bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of DPD coarse-grained models: From bulk to interfacial properties
Authors: Solano Canchaya José G. , Dequidt Alain , Goujon Florent , Malfreyt Patrice
Published: August 2016

A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve.
Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas
Authors: Izacard Olivier
Published: August 2016

In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basis sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main results, it is shown that (i) the empirical formula for the secondary electron emission is not consistent with a MDF due to the presence of super-thermal particles, (ii) the super-thermal particles can replace a diffusion parameter in the Langmuir probe current formula, and (iii) the entropy can explicitly decrease in presence of sources only for the introduced INMDF without violating the second law of thermodynamics. Moreover, the first order entropy of an infinite number of super-thermal tails stays the same as the entropy of a MDF. The latter demystifies the Maxwell's demon by statistically describing non-isolated systems.
A novel rotating experimental platform in a superconducting magnet
Authors: Chen Da , Cao Hui-Ling , Ye Ya-Jing , Dong Chen , Liu Yong-Ming , Shang Peng , Yin Da-Chuan
Published: August 2016

This paper introduces a novel platform designed to be used in a strong static magnetic field (in a superconducting magnet). The platform is a sample holder that rotates in the strong magnetic field. Any samples placed in the platform will rotate due to the rotation of the sample holder. With this platform, a number of experiments such as material processing, culture of biological systems, chemical reactions, or other processes can be carried out. In this report, we present some preliminary experiments (protein crystallization, cell culture, and seed germination) conducted using this platform. The experimental results showed that the platform can affect the processes, indicating that it provides a novel environment that has not been investigated before and that the effects of such an environment on many different physical, chemical, or biological processes can be potentially useful for applications in many fields.
Structural, dielectric, ferroelectric, and electrocaloric properties of 2% Gd2O3 doping (Na0.5Bi0.5)0.94Ba0.06TiO3 ceramics
Authors: Turki O. , Slimani A. , Seveyrat L. , Sebald G. , Perrin V. , Sassi Z. , Khemakhem H. , Lebrun L.
Published: August 2016

Structural, dielectric, and ferroelectric properties, and electrocaloric effects of pure and Gd doped (Na0.5Bi0.5)0.94Ba0.06TiO3  ceramics prepared by the conventional solid-solid method have been carried out. The X-ray diffraction analysis confirms a pure perovskite structure with the coexistence of tetragonal and rhombohedra structures in both powders. The thermal and frequency dependences of the dielectric constants of both ceramics revealed relaxor behavior. The two compounds exhibited two phase transitions: ferroelectric/antiferroelectric (FE/AFE) transition followed by an antiferroelectric/paraelectric (AFE/PE) transition at higher temperatures. Remarkably, we noticed that the small amount of Gd doping (2%) highly enhanced the dielectric properties of the parent compound by about 71%. The phase diagram was as well influenced by the Gd doping, where the FE/AFE transition temperature rose from 90 in the parent compound to 115 °C in the doped one whereas the AFE/PE transition temperature was decreased from 320 to 270 °C, respectively. The direct electrocaloric measurements performed on both compounds showed that the ferroelectric/antiferroelectric phase transition was accompanied by a significant electrocaloric effect. The Gd3+ doping improved the electrocaloric properties of the parent compound, where a remarkable temperature variation of 1.4 K was obtained in the doped ceramic. The results of the direct electrocaloric measurements will be compared and discussed with those derived from the indirect method.
Microwave-free magnetometry with nitrogen-vacancy centers in diamond
Authors: Wickenbrock Arne , Zheng Huijie , Bougas Lykourgos , Leefer Nathan , Afach Samer , Jarmola Andrey , Acosta Victor M. , Budker Dmitry
Published: August 2016

We use magnetic-field-dependent features in the photoluminescence of negatively charged nitrogen-vacancy centers to measure magnetic fields without the use of microwaves. In particular, we present a magnetometer based on the level anti-crossing in the triplet ground state at 102.4 mT with a demonstrated noise floor of 6 nT/Hz, limited by the intensity noise of the laser and the performance of the background-field power supply. The technique presented here can be useful in applications where the sensor is placed close to conductive materials, e.g., magnetic induction tomography or magnetic field mapping, and in remote-sensing applications since principally no electrical access is needed.
Switchable and tunable film bulk acoustic resonator fabricated using barium strontium titanate active layer and Ta2O5/SiO2 acoustic reflector
Authors: Sbrockey N. M. , Kalkur T. S. , Mansour A. , Khassaf H. , Yu H. , Aindow M. , Alpay S. P. , Tompa G. S.
Published: August 2016

A solidly mounted acoustic resonator was fabricated using a Ba0.60Sr0.40TiO3 (BST) film deposited by metal organic chemical vapor deposition. The device was acoustically isolated from the substrate using a Bragg reflector consisting of three pairs of Ta2O5/SiO2 layers deposited by chemical solution deposition. Transmission electron microscopy verified that the Bragg reflector was not affected by the high temperatures and oxidizing conditions necessary to process high quality BST films. Electrical characterization of the resonator demonstrated a quality factor (Q) of 320 and an electromechanical coupling coefficient (Kt2) of 7.0% at 11 V.
Far-infrared-light shadowgraphy for high extraction efficiency of extreme ultraviolet light from a CO2-laser-generated tin plasma
Authors: Matsukuma Hiraku , Hosoda Tatsuya , Suzuki Yosuke , Yogo Akifumi , Yanagida Tatsuya , Kodama Takeshi , Nishimura Hiroaki
Published: August 2016

The two-color, double-pulse method is an efficient scheme to generate extreme ultraviolet light for fabricating the next generation semiconductor microchips. In this method, a Nd:YAG laser pulse is used to expand a several-tens-of-micrometers-scale tin droplet, and a CO2 laser pulse is subsequently directed at the expanded tin vapor after an appropriate delay time. We propose the use of shadowgraphy with a CO2 laser probe-pulse scheme to optimize the CO2 main-drive laser. The distribution of absorption coefficients is derived from the experiment, and the results are converted to a practical absorption rate for the CO2 main-drive laser.
Elimination of the gate and drain bias stresses in I–V characteristics of WSe2 FETs by using dual channel pulse measurement
Authors: Park Jun-Mo , Cho In-Tak , Kang Won-Mook , Park Byung-Gook , Lee Jong-Ho
Published: August 2016

Intrinsic transfer and output characteristics of WSe2 field effect transistors are obtained by adopting the dual channel pulsed I–V measurement. Due to the DC gate bias stress during the measurement, a large hysteresis is observed and increased with increasing the sweeping range of the gate bias in the transfer curves. In addition, as a drain bias increases, the drain bias stress during the measurement induces the threshold voltage shift. The output curves measured by a DC method are significantly affected by the drain bias sweeping direction and the previous measurement, which leads to a large error in the analysis. By using the dual channel pulsed I–V measurement with a short turn-on time (10−4 s), a long turn-off time (1 s), and a base voltage (gate and drain bias during turn-off time) of 0 V, hysteretic behaviors caused by the gate bias stress and threshold voltage shift due to the drain bias stress in transfer curves are eliminated. The effect of the drain bias sweeping direction and the previous measurement in output curves are also eliminated, and the output curves show a typical field effect behavior. The intrinsic characteristics of WSe2 field effect transistors show negligible hysteresis and remarkably enhanced mobility (∼200 cm2/V s), and higher current drive capability compared to those of DC measurements.
Taking on astronomy misconceptions isn’t easy
Authors: Favia Andrej , Comins Neil F. , Batuski David J.
Published: August 2016

With the help of surveys and statistics, we tried to optimize the order in which we presented astronomy concepts. But students persisted in retaining wrong ideas about them.
Circumventing the natural, frequent oestrogen waves of the female cheetah (Acinonyx jubatus) using oral progestin (Altrenogest)
Authors: Crosier Adrienne E. , Comizzoli Pierre , Koester Diana C. , Wildt David E.
Published: August 2016

Cheetah are induced ovulators, experiencing short, variable oestrogen waves year-round. Exogenous gonadotrophin administration induces ovulation, but success is variable and often improves if ovaries are quiescent. After affirming the presence of short-term oestrogenic waves, we examined the effect of the timing of administration of exogenous equine and human chorionic gonadotrophins (eCG–hCG) within the oestrogen concentration pattern on subsequent follicle development and oocyte and corpus luteum quality. We also investigated ovarian suppression using an oral progestin (Altrenogest, 7 days) and assessed whether Altrenogest moderated adrenal activity by reducing glucocorticoid metabolites. All cheetahs exhibited short (every ~7–10 days), sporadic, year-round increases in faecal oestradiol punctuated by unpredictable periods (4–10 weeks) of baseline oestradiol (anoestrous). Gonadotrophin (eCG–hCG) efficacy was not affected by oestradiol ‘wave’ pattern if administered ≥3 days after an oestrogen peak. Such cheetahs produced normative faecal progestagen patterns and higher numbers (P < 0.06) of mature oocytes than females given gonadotrophins ≤2 days after an oestradiol peak. Altrenogest supplementation expanded the interval between oestradiol peaks to 12.9 days compared with 7.3 days without progestin pretreatment. Altrenogest-fed females excreted less (P < 0.05) glucocorticoid metabolites than non-supplemented counterparts. Results show that Altrenogest is effective for suppressing follicular activity, may contribute to reduced glucocorticoid production and may result in more effective ovulation induction via gonadotrophin therapy.
Cross-linguistic patterns in the acquisition of quantifiers
Authors: Katsos Napoleon , Cummins Chris , Ezeizabarrena Maria-José , Gavarró Anna , Kuvač Kraljević Jelena , Hrzica Gordana , Grohmann Kleanthes K. , Skordi Athina , Jensen de López Kristine , Sundahl Lone , van Hout Angeliek , Hollebrandse Bart , Overweg Jessica , Faber Myrthe , van Koert Margreet , Smith Nafsika , Vija Maigi , Zupping Sirli , Kunnari Sari , Morisseau Tiffany , Rusieshvili Manana , Yatsushiro Kazuko , Fengler Anja , Varlokosta Spyridoula , Konstantzou Katerina , Farby Shira , Guasti Maria Teresa , Vernice Mirta , Okabe Reiko , Isobe Miwa , Crosthwaite Peter , Hong Yoonjee , Balčiūnienė Ingrida , Ahmad Nizar Yanti Marina , Grech Helen , Gatt Daniela , Cheong Win Nee , Asbjørnsen Arve , Torkildsen Janne von Koss , Haman Ewa , Miękisz Aneta , Gagarina Natalia , Puzanova Julia , Anđelković Darinka , Savić Maja , Jošić Smiljana , Slančová Daniela , Kapalková Svetlana , Barberán Tania , Özge Duygu , Hassan Saima , Chan Cecilia Yuet Hung , Okubo Tomoya , van der Lely Heather , Sauerland Uli , Noveck Ira
Published: August 2016

Significance

Although much research has been devoted to the acquisition of number words, relatively little is known about the acquisition of other expressions of quantity. We propose that the order of acquisition of quantifiers is related to features inherent to the meaning of each term. Four specific dimensions of the meaning and use of quantifiers are found to capture robust similarities in the order of acquisition of quantifiers in similar ways across 31 languages, representing 11 language types.
Transition path theory analysis of c-Src kinase activation
Authors: Meng Yilin , Shukla Diwakar , Pande Vijay S. , Roux Benoît
Published: August 2016

Significance

Proteins often exhibit large-scale collective motions that are essential for biological macromolecules to perform their functions. To understand the nature of the large-scale conformational dynamics, we applied transition path theory to analyze the Markovian microstates that are obtained from extensive unrestrained molecular dynamics simulations, using the activating conformational changes in the kinase domain of c-Src nonreceptor tyrosine kinase as an example. These results elucidate the fine details of the conformational transition and offer a perspective for the interpretation of the conformational transition. Microstates that are not crucial to the thermodynamics but are important for the kinetics can be identified by transition path theory, explaining why extensive conformational sampling is needed to reproduce the accurate kinetics.
Leaky RyR2 channels unleash a brainstem spreading depolarization mechanism of sudden cardiac death
Authors: Aiba Isamu , Wehrens Xander H. T. , Noebels Jeffrey L.
Published: August 2016

Significance

Gain-of-function “leaky” ryanodine receptor-2 (RyR2) mutations are detected in many cases of human sudden cardiac death and sudden unexpected death in epilepsy. The early lethality is considered to be due to arrhythmogenic behavior of cardiomyocytes caused by excess intracellular calcium ions released from internal stores. In this study, we find that the leaky RyR2 mutation also modulates neurotransmitter release from neurons in brainstem autonomic centers and facilitates spreading depolarization, which when provoked silences autonomic microcircuitry in the dorsal medulla. When seizures were generated in mice carrying a leaky RyR2 mutation, the mice experienced sudden cardiorespiratory collapse concomitant with brainstem spreading depolarization. These findings indicate that in addition to the myocardium, the brainstem is a target of leaky RyR2 mutations.
Learning to soar in turbulent environments
Authors: Reddy Gautam , Celani Antonio , Sejnowski Terrence J. , Vergassola Massimo
Published: August 2016

Significance

Thermals are ascending currents that typically extend from the ground up to the base of the clouds. Birds and gliders piggyback thermals to fly with a reduced expenditure of energy, for example, during migration, and to extend their flying range. Flow in the thermals is highly turbulent, which poses the challenge of the orientation in strongly fluctuating environments. We combine numerical simulations of atmospheric flow with reinforcement learning methods to identify strategies of navigation that can cope with and even exploit turbulent fluctuations. Specifically, we show how the strategies evolve as the level of turbulent fluctuations increase, and we identify those sensorimotor cues that are effective at directing turbulent navigation.
Contrasting climate change impact on river flows from high-altitude catchments in the Himalayan and Andes Mountains
Authors: Ragettli Silvan , Immerzeel Walter W. , Pellicciotti Francesca
Published: August 2016

Significance

Changes in the hydrology of high-altitude catchments may have major consequences for downstream water supply. Based on model projections with a higher spatiotemporal resolution and degree of process complexity than any previous intercontinental comparative study, we show that the impacts of climate change cannot be generalized. These impacts range from a high climatic sensitivity, decreasing runoff, and significant seasonal changes in the Central Andes of Chile to increasing future runoff, limited seasonal shifts, but increases in peak flows in the Nepalese Himalaya. This study constrains uncertainty about response times and mechanisms controlling glacier and runoff response to climate and sets a benchmark for process-based modeling of the climate change impact on the hydrology of high-altitude catchments.
Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers
Authors: Schwarz Ryan S. , Moran Nancy A. , Evans Jay D.
Published: August 2016

Significance

Using a social insect model, we tested how supplementing young adult bees with a resident microbiota species affects host physiology and microbiome composition. This supplementation had significant consequences for host development and detoxification responses, parasite susceptibility, and microbiome community structure. Our results show that early perturbation of the microbiota composition can have sustained consequences for hosts. Additionally, this work provides a cautionary tale to the arbitrary use of probiotics in animal health management and highlights the importance of experimental research addressing factors that shape animal microbiome communities.
Innate immunity kinase TAK1 phosphorylates Rab1 on a hotspot for posttranslational modifications by host and pathogen
Authors: Levin Rebecca S. , Hertz Nicholas T. , Burlingame Alma L. , Shokat Kevan M. , Mukherjee Shaeri
Published: August 2016

Significance

Rab GTPases regulate vesicle traffic within the cell by switching between active (GTP-bound) and inactive (GDP-bound) states. The switch II region of Rab proteins undergoes a significant conformational change to switch between states. Rab1 is hijacked during intracellular
Legionella pneumophila
infection by bacterial effector-mediated posttranslational modifications of the switch II region, a unique mechanism for regulation of Rab function. We present new evidence that Rab1 is endogenously modified within switch II by TGF-β activated kinase 1 (TAK1), a kinase crucial for responding to infection. We show phosphorylation of Rab1 is necessary for normal Rab1 function. Interestingly, phosphorylation of Rab1 is competed during
Legionella
infection, adding to evidence that
Legionella
target substrates of the innate immunity kinase TAK1.
Unhealthy Alcohol use in Primary Care Patients who Screen Positive for Drug Use
Authors: Maynié-François Christine , Cheng Debbie M. , Samet Jeffrey H. , Lloyd-Travaglini Christine , Palfai Tibor , Bernstein Judith , Saitz Richard
Published: August 2016

Background

Unhealthy alcohol use (UAU) is common among people who use other drugs; however, little information is available about UAU among patients who screen positive for drugs in primary care, where the clinical priority might be assumed to be drug use. This study aimed at describing the occurrence of UAU and its association with substance use–related outcomes in such patients.

Methods

This cohort study is a secondary analysis of data from a randomized trial of brief intervention for primary care patients screening positive for drug use. UAU was assessed at baseline; the main independent variable was any heavy drinking day in the past month. Outcomes including drug use characteristics and substance use–related consequences were assessed at baseline and 6 months later.

Results

Of 589 primary care patients with drug use, 48% had at least 1 past-month heavy drinking day. The self-identified main drug was marijuana for 64%, cocaine for 18%, and an opioid for 16%. Any heavy drinking at baseline was negatively associated with number of days use of the main drug at 6 months (incidence rate ratio [IRR] = 0.75, 95% confidence interval [CI]: 0.62–0.91), but positively associated with the use of more than 1 drug (IRR = 1.73, 95% CI: 1.17–2.55) and unsafe sex (odds ratio [OR] = 1.90, 95% CI: 1.21–2.98).

Conclusion

Unhealthy alcohol use is common among patients identified by screening in primary care as using other drugs. Unexpectedly, UAU was negatively associated with days of main drug use. But, as expected, it was positively associated with other drug use characteristics and substance use–related consequences. These findings suggest that attention should be given to alcohol use among primary care patients who use other drugs.
From writing to reading the encyclopedia of life
Authors: Hebert Paul D. N. , Hollingsworth Peter M. , Hajibabaei Mehrdad
Published: August 2016

Prologue ‘As the study of natural science advances, the language of scientific description may be greatly simplified and abridged. This has already been done by Linneaus and may be carried still further by other invention. The descriptions of natural orders and genera may be reduced to short definitions, and employment of signs, somewhat in the manner of algebra, instead of long descriptions. It is more easy to conceive this, than it is to conceive with what facility, and in how short a time, a knowledge of all the objects of natural history may ultimately be acquired; and that which is now considered learning and science, and confined to a few specially devoted to it, may at length be universally possessed in every civilized country and in every rank of life’. J. C. Louden 1829.
Magazine of natural history
, vol.
1
.

This article is part of the themed issue ‘From DNA barcodes to biomes’.
Censusing marine eukaryotic diversity in the twenty-first century
Authors: Leray Matthieu , Knowlton Nancy
Published: August 2016

The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems.

This article is part of the themed issue ‘From DNA barcodes to biomes’.
Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches
Authors: Yahr Rebecca , Schoch Conrad L. , Dentinger Bryn T. M.
Published: August 2016

The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of ‘sequences without names’ that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.

This article is part of the themed issue ‘From DNA barcodes to biomes’.
The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life
Authors: Zhou Xin , Frandsen Paul B. , Holzenthal Ralph W. , Beet Clare R. , Bennett Kristi R. , Blahnik Roger J. , Bonada Núria , Cartwright David , Chuluunbat Suvdtsetseg , Cocks Graeme V. , Collins Gemma E. , deWaard Jeremy , Dean John , Flint Oliver S. , Hausmann Axel , Hendrich Lars , Hess Monika , Hogg Ian D. , Kondratieff Boris C. , Malicky Hans , Milton Megan A. , Morinière Jérôme , Morse John C. , Mwangi François Ngera , Pauls Steffen U. , Gonzalez María Razo , Rinne Aki , Robinson Jason L. , Salokannel Juha , Shackleton Michael , Smith Brian , Stamatakis Alexandros , StClair Ros , Thomas Jessica A. , Zamora-Muñoz Carmen , Ziesmann Tanja , Kjer Karl M.
Published: August 2016

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.

This article is part of the themed issue ‘From DNA barcodes to biomes’.
Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
Authors: Rice Edward S. , Kohno Satomi , John John St. , Pham Son , Howard Jonathan , Lareau Liana , O’Connell Brendan , Hickey Glenn , Armstrong Joel , Deran Alden , Fiddes Ian , Platt Roy N. , Gresham Cathy , McCarthy Fiona , Kern Colin , Haan David , Phan Tan , Schmidt Carl , Sanford Jeremy , Ray David A. , Paten Benedict , Guillette Louis J. , Green Richard E.
Published: August 2016

The American alligator,Alligator mississippiensis, like all crocodilians, has temperature-dependent sex determination, in which the sex of an embryo is determined by the incubation temperature of the egg during a critical period of development. The lack of genetic differences between male and female alligators leaves open the question of how the genes responsible for sex determination and differentiation are regulated. One insight into this question comes from the fact that exposing an embryo incubated at male-producing temperature to estrogen causes it to develop ovaries. Because estrogen response elements are known to regulate genes over long distances, a contiguous genome assembly is crucial for predicting and understanding its impact.

We present an improved assembly of the American alligator genome, scaffolded within vitroproximity ligation (Chicago) data. We use this assembly to scaffold two other crocodilian genomes based on synteny. We perform RNA sequencing of tissues from American alligator embryos to find genes that are differentially expressed between embryos incubated at male-versus female-producing temperature. Finally, we use the improved contiguity of our assembly along with the current model of CTCF-mediated chromatin looping to predict regions of the genome likely to contain estrogen-responsive genes. We find that these regions are significantly enriched for genes with female-biased expression in developing gonads after the critical period during which sex is determined by incubation temperature. We thus conclude that estrogen signaling is a major driver of female-biased gene expression in the post-temperature sensitive period gonads.
A global view of meiotic double-strand break end resection
Authors: Mimitou Eleni P. , Yamada Shintaro , Keeney Scott
Published: August 2016

The DNA double-strand breaks that initiate homologous recombination during meiosis are subject to extensive 5′→3′ exonucleolytic processing. This resection is a central and conserved feature of recombination, yet its mechanism is poorly understood. Using a purpose-made deep-sequencing method, we mapped meiotic resection endpoints genome-wide at high spatial resolution inSaccharomyces cerevisiae. Generating full-length resection tracts requires Exo1 exonuclease activity and the DNA-damage responsive kinase Tel1, but not the helicase Sgs1. Tel1 is also required for efficient and timely initiation of resection. We find that distributions of resection endpoints at individual genomic loci display pronounced heterogeneity that reflects a tendency for nucleosomes to block Exo1 in vivo, yet modeling experiments indicate that Exo1 digests chromatin with high apparent processivity and at rates approaching those for naked DNA in vitro. This paradox points to nucleosome destabilization or eviction as a determining feature of the meiotic resection landscape.
Investigating and implementing an extensible, adaptable game plan for digital initiatives at a large state university
Authors: Dressler Virginia A.
Published: August 2016

Purpose

The purpose of this paper is to explore the process of assessing the needs of a digital repository. The study’s institution – Kent State University, a large state university – is currently re-envisioning their digital library services to accommodate emerging technologies with an agile framework and platform. This paper includes discussion on the process of creating a sustainable digital initiatives program, a plan of action for migration, platform decision rationale and an overview of planning for future projects that is both flexible and extensible in nature.

Design/methodology/approach

The article’s approach is to examine the process of review and selection of the digital repository at Kent State University through the needs and requirements checklist the team devised according to the institution’s specifications. Literature published in the past five years is reviewed and applied to the selection process. The author maps out a plan that can be adaptable for growth and sustainability for a content management system.

Findings

Using models identified in the article, the team mapped a solution that can enhance the use and interaction by patrons to digital collections as well as provide a method to ensure the longevity of digital assets.

Originality/value

The article addresses issues that are inherent to digital content management systems of all shapes and sizes, and strives to provide a solution that would be relevant and applicable to many types of institutions in regard to digital repositories.
Academic use of smartphones by university students: a developing country perspective
Authors: Hossain Md. Emran , Ahmed S.M. Zabed
Published: August 2016

Purpose

This paper aims to investigate the use of smartphones for academic purposes by students at Dhaka University, the top-ranked university in Bangladesh.

Design/methodology/approach

Students currently using smartphones answered a questionnaire survey, which focused on whether or not students used smartphones for academic works and, if so, for what purposes they used them and their opinion on the advantages of using smartphones for academic purposes. Descriptive statistics were used to analyze demographic and academic characteristics of the students in relation to their smartphone usage. Non-parametric analyses were performed using Mann–Whitney and Kruskal–Wallis tests to compare between students’ demographic and academic variables and their opinion on the advantages of academic use of smartphones.

Findings

The findings indicate that a vast majority of university students used smartphones for academic purposes. They, on average and across the board, had a positive perception toward academic use of smartphones. Although there were some differences in terms of gender, age, place of origin and duration of smartphone use, these differences were largely due to fact that a smartphone is a relatively new addition to the life of most students who participated in this study.

Originality/value

Research investigating the academic use of smartphones in the perspective of developing countries is virtually non-existent. This is the first time an effort has been made to examine the use of smartphones by a large sample of university students in Bangladesh.
Deploying Lean Six Sigma framework in an automotive component manufacturing organization
Authors: Swarnakar Vikas , Vinodh S.
Published: August 2016

Purpose

This paper aims to deploy Lean Six Sigma (LSS) framework to facilitate defect reduction and enhance bottom line results of an automotive component manufacturing organization.

Design/methodology/approach

LSS is a business process improvement strategy widely used in the manufacturing field for enhancing manufacturing organization performance. The integration of Lean and Six Sigma will enable the attainment of defects reduction by eliminating non-value-adding activities from production line. LSS framework has been developed with the integration of define–measure–analysis–improve–control (DMAIC) tools and techniques.

Findings

The finding of this study is that the LSS framework has been successfully implemented in automotive component manufacturing organization, and non-value-adding activities and defects from assembly line have been reduced. The proposed LSS framework applies lean tools within Six Sigma DMAIC approach to facilitate waste elimination and defect reduction. The developed framework with linkage of DMAIC tools and techniques reduces defects and non-value-adding activities with enhanced bottom line results. The implementation of proposed LSS framework shows effective improvement in key metrics.

Research limitations/implications

The developed framework has been test implemented in an automotive component manufacturing organization. In future, more number of studies could be conducted. Further, advanced lean tools and techniques could be included in the framework for increasing the effectiveness of production line.

Practical implications

The proposed LSS framework with linkage of DMAIC tools and techniques has been successfully implemented in an assembly line of automotive component manufacturing organization. This method is presently applied for an automotive component manufacturing organization; in future, the approach could be applied in different industrial sectors with addition of new tools and techniques for improving its effectiveness.

Originality/value

LSS framework has been designed and test implemented in an assembly line of an automotive component manufacturing organization. Hence, the inferences are practical and key results of the study.
Credit card account opening excellence using six sigma methodology
Authors: Islam Samsul
Published: August 2016

Purpose

This study aims to expand the current knowledge of the Six Sigma approach in a period of time when there is little direct evidence of the need to improve the credit card account opening process. This is an important but neglected area of focus in the Six Sigma literature. This study explores the extent to which process improvement practices are extended to the credit card department.

Design/methodology/approach

A case study methodology is adopted in this study to facilitate an exploration of the implemented Six Sigma approach in the credit card department of a leading commercial bank. The process improvement tool used is the define, measure, analyze, improve and control (DMAIC) cycle.

Findings

The study’s results confirm that the Six Sigma approach improves the quality of the credit card account opening process. So, the Six Sigma approach can account for a reduced number of keying-in errors, resulting in better data accuracy and improved customer satisfaction.

Research limitations/implications

The authors, in an attempt to render the study results more feasible for data collection, have chosen to focus on the process of the new accounts unit of the credit card department. Therefore, the authors have not taken into account the other units (e.g. transaction processing) of the same department.

Practical implications

The results of this study will be useful in persuading bank management to evaluate and implement the Six Sigma approach. Hence, this research will assist bank managers with replies to questions, such as: “What impact will Six Sigma have on process-centric improvement, such as the new accounts opening process of a credit card department?”

Originality/value

Within the literature on the Six Sigma practice, there is little research that focuses on the implementation of this particular toolset especially for credit card departments. This indicates a gap in the field. A new contribution to bridging that gap comes from the analysis of the results for the Six Sigma concept, which addresses the new accounts opening process.
Adding store to web: migration and synergy effects in multi-channel retailing
Authors: Fornari Edoardo , Fornari Daniele , Grandi Sebastiano , Menegatti Mario , Hofacker Charles F.
Published: August 2016

Purpose

– The purpose of this paper is to investigate the topic of multi-channel retailing. Specifically, the research intends to determine if and to what extent the opening of physical stores by a former web-only retailer reduces or extends overall retail sales, and whether such effects tend to change over time. Empirical analysis focuses on data elaboration from a retailer who has passed from the initial mono-channel model (pure online), to a multi-channel one with the opening of stores.

Design/methodology/approach

– Through the analysis of an internal data set of a leading consumer electronics retailer applying Probit and Logit estimation techniques, the authors extract information about actual customers’ purchases (or rather retail sales) in three newly opened stores and about online purchases (through an e-commerce web site managed by the same retailer with the same store brand) by people living in the new store service areas before and after the openings.

Findings

– The paper shows that, for the single customer, the probability of purchasing online is reduced by the store opening in the short term, but tends to increase in the long term. Besides, results indicate that long-term synergy between the two channels depends mainly on indirect influence due to the mere presence of the store brand in the area rather than on the direct experience of shopping in the store.

Research limitations/implications

– The study highlights that channel portfolio enlargement from mono- to multi-channel retailing tends to activate a sort of life cycle; while in the early phase of store addition web sales tend to be cannibalized because the two channels are perceived as “substitutes” for each other, in the long run migration turns into a synergy effect; different channels tend to interact with and reinforce each other as customer touch points of the same retailer, in an omni-channel perspective.

Originality/value

– The paper herein presents various original elements concerning types of available data (actual sales rather than consumers’ intentions/perceptions and individual level data rather than aggregate level ones), estimation technique used (binary choice model) and research hypotheses (distinguishing between “direct” and “indirect” synergy effects in multi-channel retailing).
An economic analysis of the philosophical common good
Authors: Murphy Tim , Parkey Jeff
Published: August 2016

Purpose

– The purpose of this paper is to analyze economically several versions of the philosophical common good in order to contribute to the search for a viable conceptualization of the common good.

Design/methodology/approach

– The paper presents an economic analysis of the common good by examining the extent to which eight different versions of the philosophical concept possess the consumption characteristics of excludability and rivalry – and thus how each version may be classified as an economic good: private, public, common, or club.

Findings

– One of the examined versions of the philosophical common good is an economic common good; three versions are club goods; and four versions are public goods. Only those versions of the common good that are classifiable as public goods merit consideration as adequate conceptualizations in political and philosophical thought. In assessing the admissible versions the authors conclude that a viable conceptualization of the common good may simply be the maintenance of a peaceful social order that allows people to pursue their individual and collective goals in community.

Originality/value

– The paper shows that an analysis of the philosophical common good using the economic criteria of excludability and rivalry can contribute to common good discourse.
Energy use as skilled process: Gardeners and wind in highland Scotland
Authors: Senior Louise
Published: August 2016

Using everyday human encounters with the wind as a starting point for exploring ideas about energy, I argue that human experiences of energy are not experiences of a ‘thing‐in‐itself’, but emerge through a skilled process. Following Rupp (2013), who states that success is achieved through managing flows of energy, I discuss how people become proficient at managing wind flow in relation to specific tasks and places and what this process entails for them. I advance the notion that wind energy can be understood both as an influence that mediates action and as subject to influence by actions, creating an emerging point of continual negotiation. People become skilled at managing energetic flows in order to obtain desired results.
The rhythms of infrastructure
Authors: Jalas Mikko , Rinkinen Jenny , Silvast Antti
Published: August 2016

Technology organizes social life in different ways. This article focuses on the temporal ordering brought about by household energy technologies and the broader infrastructures upon which they depend. Such technology saves time, and the energy services so provided allow for comfort, flexibility and the independence from natural rhythms. While many such services are produced by distant infrastructures, the technology is neither invisible nor impermeable. On the contrary, our empirical results show that routinized human labour is needed to achieve comfort and convenience and to respond to the weather. Moreover, infrastructure failures, such as blackouts, create moments in which the rhythms of everyday life and the relationship between humans and technological systems are renegotiated. Surprisingly, the rhythms of heating work and those of sudden infrastructure failures are not only a source of inconvenience and trouble, but are also appreciated.
A 2‐Year Study of Δ 9‐tetrahydrocannabinol Concentrations in Drivers: Examining Driving and Field Sobriety Test Performance,,
Authors: Declues Kari , Perez Shelli , Figueroa Ariana
Published: August 2016

From November 1, 2010 through November 30, 2012, 1204 whole‐blood samples were confirmed to contain THC alone or in combination with other drugs out of nearly 5000 Orange County, California, drivers suspected of driving under the influence of drugs. The goal of this study was to examine police reports and drug recognition expert evaluations of THC‐positive samples within this 2‐year time frame to determine whether there is a correlation between whole‐blood THC concentrations and field sobriety tests performance on DRE and non‐DRE evaluations. The FSTs prove to be sensitive to impairment by marijuana although as suspected, the findings of this study did not find a correlation between performance on field sobriety tests and the concentration of THC tested in whole‐blood samples. Driving behaviors were also examined and found to be similar to those seen in alcohol impairment. Future studies examining DRE findings are needed to confirm the results.