “positive” or “negative” emotion were sites of control and resistance, particularly within their educational experiences. Youth engaged as a peer group to encourage and validate outlaw emotions and indirectly critiqued emotion as control.

Originality/value

Although many scholars have demonstrated the positive effects of out-of-school book clubs, there is scant research regarding how youth respond to culturally diverse literature with emotion, both outlaw and otherwise. Analyzing our own and characters’ outlaw emotions may help ELA educators and students deconstruct dominant ideologies about power, language and identity. This study, which demonstrates how youth responded with outlaw emotions and gave evidence of emotions as control and resistance, shows how ELA classrooms might encourage outlaw emotions as literary response. These findings suggest that ELA classrooms attempting culturally sustaining pedagogies might center youth emotion in responding to literature to critique power structures across the self, schools and society.
Alternative tourism and civil society in Athens
Authors: Vergopoulos Hecate
Published: November 2018

Purpose

The purpose of this paper is to tackle the issue of the meaning of tourism as it is being crippled by the economic crisis in Greece.

Design/methodology/approach

To do so, it brings together the findings of three different fieldworks related to tourism in Athens in times of crisis. Each one of these focuses on a specific player of tourism: a linguistic and semiological analysis led mainly on travel guides and ad campaigns deals with the industry of tourism; a linguistic analysis of tourists’ posts on a French web forum deals with the tourists themselves; and an ethnographical approach of alternative guided tours of Athens focuses on local players (associations and cooperatives offering out of the beaten tracks tours).

Findings

The whole study reveals that there is a misunderstanding between the industry and the consumers toward what the tourist practice should mean: whereas the tourists are in search of an ethical meaning, the industry claims there is no room for such issues. The alternative players, however, offer a political perspective that embraces the ethical issues raised by tourists.

Originality/value

They thus might, in the end, show us the way a so-called “civil society” could also have its own role to perform in tourism.
The role of consumer-cause identification and attitude in the intention to purchase cause-related products
Authors: Duarte Paulo Alexandre de Oliveira , Silva Susana C.
Published: November 2018

Purpose

The purpose of this paper is to extend prior research on the influence of consumer-cause identification on the intention to purchase products from the companies supporting the cause and re-evaluates the role of attitude toward the cause as a mediator of the relationship between identification and intention to purchase.

Design/methodology/approach

Using a questionnaire, a sample of 156 Portuguese consumers evaluated their personal identification and attitude to one of four causes. Partial least squares path modeling was used to evaluate the proposed conceptual model.

Findings

The results reveal that more than identification, a positive attitude is vital to be able to predict the intention to purchase. Together, consumer-cause identification and attitude explain 35.1 percent of the variance in purchase intention. The findings show also that attitude acts as a mediator in the relationship between the identification with the cause and intention to purchase. Several differences regarding gender and age are also revealed.

Originality/value

While the majority of studies were single cause evaluations, the current results are based on the assessment of multiple causes. Consequently, the findings are more comprehensive and robust, providing important insights to researchers. The conclusions confirm within a wider context the role of attitude as a mediator of the identification and intention to purchase and can further assist companies in designing better targeted cause-related marketing campaigns.
Emotional intelligence in transcendent customer experiences
Authors: Sukhu Anupama , Seo Soobin , Scharff Robert , Kidwell Blair
Published: November 2018

Purpose

This services marketing research provides a theoretical framework for experiential and relationship marketing and extends the theory of transcendent customer experience (TCE). Specifically, this paper aims to identify how the drivers (emotional intelligence [EI]), outcomes (customer loyalty, willingness to pay and word of mouth [WOM] intentions) and influences (openness to experience) of TCE are integrated. The research contributes to the theoretical debate regarding ability-based and self-reported EI measures by examining their influence on TCE.

Design/methodology/approach

Students and general consumers provided data through structured online surveys in three survey-based experiments. Linear and multiple regressions, mediation analyses and simple effects tests were used for data analysis.

Findings

Findings suggest that self-reported and ability-based measures of EI influence TCE differently. Participants who had high self-reported EI evaluated positive service encounters as more transcendent than they evaluated negative service encounters. Participants who had high ability-based EI evaluated positive service encounters as less transcendent than they evaluated negative service encounters. TCE experiences evoked higher loyalty, willingness to pay (WTP) and WOM recommendations. Furthermore, dispositional factors were significant in forming TCE: participants who were highly open to experience and had high ability-based EI interpreted their service encounter as less transcendent than did participants who were more closed to experience and had low ability-based EI.

Research limitations/implications

TCE, a relatively new concept, offers theoretical advancement in context and constructs. The student-provided data gave high internal validity; the general consumer-provided data gave external validity. Ideally, a future field study in an actual consumption setting should replicate the findings. A self-reported questionnaire used to measure constructs may have introduced common method variance that biased the results.

Practical implications

By understanding that EI affects perceptions of transcendence in positive/negative service encounters, marketers can better implement consumer-oriented marketing strategies that will enhance TCE, customer loyalty, WTP and WOM.

Originality/value

Despite considerable research in experiential and relationship marketing, room remains for theoretical and practical enhancement in the under-researched concept of TCE. This research is the first attempt to extend TCE theory to marketing by identifying the drivers, outcomes and moderators of TCE in service encounters. The research also provides theoretical advancement in EI research. The results contradict previous research claiming that ability-based and self-reported measures are equally valid. Instead, using the two EI scales interchangeably leads to potentially different outcomes.