bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoinduced valence tautomerism of a cobalt-dioxolene complex revealed with femtosecond M-edge XANES
Authors: Ash Ryan , Zhang Kaili , Vura-Weis Josh
Published: September 2019

Cobalt complexes that undergo charge-transfer induced spin-transitions or valence tautomerism from low spin CoIII to high spin (HS) CoII are potential candidates for magneto-optical switches. We use M2,3-edge X-ray absorption near-edge structure (XANES) spectroscopy with 40 fs time resolution to measure the excited-state dynamics of CoIII(Cat-N-SQ)(Cat-N-BQ), where Cat-N-BQ and Cat-N-SQ are the singly and doubly reduced forms of the 2-(2-hydroxy-3,5-di-tert-butylphenyl-imino)-4,6-di-tert-butylcyclohexa-3,5-dienone ligand. The extreme ultraviolet probe pulses, produced using a tabletop high-harmonic generation light source, measure 3p → 3d transitions and are sensitive to the spin and oxidation state of the Co center. Photoexcitation at 525 nm produces a low-spin CoII ligand-to-metal charge transfer state which undergoes intersystem crossing to high-spin CoII in 67 fs. Vibrational cooling from this hot HS CoII state competes on the hundreds-of-fs time scale with back-intersystem crossing to the ground state, with 60% of the population trapped in a cold HS CoII state for 24 ps. Ligand field multiplet simulations accurately reproduce the ground-state spectra and support the excited-state assignments. This work demonstrates the ability of M2,3-edge XANES to measure ultrafast photophysics of molecular Co complexes.
Nonlocal global symmetries of a free scalar field in a bounded spatial domain
Authors: Balondo Iyela Daddy , Govaerts Jan
Published: September 2019

Bondi-Metzner-Sachs (BMS) symmetries have been attracting a great deal of interest in recent years. Originally discovered as being the symmetries of asymptotically flat spacetime geometries at null infinity in general relativity, BMS symmetries have also been shown to exist for free field theories over Minkowski spacetime. In wanting to better understand their status and the underlying reasons for their existence, this work proposes a general rationale toward identifying all possible global symmetries of a free field theory over Minkowski spacetime, by allowing the corresponding conserved generators not to be necessarily spatially local in phase space. As a preliminary toward a separate study of the role of asymptotic states for BMS symmetries in an unbounded Minkowski spacetime, the present discussion focuses first onto a 2 + 1 dimensional free scalar field theory in a bounded spatial domain with the topology of a disk and an arbitrary radial Robin boundary condition. The complete set of global symmetries of that system, most of which are dynamical symmetries but include as well those generated by the local total energy and angular-momentum of the field, is thereby identified.
The equation of state of TaC0.99 by X-ray diffraction in radial scattering geometry to 32 GPa and 1073 K
Authors: Speziale S. , Immoor J. , Ermakov A. , Merkel S. , Marquardt H. , Liermann H.-P.
Published: September 2019

We have performed in situ synchrotron X-ray diffraction experiments on TaC0.99 compressed in a diamond anvil cell along 3 isothermal paths to maximum pressure (P)-temperature (T) conditions of 38.8 GPa at 1073 K. By combining measurements performed in axial diffraction geometry at 296 K and in radial geometry at 673 K and 1073 K, we place constraints on the pressure-volume-temperature (P-V-T) equation of state of TaC in a wide range of conditions. A fit of the Birch-Murnaghan equation to the measurements performed in axial geometry at ambient temperature yields a value of the isothermal bulk modulus at ambient conditions KT0=305±5(1σ)GPa and its pressure derivative (∂KT/∂P)T0=6.1±0.5. The fit of the Birch-Murnaghan-Debye model to our complete P-V-T dataset allows us to constrain the Grüneisen parameter at ambient pressure γ0=V(∂P/∂E)V0 to the value of 1.2 ± 0.1.
Study of the effect of external noise pickups on the performance of a cryogenic bolometer
Authors: Garai A. , Reza A. , Mazumdar A. , Krishnamoorthy H. , Gupta G. , Pose M. S. , Mallikarjunachary S. , Nanal V. , Pillay R. G. , Ramakrishnan S.
Published: September 2019

This paper reports the detailed noise characterization, investigation of various noise sources, and its mitigation to improve the performance of a cryogenic bolometer detector for the TIN.TIN experiment. The noise spectrum has been measured for a sapphire bolometer test setup with an indigenously developed neutron transmutation doped Ge sensor in the cryogen free dilution refrigerator system at Mumbai. The effect of external noise, arising either from ground loops in the system or from the diagnostic and control electronics of the cryostat, on the performance of the bolometer is assessed. A systematic comparison of the influence of different noise pickups on the bolometer resolution is also presented. The best-achieved resolution (σE) at 15 mK is ∼15 keV for heater pulses and appears to be mainly limited by the noise due to the pulse tube cryocooler.
Muon probes of temperature-dependent charge carrier kinetics in semiconductors
Authors: Yokoyama K. , Lord J. S. , Mengyan P. W. , Goeks M. R. , Lichti R. L.
Published: September 2019

We have applied the photoexcited muon spin spectroscopy technique to intrinsic germanium with the goal of developing a method for characterizing excess carrier kinetics in a wide range of semiconductors. Muon spin relaxation rates can be a unique measure of excess carrier density and utilized to investigate carrier dynamics. By virtue of the localized nature of implanted muons, the obtained carrier lifetime spectrum can be modeled with a simple 1-dimensional diffusion equation to determine bulk recombination lifetime and carrier diffusivity. Temperature dependent studies of these parameters can reveal the recombination and diffusion mechanism.
An explicit expression for the calculation of the Rortex vector
Authors: Xu Wenqian , Gao Yisheng , Deng Yue , Liu Jianming , Liu Chaoqun
Published: September 2019

Recently, a vector called Rortex was proposed and successfully applied to identify the local fluid rotation with both the rotation axis and strength. The first implementation relies on the real Schur decomposition of the velocity gradient tensor, resulting in a relatively long computational time. Subsequently, a mathematically equivalent eigenvector-based definition of Rortex was introduced with an improved implementation. Unfortunately, this definition still tends to be an algorithmic description rather than an explicit one and involves two successive cumbersome coordinate rotations. In this paper, a simple and explicit expression for the calculation of the Rortex vector, which is based on a special (transposed) Schur form of the velocity gradient tensor, is presented. The explicit expression is consistent with the previous definition but avoids the explicit calculation of the coordinate rotation, and thus can significantly simplify the implementation. According to the explicit expression, a new implementation is proposed and validated by a large eddy simulation of the flow transition around a NACA0012 airfoil and a direct numerical simulation of the boundary layer transition on a flat plate.
Multi-scroll hidden attractors with two stable equilibrium points
Authors: Deng Quanli , Wang Chunhua
Published: September 2019

Multiscroll hidden attractors have attracted extensive research interest in recent years. However, the previously reported multiscroll hidden attractors belong to only one category of hidden attractors, namely, the hidden attractors without equilibrium points. Up to now, multiscroll hidden attractors with stable equilibrium points have not been reported. This paper proposes a multiscroll chaotic system with two equilibrium points. The number of scrolls can be increased by adding breakpoints of a nonlinear function. Moreover, the two equilibrium points are stable node-foci equilibrium points. According to the classification of hidden attractors, the multiscroll attractors generated by a novel system are the hidden attractors with stable equilibrium points. The dynamical characteristics of the novel system are studied using the spectrum of Lyapunov exponents, a bifurcation diagram, and a Poincaré map. Furthermore, the novel system is implemented by electronic circuits. The hardware experiment results are consistent with the numerical simulations.
Cation dependent electroosmotic flow in glass nanopores
Authors: Mc Hugh Jeffrey , Andresen Kurt , Keyser Ulrich F.
Published: September 2019

We present our findings on the changes to electroosmotic flow outside glass nanopores with respect to the choice of Group 1 cation species. In contrast to standard electrokinetic theory, flow reversal was observed for all salts under a negative driving voltage. Moving down Group 1 resulted in weaker flow when the driving voltage was negative, in line with the reduction in the zeta potential on the glass surface going down the periodic table. No trend emerged with a positive driving voltage; however, for Cs, flow was uniquely found to be in reverse. These results are explained by the interplay between the flow inside the nanopore and flow along the outer walls in the vicinity of the nanopore.
An equation of state for Stockmayer fluids based on a perturbation theory for dipolar hard spheres
Authors: Theiss Marc , van Westen Thijs , Gross Joachim
Published: September 2019

We develop a perturbation theory for the difference between the Helmholtz energy of a Stockmayer fluid, i.e., a fluid interacting by a Lennard-Jones plus point-dipole potential, and a Lennard-Jones fluid. We show that the difference can be approximated by the perturbational Helmholtz energy contribution of a dipolar hard-sphere fluid with a suitably chosen effective hard-sphere diameter, relative to a hard-sphere fluid with the same effective diameter. We analyze both a third and fourth order perturbation theory, both written as Padé approximations. Several recipes for calculating the hard-sphere diameter are investigated; we find that the Weeks-Chandler-Andersen diameter is most suitable. Results of the perturbation theory are shown to be in good agreement with reference data for the Helmholtz energy, internal energy, and isochoric heat capacity as obtained from molecular simulations performed in this work and to vapor-liquid equilibrium data from the literature. Theoretical predictions of the proposed model are compared to results from the perturbation theory of Gubbins and Twu [Chem. Eng. Sci. 33, 863 (1978)], which is a theory based on a Lennard-Jones reference fluid. We find the theories are in good agreement. Our approach can easily be applied to van der Waals potentials, other than Lennard-Jones potentials. If a dipolar Mie fluid is considered, the approach merely requires calculation of the effective hard-sphere diameter for a Mie potential. We further note that the approach has a reduction in the variable space of the underlying correlation integrals, i.e., the correlation functions of a hard-sphere fluid depend on density only, whereas the Lennard-Jones reference correlation functions depend on density and temperature.
Solitary wave slamming induced by an asymmetric wedge through three degrees of freedom free motions
Authors: Cheng Yong , Yuan Dongchuang , Ji Chunyan , Li Gen
Published: September 2019

A time-domain higher-order boundary element method with fully nonlinear boundary conditions is developed to simulate the slamming of an asymmetric wedge entering freely and obliquely into a solitary wave in three degrees of freedom (3DOF). A third order analytical solution based on the Korteweg-de Vries equation is used to simulate the solitary wave incident boundary conditions. In the numerical model of slamming, a stretched coordinate system is applied to maintain numerical accuracy and stability at the initial stage. The thin long jet layer is generated along the wedge surface by assuming linear variation of the jet layer potential. A rotation scheme of the stretched coordinate system is adopted to avoid fluid particle leaving or entering the wedge surface. Some auxiliary functions are employed to decouple the intercoupling motions in 3DOF. The present model is verified by comparing with the published numerical results. Various parametric studies are carried out. Detailed results through the free surface, pressure distribution, accelerations, and velocities are provided to show the slamming effects, and their physical implications are discussed.
Tropical biodiversity faces intersecting threats
Authors: Miller Johanna L.
Published: September 2019

As global climate and land use both change, many rainforest species could struggle to find new habitats.
Environmental sustainability goals drive changes in conference practices
Authors: Middleton Christine
Published: September 2019

Alternative formats for sharing information and facilitating discussion help scientists lower their carbon footprints.
The stormy fluid dynamics of the living cell
Authors: Needleman Daniel , Shelley Michael
Published: September 2019

The flows inside cells are intricate and often counterintuitive. Measurements, models, and simulations are helping to unravel the complexities.
Performance-based pharmacy payment models: the case for change
Authors: Jackson John , Urick Ben
Published: September 2019

In response to rising healthcare costs, healthcare payers across the globe have been experimenting with performance-based payment models that link payments to providers with the quality of care that they provide. Community pharmacy in Australia has yet to be significantly affected by these changes. Initial steps have been taken to fund quality-linked interventions by pharmacists, such as the provision of medicines in dose administration aids, but funding for dispensing prescriptions remains solely based on a fee-for-service model. At the foundation of any performance-based payment model are measures that, in aggregate, reflect the quality of care that is provided. Patient adherence to prescription regimens can be correlated with the counselling provided by pharmacists and, as such, can serve as the measure on which a performance-based payment model for dispensing can be constructed. Experience in the US suggests per-prescription payments to a pharmacy can be increased or decreased by a small, yet meaningful, amount based on a measure of the level of adherence of patients of the pharmacy. The current dispensing payment model in the Australian Pharmaceutical Benefits Scheme may be able to be modified in a similar manner to support provision by pharmacists of improved quality of care. What is known about the topic? Dispensing in community pharmacy in Australia is currently remunerated on a fee-for-service basis that carries no incentive to deliver an enhanced performance that could lead to improved quality of care. What does this paper add? Several countries have introduced alternative payment models that link the level of funding to the quality of services provided by healthcare practitioners, and potentially to patient outcomes. Counselling is an integral aspect of pharmacists’ dispensing and, based on the principle that counselling improves adherence, which improves outcomes, remuneration paid to a pharmacy for dispensing could be adjusted in relation to the level of adherence demonstrated by patients of the pharmacy. What are the implications for practitioners? Pharmacists would be incentivised through quality-linked dispensing remuneration to provide enhanced counselling and other inputs that lead to improved patient outcomes and health system benefits.
Oligogalacturonide production upon
Arabidopsis thaliana
–
Botrytis cinerea
interaction
Authors: Voxeur Aline , Habrylo Olivier , Guénin Stéphanie , Miart Fabien , Soulié Marie-Christine , Rihouey Christophe , Pau-Roblot Corinne , Domon Jean-Marc , Gutierrez Laurent , Pelloux Jérôme , Mouille Grégory , Fagard Mathilde , Höfte Herman , Vernhettes Samantha
Published: September 2019

Despite an ever-increasing interest for the use of pectin-derived oligogalacturonides (OGs) as biological control agents in agriculture, very little information exists—mainly for technical reasons—on the nature and activity of the OGs that accumulate during pathogen infection. Here we developed a sensitive OG profiling method, which revealed unsuspected features of the OGs generated during infection of
Arabidopsis thaliana
with the fungus
Botrytis cinerea
. Indeed, in contrast to previous reports, most OGs were acetyl- and methylesterified, and 80% of them were produced by fungal pectin lyases, not by polygalacturonases. Polygalacturonase products did not accumulate as larger size OGs but were converted into oxidized GalA dimers. Finally, the comparison of the OGs and transcriptomes of leaves infected with
B. cinerea
mutants with reduced pectinolytic activity but with decreased or increased virulence, respectively, identified candidate OG elicitors. In conclusion, OG analysis provides insights into the enzymatic arms race between plant and pathogen and facilitates the identification of defense elicitors.
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock
Authors: Ray Judhajeet , Munn Paul R. , Vihervaara Anniina , Lewis James J. , Ozer Abdullah , Danko Charles G. , Lis John T.
Published: September 2019

Heat shock (HS) initiates rapid, extensive, and evolutionarily conserved changes in transcription that are accompanied by chromatin decondensation and nucleosome loss at HS loci. Here we have employed in situ Hi-C to determine how heat stress affects long-range chromatin conformation in human and
Drosophila
cells. We found that compartments and topologically associating domains (TADs) remain unchanged by an acute HS. Knockdown of Heat Shock Factor 1 (HSF1), the master transcriptional regulator of the HS response, identified HSF1-dependent genes and revealed that up-regulation is often mediated by distal HSF1 bound enhancers. HSF1-dependent genes were usually found in the same TAD as the nearest HSF1 binding site. Although most interactions between HSF1 binding sites and target promoters were established in the nonheat shock (NHS) condition, a subset increased contact frequency following HS. Integrating information about HSF1 binding strength, RNA polymerase abundance at the HSF1 bound sites (putative enhancers), and contact frequency with a target promoter accurately predicted which up-regulated genes were direct targets of HSF1 during HS. Our results suggest that the chromatin conformation necessary for a robust HS response is preestablished in NHS cells of diverse metazoan species.
Distinct intraspecies virulence mechanisms regulated by a conserved transcription factor
Authors: Connolly James P. R. , O’Boyle Nicky , Turner Natasha C. A. , Browning Douglas F. , Roe Andrew J.
Published: September 2019

Tailoring transcriptional regulation to coordinate the expression of virulence factors in tandem with the core genome is a hallmark of bacterial pathogen evolution. Bacteria encode hundreds of transcription factors forming the base-level control of gene regulation. Moreover, highly homologous regulators are assumed to control conserved genes between members within a species that harbor the same genetic targets. We have explored this concept in 2
Escherichia coli
pathotypes that employ distinct virulence mechanisms that facilitate specification of a different niche within the host. Strikingly, we found that the transcription factor YhaJ actively regulated unique gene sets between intestinal enterohemorrhagic
E. coli
(EHEC) and extraintestinal uropathogenic
E. coli
(UPEC), despite being very highly conserved. In EHEC, YhaJ directly activates expression of type 3 secretion system components and effectors. Alternatively, YhaJ enhances UPEC virulence regulation by binding directly to the phase-variable type 1 fimbria promoter, driving its expression. Additionally, YhaJ was found to override the universal GAD acid tolerance system but exclusively in EHEC, thereby indirectly enhancing type 3 secretion pleiotropically. These results have revealed that within a species, conserved regulators are actively repurposed in a “personalized” manner to benefit particular lifestyles and drive virulence via multiple distinct mechanisms.
Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits
Authors: Xiang Ruidong , Berg Irene van den , MacLeod Iona M. , Hayes Benjamin J. , Prowse-Wilkins Claire P. , Wang Min , Bolormaa Sunduimijid , Liu Zhiqian , Rochfort Simone J. , Reich Coralie M. , Mason Brett A. , Vander Jagt Christy J. , Daetwyler Hans D. , Lund Mogens S. , Chamberlain Amanda J. , Goddard Michael E.
Published: September 2019

Many genome variants shaping mammalian phenotype are hypothesized to regulate gene transcription and/or to be under selection. However, most of the evidence to support this hypothesis comes from human studies. Systematic evidence for regulatory and evolutionary signals contributing to complex traits in a different mammalian model is needed. Sequence variants associated with gene expression (expression quantitative trait loci [eQTLs]) and concentration of metabolites (metabolic quantitative trait loci [mQTLs]) and under histone-modification marks in several tissues were discovered from multiomics data of over 400 cattle. Variants under selection and evolutionary constraint were identified using genome databases of multiple species. These analyses defined 30 sets of variants, and for each set, we estimated the genetic variance the set explained across 34 complex traits in 11,923 bulls and 32,347 cows with 17,669,372 imputed variants. The per-variant trait heritability of these sets across traits was highly consistent (
r
> 0.94) between bulls and cows. Based on the per-variant heritability, conserved sites across 100 vertebrate species and mQTLs ranked the highest, followed by eQTLs, young variants, those under histone-modification marks, and selection signatures. From these results, we defined a Functional-And-Evolutionary Trait Heritability (FAETH) score indicating the functionality and predicted heritability of each variant. In additional 7,551 cattle, the high FAETH-ranking variants had significantly increased genetic variances and genomic prediction accuracies in 3 production traits compared to the low FAETH-ranking variants. The FAETH framework combines the information of gene regulation, evolution, and trait heritability to rank variants, and the publicly available FAETH data provide a set of biological priors for cattle genomic selection worldwide.
The long-term impact of the Communist Revolution on social stratification in contemporary China
Authors: Xie Yu , Zhang Chunni
Published: September 2019

Significance

Utilizing the latest, high-quality, 3-generation data, this article reports findings from a systematic study of the long-term impact of the Communist Revolution on the social stratification order in today’s China. It is found that the revolution disrupted the cross-generational reproduction of the prevailing social stratification at the time of the revolution in promoting the social status of children of the peasant and worker classes and disadvantaging those from privileged classes. Despite a tendency for “reversion” mitigating the revolution’s effects in the third generation toward the grandparents’ generation in social status, the impact of the revolution on the educational attainment of descendants by class classification immediately following the revolution remains strong even after 6 decades have passed.
Decadal increase in Arctic dimethylsulfide emission
Authors: Galí Martí , Devred Emmanuel , Babin Marcel , Levasseur Maurice
Published: September 2019

Dimethylsulfide (DMS), a gas produced by marine microbial food webs, promotes aerosol formation in pristine atmospheres, altering cloud radiative forcing and precipitation. Recent studies suggest that DMS controls aerosol formation in the summertime Arctic atmosphere and call for an assessment of pan-Arctic DMS emission (EDMS) in a context of dramatic ecosystem changes. Using a remote sensing algorithm, we show that summertime EDMS from ice-free waters increased at a mean rate of 13.3 ± 6.7 Gg S decade−1(∼33% decade−1) north of 70°N between 1998 and 2016. This trend, mostly explained by the reduction in sea-ice extent, is consistent with independent atmospheric measurements showing an increasing trend of methane sulfonic acid, a DMS oxidation product. Extrapolation to an ice-free Arctic summer could imply a 2.4-fold (±1.2) increase in EDMS compared to present emission. However, unexpected regime shifts in Arctic geo- and ecosystems could result in future EDMS departure from the predicted range. Superimposed on the positive trend, EDMS shows substantial interannual changes and nonmonotonic multiyear trends, reflecting the interplay between physical forcing, ice retreat patterns, and phytoplankton productivity. Our results provide key constraints to determine whether increasing marine sulfur emissions, and resulting aerosol–cloud interactions, will moderate or accelerate Arctic warming in the context of sea-ice retreat and increasing low-level cloud cover.
Immunogenicity of a rheumatoid arthritis protective sequence when acquired through microchimerism
Authors: Kanaan Sami B. , Sensoy Oyku , Yan Zhen , Gadi Vijayakrishna K. , Richardson Michael L. , Nelson J. Lee
Published: September 2019

Significance

HLA genes confer the strongest genetic autoimmune disease risk. SpecificHLA-DRB1alleles predispose to rheumatoid arthritis (RA), while others encoding the sequence DERAA are RA-protective. Unexpectedly, having given birth to children with DERAA+HLA-DRB1alleles prior to onset was found to increase RA risk in women. We show that microchimerism (Mc; allogeneic cell long-term legacy of pregnancy) carrying DERAA+HLA increases the odds of RA 17-fold and that allogeneic cells carrying DERAA stimulated DERAA−/−T cells in vitro. Microbial-derived DERAA peptides (among others) are known to stimulate DERAA-directed T cells naturally present in DERAA−/−individuals. Our data indicate that Mc with DERAA alloantigens can potentially activate similar adaptive immunity pathways and mechanistically link naturally occurring Mc to an autoimmune disorder.
Fine particulate matter damages and value added in the US economy
Authors: Tschofen Peter , Azevedo Inês L. , Muller Nicholas Z.
Published: September 2019

Emissions of most pollutants that result in fine particulate matter (PM
2.5
) formation have been decreasing in the United States. However, this trend has not been uniform across all sectors or regions of the economy. We use integrated assessment models (IAMs) to compute marginal damages for PM
2.5
-related emissions for each county in the contiguous United States and match location-specific emissions with these marginal damages to compute economy-wide gross external damage (GED) due to premature mortality. We note 4 key findings: First, economy-wide, GED has decreased by more than 20% from 2008 to 2014. Second, while much of the air pollution policies have focused to date on the electricity sector, damages from farms are now larger than those from utilities. Indeed, farms have become the largest contributor to air pollution damages from PM
2.5
-related emissions. Third, 4 sectors, comprising less than 20% of the national gross domestic product (GDP), are responsible for ∼75% of GED attributable to economic activities. Fourth, uncertainty in GED estimates tends to be high for sectors with predominantly ground-level emissions because these emissions are usually estimated and not measured. These findings suggest that policymakers should target further emissions reductions from such sectors, particularly in transportation and agriculture.
Evolution-based screening enables genome-wide prioritization and discovery of DNA repair genes
Authors: Brunette Gregory J. , Jamalruddin Mohd A. , Baldock Robert A. , Clark Nathan L. , Bernstein Kara A.
Published: September 2019

Significance

Genome stability is maintained through conserved DNA repair pathways. By analyzing evolutionary relationships between genes that mediate DNA repair, we show that functional relationships between DNA repair genes are reflected in the variation of their evolutionary rates. Here we ranked mammalian genes for coevolution with 6 DNA repair pathways. Direct comparison to genetic screens for DNA repair factors indicates that our evolution-based screen is comparable, if not superior, to traditional screening approaches. As a proof of principle, we identified a role for the gene
DDIAS
in double-strand break (DSB) repair. DDIAS depletion results in DSB accumulation, increased checkpoint signaling, and defective homologous recombination. Our results reveal that evolutionary analysis is a powerful tool to uncover DNA repair factors.
Global invasion history of the agricultural pest butterfly
Pieris rapae
revealed with genomics and citizen science
Authors: Ryan Sean F. , Lombaert Eric , Espeset Anne , Vila Roger , Talavera Gerard , Dincă Vlad , Doellman Meredith M. , Renshaw Mark A. , Eng Matthew W. , Hornett Emily A. , Li Yiyuan , Pfrender Michael E. , Shoemaker DeWayne
Published: September 2019

The small cabbage white butterfly,
Pieris rapae
, is a major agricultural pest of cruciferous crops and has been introduced to every continent except South America and Antarctica as a result of human activities. In an effort to reconstruct the near-global invasion history of
P. rapae
, we developed a citizen science project, the “Pieris Project,” and successfully amassed thousands of specimens from 32 countries worldwide. We then generated and analyzed nuclear (double-digest restriction site-associated DNA fragment procedure [ddRAD]) and mitochondrial DNA sequence data for these samples to reconstruct and compare different global invasion history scenarios. Our results bolster historical accounts of the global spread and timing of
P. rapae
introductions. We provide molecular evidence supporting the hypothesis that the ongoing divergence of the European and Asian subspecies of
P. rapae
(∼1,200 y B.P.) coincides with the diversification of brassicaceous crops and the development of human trade routes such as the Silk Route (Silk Road). The further spread of
P. rapae
over the last ∼160 y was facilitated by human movement and trade, resulting in an almost linear series of at least 4 founding events, with each introduced population going through a severe bottleneck and serving as the source for the next introduction. Management efforts of this agricultural pest may need to consider the current existence of multiple genetically distinct populations. Finally, the international success of the Pieris Project demonstrates the power of the public to aid scientists in collections-based research addressing important questions in invasion biology, and in ecology and evolutionary biology more broadly.
Development and utilization of human decidualization reporter cell line uncovers new modulators of female fertility
Authors: Haller Meade , Yin Yan , Ma Liang
Published: September 2019

Significance

Up to 15% of couples experience infertility. Implantation must occur in order for the pregnancy hormone hCG to be detected, and thus many pregnancies go unrecognized before being lost due to implantation failure. Decidualization is a complex differentiation process during which the uterine lining grows and dramatically changes form in response to ovarian hormone stimulus, and this process is required for successful implantation. By developing and utilizing a new reporter cell line, the present study systematically uncovers more than 4,000 genetic and chemical modulators of the human decidual response in the hopes of catalyzing new treatments for female infertility, subfertility, and recurrent pregnancy loss.
Evolution of the vomer and its implications for cranial kinesis in Paraves
Authors: Hu Han , Sansalone Gabriele , Wroe Stephen , McDonald Paul G. , O’Connor Jingmai K. , Li Zhiheng , Xu Xing , Zhou Zhonghe
Published: September 2019

Most living birds exhibit cranial kinesis—movement between the rostrum and braincase—in which force is transferred through the palatal and jugal bars. The palate alone distinguishes the Paleognathae from the Neognathae, with cranial kinesis more developed in neognaths. Most previous palatal studies were based on 2D data and rarely incorporated data from stem birds despite great interest in their kinetic abilities. Here we reconstruct the vomer of the Early Cretaceous stem birdSapeornisand the troodontidSinovenator, taxa spanning the dinosaur–bird transition. A 3D shape analysis including these paravians and an extensive sampling of neornithines reveals their strong similarity to paleognaths and indicates that morphological differences in the vomer between paleognaths and neognaths are intimately related to their different kinetic abilities. These results suggest the skull of Mesozoic paravians lacked the kinetic abilities observed in neognaths, a conclusion also supported by our identification of an ectopterygoid inSapeornishere. We conclude that cranial kinesis evolved relatively late, likely an innovation of the Neognathae, and is linked to the transformation of the vomer. This transformation increased palatal mobility, enabling the evolution of a diversity of kinetic mechanisms and ultimately contributing to the extraordinary evolutionary success of this clade.
CMT disease severity correlates with mutation-induced open conformation of histidyl-tRNA synthetase, not aminoacylation loss, in patient cells
Authors: Blocquel David , Sun Litao , Matuszek Zaneta , Li Sheng , Weber Thomas , Kuhle Bernhard , Kooi Grace , Wei Na , Baets Jonathan , Pan Tao , Schimmel Paul , Yang Xiang-Lei
Published: September 2019

Aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are the largest protein family causatively linked to neurodegenerative Charcot–Marie–Tooth (CMT) disease. Dominant mutations cause the disease, and studies of CMT disease-causing mutant glycyl-tRNA synthetase (GlyRS) and tyrosyl-tRNA synthetase (TyrRS) showed their mutations create neomorphic structures consistent with a gain-of-function mechanism. In contrast, based on a
haploid
yeast model, loss of aminoacylation function was reported for CMT disease mutants in histidyl-tRNA synthetase (HisRS). However, neither that nor prior work of any CMT disease-causing aaRS investigated the aminoacylation status of tRNAs in the cellular milieu of actual patients. Using an assay that interrogated aminoacylation levels in patient cells, we investigated a HisRS-linked CMT disease family with the most severe disease phenotype. Strikingly, no difference in charged tRNA levels between normal and diseased family members was found. In confirmation, recombinant versions of 4 other HisRS CMT disease-causing mutants showed no correlation between activity loss in vitro and severity of phenotype in vivo. Indeed, a mutation having the most detrimental impact on activity was associated with a mild disease phenotype. In further work, using 3 independent biophysical analyses, structural opening (relaxation) of mutant HisRSs at the dimer interface best correlated with disease severity. In fact, the HisRS mutation in the severely afflicted patient family caused the largest degree of structural relaxation. These data suggest that HisRS-linked CMT disease arises from open conformation-induced mechanisms distinct from loss of aminoacylation.
Phase transitions beyond post-perovskite in NaMgF
3
to 160 GPa
Authors: Dutta Rajkrishna , Greenberg Eran , Prakapenka Vitali B. , Duffy Thomas S.
Published: September 2019

Significance

The high-pressure behavior of NaMgF
3
is of interest due to its role as a low-pressure analog for phase transitions in the MgSiO
3
system. In this work, we have used the diamond anvil cell and synchrotron X-ray diffraction techniques to study structural transitions in NaMgF
3
to 1.6 Mbars. Our work has identified a sequence of high-pressure phases beyond post-perovskite in this ABX
3
system. We report the presence of a post-post-perovskite phase, followed by a partial and then complete dissociation into binary fluorides. A similar sequence of high-pressure phase transitions in MgSiO
3
at very high pressure-temperature conditions has implications for understanding the interiors of large rocky exoplanets.
The first day of the Cenozoic
Authors: Gulick Sean P. S. , Bralower Timothy J. , Ormö Jens , Hall Brendon , Grice Kliti , Schaefer Bettina , Lyons Shelby , Freeman Katherine H. , Morgan Joanna V. , Artemieva Natalia , Kaskes Pim , de Graaff Sietze J. , Whalen Michael T. , Collins Gareth S. , Tikoo Sonia M. , Verhagen Christina , Christeson Gail L. , Claeys Philippe , Coolen Marco J. L. , Goderis Steven , Goto Kazuhisa , Grieve Richard A. F. , McCall Naoma , Osinski Gordon R. , Rae Auriol S. P. , Riller Ulrich , Smit Jan , Vajda Vivi , Wittmann Axel ,   the Expedition 364 Scientists, Gulick S. P. S. , Morgan J. V. , Bralower T. , Cheno E. , Christeson G. L. , Claeys P. , Cockell C. S. , Coolen M. J. L. , Ferrière L. , Gebhardt C. , Goto K. , Green S. , Jones H. , Kring D. A. , LeBer E. , Lofi J. , Lowery C. M. , OcampoTorres R. , Cruz L. Perez , Pickersgill A. E. , Poelchau M. H. , Rae A. S. P. , Rasmussen C. , Vieyra M. Rebolledo , Riller U. , Sato H. , Schmitt D. , Smit J. , Tikoo S. M. , Tomioka N. , Fucugauchi J. Urrutia , Whalen M. T. , Wittmann A. , Xiao L. , Yamaguchi K. E.
Published: September 2019

Highly expanded Cretaceous–Paleogene (K-Pg) boundary section from the Chicxulub peak ring, recovered by International Ocean Discovery Program (IODP)–International Continental Scientific Drilling Program (ICDP) Expedition 364, provides an unprecedented window into the immediate aftermath of the impact. Site M0077 includes ∼130 m of impact melt rock and suevite deposited the first day of the Cenozoic covered by <1 m of micrite-rich carbonate deposited over subsequent weeks to years. We present an interpreted series of events based on analyses of these drill cores. Within minutes of the impact, centrally uplifted basement rock collapsed outward to form a peak ring capped in melt rock. Within tens of minutes, the peak ring was covered in ∼40 m of brecciated impact melt rock and coarse-grained suevite, including clasts possibly generated by melt–water interactions during ocean resurge. Within an hour, resurge crested the peak ring, depositing a 10-m-thick layer of suevite with increased particle roundness and sorting. Within hours, the full resurge deposit formed through settling and seiches, resulting in an 80-m-thick fining-upward, sorted suevite in the flooded crater. Within a day, the reflected rim-wave tsunami reached the crater, depositing a cross-bedded sand-to-fine gravel layer enriched in polycyclic aromatic hydrocarbons overlain by charcoal fragments. Generation of a deep crater open to the ocean allowed rapid flooding and sediment accumulation rates among the highest known in the geologic record. The high-resolution section provides insight into the impact environmental effects, including charcoal as evidence for impact-induced wildfires and a paucity of sulfur-rich evaporites from the target supporting rapid global cooling and darkness as extinction mechanisms.
Water follows polar and nonpolar protein surface domains
Authors: Qiao Baofu , Jiménez-Ángeles Felipe , Nguyen Trung Dac , Olvera de la Cruz Monica
Published: September 2019

Significance

The hydration of molecules affects their physical and chemical properties. In particular, the functions and interactions of various proteins are determined by the conformation of water molecules around polar and nonpolar protein surface domains. Therefore, understanding the local interactions between water molecules and the polar and nonpolar protein surface domains such as water molecule conformations in protein hydration layers benefits targeted protein engineering, and recognition of molecules including proteins, DNA/RNA, cell membranes, and drugs. By using atomistic simulations, we show distinct correlations between the hydration water molecules and the different types of protein surface domains.
Autism spectrum traits predict higher social psychological skill
Authors: Gollwitzer Anton , Martel Cameron , McPartland James C. , Bargh John A.
Published: September 2019

Social-cognitive skills can take different forms, from accurately predicting individuals’ intentions, emotions, and thoughts (person perception or folk psychology) to accurately predicting social phenomena more generally. Past research has linked autism spectrum (AS) traits to person perception deficits in the general population. We tested whether AS traits also predict poor accuracy in terms of predicting generalized social phenomena, assessed via participants’ accuracy at predicting social psychological phenomena (e.g., social loafing, social projection, group think). We found the opposite. In a sample of ∼6,500 participants in 104 countries, AS traits predicted slightly higher social psychological skill. A second study with 400 participants suggested that heightened systemizing underlies this relationship. Our results indicate that AS traits relate positively to a form of social cognitive skill—predicting social psychological phenomena—and highlight the importance of distinguishing between divergent types of social cognition.
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression
Authors: Xia Chenglong , Fan Jean , Emanuel George , Hao Junjie , Zhuang Xiaowei
Published: September 2019

The expression profiles and spatial distributions of RNAs regulate many cellular functions. Image-based transcriptomic approaches provide powerful means to measure both expression and spatial information of RNAs in individual cells within their native environment. Among these approaches, multiplexed error-robust fluorescence in situ hybridization (MERFISH) has achieved spatially resolved RNA quantification at transcriptome scale by massively multiplexing single-molecule FISH measurements. Here, we increased the gene throughput of MERFISH and demonstrated simultaneous measurements of RNA transcripts from ∼10,000 genes in individual cells with ∼80% detection efficiency and ∼4% misidentification rate. We combined MERFISH with cellular structure imaging to determine subcellular compartmentalization of RNAs. We validated this approach by showing enrichment of secretome transcripts at the endoplasmic reticulum, and further revealed enrichment of long noncoding RNAs, RNAs with retained introns, and a subgroup of protein-coding mRNAs in the cell nucleus. Leveraging spatially resolved RNA profiling, we developed an approach to determine RNA velocity in situ using the balance of nuclear versus cytoplasmic RNA counts. We applied this approach to infer pseudotime ordering of cells and identified cells at different cell-cycle states, revealing ∼1,600 genes with putative cell cycle-dependent expression and a gradual transcription profile change as cells progress through cell-cycle stages. Our analysis further revealed cell cycle-dependent and cell cycle-independent spatial heterogeneity of transcriptionally distinct cells. We envision that the ability to perform spatially resolved, genome-wide RNA profiling with high detection efficiency and accuracy by MERFISH could help address a wide array of questions ranging from the regulation of gene expression in cells to the development of cell fate and organization in tissues.
Language programming in rural and regional Victoria
Authors: Slaughter Yvette , Lo Bianco Joseph , Aliani Renata , Cross Russell , Hajek John
Published: September 2019

Despite decades of often ambitious policies in Australia, languages education is still characterized by intermittent commitment to the teaching of languages, with inequitable access particularly entrenched in rural and regional contexts. While research has focused on the practical and material constraints impacting on policy implementation, little research has investigated the role of the discursive terrain in shaping expectations and limitations around what seems achievable in schools, particularly, from the school principal perspective. Beginning with an overview of policy interventions and an analysis of contemporary challenges, we use Q methodology to identify and analyze viewpoints at work in similarly-positioned rural and regional schools. In doing so, we seek to determine what seems possible or impossible across settings; the role of principals in enabling and constraining pathways for the provision of school language programs, and the need for macro-level language policy to be informed by constraints specific to rural and regional contexts.
Exploring a possible relationship between the attitude of experienced English learners towards Australian English and
their L2 motivation
Authors: Farley Florence , Stracke Elke
Published: September 2019

This paper investigates a possible relationship between the motivation and attitude of learners towards L2 in the
socio-cultural context of Australia. We used an explanatory mixed-methods approach and conducted a survey with 31 international
postgraduate TESOL students at a regional university in Australia. Then we conducted semi-structured interviews with six of the
students. The survey results suggest a relationship between the way a learner viewed Australian English and their motivation
towards L2. The motivational factors were Ideal L2 Self, Linguistic Self Confidence, Cultural Interest, Instrumentality
(Promotion) and Ought-to L2 Self. While all contributed to varying degrees in motivating the learners towards L2 learning, only
the first three interacted significantly with learners’ attitudes towards Australian English. Further, our interview data
highlight that the attitude of the learners with regard to their favorite language variety was based more on Australian English’s Inner
Circle status than its linguistic characteristics.
Politically-relevant fisheries science: Reflections on the work of Henry Regier, or, lessons from the sassy scientist
Authors: Knuth Barbara A.
Published: September 2019

Throughout his career, Dr. Henry Regier’s science and scholarship includes numerous contributions that cross disciplines and inform policy. This review of examples of his politically-relevant science publications spans six decades. Regier’s publications emphasize themes that cross the various boundaries of expert-layperson, state actors-society, public-private, and government-academic sectors. His writings provide several lessons for fishery and aquatic scientists and managers throughout the Great Lakes Basin and beyond: advocate, provoke, network and combine the dualities of idealism and pragmatism.
TGFβ signaling in germinal center B cells promotes the transition from light zone to dark zone
Authors: Albright Anne R. , Kabat Juraj , Li Moyi , Raso Fiona , Reboldi Andrea , Muppidi Jagan R.
Published: September 2019

B cells in germinal centers (GCs) cycle between light zone (LZ) and dark zone (DZ). The cues in the GC microenvironment that regulate the transition from LZ to DZ have not been well characterized. In Peyer’s patches (PPs), transforming growth factor-β (TGFβ) promotes IgA induction in activated B cells that can then differentiate into GC B cells. We show here that TGFβ signaling occurs in B cells in GCs and is distinct from signaling that occurs in activated B cells in PPs. Whereas in activated B cells TGFβ signaling is required for IgA induction, in the GC it was instead required for the transition from LZ to DZ. In the absence of TGFβ signaling, there was an accumulation of LZ GC B cells and reduced antibody affinity maturation likely due to reduced activation of Foxo1. This work identifies TGFβ as a microenvironmental cue that is critical for GC homeostasis and function.