bluuebunny/crossref_metadata_2025 huggingface dataset:
Pushing the limit of Cs incorporation into FAPbBr3 perovskite to enhance solar cells performances
Authors: Sutanto Albertus A. , Queloz Valentin I. E. , Garcia-Benito Inés , Laasonen Kari , Smit Berend , Nazeeruddin Mohammad Khaja , Syzgantseva Olga A. , Grancini Giulia
Published: April 2019

Cation compositional engineering has revealed a powerful design tool to manipulate the perovskite structural and optoelectronic characteristics with a tremendous impact on device performances. Tuning the bandgap by cation and anion compositional mixing, for instance, is paramount to target different optoelectronic segments, from light emitting applications to tandem solar cells. However, structural and photo instabilities, and phase segregation come along, imposing a severe control on the material composition and structure. Here we develop highly uniform alloy of mixed cation FA(1−x)CsxPbBr3 perovskite thin films pushing for the first time the Cs content up to 30%. In contrast to what has been reported so far, this composition leads to a high quality crystalline film, maintaining a single cubic phase arrangement. In addition, a remarkably high robustness against moisture and phase purity is observed. The experimental finding is also supported by density functional theory simulations, demonstrating at the atomistic level Cs segregation starting from Cs concentration around 37.5%. Beyond that, phase segregation happens, leading to formation of an unstable pure Cs-rich region. Low temperature photoluminescence (PL) measurements reveal that the addition of Cs eliminates the non-radiative channel into mid-gap traps, as evident by the lack of the broad emission band, often associated with recombination of self-trapped exciton, present for 0% Cs. This, in turn, reduces the non-radiative recombination losses which manifests as high performance solar cells. Indeed, when embodied in solar devices, Cs incorporation leads to enhanced device performances, with an open circuit voltage beyond 1.33 V.
Thermal variation of electric field sensor bias caused by anisotropy of LiNbO3
Authors: Wang Hai , Zeng Rong , Zhuang Chijie
Published: April 2019

Electric field sensors based on LiNbO3 are attractive for use in high-intensity transient electric field measurements. However, the working bias of such sensors is easily influenced by temperature variations. Many researchers have worked to improve the thermal stability of the bias of these sensors, mostly in terms of waveguide direction selection and suppression of the pyroelectric effect. In this letter, we present an analysis of the steady-state temperature stability of an x-cut, z-propagation, straight waveguide common-path interferometer-based sensor and show that the difference between the thermo-optic coefficients of no and ne caused by the anisotropy of the LiNbO3 crystal is the main factor that affects the steady-state working bias of the electric field sensor at different working temperatures. The experimental results for the changes in the sensor bias with temperature in the steady states are in good agreement with the theoretical analysis.
Measurement of wave-particle interaction and metastable lifetime using laser-induced fluorescence
Authors: Chu F. , Hood R. , Skiff F.
Published: April 2019

Extensive information, such as ion temperature and wave-particle interactions, can be obtained by the direct measurement of ion distribution functions using laser-induced fluorescence (LIF). This nonintrusive plasma diagnostics provides an important window into the ion motions in phase-space. Previous simulation results suggest that LIF measurements, which are performed on metastable ions produced directly from neutral gas particles and also from ions in other electronic states, place restrictions on the metastable lifetime. In the case where metastable population is produced from direct ionization of neutral atoms, the velocity distribution measured using LIF will only faithfully represent processes which act on the ion dynamics in a time shorter than the metastable lifetime. In this paper, the metastable lifetime effects are explored experimentally for the first time using wave-particle interaction in an Argon multidipole plasma. We demonstrate that this systematic effect can be corrected using the theory addressed in this paper based on the metastable lifetime and relative fraction of metastables produced from pre-existing ions.
Directional motion of dielectric droplets on polymer-coated conductor driven by electric corona discharge
Authors: Li Guoliang , Pan Junheng , Zheng Huai , Liu Sheng , Tang Jau
Published: April 2019

Achieving better control of liquid droplet movement is an important subject for academic research and industrial applications. In this study, we investigate the use of electric corona discharge to drive and control oil droplet movement. For a fully covered polymer-coated copper plate, all droplets on the surface were found to move outward in the same direction. Interestingly, for a polymer coating a hole directly beneath a needle biased with a high DC voltage, we observed the existence of a zone boundary at which all of the droplets within the boundary move inward, whereas droplets outside the boundary move outward. The boundary appeared to depend on the hole size and the voltage bias. Our model simulations reasonably agree well with the experimental measurements of these peculiar phenomena.
Energy-time entanglement-based dispersive optics quantum key distribution over optical fibers of 20 km
Authors: Liu Xu , Yao Xin , Wang Heqing , Li Hao , Wang Zhen , You Lixing , Huang Yidong , Zhang Wei
Published: April 2019

An energy-time entanglement-based dispersive optics quantum key distribution (DO-QKD) is demonstrated experimentally over optical fibers of 20 km. In the experiment, the telecom band energy-time entangled photon pairs are generated through spontaneous four-wave mixing in a silicon waveguide. The arrival time of photons is registered for key generation and security test. High-dimensional encoding in the arrival time of photons is used to increase the information per coincidence of photon pairs. The bin sifting process is optimized by a three-level structure, which significantly reduces the raw quantum bit error rate (QBER) due to timing jitters of detectors and electronics. A raw key generation rate of 151 kbps with a QBER of 4.95% is achieved, in a time bin encoding format with 4 bits per coincidence. This experiment shows that the entanglement-based DO-QKD can be implemented in an efficient and convenient way, which has great potential for quantum secure communication networks in the future.
Crystal orientation dependence of spin-orbit torques in Co/Pt bilayers
Authors: Ryu Jeongchun , Avci Can Onur , Karube Shutaro , Kohda Makoto , Beach Geoffrey S. D. , Nitta Junsaku
Published: April 2019

We study the role of Pt crystal orientation in spin-orbit torques in Co/Pt bilayers by means of the harmonic Hall effect and current-induced switching measurements. Perpendicularly magnetized Co/Pt bilayers were fabricated with the Pt layer exhibiting either a polycrystalline grain structure or an epitaxial (111)-oriented film on MgO substrates by magnetron sputtering. We find that the damping-like spin-orbit torque is 1.3 times smaller in the epitaxial Co/Pt(111) bilayers compared to the polycrystalline films, whereas the field-like spin-orbit torque values are of comparable magnitude. Current-induced magnetization switching measurements show good agreement with the results of harmonic measurements of damping-like torque, i.e., the critical switching current is about 30% higher in epitaxial Co/Pt(111). These results highlight the importance of crystal orientation effects on spin-orbit torques in nominally identical bilayer structures.
A spectrum matching method for accurate frequency estimation of real sinusoids
Authors: Wang Kui , Tu Yaqing , McLernon Des , Shen Yanlin , Chen Peng
Published: April 2019

It is well-known that incoherent sampling is detrimental for frequency estimation of a real sinusoid, and the estimation errors get worse when the signal lengths are very short. In this paper, a spectrum matching based frequency estimator is proposed as well as evaluated against other four two-step methods developed to suppress the effect of incoherent sampling. The spectral interference introduced by incoherent sampling is eliminated via a spectrum matching process including modulation and spectral analysis. A further error correction based on Fourier transform is conducted to generate the fine frequency estimate. Simulation results are carried out to show that the proposed method can closely approach the Cramér-Rao lower bound without any error floor, and it can outperform the other four methods particularly for short signal lengths.
Effect of implantation of Sm+ ions into RF sputtered ZnO thin film
Authors: Otieno Francis , Airo Mildred , Njoroge Eric G. , Erasmus Rudolph , Ganetsos Theodore , Quandt Alexander , Wamwangi Daniel , Billing David G.
Published: April 2019

The effects of implantation of Samarium ions (Sm+), a rare earth ion (RE) on the properties of ZnO films grown on Si (001) substrate by RF sputtering system are presented. The structural properties of the virgin and Sm–implanted ZnO thin films were investigated by Atomic force microscopy, Rutherford backscattering spectroscopy and Raman spectroscopy. Local lattice softening caused by the incorporation of highly mismatched Sm+ (ionic radii 0.096 nm and 0.113 nm for Sm3+ and Sm2+ respectively) into Zn antisites was detected as a red shift in E2 (high) mode likely caused by reduction in the crystallinity of the ZnO film. Photoluminescence on the pristine ZnO film showed a strong near band gap (NBE) emission and an intrinsic defect related blue, green-orange emission. The NBE is suppressed after implantation of Sm+ while the blue, green – orange emission intensities are enhanced as a result of increased structural defects with mismatched charge states. Moreover the effect of varying the concentration of Sm+ ions is presented and compared with predictions made from Stopping and Range of Ions in Matter (SRIM) calculation.
Switching dynamics of ferroelectric HfO2-ZrO2 with various ZrO2 contents
Authors: Li Yuxing , Li Jingzhou , Liang Renrong , Zhao Ruiting , Xiong Benkuan , Liu Houfang , Tian He , Yang Yi , Ren Tian-Ling
Published: April 2019

To explore the effect of the ZrO2 content on the switching speed of ferroelectric HfO2-ZrO2 (FE-HZO), we demonstrate 10 nm FE-HZO capacitors fabricated with 5:5, 6:4, and 7:3 HfO2 and ZrO2 atomic-layer-deposition-cycling ratios. The FE-HZO devices show high remanent polarization (Pr) of 26, 20, and 11 μC/cm2 for the 5:5, 6:4, and 7:3 samples, respectively. The FE-HZO capacitors with lower ZrO2 contents show increasing coercive fields, which intuitively seem to increase switching difficulty. However, the FE-HZO devices with 50 mol. %, 40 mol. %, and 30 mol. % ZrO2 contents show decreasing switching times for 80% polarization, namely, 1.2, 0.9, and 0.7 μs, respectively. Because of the polycrystalline nature of FE-HZO, the distribution of local fields in the film is analyzed based on the inhomogeneous field mechanism model. The results show that the FE-HZO devices with lower ZrO2 contents have higher active fields and less uniform distribution of local fields. However, time constants for the 5:5, 6:4, and 7:3 samples decrease dramatically, being 137, 98, and 14 ps, respectively. These results unveil the distribution of the local fields in FE-HZO with varying ZrO2 contents and are helpful for understanding and optimizing the switching dynamics of FE-HZO for non-volatile memory applications.
Mind the gap: is it time to invest in embedded researchers in regional, rural and remote health services to address health outcome discrepancies for those living in rural, remote and regional areas?
Authors: Moran Anna , Haines Helen , Raschke Nicole , Schmidt David , Koschel Alison , Stephens Alexandre , Opie Cynthia , Nancarrow Susan
Published: April 2019

Research capacity building in healthcare works to generate and apply new knowledge to improve health outcomes; it creates new career pathways, improves staff satisfaction, retention and organisational performance. While there are examples of investment and research activity in rural Australia, overall, rural research remains under-reported, undervalued and under-represented in the evidence base. This is particularly so in primary care settings. This lack of contextual knowledge generation and translation perpetuates rural–metropolitan health outcome disparities. Through greater attention to and investment in building research capacity and capability in our regional, rural and remote health services, these issues may be partially addressed. It is proposed that it is time for Australia to systematically invest in rurally focussed, sustainable, embedded research capacity building.
Implementation of an occupancy-based monitoring protocol for a widespread and cryptic species, the New England cottontail (Sylvilagus transitionalis)
Authors: Shea Colin P. , Eaton Mitchell J. , MacKenzie Darryl I.
Published: April 2019

Context
Designing effective long-term monitoring strategies is essential for managing wildlife populations. Implementing a cost-effective, practical monitoring program is especially challenging for widespread but locally rare species. Early successional habitat preferred by the New England cottontail (NEC) has become increasingly rare and fragmented, resulting in substantial declines from their peak distribution in the mid-1900s. The introduction of a possible competitor species, the eastern cottontail (EC), may also have played a role. Uncertainty surrounding how these factors have contributed to NEC declines has complicated management and necessitated development of an appropriate monitoring framework to understand possible drivers of distribution and dynamics.

Aims
Because estimating species abundance is costly, we designed presence–absence surveys to estimate species distributions, test assumptions about competitive interactions, and improve understanding of demographic processes for eastern cottontails (EC) and New England cottontails (NEC). The survey protocol aimed to balance long-term management objectives with practical considerations associated with monitoring a widespread but uncommon species. Modelling data arising from these observations allow for estimation of covariate relationships between species status and environmental conditions including habitat and competition. The framework also allows inference about species status at unsurveyed locations.

Methods
We designed a monitoring protocol to collect data across six north-eastern USA states and, using data collected from the first year of monitoring, fit a suite of single-season occupancy models to assess how abiotic and biotic factors influence NEC occurrence, correcting for imperfect detectability.

Key results
Models did not provide substantial support for competitive interactions between EC and NEC. NEC occurrence patterns appear to be influenced by several remotely sensed habitat covariates (land-cover classes), a habitat-suitability index, and, to a lesser degree, plot-level habitat covariates (understorey density and canopy cover).

Conclusions
We recommend continuing presence–absence monitoring and the development of dynamic occupancy models to provide further evidence regarding hypotheses of competitive interactions and habitat influences on the underlying dynamics of NEC occupancy.

Implications
State and federal agencies responsible for conserving this and other threatened species can engage with researchers in thoughtful discussions, based on management objectives, regarding appropriate monitoring design to ensure that the allocation of monitoring efforts provides useful inference on population drivers to inform management intervention.
Peroxisome protein import recapitulated in Xenopus egg extracts
Authors: Romano Fabian B. , Blok Neil B. , Rapoport Tom A.
Published: April 2019

Peroxisomes import their luminal proteins from the cytosol. Most substrates contain a C-terminal Ser-Lys-Leu (SKL) sequence that is recognized by the receptor Pex5. Pex5 binds to peroxisomes via a docking complex containing Pex14, and recycles back into the cytosol following its mono-ubiquitination at a conserved Cys residue. The mechanism of peroxisome protein import remains incompletely understood. Here, we developed an in vitro import system based on Xenopus egg extracts. Import is dependent on the SKL motif in the substrate and on the presence of Pex5 and Pex14, and is sustained by ATP hydrolysis. A protein lacking an SKL sequence can be coimported, providing strong evidence for import of a folded protein. The conserved cysteine in Pex5 is not essential for import or to clear import sites for subsequent rounds of translocation. This new in vitro assay will be useful for further dissecting the mechanism of peroxisome protein import.
Thermoelectrics versus thermophotovoltaics: two approaches to convert heat fluxes into electricity
Authors: Okanimba Tedah Irene Ambo , Maculewicz Franziska , Wolf Dietrich E , Schmechel Roland
Published: April 2019

Direct conversion of heat fluxes into electricity is usually done by thermoelectric generators (TEGs). For hot-side temperatures above 1000 K, thermal radiation carries a high energy density, comparable with the energy density extracted from TEGs and therefore a direct conversion of thermal radiation into electricity, named thermophotovoltaics (TPV), would also be an option. This paper compares both methods with respect to efficiency and extractable power density. The physical limits are estimated under simplified but realistic boundary conditions. For TPV the radiative detailed balance limit under black body radiation, which was calculated for different hot-side temperatures from 310 K to 3000 K for an optimized bandgap of the applied material was used. But, since very narrow bandgaps leading to strong non-radiative recombination mechanisms, the bandgap was limited to

. The effect of suppressing sub-bandgap radiation as well as an enhanced radiation density in the nearfield (near-field TPV) were also included. The TEG efficiency and power density was calculated under thermal matching conditions with a heat transfer coefficient of

and an average device

. The results are compared with experimental data for TPV and TEGs from literature. It is shown, that up to 600 K hot-side temperature TEGs are superior to TPV, due to a significant higher power density. Above 1000 K TPV profits from higher efficiency by a similar power density. But above 2000 K TPV suffers from cell heating. The range 600 K to 1000 K is currently captured by high temperature thermoelectrics, but near-field TPV (NF-TPV) has good chances to compete with TEGs in this temperature range in the future.
Joint effort among research infrastructures to quantify the impact of plastic debris in the ocean
Authors: Conchubhair Diarmuid Ó , Fitzhenry Deirdre , Lusher Amy , King Andrew L , van Emmerik Tim , Lebreton Laurent , Ricaurte-Villota Constanza , Espinosa Luisa , O’Rourke Eleanor
Published: April 2019

Marine debris is one of the most significant problems facing the marine environment, endangering wildlife, polluting oceans and is an issue which holds global significance. Plastics constitute a large proportion of marine debris, and their persistence can cause a number of negative consequences for biota and the environment, including entanglement and ingestion, which can lead to mortality. Most plastics never biodegrade and instead break down into smaller pieces which are more difficult to monitor and eventually become so small (micro and nanoplastics), that they are challenging to observe or intercept in the ocean. Marine-based Research Infrastructures (RIs) monitor several environmental parameters and are situated around the globe; however, none of these are routinely monitoring marine debris or plastics. Currently, the only infrastructures in place with regard to marine debris are ‘physical debris interception infrastructure’ in the form of barriers constructed to prevent marine debris from entering the ocean. Several knowledge gaps and restraints exist within current in situ infrastructure including technological immaturity, diverse methodologies and lack of data harmonisation. Nevertheless, marine RIs could monitor microplastics within the water column on a long-term basis and initial steps towards developing technology are promising.
Climate change impacts on Canadian yields of spring wheat, canola and maize for global warming levels of 1.5 °C, 2.0 °C, 2.5 °C and 3.0 °C
Authors: Qian Budong , Zhang Xuebin , Smith Ward , Grant Brian , Jing Qi , Cannon Alex J , Neilsen Denise , McConkey Brian , Li Guilong , Bonsal Barrie , Wan Hui , Xue Li , Zhao Jun
Published: April 2019

Science-based assessments of climate change impacts on cropping systems under different levels of global warming are essential for informing stakeholders which global climate targets and potential adaptation strategies may be effective. A comprehensive evaluation of climate change impacts on Canada’s crop production under different levels of global warming is currently lacking. The DayCent, DNDC and DSSAT models were employed to estimate changes in crop yield and production for three prominent crops including spring wheat, canola and maize in current agricultural regions of Canada. Four warming scenarios with global mean temperature changes of 1.5 °C, 2.0 °C, 2.5 °C and 3.0 °C above the pre-industrial level were investigated. Climate scenarios from 20 Global Climate Models, included in the Coupled Model Intercomparison Project Phase 5 and downscaled with a multivariate quantile mapping bias correction method, were used to drive the crop simulation models. Simulated yield changes demonstrate a potentially positive impact on spring wheat and canola yields at all four temperature levels, particularly when shifting planting date is considered in the simulations. There was less consensus for the currently utilized short-season maize cultivars, as yields were only projected to increase by DNDC compared to a slight decrease by DayCent and a slight increase up to 2.5 °C followed by a decrease at 3.0 °C by DSSAT. These findings indicate that climate at the global warming levels up to 3.0 °C above the pre-industrial level could be beneficial for crop production of small grains in Canada. However, these benefits declined after warming reached 2.5 °C.
Moufang Sets and Structurable Division Algebras
Authors: Boelaert Lien , De Medts Tom , Stavrova Anastasia
Published: April 2019

A Moufang set is essentially a doubly transitive permutation group such that each point stabilizer contains a normal subgroup which is regular on the remaining vertices; these regular normal subgroups are called the root groups, and they are assumed to be conjugate and to generate the whole group.

It has been known for some time that every Jordan division algebra gives rise to a Moufang set with abelian root groups. We extend this result by showing that every structurable division algebra gives rise to a Moufang set, and conversely, we show that every Moufang set arising from a simple linear algebraic group of relative rank one over an arbitrary field

k
k

of characteristic different from

2
2

and

3
3

arises from a structurable division algebra.

We also obtain explicit formulas for the root groups, the

τ
\tau

-map and the Hua maps of these Moufang sets. This is particularly useful for the Moufang sets arising from exceptional linear algebraic groups.
Monotone maps of 𝐺-like continua with positive topological entropy yield indecomposability
Authors: Kato Hisao
Published: April 2019

In the previous paper Adv. Math. 304 (2017), pp. 793–808, we proved that if for any graph

G
G

, a homeomorphism on a

G
G

-like continuum

X
X

has positive topological entropy, then the continuum

X
X

contains an indecomposable subcontinuum. Also, if for a tree

G
G

, a monotone map on a

G
G

-like continuum

X
X

has positive topological entropy, then the continuum

X
X

contains an indecomposable subcontinuum. In this note, we extend these results. In fact, we prove that if for any graph

G
G

, a monotone map on a

G
G

-like continuum

X
X

has positive topological entropy, then the continuum

X
X

contains an indecomposable subcontinuum. Also we study topological entropy of monotone maps on Suslinean continua.
Ulrich bundles on smooth projective varieties of minimal degree
Authors: Aprodu M. , Huh S. , Malaspina F. , Pons-Llopis J.
Published: April 2019

We classify Ulrich vector bundles of arbitrary rank on smooth projective varieties of minimal degree. In the process, we prove the stability of the sheaves of relative differentials on rational scrolls.
On Kierstead’s conjecture
Authors: Ng Keng Meng , Zubkov Maxim
Published: April 2019

We settle the long-standing Kierstead conjecture in the negative. We do this by constructing a computable linear order with no rational subintervals, where every block has order type finite or

ζ
\zeta

, and where every computable copy has a strongly nontrivial

Π
1
0

\Pi ^0_1

automorphism. We also construct a strongly

η
\eta

-like linear order where every block has size at most

4
4

with no rational subinterval such that every

Δ
2
0

\Delta ^0_2

isomorphic computable copy has a nontrivial

Π
1
0

\Pi ^0_1

automorphism.
Simple ℒ-invariants for GL_{𝓃}
Authors: Ding Yiwen
Published: April 2019

Let

L
L

be a finite extension of

Q

p

{\mathbb Q}_p

, and

ρ
L

\rho _L

be an

n
n

-dimensional semistable noncrystalline

p
p

-adic representation of

G
a
l

L

{\mathrm {Gal}}_L

with full monodromy rank. Via a study of Breuil’s (simple)

L

{\mathcal L}

-invariants, we attach to

ρ
L

\rho _L

a locally

Q

p

{\mathbb Q}_p

-analytic representation

Π
(

ρ
L

)

\Pi (\rho _L)

of

G
L

n

(
L
)

{\mathrm {GL}}_n(L)

, which carries the exact information of the Fontaine–Mazur simple

L

{\mathcal L}

-invariants of

ρ
L

\rho _L

. When

ρ
L

\rho _L

comes from an automorphic representation of

G
(

A

F
+

)

G({\mathbb A}_{F^+})

(for a unitary group

G
G

over a totally real field

F
+

F^+

which is compact at infinite places and

G
L

n

{\mathrm {GL}}_n

at

p
p

-adic places), we prove under mild hypothesis that

Π
(

ρ
L

)

\Pi (\rho _L)

is a subrepresentation of the associated Hecke-isotypic subspaces of the Banach spaces of

p
p

-adic automorphic forms on

G
(

A

F
+

)

G({\mathbb A}_{F^+})

. In other words, we prove the equality of Breuil’s simple

L

{\mathcal L}

-invariants and Fontaine–Mazur simple

L
L

-invariants.
Vanishing theorems and Brauer–Hasse–Noether exact sequences for the cohomology of higher-dimensional fields
Authors: Izquierdo Diego
Published: April 2019

Let

k
k

be a finite field, a

p
p

-adic field, or a number field. Let

K
K

be a finite extension of the Laurent series field in

m
m

variables

k
(
(

x
1

,
…
,

x
m

)
)

k((x_1,\ldots ,x_m))

. When

r
r

is an integer and

ℓ
\ell

is a prime number, we consider the Galois module

Q

ℓ

/

Z

ℓ

(
r
)

\mathbb {Q}_{\ell }/\mathbb {Z}_{\ell }(r)

over

K
K

, and we prove several vanishing theorems for its cohomology. In the particular case in which

K
K

is a finite extension of the Laurent series field in two variables

k
(
(

x
1

,

x
2

)
)

k((x_1,x_2))

, we also prove exact sequences that play the role of the Brauer–Hasse–Noether exact sequence for the field

K
K

and that involve some of the cohomology groups of

Q

ℓ

/

Z

ℓ

(
r
)

\mathbb {Q}_{\ell }/\mathbb {Z}_{\ell }(r)

which do not vanish.
Arf6, JIP3, and dynein shape and mediate macropinocytosis
Authors: Williamson Chad D. , Donaldson Julie G.
Published: April 2019

Macropinocytosis is an actin-driven form of clathrin-independent endocytosis that generates an enlarged structure, the macropinosome. Although many studies focus on signaling molecules and phosphoinositides involved in initiating macropinocytosis, the commitment to forming a macropinosome and the handling of that membrane have not been studied in detail. Here we show in HT1080 cells, a human fibrosarcoma cell line, a requirement for microtubules, dynein, the JIP3 microtubule motor scaffold protein, and Arf6, a JIP3 interacting protein, for the formation and inward movement of the macropinosome. While actin and myosin II also play critical roles in the formation of ruffling membrane, microtubules provide an important tract for initiation, sealing, and transport of the macropinosome through the actin- and myosin-rich lamellar region.
Effects of manipulated levels of predation threat on parental provisioning and nestling begging
Authors: Mutzel Ariane , Olsen Anne-Lise , Mathot Kimberley J , Araya-Ajoy Yimen G , Nicolaus Marion , Wijmenga Jan J , Wright Jonathan , Kempenaers Bart , Dingemanse Niels J
Published: April 2019

Parental provisioning behavior is a major determinant of offspring growth and survival, but high provisioning rates might come at the cost of increased predation threat. Parents should thus adjust provisioning activity according to current predation threat levels. Moreover, life-history theory predicts that response to predation threat should be correlated with investment in current reproduction. We experimentally manipulated perceived predation threat in free-living great tits (Parus major) by presenting parents with a nest predator model while monitoring different aspects of provisioning behavior and nestling begging. Experiments were conducted in 2 years differing greatly in ecological conditions, including food availability. We further quantified male territorial aggressiveness and male and female exploratory tendency. Parents adjusted provisioning according to current levels of threat in an apparently adaptive way. They delayed nest visits during periods of elevated perceived predation threat and subsequently compensated for lost feeding opportunities by increasing provisioning once the immediate threat had diminished. Nestling begging increased after elevated levels of predation threat, but returned to baseline levels by the end of the experiment, suggesting that parents had fully compensated for lost feeding opportunities. There was no evidence for a link between male exploration behavior or aggressiveness and provisioning behavior. In contrast, fast-exploring females provisioned at higher rates, but only in the year with poor environmental conditions, which might indicate a greater willingness to invest in current reproduction in general. Future work should assess whether these personality-related differences in delivery rates under harsher conditions came at a cost of reduced residual reproductive value.
Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants
Authors: Monger Steven , Troup Michael , Ip Eddie , Dunwoodie Sally L , Giannoulatou Eleni
Published: April 2019

Motivation

In silico prediction tools are essential for identifying variants which create or disrupt cis-splicing motifs. However, there are limited options for genome-scale discovery of splice-altering variants.

Results

We have developed Spliceogen, a highly scalable pipeline integrating predictions from some of the individually best performing models for splice motif prediction: MaxEntScan, GeneSplicer, ESRseq and Branchpointer.

Availability and implementation

Spliceogen is available as a command line tool which accepts VCF/BED inputs and handles both single nucleotide variants (SNVs) and indels (https://github.com/VCCRI/Spliceogen). SNV databases with prediction scores are also available, covering all possible SNVs at all genomic positions within all Gencode-annotated multi-exon transcripts.

Supplementary information

Supplementary data are available at Bioinformatics online.
PyPore: a python toolbox for nanopore sequencing data handling
Authors: Semeraro Roberto , Magi Alberto
Published: April 2019

Motivation

The recent technological improvement of Oxford Nanopore sequencing pushed the throughput of these devices to 10–20 Gb allowing the generation of millions of reads. For these reasons, the availability of fast software packages for evaluating experimental quality by generating highly informative and interactive summary plots is of fundamental importance.

Results

We developed PyPore, a three module python toolbox designed to handle raw FAST5 files from quality checking to alignment to a reference genome and to explore their features through the generation of browsable HTML files. The first module provides an interface to explore and evaluate the information contained in FAST5 and summarize them into informative quality measures. The second module converts raw data in FASTQ format, while the third module allows to easily use three state-of-the-art aligners and collects mapping statistics.

Availability and implementation

PyPore is an open-source software and is written in Python2.7, source code is freely available, for all OS platforms, in Github at https://github.com/rsemeraro/PyPore

Supplementary information

Supplementary data are available at Bioinformatics online.
The Dynamics of Speech Motor Control Revealed with Time-Resolved fMRI
Authors: Janssen Niels , Mendieta Cristian Camilo Rincón
Published: April 2019

Holding a conversation means that speech must be started, maintained, and stopped continuously. The brain networks that underlie these aspects of speech motor control remain poorly understood. Here we collected functional magnetic resonance imaging (fMRI) data while participants produced normal and fast rate speech in response to sequences of visually presented objects. We took a non-conventional approach to fMRI data analysis that allowed us to study speech motor behavior as it unfolded over time. To this end, whole-brain fMRI signals were extracted in stimulus-locked epochs using slice-based fMRI. These data were then subjected to group independent component analysis to discover spatially independent networks that were associated with different temporal activation profiles. The results revealed two basic brain networks with different temporal dynamics: a cortical network that was activated continuously during speech production, and a second cortico-subcortical network that increased in activity during the initiation and suppression of speech production. Additional analyses explored whether key areas involved in motor suppression such as the right inferior frontal gyrus, sub-thalamic nucleus and pre-supplementary motor area provide first-order signals to stop speech. The results reveal for the first time the brain networks associated with the initiation, maintenance, and suppression of speech motor behavior.
How Introducing a Registry With Automated Alerts for Carbapenem-resistant Enterobacteriaceae (CRE) May Help Control CRE Spread in a Region
Authors: Lee Bruce Y , Bartsch Sarah M , Hayden Mary K , Welling Joel , DePasse Jay V , Kemble Sarah K , Leonard Jim , Weinstein Robert A , Mueller Leslie E , Doshi Kruti , Brown Shawn T , Trick William E , Lin Michael Y
Published: April 2019

Background

Regions are considering the use of electronic registries to track patients who carry antibiotic-resistant bacteria, including carbapenem-resistant Enterobacteriaceae (CRE). Implementing such a registry can be challenging and requires time, effort, and resources; therefore, there is a need to better understand the potential impact.

Methods

We developed an agent-based model of all inpatient healthcare facilities (90 acute care hospitals, 9 long-term acute care hospitals, 351 skilled nursing facilities, and 12 ventilator-capable skilled nursing facilities) in the Chicago metropolitan area, surrounding communities, and patient flow using our Regional Healthcare Ecosystem Analyst software platform. Scenarios explored the impact of a registry that tracked patients carrying CRE to help guide infection prevention and control.

Results

When all Illinois facilities participated (n = 402), the registry reduced the number of new carriers by 11.7% and CRE prevalence by 7.6% over a 3-year period. When 75% of the largest Illinois facilities participated (n = 304), registry use resulted in a 11.6% relative reduction in new carriers (16.9% and 1.2% in participating and nonparticipating facilities, respectively) and 5.0% relative reduction in prevalence. When 50% participated (n = 201), there were 10.7% and 5.6% relative reductions in incident carriers and prevalence, respectively. When 25% participated (n = 101), there was a 9.1% relative reduction in incident carriers (20.4% and 1.6% in participating and nonparticipating facilities, respectively) and 2.8% relative reduction in prevalence.

Conclusions

Implementing an extensively drug-resistant organism registry reduced CRE spread, even when only 25% of the largest Illinois facilities participated due to patient sharing. Nonparticipating facilities garnered benefits, with reductions in new carriers.
Pharmacokinetics and Pharmacodynamics of Oral and Intravenous Omadacycline
Authors: Rodvold Keith A , Pai Manjunath P
Published: April 2019

Oral and intravenous (IV) omadacycline formulations are approved in the United States for treating acute bacterial skin and skin structure infections and community-acquired bacterial pneumonia in adults. Oral omadacycline bioavailability is 34.5%; similar exposures are obtained following 300 mg oral and 100 mg IV doses. Oral administration should be in a fasted state, with dairy products, antacids, or multivitamins avoided for ≥4 hours after dosing. Low protein binding (21%), large volume of distribution (190 L), low systemic clearance (10 L/hour), and long elimination half-life (16–17 hours) support once-daily dosing. Omadacycline is excreted unchanged in feces (81.1%) and urine (14.4%), with low potential for drug–drug interactions. Dose adjustments are unnecessary for age, sex, and renal or hepatic impairment. Pharmacokinetic–pharmacodynamic studies identify fAUC0–24/MIC ratio as the parameter that correlates with in vivo efficacy. Systemic exposure of omadacycline in epithelial lining fluid is greater than/equal to plasma concentrations in healthy adults.
Near-optimal recovery of linear and N-convex functions on unions of convex sets
Authors: Juditsky Anatoli , Nemirovski Arkadi
Published: April 2019

In this paper we build provably near-optimal, in the minimax sense, estimates of linear forms and, more generally, ‘$N$-convex functionals’ (an example being the maximum of several fractional-linear functions) of unknown ‘signal’ from indirect noisy observations, the signal assumed to belong to the union of finitely many given convex compact sets. Our main assumption is that the observation scheme in question is good in the sense of Goldenshluger et al. (2015, Electron. J. Stat., 9, 1645–1712), the simplest example being the Gaussian scheme, where the observation is the sum of linear image of the signal and the standard Gaussian noise. The proposed estimates, same as upper bounds on their worst-case risks, stem from solutions to explicit convex optimization problems, making the estimates ‘computation-friendly’.
Early Clearance of Mycobacterium tuberculosis: The INFECT Case Contact Cohort Study in Indonesia
Authors: Verrall Ayesha J , Alisjahbana Bachti , Apriani Lika , Novianty Novianty , Nurani Andini C , van Laarhoven Arjan , Ussher James E , Indrati Agnes , Ruslami Rovina , Netea Mihai G , Sharples Katrina , van Crevel Reinout , Hill Philip C
Published: April 2019

Background

Early clearance of Mycobacterium tuberculosis is the eradication of infection before an adaptive immune response develops. We aimed to identify host factors associated with early clearance.

Methods

Indonesian household contacts patients with smear-positive tuberculosis (TB) had an interferon-γ release assay (IGRA) at baseline and 14 weeks later. Early clearance was defined as a persistently negative IGRA. Contact characteristics, exposure, and disease phenotype were assessed for association with a positive IGRA at each time point.

Results

Of 1347 contacts of 462 TB cases, 780 (57.9%) were IGRA positive and 490 (36.3%) were IGRA negative. After 14 weeks, 116 of 445 (26.1%) initially negative contacts were IGRA converters; 317 (71.2%) remained persistently negative. BCG vaccination reduced the risk of a positive baseline IGRA (relative risk [RR], 0.89 [95% confidence interval {CI} .83–.97]; P = .01), and strongly reduced the risk of IGRA conversion (RR, 0.56 [95% CI, .40–.77]; P < .001). BCG protection decreased with increasing exposure (P = .05) and increasing age (P = .004). Risk of IGRA conversion was positively associated with hemoglobin concentration (P = .04).

Conclusions

A quarter of household TB case contacts were early clearers. Protection against M. tuberculosis infection was strongly associated with BCG vaccination. Lower protection from BCG with increasing M. tuberculosis exposure and age can inform vaccine development.
Sphingosine 1-phosphate and inflammation
Authors: Obinata Hideru , Hla Timothy
Published: April 2019

AbstractSphingosine 1-phosphate (S1P), a sphingolipid mediator, regulates various cellular functions via high-affinity G protein-coupled receptors, S1P1-5. The S1P-S1P receptor signaling system plays important roles in lymphocyte trafficking and maintenance of vascular integrity, thus contributing to the regulation of complex inflammatory processes. S1P is enriched in blood and lymph while maintained low in intracellular or interstitial fluids, creating a steep S1P gradient that is utilized to facilitate efficient egress of lymphocytes from lymphoid organs. Blockage of the S1P-S1P receptor signaling system results in a marked decrease in circulating lymphocytes because of a failure of lymphocyte egress from lymphoid organs. This provides a basis of immunomodulatory drugs targeting S1P1 receptor such as FTY720, an immunosuppressive drug approved in 2010 as the first oral treatment for relapsing–remitting multiple sclerosis. The S1P-S1P receptor signaling system also plays important roles in maintenance of vascular integrity since it suppresses sprouting angiogenesis and regulates vascular permeability. Dysfunction of the S1P-S1P receptor signaling system results in various vascular defects, such as exaggerated angiogenesis in developing retina and augmented inflammation due to increased permeability. Endothelial-specific deletion of S1P1 receptor in mice fed high-fat diet leads to increased formation of atherosclerotic lesions. This review highlights the importance of the S1P-S1P receptor signaling system in inflammatory processes. We also describe our recent findings regarding a specific S1P chaperone, apolipoprotein M, that anchors to high-density lipoprotein and contributes to shaping the endothelial-protective and anti-inflammatory properties of high-density lipoprotein.
BOARD INVITED REVIEW: Post-transfer consequences of in vitro-produced embryos in cattle
Authors: Ealy Alan D , Wooldridge Lydia K , McCoski Sarah R
Published: April 2019

In vitro embryo production (IVP) in cattle has gained worldwide interest in recent years, but the efficiency of using IVP embryos for calf production is far from optimal. This review will examine the pregnancy retention rates of IVP embryos and explore causes for pregnancy failures. Based on work completed over the past 25 yr, only 27% of cattle receiving IVP embryos will produce a live calf. Approximately 60% of these pregnancies fail during the first 6 wk of gestation. When compared with embryos generated by superovulation, pregnancy rates are 10% to 40% lower for cattle carrying IVP embryos, exemplifying that IVP embryos are consistently less competent than in vivo-generated embryos. Several abnormalities have been observed in the morphology of IVP conceptuses. After transfer, IVP embryos are less likely to undergo conceptus elongation, have reduced embryonic disk diameter, and have compromised yolk sac development. Marginal binucleate cell development, cotyledon development, and placental vascularization have also been documented, and these abnormalities are associated with altered fetal growth trajectories. Additionally, in vitro culture conditions increase the risk of large offspring syndrome. Further work is needed to decipher how the embryo culture environment alters post-transfer embryo development and survival. The risk of these neonatal disorders has been reduced by the use of serum-free synthetic oviductal fluid media formations and culture in low oxygen tension. However, alterations are still evident in IVP oocyte and embryo transcript abundances, timing of embryonic cleavage events and blastulation, incidence of aneuploidy, and embryonic methylation status. The inclusion of oviductal and uterine-derived embryokines in culture media is being examined as one way to improve the competency of IVP embryos. To conclude, the evidence presented herein clearly shows that bovine IVP systems still must be refined to make it an economical technology in cattle production systems. However, the current shortcomings do not negate its current value for certain embryo production needs and for investigating early embryonic development in cattle.
Phylogeography of Simulium Subgenus Wilhelmia (Diptera: Simuliidae)—Insights From Balkan Populations
Authors: Đuknić Jelena , Jovanović Vladimir M , Popović Nataša , Živić Ivana , Raković Maja , Čerba Dubravka , Paunović Momir
Published: April 2019

Many morphologically similar species of the simuliid (Diptera: Simuliidae) subgenus Wilhelmia, Enderlein are difficult to distinguish. Thus, the revision of the subgenus using various morphological, cytogenetic, and genetic analyses has been attempted. Neglected until now, the Balkan Peninsula, a crossroad between Europe and Anatolia, provides insight which could resolve problematic interrelationships of the taxa within this subgenus. To uncover the status and relations within the subgenus Wilhelmia, mtDNA was extracted from 47 individuals of six morphospecies: Simulium balcanicum (Enderlein, 1924), Simulium turgaicum Rubtsov, 1940, Simulium lineatum (Meigen, 1804), Simulium pseudequinum Séguy, 1921, Simulium equinum (Linnaeus, 1758), and Simulium paraequinum Puri, 1933 from 21 sites throughout the Balkan Peninsula. Phylogenetic analysis of the Wilhelmia species using mitochondrial DNA barcoding (COI) gene showed two major branches, the lineatum branch, which includes the lineages sergenti, paraequinum, and lineatum, and the equinum branch. In the equinum branch, the mtDNA sequences formed six clades, with high genetic distances, suggesting the existence of different species. Historically, the clades of the equinum branch appeared at numerous islands, perhaps as a result of allopatric speciation. The paraequinum lineage (lineatum branch) is composed of two species. However, six clades of the lineatum lineage overlapped with intra- and interspecific genetic distances. Our results revealed that the species S. balcanicum, S. pseudequinum B, and S. equinum were omnipresent in the Balkans. The results point to not only the fair diversity of Wilhelmia species in the Balkans, but also indicate that most Wilhelmia species live in sympatry.
Proliferating Bias? American Political Science, Nuclear Weapons, and Global Security
Authors: Braut-Hegghammer Målfrid
Published: April 2019

This article examines whether there is a US bias affecting how American political scientist study nuclear weapons and their effects. US dominance in the production and dissemination of political science literature on nuclear weapons is reflected in concepts and theories of their spread and use, as well as prominent datasets on nuclear proliferation. More broadly, is there a US bias in scholarship on nuclear weapons produced by American political scientist? In this article I examine whether there is a US bias that affects what is studied, what kinds of questions are asked and what cases are examined, and how the evidence is interpreted.