bluuebunny/crossref_metadata_2025 huggingface dataset:
Paying the reviewer debt.
Authors: Calver Mike
Published: November 2018

A COMMON complaint amongst conservation biologists, whether academics, government employees, in private industry or self-employed, is a growing workload. If sinecures ever existed, it seems that they are long gone. Many of the self-help directives for busy professionals tell us that part of the solution is to cull demands on our time that return no benefit to us, so in
recent months several of my colleagues have questioned the wisdom of spending time reviewing manuscripts or examining theses. I disagree and argue that reviewing and examining are helpful to the whole scientific community, including reviewers and examiners.
Scheme for direct measurement of the two-mode Wigner function in cavity QED and ion traps.
Authors: Zheng Shi-Biao
Published: November 2018

A scheme is proposed for the reconstruction of two-mode entangled states in
cavity QED and ion traps. For a two-mode field we show that the Wigner
function can be obtained by measuring the probability of a two-level atom
being in ground states after resonant interaction with two classical fields
and dispersive interaction with the two-mode cavity field displaced by
resonant sources. For the two-dimensional motion of a trapped ion the Wigner
function is obtained by measuring the probability of the ion in its ground
electronic state after displacing the ion motion and then resonantly exciting
the ion.
Composition of the 7Li(p,g) Radiation Below the 441 keV Resonance
Authors: Campbell JG
Published: November 2018

The only published determinations of the energy of the ?-radiation emitted when lithium is bombarded by protons with energy less than 400 keV have been made by absorption measurements of secondary electrons in aluminium. Gentner (1937) found that the radiation at 90� from a thick lithium target at 300 keV, had the same half-value thickness as that at 550 keV, corresponding to about 17 MeV. Tangen (1946), however, reported that the radiation emitted at 0� at both 300 and 400 keV had energy 14�5 � 0�5 MeV.
Processes Controlling Ionization Distribution in the F2 Region of the Ionosphere
Authors: Martyn DF
Published: November 2018

It has been known for more than 20 years that the morphology of the principal (F2) region of the ionosphere is complex, and inexplicable in terms only of solar ionizing radiation and recombination. The hypothesis was advanced (Martyn 1947) that movement, and especially vertical movement, of F2 ionization was the main reason why the morphology of this region differed so profoundly from that of the lower regions E and F1, which conform closely with Chapman's well-known theory. A principal cause of movement of F2 ionization was held to be the drift occasioned by the electrodynamic forces and winds associated with the ionospheric electric current systems whose existence is manifested by the daily magnetic variations at the ground. There is now considerable evidence, both theoretical and observational, to show that this view may be essentially correct.
Near-threshold Rotational and Vibrational Excitation of H2 by Electron Impact: Theory and Experiment
Authors: Morrison MA , Crompton RW , Saha Bidhan C , Petrovic ZLj
Published: November 2018

A joint experimental-theoretical attack on low-energy e-H2 scattering is described. The cross sections calculated from a highly converged numerical solution of the nonrelativistic Schrodinger equation, using a parameter-free interaction potential, are first compared with results from swarm experiments, and are later used to improve the accuracy of the swarm analysis at energies above the first vibrational threshold. To provide further perspective, the theoretical results are compared with a variety of other experimental data. The theoretical results for the momentum-transfer and rotational-excitation cross sections are in excellent agreement with the results from swarm experiments, but there is an unresolved and significant difference in the threshold behaviour of the vibrational-excitation cross sections. Both the theoretical and experimental approaches are subjected to close scrutiny in an attempt to uncover possible sources of error that could explain this difference. The failure to locate likely sources points to the need for further independent theoretical and experimental work to resolve a problem that has serious implications.
Diffuse Background X Rays and the Density of the Intergalactic Medium
Authors: F Crawford David
Published: November 2018

Most of the 3-300 keY spectrum of the unresolved X-ray background can be explained as thermal bremsstrahlung from a hot intergalactic gas plus a small non-thermal component at higher energies. The model used assumes a static Universe with an exponential redshift with distance relationship that is due to photon interactions with curved space-time. The interglactic gas is found to have a temperature of 1 �3 x 109 K and a density of 2.05 C - 213 hydrogen atoms m - 3, where C is an unknown factor that depends on the dumpiness of the intergalactic gas.
On the Lifetimes of Antisteady States
Authors: J Searles Debra , J Evans Denis
Published: November 2018

The influence of Lyapunov instability on the lifetimes of antisteady states is investigated using nonequilibrium molecular dynamics simulations. It is found that the lifetime is inversely proportional to the smallest Lyapunov exponent of the steady state system and proportional to the logarithm of the trajectory error per timestep.
Bonding without ionisation.
Authors: Maslen E. N. , Etschmann B. E.
Published: November 2018

Charges are calculated for diatomic molecules by partitioning the promolecular
density with projection operators derived from free atom potentials. The
promolecular charges thus obtained have physically reasonable magnitudes,
which are moderately sensitive to interatomic distances and thus to bond type.
Their signs are negative for cations and positive for anions. Trends in these
charges correlate with subshell structure. Due to the long range of their
electrostatic potentials, the cations compete successfully for electrons at
the expense of the anions in the density partitioning. This implies that the
cation states become overfilled when the atoms overlap, favouring a flow of
electrons away from the cation towards the vacant anion states. That accounts
for the positive cations and negative anions observed when molecular densities
are partitioned with projection operators based on free atom electron
densities.
An atomistic interpretation of Planck's 1900 derivation of his radiation law.
Authors: Irons F. E.
Published: November 2018

In deriving his radiation law in 1900, Max Planck employed a simple harmonic
oscillator to model the exchange of energy between radiation and matter.
Traditionally the harmonic oscillator has been viewed as modelling an entity
which is itself oscillating, although a suitable oscillating entity has not
been forthcoming. (Opinion is divided between a material oscillator, an
imaginary oscillator and a need to revise Planck"s derivation to apply to
cavity modes of oscillation). We offer a novel, atomistic interpretation of
Planck"s derivation wherein the harmonic oscillator models a transition
between the internal quantum states of an atom|not a normal electronic
atom characterised by possible energies 0 and hv, but an
atom populated by subatomic bosons (such as pions) and characterised by
multiple occupancy of quantum states and possible energies
nhv (n= 0;1;2; :::). We
show how Planck"s derivation can be varied to accommodate electronic
atoms. A corollary to the atomistic interpretation is that Planck"s
derivation can no longer be construed as support for the postulate that
material oscillating entities can have only those energies that are multiples
of hv.
The low-energy 9Be(g, n)8Be cross section.
Authors: Barker F. C.
Published: November 2018

Fits are made to low-energy 9 Be(g;n)
8 Be cross-section data using one-level R-matrix
formulae including channel contributions. Fits with reasonable parameter
values are found for the newer radioactive-isotope data, and also for data
obtained from inelastic electron scattering on 9 Be, but
not for older radioactive-isotope data. This differs from the result of recent
fits using a semi-microscopic model, which supported the older data. The
difference is attributed to the use in the latter calculation of a
single-particle potential description of the continuum wave function.
Elastic scattering of low-energy electrons by OCS molecules.
Authors: Bettega M. H. F. , Lima M. A. P. , Ferreira L. G.
Published: November 2018

We report results from an ab initio calculation of
low-energy electron scattering by OCS molecules. We used the Schwinger
multichannel method with pseudopotentials at the fixed-nuclei static-exchange
approximation to calculate elastic integral, differential and momentum
transfer cross sections in the energy range from 5 to 50 eV. We compare our
results with available theoretical results and experimental data. Through the
symmetry decomposition of our integral cross section and eigenphase sum
analysis, we found structures in the cross sections that may be interpreted as
shape resonances for ∑, ∏ and Δ symmetries. We compared the
results for OCS with our previous results on the
e––CS2 collision. In
particular, we found a similar behaviour in the shape of the symmetry
decomposed cross sections of OCS and of CS2 when, for
the latter, we sum over the ‘g’ and
‘u’ contributions.
Optical Multistability from a Squeezed Vacuum in the Presence of Quantum Interference
Authors: Du Chunguang , Li Shiqun
Published: November 2018

The effect of a squeezed vacuum on the optical bistable and multistable
behaviour of a system of N three-level atoms is
investigated, where the quantum interference between the atomic transition
paths is considered. It is shown that the squeezed vacuum can profoundly
affect the output field of this system. A strong squeezed vacuum can lead to
multistable behaviour, even in the case where the cooperation parameter
C is so small that the input–output
relationship curve is monotone in the absence of the squeezed vacuum. The
optical multistability is most significant when the quantum interference is
perfect. The bistability and multistability can be controlled by the squeezing
photon number and the strength of the two-photon correlation.
The Importance of Numbers: Using Capture-recapture to make the Homeless Count in Adelaide
Authors: D'Onise Katina , Wang Yan , McDermott Robyn
Published: November 2018

An important problem for the homeless service sector is understanding the size of homeless populations, which has implications on planning services and social policy. The aim of this study is to apply capture-recapture methods to count the primary homeless population in the Adelaide city council area, to examine the use of an alternative method to the Australian Bureau of Statistics census. Capture-recapture techniques were used to analyse homeless registers from three different services to estimate the number of primary homeless people in the Adelaide city council area from 19 June to 19 September 2005. Log-linear model and the sample coverage method were employed to analyse the data. The log-linear model results gave a population estimate of 455 (95% confidence interval 299, 762), and the sample coverage method of 311 (95% confidence interval 229, 466), compared with 104 from the Australian Bureau of Statistics census. Multiple sources of information utilising different methodologies should be considered together when attempting to plan services for primary homeless people, as all available techniques have important limitations. Capture-recapture is an important method to supplement any attempt at enumeration of hidden, mobile or difficult-to-reach populations.
175 Testis-Specific Protein Y Encoded Copy Number Variation in In Vitro-Produced Bovine Early Embryos
Authors: Rho N.Y. , Favetta L. A. , Mogas T. , King W. A.
Published: November 2018

Testis-specific protein Y (TSPY) is one of the genes located in the male-specific region of the Y chromosome involved in male reproduction, particularly in spermatogenesis. It has been shown to have different copy number (CN) in different species, in different individuals within a species and in the same family (i.e. among brothers from the same father). Previous studies from our laboratory in the bovine species showed that different TSPY CN was correlated with fertility, as bulls with higher CN showed higher fertility rate. In this study, we investigated development rate in in vitro-produced (IVP) bovine early embryos produced by sex-sorted semen (X and Y) from 3 bulls (1, 2, and 3) and TSPY copy number variation (CNV) in the male blastocysts. The IVP embryos by the 3 different types of semen (sub-divided: 1X, 1Y, 2X, 2Y, 3X, 3Y) and parthenotes (PART) for the negative control were assessed for developmental rates (shown in Table 1 below) and individually collected at each cell stage from zygote to blastocyst to extract DNA for TSPY CN analysis. The DNA from individual blastocysts was treated with a restriction enzyme for relative quantification of TSPY CN using digital droplet PCR (ddPCR) with SRY, known to have only one copy in bovine, as a reference gene. Developmental data showed that Y-carrying semen had higher rates both in cleavage and blastocyst compared with X-carrying semen from the same bull. Particularly, bull 3 (both 3X and 3Y) had the highest developmental rates compared with the other 2 types of bulls. TSPY was detected in male blastocyst, where both parthenotes and female embryos were negative. Relative CN of TSPY versus SRY from blastocysts produced from bulls 1, 2, and 3 averaged to 87.5, 55, and 20, respectively. Interestingly, the CN among brother blastocysts showed a variation of less than 7.5, where bull-to-bull variation was approximately from 20 to 60 copies. Our results show that TSPY CN in the embryo varies according to the sire and among brother blastocysts. Moreover, TSPY CNV among brother blastocysts allows us to speculate that individually different recombination events occurred in meiosis during spermatogenesis.

Table 1.Embryo development rate by semen type

This research was funded by the Canada Research Chair’s program, Natural Sciences and Engineering Research Council of Canada and the Ontario Veterinary College.
The impact of a chlamydia education program on practice nurse’s knowledge and attitudes in relation to chlamydia testing: a cross-sectional survey
Authors: Lorch Rebecca , Guy Rebecca , Temple-Smith Meredith , Vaisey Alaina , Wood Anna , Ford Belinda , Murray Carolyn , Bourne Chris , Tomnay Jane , Hocking Jane , on behalf of the ACCEPt Consortium
Published: November 2018

Background
We aimed to determine the impact of a chlamydia (Chlamydia trachomatis) education program on the knowledge of and attitudes towards chlamydia testing of practice nurses (PNs). Methods: A cross-sectional survey was conducted at baseline and 6–12 months following recruitment with PNs in the Australian Chlamydia Control Effectiveness Pilot. Likert scales were analysed as continuous variables (scores), and t-tests were used to assess changes in mean scores between survey rounds and groups. Results: Of the 72 PNs who completed both surveys, 42 received education. Epidemiology knowledge scores increased significantly between surveys in the education group (P < 0.01), with change in knowledge being greater in the education group compared with the non-education group (P < 0.01). Knowledge of recommended testing scenarios (P = 0.01) and retesting following treatment (P < 0.01) increased in the education group. Attitudes to testing scores improved over time in the education group (P = 0.03), with PNs more likely to want increased involvement in chlamydia testing (P < 0.01). Change in overall attitude scores towards testing between surveys was higher in the education group (P = 0.05). Barriers to chlamydia testing scores also increased in the education group (P = 0.03), with change in barriers greater in the education vs the non-education group (P = 0.03). Conclusion: The education program led to improved knowledge and attitudes to chlamydia, and could be made available to PNs working in general practice. Future analyses will determine if the education program plus other initiatives can increase testing rates.
Survival of Escherichia coli in a tropical estuary
Authors: Chandran Abirosh , Hatha A. A. Mohamed
Published: November 2018

The survival of Escherichia coli in tropical estuarine water has been studied under controlled laboratory conditions using microcosms. The survival has been assessed in terms of various self purifying factors of the natural waters such as biological, chemical and physical factors. The biological factors considered included competition from other microorganisms, predation by protozoa and coliphages. The suitability of the chemical composition of estuarine water has been studied under chemical factors and negative impact of sunlight has been studied under physical factors. The results revealed that sunlight exerted maximum negative impact, followed by biotic factors contained in the estuarine water. However, the chemical composition of the estuarine water is found to be suitable for the growth and survival of E. coli. The injury exerted by each of the above factors was also evaluated by using a selective and non-selective medium in conjunction. It was found that sunlight resulted in 100% injury of the cells as the cells failed to develop in a selective medium. While, sunlight resulted in the extinction of 90% of the E. coli cells within the first two hours of exposure, biotic factors took nearly 24 hours to remove the same amount of population.
Temperature trends in Fiji: a clear signal of climate change
Authors: Kumar Ravind , Stephens Mark , Weir Tony
Published: November 2018

This paper analyses trends in temperature in Fiji, using data from more stations (10) and longer periods (52-78 years) than previous studies. All the stations analysed show a statistically significant trend in both maximum and minimum temperature, with increases ranging from 0.08 to 0.23°C per decade. More recent temperatures show a higher rate of increase, particularly in maximum temperature (0.18 to 0.69°C per decade from 1989 to 2008). This clear signal of climate change is consistent with that found in previous studies of temperatures in Fiji and other Pacific Islands. Trends in extreme values show an even stronger signal of climate change than that for mean temperatures. Our preliminary analysis of daily maxima at 6 stations indicates that for 4 of them (Suva, Labasa, Vunisea and Rotuma) there has been a tripling in the number of days per year with temperature >32°C between 1970 and 2008. The correlations between annual mean maximum (minimum) temperature and year are mostly strong: for about half the stations the correlation coefficient exceeds 60% over 50+ years. Trends do not vary systematically with location of station. At all 7 stations for which both trends are available there is no statistically significant difference between the trends in maximum and minimum temperatures.
Estimating distribution and abundance of feral horses (Equus caballus) in a coniferous plantation in Australia, using line-transect surveys of dung
Authors: Zabek Magdalena A. , Berman David M. , Blomberg Simon , Wright John
Published: November 2018

Context
Feral horses are a growing problem in Australia, despite implementation of management strategies. The incidence of horse sightings and horse-associated vehicle collisions within the Tuan and Toolara State Forest (TTSF), a coniferous plantation in south-eastern Queensland, has increased in the past decade, indicating an increase in population and the necessity to undertake an accurate appraisal of population abundance.

Aim
To determine the feasibility of using dung counts, defecation and dung-decay rates to determine the distribution and abundance of feral horse population in a managed coniferous plantation where dense vegetation prohibits the use of visual-based animal detection methods.

Methods
Population distribution was assessed by dung count incorporated into a vehicle strip-transect survey on 582 km of forest tracks. Population abundance was estimated from dung density, the mean defecation frequency of feral horses, and the mean number of days required for dung to decay. Dung density was obtained from on-ground distance line-transect survey that sampled all representative plantation habitats and consisted of 111 transects totalling 44.3 km.

Key results
The strip-transect survey clearly showed that although feral horses were dispersed across the plantation, the distribution was uneven, with the central region of the plantation being the most heavily populated. The combination of dung counts, defecation rate (mean ± s.d., 7.97 ± 8.74) over 24 h and dung-decay rate (444 ± 150.7 days) provided an estimation of the density of feral horses in various habitats and indicated that the plantation was occupied by 1321 (95% CI 940–1965) horses, which corresponded to an average density of 1.8 horses km–2. The method clearly identified variations in horse abundance among the various habitats within the surveyed areas. Open habitats, created following harvesting, showed higher occurrence rates, whereas the habitats of mature forest were scantily occupied.

Key conclusions
Dung counts are a simple, effective and practical technique that can provide information on distribution and abundance of feral horse population in densely forested habitats where visual-based techniques are not applicable. However, unbiased and precise defecation and decay rates must be estimated.

Implications
The study validated the use of dung counts to provide information on feral horse distribution and abundance in densely forested environments where direct methods of census may be difficult to obtain. The methods are applicable to a range of ecosystems, but defecation and dung-decay rates must be determined separately for each ecosystem.
Effect of strain rate on microstructures and mechanical properties of Fe–18Cr–8Ni steel
Authors: Xu D. M. , Wan X. L. , Yu J. X. , Xu G. , Li G. Q.
Published: November 2018

The effect of strain rate on deformation microstructures and mechanical properties of Fe–18Cr–8Ni austenitic stainless steel was investigated at strain rates of from 10−3 to 100 s−1. The results indicated that the deformation mechanism of steel changes from transformation induced plasticity (TRIP) to TRIP + twinning induced plasticity (TWIP) effect when the strain rate is increased from 10−3 to 100 s−1. The yield strength of steel increases gradually with strain rate increased, while the tensile strength and elongation first decreases and then increases slowly. The changes in tensile strength and elongation are due to the change of deformation mechanism with the strain rate increased.
‘The fourth commandment effect’: church attendance and intergenerational support in late parent–child relationships
Authors: Tosi Marco , Oncini Filippo
Published: November 2018

We examine whether church attendance is related to intergenerational support from children to older parents in Italy. First, we focus on the role of church attendance on different forms of assistance, by distinguishing between practical support and personal assistance. Second, we attempt to disentangle the role of church attendance from that of traditionalism. We analyse data from the ISTAT survey ‘Family and Social Subject’ 2003 using multinomial logistic regression models and the KHB method for the decomposition of direct and indirect effects. Results show the existence of an association between church attendance and the probability of providing practical support to older parents, whereas there is no association with personal assistance. Regular churchgoers are more likely to provide practical support to their parents than the non-catholic, with occasional churchgoers falling somewhere in between. We find little support to the hypothesis that the association between religious practices and intergenerational support is explained by traditional family attitudes, although more traditional children are more likely to live with their parents. In the discussion, we argue that church attendance offers the opportunity for adult children to learn pro-family teachings that are positively related to supportive behaviors in later life.
Examiner accuracy in cognitive testing in multisite brain-tumor clinical trials: an analysis from the Alliance for Clinical Trials in Oncology
Authors: Cerhan Jane H , Anderson S Keith , Butts Alissa M , Porter Alyx B , Jaeckle Kurt , Galanis Evanthia , Brown Paul D
Published: November 2018

Background

Cognitive function is an important outcome in brain-tumor clinical trials. Cognitive examiners are often needed across multiple sites, many of whom have no prior testing experience. To ensure quality, we looked at examiner errors in administering a commonly used cognitive test battery, determined whether the errors were correctable upon central review, and considered whether the same errors would be detected using onsite electronic data entry.

Methods

We looked at 500 cognitive exams administered for brain-tumor trials led by the Alliance for Clinical Trials in Oncology (Alliance). Of 2277 tests examined, 32 noncorrectable errors were detected with routine central review (1.4% of tests administered), and thus removed from the database of the respective trial. The invalidation rate for each test was 0.8% for each part of the Hopkins Verbal Learning Test-Revised, 0.8% for Controlled Oral Word Association, 1.8% for Trail Making Test-A and 2.6% for Trail Making Test-B. It was estimated that, with onsite data entry and no central review, 4.9% of the tests entered would have uncorrected errors and 1.3% of entered tests would be frankly invalid but not removed.

Conclusions

Cognitive test results are useful and robust outcome measures for brain-tumor clinical trials. Error rates are extremely low, and almost all are correctable with central review of scoring, which is easy to accomplish. We caution that many errors could be missed if onsite electronic entry is utilized instead of central review, and it would be important to mitigate the risk of invalid scores being entered.

ClinicalTrials.gov identifiers

NCT01781468 (Alliance A221101), NCT01372774 (NCCTG N107C), NCT00731731 (NCCTG N0874), and NCT00887146 (NCCTG N0577).
RADIATION SHIELDING STUDY FOR THE VERTICAL TEST SYSTEM FOR SUPERCONDUCTING RF CAVITIES
Authors: Zhou Dejun , Lin Lin , Feng Liwen , Quan Shengwen
Published: November 2018

A vertical test system (VTS) for superconducting radio frequency cavities had been designed and constructed at Peking University. During the test, field emission electrons in the cavity will be accelerated and some of them will hit the flange of cavity with high-energy. These high-energy electrons will have a significant impact on the radiation safety of the system and environment. In this paper, the Particle-in-Cell solver in CST software was used to analyze the behavior of electrons emitted from different field emission positions and found the worst field emission site which deposited the most energy on the cavity wall. The impact information of the electrons emitted from the worst field emission site was utilized to character the source term. Prompt dose equivalent rate distribution and residual radioactivity was predicted by using the Monte Carlo simulation program FLUKA. Further vertical test results are consistent with the simulation results.
BioKEEN: A library for learning and evaluating biological knowledge graph embeddings
Authors: Ali Mehdi , Hoyt Charles Tapley , Domingo-Fernández Daniel , Lehmann Jens , Jabeen Hajira
Published: November 2018

Knowledge graph embeddings (KGEs) have received significant attention in other domains due to their ability to predict links and create dense representations for graphs’ nodes and edges. However, the software ecosystem for their application to bioinformatics remains limited and inaccessible for users without expertise in programming and machine learning. Therefore, we developed BioKEEN (Biological KnowlEdge EmbeddiNgs) and PyKEEN (Python KnowlEdge EmbeddiNgs) to facilitate their easy use through an interactive command line interface. Finally, we present a case study in which we used a novel biological pathway mapping resource to predict links that represent pathway crosstalks and hierarchies.

Availability

BioKEEN and PyKEEN are open source Python packages publicly available under the MIT License at https://github.com/SmartDataAnalytics/BioKEEN and https://github.com/SmartDataAnalytics/PyKEEN as well as through PyPI.
Explorations with Conditioned Stimuli in Autoshaping Procedures
Authors: Nehrbas Jill F. , Smedley Elizabeth B. , Kyle S. Smith
Published: November 2018

Sign-tracking is a form of autoshaping where by animals reliably develop conditioned responses toward stimuli that predict an outcome. While the assignment of some value to a predictive cue may be adaptive (i.e., to be alerted to food and water sources), the attribution of value to predictive cues can be maladaptive as seen in behaviors elicited during addiction. Here we test if responding to the predictive cue changes in the context of other cues that are only partially predictive (Experiment 1). Previous work on sequential cues leading to reward have shown a bias in responding toward the first cue in the sequence over learning (Smedley and Smith 2018a, 2018b). Here we test if this effect is unique to discrete cues or if a bias in responding can be seen in a single, long cue (Experiment 2). Finally, we investigate if sign-tracking responses can reliably develop towards a cue that arrives after the delivery of reward (backwards conditioning, Experiment 3). Together, we aim to address various gaps in knowledge about the nature of the sign-tracking response.
APPLES: Scalable Distance-based Phylogenetic Placement with or without Alignments
Authors: Balaban Metin , Sarmashghi Shahab , Mirarab Siavash
Published: November 2018

Abstract

Placing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming, or metagenomic data. Maximum likelihood (ML) methods of phylogenetic placement exist, but these methods are not scalable to reference trees with many thousands of leaves, limiting their ability to enjoy benefits of dense taxon sampling in modern reference libraries. They also rely onassembledsequences for the reference set and aligned sequences for the query. Thus, ML methods cannot analyze datasets where the reference consists of unassembled reads, a scenario relevant to emerging applications of genome-skimming for sample identification. We introduce APPLES, a distance-based method for phylogenetic placement. Compared to ML, APPLES is an order of magnitude faster and more memory efficient, and unlike ML, it is able to place on large backbone trees (tested for up to 200,000 leaves). We show that using dense references improves accuracy substantially so that APPLES on dense trees is more accurate than ML on sparser trees, where it can run. Finally, APPLES can accurately identify samples without assembled reference or aligned queries using kmer-based distances, a scenario that ML cannot handle. APPLES is available publically atgithub.com/balabanmetin/apples.
Methamphetamine Administration Increases Proceptive Behavior by Activating Src Kinase and Upregulating Progesterone Receptor in the Medial Amygdala
Authors: Williams Katrina M , Rudzinskas Sarah A , Mong Jessica A
Published: November 2018

Methamphetamine, a psychostimulant drug of abuse, increases sexual motivation both in humans and in rodent models. The activation of dopamine type-1 receptors (D1Rs) within the medial amygdala, in the presence of ovarian hormones (EB+P), are both necessary and sufficient for increases in proceptive, or sexually motivated, behaviors. Here, we demonstrate that methamphetamine increases progesterone receptor expression in the medial amygdala independently of D1R activation, and that lentiviral overexpression of the progesterone receptor was able to recapitulate the methamphetamine-induced enhancement of proceptive behaviors. Furthermore, we found that within the medial amygdala, these progesterone receptors show an increase in phosphorylation of serine 294 of the progesterone receptor in a region-specific manner. The involvement of this phosphorylation site suggests a role for cytosolic kinases, which may be responsible for enhanced progesterone receptor action. The phosphorylation of serine 294 is blocked by D1R antagonists, and by inhibiting cSrc and ERK1/2, downstream of D1R signaling, we identified that Src and ERK1/2 are required for enhanced proceptive behavior. Taken together, we propose that within the medial amygdala, methamphetamine enhances progesterone receptors sensitivity to its cognate ligand via interaction with cSrc kinase and ERK1/2, as well as an increase total progesterone receptors, thus leading to enhanced proceptive behaviors in the rat.
ExtendAlign: the post-analysis tool to correct and improve the alignment of dissimilar short sequences
Authors: Flores-Torres Mariana , Gómez-Romero Laura , Haase-Hernández Joshua I. , Aguilar-Ordóñez Israel , Tovar Hugo , Avendaño-Vázquez S. Eréndira , Flores-Jasso C. Fabián
Published: November 2018

In this work, we evaluated several tools used for the alignment of short sequences and found that most aligners execute reasonably well for identical sequences, whereas a variety of alignment errors emerge for dissimilar ones. Since alignments are essential in computational biology, we developed ExtendAlign, a post-analysis tool that corrects these errors and improves the alignment of dissimilar short sequences. We used simulated and biological data to show that ExtendAlign outperforms the other aligners in most metrics tested. ExtendAlign is useful for pinpointing the identity percentage for alignments of short sequences in the range of ∼35–50% similarity.
Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
Authors: Gaublomme Jellert T. , Li Bo , McCabe Cristin , Knecht Abigail , Drokhlyansky Eugene , Wittenberghe Nicholas Van , Waldman Julia , Dionne Danielle , Nguyen Lan , Jager Phil De , Yeung Bertrand , Zhao Xinfang , Habib Naomi , Rozenblatt-Rosen Orit , Regev Aviv
Published: November 2018

Single-nucleus RNA-Seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate, including frozen clinical samples. This opens the way, in principle, to large studies, such as those required for human genetics, clinical trials, or precise cell atlases of large organs. However, such applications are currently limited by batch effects, sequential processing, and costs. To address these challenges, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies against the nuclear pore complex to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled in multiplex with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter the recovered transcriptome profiles. We further developed demuxEM, a novel computational tool that robustly detects inter-sample nucleus multiplets and assigns singlets to their samples of origin by antibody barcodes, and validated its accuracy using gender-specific gene expression, species-mixing and natural genetic variation. Nucleus hashing significantly reduces cost per nucleus, recovering up to about 5 times as many single nuclei per microfluidc channel. Our approach provides a robust technique for diverse studies including tissue atlases of isogenic model organisms or from a single larger human organ, multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.
Riding the wave of genomics, to investigate aquatic coliphage diversity and activity
Authors: Michniewski Slawomir , Redgwell Tamsin , Grigonyte Aurelija , Rihtman Branko , Aguilo-Ferretjans Maria , Christie-Oleza Joseph , Jameson Eleanor , Scanlan David J. , Millard Andrew D.
Published: November 2018

Bacteriophages infectingEscherichia colihave been used as a proxy for faecal matter and water quality from a variety of environments. However, the diversity of coliphages that are present in seawater remains largely unknown, with previous studies largely focusing on morphological diversity. Here, we isolated and characterised coliphages from three coastal locations in the UK and Poland. This revealed a surprising genetic diversity, with comparative genomics and phylogenetic analysis of phage isolates facilitating the identification of putative new species within the generaRB69virusandT5virusand a putative new genus within the subfamilyTunavirinae. Furthermore, by combining this genomic data with proteomic and host range analyses a number of phage structural proteins were identified, one of which is likely to be responsible for the observed differences in host range.
ProtMiscuity: a database of promiscuous proteins
Authors: Rueda Ana Julia Velez , Palopoli Nicolas , Zacarías Matías , Parisi Gustavo
Published: November 2018

ProtMiscuity is a manually-curated database of promiscuous proteins. It is annotated with information about canonical and promiscuous activities comprising 88 different reactions in 57 proteins from 40 organisms. ProtMiscuity could assist in the study of the underlying mechanisms of promiscuous reactions by offering a collection of experimentally derived data, extensively linked with other databases providing biological, structural and functional information.

Availability and Implementation

The responsive web interface of ProtMiscuity provides support for easier navigation and visualization of the database contents on multiple devices. It is implemented in HTML, CSS, JavaScript, Angular4 and NodeJS. ProtMiscuity is hosted on our server and can be freely accessed at http://ufq.unq.edu.ar/protmiscuity

Contact

Gustavo Parisi (gustavo@unq.edu.ar)
Relating excitatory and inhibitory neurochemicals to visual perception: a magnetic resonance study of occipital cortex between migraine events
Authors: Chan Yu Man , Pitchaimuthu Kabilan , Wu Qi-Zhu , Carter Olivia L , Egan Gary F , Badcock David R , McKendrick *Allison M
Published: November 2018

Certain perceptual measures have been proposed as indirect assays of brain neurochemical status in people with migraine. One such measure is binocular rivalry, however, previous studies have not measured rivalry characteristics and brain neurochemistry together in people with migraine. This study compared spectroscopy-measured levels of GABA and Glx (glutamine and glutamate complex) in visual cortex between 16 people with migraine and 16 non-headache controls, and assessed whether the concentration of these neurochemicals explains, at least partially, inter-individual variability in binocular rivalry perceptual measures. Mean Glx level was significantly reduced in migraineurs relative to controls, whereas mean occipital GABA levels were similar between groups. Neither GABA levels, nor Glx levels correlated with rivalry percept duration. Our results thus suggest that the previously suggested relationship between rivalry percept duration and GABAergic inhibitory neurotransmitter concentration in visual cortex is not strong enough to enable rivalry percept duration to be reliably assumed to be a surrogate for GABA concentration, at least in the context of healthy individuals and those that experience migraine.
Differential physiological role of BIN1 isoforms in skeletal muscle development, function and regeneration
Authors: Prokic Ivana , Cowling Belinda , Kutchukian Candice , Kretz Christine , Tasfaout Hichem , Hergueux Josiane , Wendling Olivia , Ferry Arnaud , Toussaint Anne , Gavriilidis Christos , Nattarayan Vasugi , Koch Catherine , Lainné Jeanne , Combe Roy , Tiret Laurent , Jacquemond Vincent , Pilot-Storck Fanny , Laporte Jocelyn
Published: November 2018

Skeletal muscle development and regeneration are tightly regulated processes. How the intracellular organization of muscle fibers is achieved during these steps is unclear. Here we focus on the cellular and physiological roles of amphiphysin 2 (BIN1), a membrane remodeling protein mutated in both congenital and adult centronuclear myopathies, that is ubiquitously expressed and has skeletal muscle-specific isoforms. We created and characterized constitutive, muscle-specific and inducible Bin1 homozygous and heterozygous knockout mice targeting either ubiquitous or muscle-specific isoforms. Constitutive Bin1-deficient mice died at birth from lack of feeding due to a skeletal muscle defect. T-tubules and other organelles were misplaced and altered, supporting a general early role of BIN1 on intracellular organization in addition to membrane remodeling. Whereas restricted deletion of Bin1 in unchallenged adult muscles had no impact, the forced switch from the muscle-specific isoforms to the ubiquitous isoforms through deletion of the in-frame muscle–specific exon delayed muscle regeneration. Thus, BIN1 ubiquitous function is necessary for muscle development and function while its muscle-specific isoforms fine-tune muscle regeneration in adulthood, supporting that BIN1 centronuclear myopathy with congenital onset are due to developmental defects while later onset may be due to regeneration defects.
Joint optimal decision of the shared distribution system through revenue-sharing and cooperative investment contracts
Authors: Wei Qiang , Li Sheng , Gou Xinyu , Huo Baofeng
Published: November 2018

Purpose

The rapid development of e-commerce has caused not only explosive growth of the express delivery industry, but also ever-greater operational pressures. Models from the sharing economy may provide new ideas for operational improvement. The purpose of this paper is to consider an optimization method that reduces costs and increases efficiency. The proposed method enables a shared distribution system based on revenue-sharing and cooperative investment contracts.

Design/methodology/approach

The authors design a two-echelon supply chain (SC) of the shared distribution system with one shared distribution company and N express companies. In this SC, the express companies provide only inter-city transportation, and they outsource internal-city transportation to a shared distribution company. This distribution system differs from that of the traditional express delivery industry. The traditional system of delivery requires large numbers of empty trips (with no load to deliver), because the operating mode of urban distribution has been the franchise. To offer greater efficiency and performance, the authors introduce the sharing economy mode of express delivery. The authors examine the potential of a joint optimal decision-making strategy that involves revenue-sharing and cooperative investment contracts based on an order flow proportion (OFP) and a revenue-sharing factor (RSF). In this shared distribution system, the most important innovation is that all of the express companies jointly invest in and establish a shared distribution company based on OFP or RSF principles.

Findings

The profitability of an SC with revenue-sharing contracts based on an OFP system is much higher than that of a decentralized SC, and it is very close to the profitability of a centralized SC. In SCs with revenue-sharing contracts that are based on RSFs, there are many possible combinations of RSFs that can increase the overall profitability. The analyses indicate that the OFP system offers the best solution in designing revenue-sharing contracts based on RSFs.

Practical implications

This study indicates that revenue-sharing contracts based on both OFP and RSF principles can increase overall SC returns by 0.21 to 0.44 percent. In sum total, this improvement could mean a 0.84 to 1.76bn Yuan increase in revenues for the 400+ bn-Yuan express delivery industry.

Originality/value

The authors find that a combination of equity investment and SC coordination contracts makes the cooperation between SC members much more stable. Through this kind of shared distribution system, the scale of economy can further reduce the costs and increase the efficiency of the express delivery industry.
What geographical scope works best for rapidly internationalizing SMEs?
Authors: Melén Hånell Sara , Rovira Nordman Emilia
Published: November 2018

Purpose

This paper aims to explore the benefits of a regional internationalization strategy and investigate how a rapidly internationalizing SME’s development of market knowledge relates to this strategy.

Design/methodology/approach

After a brief overview of the literature on international SMEs, the internalization approach and the IP-approach, a case study is introduced and analyzed.

Findings

The case findings illustrate that market knowledge steers the investigated firm to follow a regional approach of operations. The regional strategy lessens perceived risks, saves costs and generates sufficient knowledge about one market at a time.

Practical implications

It is important for managers in rapidly internationalizing SMEs and for policymakers to recognize the benefits of supporting regional orientation initiatives for enhancing these firms’ internationalization.

Originality/value

This paper presents a longitudinal case study that contributes to further the understanding and insights into the operations of born regionals. By probing deeper into the ideas provided by the internalization approach, the IP-approach and research about international SMEs, the study contributes with a unified framework for understanding the benefits for rapidly internationalizing SMEs to operate on a regional scope.
Backshoring readiness
Authors: Nujen Bella Belerivana , Mwesiumo Deodat Edward , Solli-Sæther Hans , Slyngstad Andrea Blindheim , Halse Lise Lillebrygfjeld
Published: November 2018

Purpose

The purpose of this study is to delineate key aspects of backshoring readiness and discuss how such aspects contribute to a smooth shift-back from global sourcing operations. It aims to answer the following questions: which factors constitute backshoring readiness and how these factors affect the backshoring transition.

Design/methodology/approach

Based on theory departure from the organizational readiness field and the emerging field on backshoring, a conceptual model is developed. A multiple qualitative case study is then conducted to exemplify the backshoring readiness factors delineated in the study.

Findings

The study indicates that due to previous outsourcing, limitations concerning the availability of firms’ capabilities are affected by ownership structures and that backshoring appears to be time-sensitive. The study delineates three key aspects of backshoring readiness and proposes a comprehensive understanding of readiness as an important construct to enhance successful backshoring.

Research limitations/implications

The findings are limited by the nature of this conceptual study, the restriction to a high-cost context and the small number of cases. Therefore, conclusions and proposed recommendations need to be further investigated in preferably larger samples of case studies.

Practical implications

By introducing contextual variables that go beyond traditional cost considerations, this work should be of special interest for both practitioners and academics, because the absorptive capacity for the exploitation of cutting-edge knowledge is globally scarce and hence rather expensive in Western countries compared with traditionally low-cost countries. Another practical contribution of this study is the conceptual backshoring readiness framework itself, as it can guide firms acquainting themselves with the resource availability in their home environment.

Originality/value

The research defines key resources needed to facilitate backshoring readiness in a conceptual framework developed from literature, which is then exemplified by a case study. This framework conceptualizes backshoring readiness as aspects of requirements to knowledge, technology and supplier infrastructures. Furthermore, the readiness framework developed provides firms and their managers with six recommendations that can enable a rigorous evaluation of a firm’s readiness to embark on backshoring and reflect on the aspect of fitness of its current strategies.