bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding the unique sorption of alkane-α, ω-diols in silicalite-1
Authors: DeJaco Robert F. , Elyassi Bahman , Dorneles de Mello Matheus , Mittal Nitish , Tsapatsis Michael , Siepmann J. Ilja
Published: July 2018

Adsorption equilibria of alkane-α, ω-diols (propane-1,3-diol, butane-1,4-diol, pentane-1,5-diol, and hexane-1,6-diol) from aqueous solution onto an all-silica zeolite of the type mordenite framework inverted (MFI, also known as silicalite-1) are obtained by simulations and experiments at T = 323 K and also for pentane-1,5-diol (C5) at 348 and 383 K. After an initial slow rise, isotherms at T = 323 K exhibit steep changes in loading, reaching saturation at 10, 9, 8, and 7 molec/uc as the number of carbon atoms of the diols increases from 3 to 6. The abrupt change in loading corresponds to a minimum in the free energy of adsorption (from vapor to zeolite) that is associated with a rapid rise in the number of hydrogen bonds per sorbate molecule due to the formation of large clusters. For C5 at low loading, the centers-of-mass primarily occupy the channel intersections with oxygens oriented along the straight channels where intermolecular hydrogen bonds are formed. At saturation loading, the C5 centers-of-mass instead occupy the straight and zig-zag channels, and nearly all C5 molecules are involved in a percolating hydrogen-bonding network (this also occurs for C6). With increasing temperature, the C5 isotherm decreases in steepness as the minimum in free energy of adsorption decreases in depth and a less-ordered structure of the adsorbed molecules results in a lower number of diol–diol hydrogen bonds. However, the C5 isotherm does not shift significantly in concentration of the adsorption onset, as the free energies of solvation and adsorption increase by similar and compensating amounts. At T = 323 and 348 K, the steep change for the C5 adsorption isotherm is found to be a phase transition (as indicated by a bimodal distribution of unit cell occupancies at intermediate loading) from a less-dense phase with only small hydrogen-bonded clusters to an ordered solid phase with loadings of 8 molec/uc. At T = 383 K, the sorbates are less ordered, the distribution of occupancies becomes unimodal at intermediate loading, and the loading rises more gradually with concentration. Several different enhanced sampling methods are utilized for these simulations.
Gate controlled Majorana zero modes of a two-dimensional topological superconductor
Authors: Djavid Nima , Yin Gen , Barlas Yafis , Lake Roger K.
Published: July 2018

Half-integer conductance, the signature of Majorana edge modes, was recently observed in a thin-film magnetic topological insulator/superconductor bilayer. This letter analyzes a scheme for gate control of Majorana zero modes in such systems. Gating the top surface of the thin-film magnetic topological insulator controls the topological phase in the region underneath the gate. The voltage of the transition depends on the gate width, and narrower gates require larger voltages. Relatively long gates are required, on the order of 2 μm, to prevent hybridization of the end modes and to allow the creation of Majorana zero modes at low gate voltages. Applying voltage to T-shaped and I-shaped gates localizes the Majorana zero modes at their ends. This scheme may provide a facile method for implementing quantum gates for topological quantum computing.
Aerodynamic characteristics of unsteady gap flow in a bristled wing
Authors: Lee Seung Hun , Lahooti Mohsen , Kim Daegyoum
Published: July 2018

A micro-scale flying insect has a unique wing configuration consisting of a central frame and several bristles. For the low-Reynolds-number regime in which the insect lives, the bristled wing utilizes a virtual fluid barrier inside gaps produced by strong viscous diffusion of shear layers to overcome its morphological limitations. Considering the unsteady flapping motion of such a wing, the aerodynamic characteristics of gap flow formation are investigated numerically using a two-dimensional bristled wing model for a wide range of Reynolds numbers. Inside a gap between bristles, the development of a stopping vortex during the deceleration phase and its effect on the extinction of an existing vortex generated at the same edge are dependent on the Reynolds number, which leads to a significant change in vorticity distribution at stroke reversal even with just a small change in the Reynolds number. As the Reynolds number decreases, the gap flow responds more rapidly to wing motion, and its pattern does not deviate significantly from the kinematics of the wing. A noticeable difference is also observed in the behavior of the aerodynamic force acting on each bristle at low and high Reynolds numbers. With regard to aerodynamic force generation by the bristles, each bristle behaves independently and produces similar force because of strong gap flows relative to the wing at high Reynolds numbers. Meanwhile, at low Reynolds numbers, each bristle experiences a different force depending on its relative position, which indicates the existence of collective interaction of bristles through a virtual fluid barrier.
Observations of core ion cyclotron emission on ASDEX Upgrade tokamak
Authors: Ochoukov R. , Bobkov V. , Chapman B. , Dendy R. , Dunne M. , Faugel H. , García-Muñoz M. , Geiger B. , Hennequin P. , McClements K. G. , Moseev D. , Nielsen S. , Rasmussen J. , Schneider P. , Weiland M. , Noterdaeme J.-M. ,   ASDEX Upgrade Team,   EUROfusion MST1 Team
Published: July 2018

The B-dot probe diagnostic suite on the ASDEX Upgrade tokamak has recently been upgraded with a new 125 MHz, 14 bit resolution digitizer to study ion cyclotron emission (ICE). While classic edge emission from the low field side plasma is often observed, we also measure waves originating from the core with fast fusion protons or beam injected deuterons being a possible emission driver. Comparing the measured frequency values with ion cyclotron harmonics present in the plasma places the origin of this emission on the magnetic axis, with the fundamental hydrogen/second deuterium cyclotron harmonic matching the observed values. The actual values range from ∼27 MHz at the on-axis toroidal field BT = −1.79 T to ∼40 MHz at BT = −2.62 T. When the magnetic axis position evolves during this emission, the measured frequency values track the changes in the estimated on-axis cyclotron frequency values. Core ICE is usually a transient event lasting ∼100 ms during the neutral beam startup phase. However, in some cases, core emission occurs in steady-state plasmas and lasts for longer than 1 s. These observations suggest an attractive possibility of using a non-perturbing ICE-based diagnostic to passively monitor fusion alpha particles at the location of their birth in the plasma core, in deuterium-tritium burning devices such as ITER and DEMO.
Hydration and dehydration of monovalent cations near an electrode surface
Authors: Kiyohara Kenji , Minami Riho
Published: July 2018

The mechanism of hydration and dehydration of monovalent ions, Li+, Na+, K+, and Cs+, in a dilute solution near an electrode surface was studied by molecular dynamics simulations. The potentials of mean force for these ions were calculated as a function of the distance from the electrode surface and the potential barriers for dehydrating the first and the second hydration shell near the electrode surface and were estimated for each ion species. It was found that the mechanism of hydration for Li+ is distinct from those for Na+, K+, and Cs+. Penetration of ions into the first layer of water molecules on the electrode surface is unlikely to occur for the case of Li+, while that would occur with certain probabilities for the case of Na+, K+, or Cs+, whether or not voltage is applied to the electrode. Li+ ions would be adsorbed on the electrode surface in a doubly hydrated form with a significant probability, while Na+, K+, and Cs+ ions would be adsorbed most likely in a singly hydrated form. Furthermore, the theory of ionic radii, which has been successfully used in the analysis of bulk solutions, was applied to the electrode/electrolyte interface. It was found that the theory of ionic radii is also useful in explaining the structural behaviors of ions near an electrode surface. The distance between an ion and the layers of water molecules on the electrode surface showed almost linear dependence on the radius of the ion, as predicted by the theory of ionic radii. Analysis of the deviation from the linearity showed that Li+ ions are most likely adsorbed in the first layer of water molecules on the electrode surface, while Na+, K+, and Cs+ ions are adsorbed on the second layer of water molecules. These analyses indicate that Li+ is a structure maker, while Na+, K+, and Cs+ are structure breakers, which is consistent with the widely accepted idea in explaining the behaviors of the bulk solutions.
An impedimetric bioaffinity sensing chip integrated with the long-range DC-biased AC electrokinetic centripetal vortex produced in a high conductivity solution
Authors: Lin Ming-Jie , Liu Yen-Fu , Wu Ching-Chou
Published: July 2018

Immunoreaction of specific antibodies to antigens is widely used in numerous immunoanalysis applications. However, diffusion-dominated transport in stationary solutions limits the rate and binding density of immunoreaction. This research describes the construction of chip-type concentric multi-double ring electrodes and single central disk electrode. A +1 V-biased 6 Vpp voltage was applied to the multi-double ring electrodes to induce a long-range DC-biased AC electrokinetic flow (ACEKF). The immunoreaction was quantified by electrochemical impedance spectrum (EIS). Fluorescence-labeled secondary antibody (FLSA) and protein A were exemplified as an immunoreacting model to demonstrate the effect of ACEKF on immunoreaction efficiency. The results showed that FLSA binding can reach a plateau in 8 min with the DC-biased ACEKF vortex, and the increment of electron transfer resistance is 2.26 times larger than that obtained in the unstirred solution. The sensitivity of the calibration curves obtained by EIS detection with the aid of DC-biased ACEKF vortex is 1.51 times larger than that obtained in an unstirred solution. The label-free EIS-based sensing chip integrated with the long-range DC-biased ACEKF vortex promises to facilitate immunoreaction efficiency, which is beneficial for the development of a miniature and fast-detection in vitro diagnostic device.
Localized excitations and scattering of spin waves in ferromagnetic chains containing magnetic nanoclusters
Authors: Charkina O. V. , Bogdan M. M.
Published: July 2018

The spectrum of localized excitations in an anisotropic one-dimensional ferromagnet containing a spin cluster of arbitrary size was found accurately within the framework of the discrete Takeno-Homma model. The stability boundaries of spin nanoclusters are determined depending on their size and the ferromagnet's exchange and anisotropy parameters. The problem of scattering of spin waves by nanoclusters is solved and explicit analytical expressions are obtained for their reflection and transmission coefficients. A model of a metamaterial consisting of weakly interacting magnetic molecular nanoclusters with the discovered dynamic properties is proposed.
Phase dynamics of discrete breathers periodically tunneling in weakly coupled nonlinear chains
Authors: Kosevich Yuriy A.
Published: July 2018

We present a brief discussion of the phase-coherent dynamics of discrete breathers (intrinsic localized modes) in a system of two weakly coupled nonlinear chains and its comparison with periodic tunneling of quantum particles in a double-well potential and with macroscopic quantum tunneling of two weakly linked Bose–Einstein condensates. We consider the dynamics of relative phase of classically-tunneling discrete breathers in two weakly coupled nonlinear chains and show that the dynamics of the relative phase in the π/2 tunneling mode coincides with the experimentally observed dynamics of the relative phase of quantum particles, periodically tunneling in a double-well potential, both for noninteracting and strongly repulsively interacting particles. The observed coincidence demonstrates the correspondence between the dynamics of classical localized excitations in two weakly coupled nonlinear chains and tunneling dynamics of quantum object in the double-well potential. We show that in both π/2 and winding tunneling modes the relative phase experiences periodic jumps by π in the instants of complete depopulation of one of the weakly coupled chains or potential wells. The connection of the observed phase dynamics with the non-quantum uncertainty principle is discussed.
Computer modeling and analytical description of structural defects in two-dimensional crystals of bounded sizes: Free boundary, dislocations, and crowdions
Authors: Natsik V. D. , Smirnov S. N. , Belan V. I.
Published: July 2018

Two-dimensional crystals of bounded sizes formed by atoms with centrallysymmetric interaction between them (Lennard-Jones potential) are examined. Methodologies of molecular dynamics have established the atomic structure of clusters of approximately circular form with radii on the nanometer scale. Deviations of atomic configurations from the ideal lattice of a 2D crystal, caused both by the free boundary of a cluster and by the defects introduced into its center, dislocations and crowdions, are investigated. The values of the self-energy of these defects are calculated, and their dependencies on the cluster radius and the parameters of the potential of interatomic interaction are analyzed. Methodologies of continuum mechanics of crystals described the features of uniform elastic strain of 2D crystal circles and bands in comparison with deformation of 3D crystal spheres and rods. Two-dimensional analogues of the main characteristics of elasticity, namely the coefficient of compression, Young's modulus, shear modulus, and Poisson coefficient, as well as their connection with Lamé coefficients, are discussed. The dependencies of the enumerated parameters of elasticity on the parameters of the potential of interatomic interaction are established, and estimates for the effective sizes of kernels of dislocation and crowdion are derived.
On the possibility of estimating the position of the mobility edge for charge carriers using single-particle averages
Authors: Skrypnyk Yu. V. , Loktev V. M.
Published: July 2018

The dependence of the position of the mobility edge on the impurity concentration during the transformation of the electronic band structure is considered in a disordered system described by the Lifshitz model. Concentration dependence of the mobility threshold caused by variation of the threshold parameter in the Ioffe–Regel criterion is analyzed. It is demonstrated that the critical concentration of the impurity, which triggers the transformation of the band structure, changes slightly with variation of this parameter, while the corresponding position of the mobility edge at this concentration remains stable. The prerequisites for the existence of such concentration intervals, within which the mobility edge is shifted in proportion to the cubic root of the impurity concentration, are discussed.
Soil quality change 50 years after forestland conversion to tea farming
Authors: Gholoubi Azadeh , Emami Hojat , Alizadeh Amin
Published: July 2018

Land-use change has been shown to affect soil quality and may lead to soil degradation. The effects of land-use change from natural forest to tea farming on soil properties and quality were studied within Guilan Province of northern Iran. Thirty-six soil samples (0–30 cm) were randomly collected from six sites with three replications at each site. The soil quality of forest and tea farms was determined using the cumulative rating (CR) index and the Cornell Comprehensive Assessment of Soil Health (CASH) scoring function. Effects of land-use change on soil quality or health were significant (P < 0.01) using both methods. Both methods for all regions (forest and tea fields) showed that forest land-use was more sustainable based on lower CR (lower limitation to crop production) and higher CASH scores (higher soil productivity and quality) than tea farm soils. Both methods were also negatively correlated with each other. Despite pH being a limiting factor for soil quality, it was not influenced by land-use change in most locations because the studied soils were acidic. However, organic carbon was the most important soil quality indicator, which was significantly correlated with soil physical, chemical and biological (respiration rate) properties. Therefore, land-use management practices that are continuously cultivated should include increases in organic carbon.
Nu-prefaced responses in Russian
conversation
Authors: Bolden Galina B.
Published: July 2018

This chapter examines the Russian particle nu,
focusing on its use in responses to polar and question-word
questions. I show that nu prefaces responses that
are, in some way, misaligned vis-à-vis the initiating action. First,
nu may preface
non-type-conforming responses, i.e., responses
that “depart from the constraints embodied in the grammatical form”
of the question (Raymond
2003, 946). Such responses may operate on the terms
of the question, correct its presuppositions, resist the action the
question implements, and problematize its assumption of
answerability. Second, nu may preface responses
that conform to the question’s grammatical constraints and forward
its action agenda, but convey an incongruent epistemic stance by
suggesting that the questioner already knows the solicited
information.
Turn-initial particles in English
Authors: Heritage John
Published: July 2018

This chapter examines the English turn-initial particles
oh and well. It begins with a
consideration of their distinctive usages and functions in three
basic sequential positions (first, second and third), arguing that
both exhibit what Schegloff
(1996) terms ‘positional sensitivity’. The chapter then
considers some larger contrasts between the two particles, including
distinctions between epistemic (oh) and
action-projecting (well) functions, forward-
(well) and backward- (oh)
looking orientations, and their underlying semantic
characteristics.
Making up one’s mind in second position
Authors: Keevallik Leelo
Published: July 2018

This chapter discusses preferred responses that are delayed in their
turn by the initial particle no in Estonian. It
demonstrates that the turn-initial time-space may be employed for a
display of “making up one’s mind”, either weighing matters outside
the conversation or something already discussed in the talk. The
paper argues that besides the dichotomous choice between the
preferred and the dispreferred answer format, there are individual
contingencies to consider in committing to future actions as made
relevant in requests, proposals and suggestions. By marking a
transition from prior resistance to compliance with a
no-preface, the speaker indexes that the
emerging response is carefully considered and therefore socially
cohesive.
Justifying departures from progressivity
Authors: Heinemann Trine , Steensig Jakob
Published: July 2018

This chapter investigates the use of the Danish particle
altså in turn-initial position. Turn-initial
altså can be employed for prefacing a wide
range of actions, including self- and other-initiated repair,
questions, second stories and answers to both yes/no and
wh-questions. We show that across these actions, participants in
interaction produce altså to indicate (1) that the
action they will produce departs from progressivity, (2) that it
will expand on something prior, (3) that the departure is,
therefore, justified, and (4) that it will contribute to
reinstalling the progression of the larger on-going activity. Some
of the actions that altså prefaces can also be
prefaced by phrases that function like ‘you know’ or ‘I mean’, which
seem to do at least some of the work that altså
does, but altså is used more frequently and across
a wider range of actions. In our discussion, we raise the
possibility that the usefulness of altså is due to
the fact that it allows its producer to indicate that no one party
in the interaction was accountable or at fault for the
departure.
Off-target predictions in CRISPR-Cas9 gene editing using deep learning
Authors: Lin Jiecong , Wong Ka-Chun
Published: July 2018

Motivation

The prediction of off-target mutations in CRISPR-Cas9 is a hot topic due to its relevance to gene editing research. Existing prediction methods have been developed; however, most of them just calculated scores based on mismatches to the guide sequence in CRISPR-Cas9. Therefore, the existing prediction methods are unable to scale and improve their performance with the rapid expansion of experimental data in CRISPR-Cas9. Moreover, the existing methods still cannot satisfy enough precision in off-target predictions for gene editing at the clinical level.

Results

To address it, we design and implement two algorithms using deep neural networks to predict off-target mutations in CRISPR-Cas9 gene editing (i.e. deep convolutional neural network and deep feedforward neural network). The models were trained and tested on the recently released off-target dataset, CRISPOR dataset, for performance benchmark. Another off-target dataset identified by GUIDE-seq was adopted for additional evaluation. We demonstrate that convolutional neural network achieves the best performance on CRISPOR dataset, yielding an average classification area under the ROC curve (AUC) of 97.2% under stratified 5-fold cross-validation. Interestingly, the deep feedforward neural network can also be competitive at the average AUC of 97.0% under the same setting. We compare the two deep neural network models with the state-of-the-art off-target prediction methods (i.e. CFD, MIT, CROP-IT, and CCTop) and three traditional machine learning models (i.e. random forest, gradient boosting trees, and logistic regression) on both datasets in terms of AUC values, demonstrating the competitive edges of the proposed algorithms. Additional analyses are conducted to investigate the underlying reasons from different perspectives.

Availability and implementation

The example code are available at https://github.com/MichaelLinn/off_target_prediction. The related datasets are available at https://github.com/MichaelLinn/off_target_prediction/tree/master/data.
Biblical Hebrew Bal and Privative Negation
Authors: Sjörs Ambjörn
Published: July 2018

The Biblical Hebrew lexeme bal has been described as a poetic and prophetic synonym with lō’ in previous research. However, cognate morphemes in the Semitic languages outside Northwest Semitic, as well as other Biblical Hebrew lexemes derived from the relevant root morpheme, e.g. bǝlî and lǝḇiltî, may be identified with privative grammatical morphemes, i.e. grammatical morphemes that cancel an association. It is argued that, most of the time, bal too should be identified with privative negation, and that it is a poetic and prophetic synonym with lǝḇiltî (with different co-occurrence restrictions). Other times, the uses of bal can be explained as typical for the grammaticalization of privative expressions. The use of bal as a negator, for example, can be explained in terms of the grammaticalization of a conventional implicature, by which a salient feature, privation, became bleached semantically in favour of its implicature, negation.1
Evaluation of the Florida Strawberry Advisory System for Control of Botrytis and Anthracnose Fruit Rots in Ohio
Authors: Cordova L. G. , Ellis M. A. , Wilson L. L. , Madden L. V. , Peres N. A.
Published: July 2018

The Florida Strawberry Advisory System (StAS) forecasts the need for fungicide applications for control of Botrytis fruit rot (BFR) and anthracnose fruit rot (AFR) based on leaf wetness and temperature during the moist period. StAS was evaluated in Ohio for four seasons from 2011 to 2014 and compared with the calendar-based system currently used by growers. BFR was severe in 2011 and 2013 and nearly absent in the other years, whereas AFR was not a problem in any of the four years. Using the calendar-based system, five to six applications were made each year for BFR, whereas only two or fewer were recommended using StAS. For AFR control, six to seven applications were made based on the calendar system, whereas three or fewer were recommended by StAS. There was no case in which the calendar program outperformed the StAS in disease management. Use of StAS would greatly reduce the number of sprays needed for control of fruit rot diseases and result in significant savings for Ohio strawberry growers.
Mutations in ORP1 Conferring Oxathiapiprolin Resistance Confirmed by Genome Editing using CRISPR/Cas9 in Phytophthora capsici and P. sojae
Authors: Miao Jianqiang , Chi Yuandong , Lin Dong , Tyler Brett M. , Liu Xili
Published: July 2018

Oxathiapiprolin is a novel fungicide that was recently registered in a number of countries to control plant-pathogenic oomycetes such as Phytophthora capsici. In our previous study, point mutations G770V and G839W in oxysterol binding protein-related protein 1 (ORP1) were detected in oxathiapiprolin-resistant P. capsici isolates (PcORP1). Here, we used the CRISPR/Cas9 system to verify the effects of these two point mutations on P. capsici phenotypes. Transformants containing heterozygous G770V and G839W mutations in PcORP1 showed high levels of oxathiapiprolin resistance. The G770V transformants showed otherwise similar phenotypes compared with the wild-type isolate BYA5, including sporangia and zoospore production, cyst germination, and pathogenicity. However, two independent transformants with heterozygous G839W mutations in PcORP1 could not produce sporangia. Three transformants with an unexpected point mutation in PcORP1 (ΔN837) showed high oxathiapiprolin resistance, and either similar or significantly reduced fitness compared with BYA5. The same deletion (ΔN837) was confirmed to confer oxathiapiprolin resistance in P. sojae by using CRISPR/Cas9. These homozygous P. sojae mutants also showed either similar or strongly reduced fitness compared with the wild-type parent isolate P6497. These results improve our understanding of oxathiapiprolin resistance in Phytophthora spp., and will be useful for the development of novel oxysterol-binding protein homolog inhibitor fungicides.
How Does Phytophthora infestans Evade Control Efforts? Modern Insight Into the Late Blight Disease
Authors: Leesutthiphonchai Wiphawee , Vu Andrea L. , Ah-Fong Audrey M. V. , Judelson Howard S.
Published: July 2018

The infamous oomycete Phytophthora infestans has been a persistent threat to potato and tomato production worldwide, causing the diseases known as late blight. This pathogen has proved to be remarkably adept at overcoming control strategies including host-based resistance and fungicides. This review describes the features of P. infestans that make it such a daunting challenge to agriculture. These include a stealthy lifestyle that helps P. infestans evade plant defenses, effectors that suppress host defenses and promote susceptibility, profuse sporulation with a short latent period that enables rapid dissemination, and a genome structure that promotes the adaptive evolution of P. infestans by fostering genetic diversity. Nevertheless, there is reason to be optimistic that accumulated knowledge about the biology of P. infestans and its hosts will lead to improved management of late blight.
Intergenerational effects on mouse sperm quality after in utero exposure to acetaminophen and ibuprofen
Authors: Rossitto Moïra , Marchive Candice , Pruvost Alain , Sellem Eli , Ghettas Aurélie , Badiou Stéphanie , Sutra Thibault , Poulat Francis , Philibert Pascal , Boizet-Bonhoure Brigitte
Published: July 2018

Nonsteroidal antiinflammatory drugs and analgesic drugs, such as N‐acetyl‐p‐aminophenol (APAP; acetaminophen, paracetamol), are widely used by pregnant women. Accumulating evidence has indicated that these molecules can favor genital malformations in newborn boys and reproductive disorders in adults. However, the consequences on postnatal testis development and adult reproductive health after exposure during early embryo‐genesis are still unknown. Using the mouse model, we show that in utero exposure to therapeutic doses of the widely used APAP‐ibuprofen combination during the sex determination period leads to early differentiation and decreased proliferation of male embryonic germ cells, and early 5‐mefhylcytosine and extracellular matrix protein deposition in 13.5 d postcoitum exposed testes. Consequently, in postnatal testes, Sertoli‐cell maturation is delayed, the Leydig‐cell compartment is hyperplasia and the spermatogonia A pool is decreased. This results in a reduced production of testosterone and in epididymal sperm parameter defects. We observed a reduced sperm count (19%) in utero–exposed (FO) adult males and also a reduced sperm motility (40%) in their offspring (Fl) when both parents were exposed, which leads to subfertility among the 6 mo old Fl animals. Our study suggests that the use of these drugs during the critical period of sex determination affects the germ‐line development and leads to adverse effects that could be passed to the offspring.—Rossitto, M., Marchive, C., Pruvost, A., Sellem, E., Ghettas, A., Badiou, S., Sutra, T., Poulat, F., Philibert, P., Boizet‐Bonhoure, B. Intergenerational effects on mouse sperm quality after in utero exposure to acetaminophen and ibuprofen. FASEB J. 33, 339–357 (2019). www.fasebj.org
Charting Tissue Expression Anatomy by Spatial Transcriptome Decomposition
Authors: Maaskola Jonas , Bergenstråhle Ludvig , Jurek Aleksandra , Navarro José Fernández , Lagergren Jens , Lundeberg Joakim
Published: July 2018

We create data-driven maps of transcriptomic anatomy with a probabilistic framework for unsupervised pattern discovery in spatial gene expression data. With convolved negative binomial regression we discover patterns which correspond to cell types, microenvironments, or tissue components, and that consist of gene expression profiles and spatial activity maps. Expression profiles quantify how strongly each gene is expressed in a given pattern, and spatial activity maps reflect where in space each pattern is active. Arbitrary covariates and prior hierarchies are supported to leverage complex experimental designs.

We demonstrate the method with Spatial Transcriptomics data of mouse brain and olfactory bulb. The discovered transcriptomic patterns correspond to neuroanatomically distinct cell layers. Moreover, batch effects are successfully addressed, leading to consistent pattern inference for multi-sample analyses. On this basis, we identify known and uncharacterized genes that are spatially differentially expressed in the hippocampal field between Ammon’s horn and the dentate gyrus.
A Framework for Predicting Design Failures in Engineered Genetic Codes
Authors: Yu Bea , Murphy Matthew , Carr Peter A.
Published: July 2018

Extreme engineering of an organism’s genetic code could impart true genetic incompatibility, even blocking effects of horizontal gene transfer and viral infection. Recent experiments exploring this possibility demonstrate that such radical genome engineering achievements are plausible. However, it is unclear when the modifications will compromise the fitness of an organism. Efforts to reformat an entire genome are difficult and expensive; computational methods predicting fruitful experimental trajectories could play a pivotal role in advancing such efforts. We present a framework for building in silico models to assist genome-scale engineering. Genetic code engineering requires choosing from many possible codon-usage schemes, to find a design that is viable and effective. We use machine learning to identify which alternative codon-usage schemes are likely to result in no observed viable cells. Our data-driven approach employs observations of how modifying codon usage in individual genes impacted observed viability in E. coli, revealing salient features for early identification of problematic genetic code designs. We achieved an average area under the receiver operating characteristic of 0.72 on out-ofsample data.

Author Summary

As machine learning and artificial intelligence play an increasingly central role in science and engineering, it will be important to establish standardized techniques that facilitate the dialogue between experimentation and modeling. Biological experimental techniques are concurrently evolving at a rapid pace, providing unique opportunities to collect high-quality, novel information that was previously unobtainable. This work navigates the landscape of this vast, new territory, identifies interesting landmarks for exploration and posits new approaches towards advancing our research efforts in these areas. In this work, we show that, using a small dataset of 47 observations and rigorous nested cross validation techniques, we can build a model that makes better-than-random predictions of how codon usage changes in essential genes influence viability in E. coli. These predictions can be used to inform experimental trajectories in both genetic code and codon optimization experiments. We discuss ways to improve this model, iteratively, by performing high value experiments that decrease uncertainty in predictions and extrapolation error. Finally, we present novel visualization methods to aid in developing intuitions for how re-coding impacts groups of genes. These methods are also useful tools in building important insights into how well machine learning algorithms can generalize to new data.
Leucine rich repeat kinase 2 (LRRK2) gly2019ser mutation is absent in a second cohort of nigerian africans with parkinson disease
Authors: Okubadejo Njideka U , Rizig Mie , Ojo Oluwadamilola O , Jonvik Hallgeir , Oshinaike Olajumoke , Brown Emmeline , Houlden Henry
Published: July 2018

To date the LRRK2 p.G2019S mutation remains the most common genetic cause of Parkinson disease (PD) worldwide. It accounts for up to 6% of familial and approximately 1.5% of sporadic cases. LRRK2 has a kinase enzymatic domain which provides an attractive potential target for drug therapies and LRRK2 kinase inhibitors are in development. Prevalence of the p.G2019S has a variable ethnic and geographic distribution, the highest was reported among Ashkenazi Jews (30% in patients with familial PD, 14% in sporadic PD, 2.0% in controls) and North African Berbers (37% in patients with familial PD, 41% in sporadic PD, and 1% in controls). Little is known about the frequency of the LRRK2 p.G2019S among populations in Sub Saharan Africa. Our group and others previously reported that the p.G2019S is absent in a small cohort from Nigerian PD patients and controls. Here we used Kompetitive Allele Specific PCR (KASP) assay to screen for the p.G2019S in a larger cohort of Black African PD patients (n =126) and healthy controls (n = 55) from Nigeria. Our analysis confirmed that all patients and controls are negative for the p.G2019S mutation. This report provides further evidence that the LRRK2 p.G2019S is not implicated in PD in black populations from Nigeria and support the notion that p.G2019S mutation originated after the early human dispersal from sub-Saharan Africa. Further studies using larger cohorts and advance sequencing technology are required to underpin the genetic causes of PD in this region.
Employee indifference and inaction against abusive supervision
Authors: Zhang Yucheng , Frenkel Stephen J.
Published: July 2018

Purpose

The purpose of this paper is to investigate how part-time waiters perceive and respond to abusive supervision by the owner-manager of a small restaurant.

Design/methodology/approach

An ethnographic approach was used to collect data. One of the authors worked as a participant observer for three months. In addition, 13 interviews and three focus group discussions were conducted.

Findings

Data analysis showed how neutral identification based on a primary identity—liu xu sheng(overseas student)—overshadows employees’ occupational identity (waiter), which helps waiters to cope with abusive supervision.

Originality/value

Development and application of the concept of neutral organizational identification orientation encourages emotional suppression and reframing, leading to waiters’ indifference and acquiescence in abusive supervision. Implications are drawn for theory and the practice of managing part-time and temporary workers.
Numerical simulation of two-phase flow regime in horizontal pipeline and its validation
Authors: Ban Sam , Pao William , Nasif Mohammad Shakir
Published: July 2018

Purpose

The purpose of this paper is to investigate oil-gas slug formation in horizontal straight pipe and its associated pressure gradient, slug liquid holdup and slug frequency.

Design/methodology/approach

The abrupt change in gas/liquid velocities, which causes transition of flow patterns, was analyzed using incompressible volume of fluid method to capture the dynamic gas-liquid interface. The validity of present model and its methodology was validated using Baker’s flow regime chart for 3.15 inches diameter horizontal pipe and with existing experimental data to ensure its correctness.

Findings

The present paper proposes simplified correlations for liquid holdup and slug frequency by comparison with numerous existing models. The paper also identified correlations that can be used in operational oil and gas industry and several outlier models that may not be applicable.

Research limitations/implications

The correlation may be limited to the range of material properties used in this paper.

Practical implications

Numerically derived liquid holdup and holdup frequency agreed reasonably with the experimentally derived correlations.

Social implications

The models could be used to design pipeline and piping systems for oil and gas production.

Originality/value

The paper simulated all the seven flow regimes with superior results compared to existing methodology. New correlations derived numerically are compared to published experimental correlations to understand the difference between models.
Exploration and prioritization of lean techniques in a hotel supply chain
Authors: Al-Aomar Raid , Hussain Matloub
Published: July 2018

Purpose

The purpose of this paper is to develop a framework for identification, categorization and prioritization of lean techniques adopted in a hotel supply chain.

Design/methodology/approach

A survey tool is used for the identification of lean techniques that are relevant to a hotel supply chain. The targeted sample includes experts from 50 four- and five-star hotels in the United Arab Emirates (UAE) that confirmed experience in implementing lean practices across hotels supply chain. A Supplier-Inputs-Process-Outputs-Customers (SIPOC) chart and experts’ opinion are used to allocate and categorize the identified lean techniques across the construct of the hotel supply chain. Finally, analytical hierarchy process (AHP) is used to prioritize the criteria and sub-criteria of adopted lean techniques.

Findings

Study results have identified six main categories of lean practices and 19 specific lean techniques as relevant to a hotel supply chain. The identified categories include JIT, Kaizen, Quality, Inventory, Maintenance and Standardization. The study found that JIT and Kaizen take the top priority among the identified categories of lean practices. In line with that, on-time service to customers, effective improvement system and on-time delivery from suppliers were found to be the three most relevant lean techniques to a hotel supply chain.

Research limitations/implications

The study has targeted a representative sample of hotels with experience in implementing lean practices. Study findings have several implications to researchers and practitioners for effective adoption of lean techniques within a hotel supply chain. However, the accuracy and credibility of results obtained from this research including SIPOC allocation and lean categorization are highly dependent on the accuracy and credibility of collected empirical data from surveyed hotels within the study context. Results of AHP prioritization also depend on the credibility of judgements made by the hotels’ supply chain experts.

Practical implications

The study provides the hospitality industry with a structured approach that can help in a prioritized adoption of most relevant lean techniques across the hotel supply chain to reduce wastes, create value, increase efficiency and improve the service level. Study findings can be used by hotel management to direct and focus the effort of lean capacity building, resources allocation and implementation plans.

Originality/value

Limited research is available on lean management in the context of a hotel supply chain. Also, most of the previous research is focused on lean impacts, while academics and practitioners agree that the identification and prioritization of most relevant lean techniques is crucial to the successful implementation of lean management for waste reduction and value creation. This research addresses this important issue in hotel supply chains and proposes a structured approach for effective lean adoption.
Does financial development accelerate economic growth?
Authors: Fetai Besnik Taip
Published: July 2018

Purpose

This study aims to empirically explore whether there is causality and in which direction, i.e. whether financial development generates economic growth or whether financial development merely follows economic growth in transition European countries, including Russian Federation and Turkey, during 1998-2015.

Design/methodology/approach

The study uses different techniques such as pooled OLS, fixed and random effects and the Hausman–Taylor model with instrumental variables.

Findings

The regression results show a positive relationship between financial development indicators and real GDP per capita growth, thus supporting the hypothesis that finance leads economic growth. The result also shows that financial crisis has a negative effect on real GDP per capita growth. Furthermore, these findings show that government spending and inflation have a negative impact on real GDP per capita growth. The study also shows that financial development plays growth-supporting role in real GDP per capita growth in 20 European countries in transition, including Russian Federation and Turkey.

Practical implications

As financial development generates real GDP per capita growth, on the basis of the results of the study, a course of action that involves institutional improvement and incentivizing competition in the financial sector is recommended to the Central Banks’ policymakers in transition economies. These will in turn lead to higher real GDP per capita growth.

Originality/value

The study is original in nature and makes effort to promote financial development in transition European countries, including Russian Federation and Turkey. The findings of this study will be of value to Central Banks and other policymakers.
Professional development of future foreign language teachers during short-term exchanges
Authors: Helmchen Christian , Melo-Pfeifer Sílvia
Published: July 2018

Purpose

The purpose of this paper is to analyze the self-perceived influence of short-term exchanges in schools abroad on future foreign language teacher’s professionalization, regarding professional values and pedagogy and practice. It grasps students’ changes in the perception of values attached to short-term exchanges in a professional setting.

Design/methodology/approach

In the scope of the European project SPIRAL, four prospective foreign language teachers attended a two-week internship at schools in another country. This paper explores, resorting to a combined content and discourse analysis, their letters of motivation (two months before the exchange), emails sent individually to the local coordinator (one week after the arrival) and a focus-group interview (two months after the arrival).

Findings

Future foreign language teachers change their focus when referring to the values attached to their experiences at schools abroad: from an initial focus on language skills improvement, they come to value the intercultural pedagogic experience they lived, focusing on differences and similarities between professional values and pedagogical practices across the contexts.

Practical implications

A generalized introduction of professional exchange programs, both in pre-service and continuing teacher education, could improve teachers’ perceptions of global structural, educational, political and curricular contexts and demands. It would also help the teachers decenter from educational practices and professional habitus taken for granted, and raise their awareness of what it means to be educated and professionalized in other contexts.

Originality/value

Few studies have focused on short-term exchanges and their impact on teachers’ professional development. The present paper highlights the pedagogical, intercultural and identity-building potential of short-term exchanges in foreign language teacher education.
Design Elements of Listeria Environmental Monitoring Programs in Food Processing Facilities: A Scoping Review of Research and Guidance Materials
Authors: Zoellner Claire , Ceres Kristina , Ghezzi‐Kopel Kate , Wiedmann Martin , Ivanek Renata
Published: July 2018

Occurrence of Listeria monocytogenes (Lm), the causative agent of listeriosis, in food processing facilities presents considerable challenges to food producers and food safety authorities. Design of an effective, risk‐based environmental monitoring (EM) program is essential for finding and eliminating Lm from the processing environment to prevent product contamination. A scoping review was conducted to collate and synthesize available research and guidance materials on Listeria EM in food processing facilities. An exhaustive search was performed to identify all available research, industry and regulatory documents, and search results were screened for relevance based on eligibility criteria. After screening, 198 references were subjected to an in‐depth review and categorized according to objectives for conducting Listeria sampling in food processing facilities and food sector. Mapping of the literature revealed research and guidance gaps by food sector, as fresh produce was the focus in only 10 references, compared to 72 on meat, 52 on fish and seafood, and 50 on dairy. Review of reported practices and guidance highlighted key design elements of EM, including the number, location, timing and frequency of sampling, as well as methods of detection and confirmation, and record‐keeping. While utilization of molecular subtyping methods is a trend that will continue to advance understanding of Listeria contamination risks, improved study design and reporting standards by researchers will be essential to assist the food industry optimize their EM design and decision‐making. The comprehensive collection of documents identified and synthesized in this review aids continued efforts to minimize the risk of Lm contaminated foods.
Mycotoxin Biomarkers of Exposure: A Comprehensive Review
Authors: Vidal Arnau , Mengelers Marcel , Yang Shupeng , De Saeger Sarah , De Boevre Marthe
Published: July 2018

To date, the use of biomarkers has become generally accepted. Biomarker‐driven research has been proposed as a successful method to assess the exposure to xenobiotics by using concentrations of the parent compounds and/or metabolites in biological matrices such as urine or blood. However, the identification and validation of biomarkers of exposure remain a challenge. Recent advances in high‐resolution mass spectrometry along with new analytical (post‐acquisition data‐mining) techniques will improve the quality and output of the biomarker identification process. Chronic or even acute exposure to mycotoxins remains a daily fact, and therefore it is crucial that the mycotoxins’ metabolism is unravelled so more knowledge on biomarkers in humans and animals is acquired. This review aims to provide the scientific community with a comprehensive overview of reported in vitro and in vivo mycotoxin metabolism studies in relation to biomarkers of exposure for deoxynivalenol, nivalenol, fusarenon‐X, T‐2 toxin, diacetoxyscirpenol, ochratoxin A, citrinin, fumonisins, zearalenone, aflatoxins, and sterigmatocystin.