bluuebunny/crossref_metadata_2025 huggingface dataset:
Different flavors of nonadiabatic molecular dynamics
Authors: Agostini Federica , Curchod Basile F. E.
Published: April 2019

The Born‐Oppenheimer approximation constitutes a cornerstone of our understanding of molecules and their reactivity, partly because it introduces a somewhat simplified representation of the molecular wavefunction. However, when a molecule absorbs light containing enough energy to trigger an electronic transition, the simplistic nature of the molecular wavefunction offered by the Born‐Oppenheimer approximation breaks down as a result of the now non‐negligible coupling between nuclear and electronic motion, often coined nonadiabatic couplings. Hence, the description of nonadiabatic processes implies a change in our representation of the molecular wavefunction, leading eventually to the design of new theoretical tools to describe the fate of an electronically‐excited molecule. This Overview focuses on this quantity—the total molecular wavefunction—and the different approaches proposed to describe theoretically this complicated object in non‐Born‐Oppenheimer conditions, namely the Born‐Huang and Exact‐Factorization representations. The way each representation depicts the appearance of nonadiabatic effects is then revealed by using a model of a coupled proton–electron transfer reaction. Applying approximations to the formally exact equations of motion obtained within each representation leads to the derivation, or proposition, of different strategies to simulate the nonadiabatic dynamics of molecules. Approaches like quantum dynamics with fixed and time‐dependent grids, traveling basis functions, or mixed quantum/classical like surface hopping, Ehrenfest dynamics, or coupled‐trajectory schemes are described in this Overview.

This article is categorized under:

Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics

Software > Simulation Methods

Theoretical and Physical Chemistry > Spectroscopy
Effect of paternal age on the birth sex ratio in captive populations of aye‐aye (Daubentonia madagascariensis (Gmelin))
Authors: Tanaka Yosuke , Fukano Yuya , Nakamura Masato
Published: April 2019

For the management of captive populations of zoo animals, it is important to elucidate factors that affect the offspring birth sex ratio. On the basis of the sex allocation theory, the Trivers–Willard and mate attractive/quality hypotheses predict that maternal and paternal conditions affect offspring birth sex ratios. We examined these predictions for the birth sex ratio of aye‐aye Daubentonia madagascariensis (Gmelin) by analyzing the pedigree information in the International Studbook. We found that the birth sex ratio of the aye‐aye was affected by the paternal age, but not maternal age and other environmental factors (birth year, season, and institution). The younger the sire, the more the offspring sex ratio was biased toward males. These results are useful for the effective population management of captive aye‐aye and illustrated the usefulness of the sex allocation theory in the sex ratio management of zoo animals.
Complexity of holographic superconductors
Authors: Yang Run-Qiu , Jeong Hyun-Sik , Niu Chao , Kim Keun-Young
Published: April 2019

Abstract

We study the complexity of holographic superconductors (Einstein-Maxwell-complex scalar actions in d + 1 dimension) by the “complexity = volume” (CV) conjecture. First, it seems that there is a universal property: the superconducting phase always has a smaller complexity than the unstable normal phase below the critical temperature, which is similar to a free energy. We investigate the temperature dependence of the complexity. In the low temperature limit, the complexity (of formation) scales as T

α
, where α is a function of the complex scalar mass m
2, the U(1) charge q, and dimension d. In particular, for m
2 = 0, we find α = d−1, independent of q, which can be explained by the near horizon geometry of the low temperature holographic superconductor. Next, we develop a general numerical method to compute the time-dependent complexity by the CV conjecture. By this method, we compute the time-dependent complexity of holographic superconductors. In both normal and superconducting phase, the complexity increases as time goes on and the growth rate saturates to a temperature dependent constant. The higher the temperature is, the bigger the growth rate is. However, the growth rates do not violate the Lloyd’s bound in all cases and saturate the Lloyd’s bound in the high temperature limit at a late time.
Beyond Belief: How Membership in Congregations Affects the Fertility of U.S. Mormons and Jews
Authors: Shain Michelle
Published: April 2019

Scholars have long recognized that participation in religious congregations is strongly linked to fertility outcomes, and this relationship has practical implications for religious, social and political life in the United States. Yet, the way in which congregational participation affects fertility is not well understood. The Theory of Conjunctural Action suggests that congregational participation affects fertility both by teaching schemas that valorize family formation and by creating material conditions conducive to family formation. However, other research found that congregational participation was simply a proxy for learned schemas, with no additional impact on fertility. The present study explores this question using the Pew Research Center's 2011 National Survey of Mormons and the 2013 Survey of U.S. Jews. These two minority religious groups represent similarly pronatalist religious traditions but opposite extremes in terms of both fertility (i.e., Mormons have higher fertility) and congregational participation (i.e., Mormons have higher participation). The analysis reveals that congregational participation and intra-group friendships have an independent effect on fertility, even controlling for learned schemas. This suggests that the influence of group participation on fertility is not solely due to its impact on learned schemas, but also due to the impact of material elements such as religious social networks. Limitations and directions for future research are discussed.
Predicting enhancer‐promoter interaction from genomic sequence with deep neural networks
Authors: Singh Shashank , Yang Yang , Póczos Barnabás , Ma Jian
Published: April 2019

Background

In the human genome, distal enhancers are involved in regulating target genes through proximal promoters by forming enhancer‐promoter interactions. Although recently developed high‐throughput experimental approaches have allowed us to recognize potential enhancer‐promoter interactions genome‐wide, it is still largely unclear to what extent the sequence‐level information encoded in our genome help guide such interactions.

Methods

Here we report a new computational method (named “SPEID”) using deep learning models to predict enhancer‐promoter interactions based on sequence‐based features only, when the locations of putative enhancers and promoters in a particular cell type are given.

Results

Our results across six different cell types demonstrate that SPEID is effective in predicting enhancer‐promoter interactions as compared to state‐of‐the‐art methods that only use information from a single cell type. As a proof‐of‐principle, we also applied SPEID to identify somatic non‐coding mutations in melanoma samples that may have reduced enhancer‐promoter interactions in tumor genomes.

Conclusions

This work demonstrates that deep learning models can help reveal that sequence‐based features alone are sufficient to reliably predict enhancer‐promoter interactions genome‐wide.
Current challenges and solutions of de novo assembly
Authors: Liao Xingyu , Li Min , Zou You , Wu Fang‐Xiang , Yi‐Pan  , Wang Jianxin
Published: April 2019

Background

Next‐generation sequencing (NGS) technologies have fostered an unprecedented proliferation of high‐throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. However, numerous technical or computational challenges in de novo assembly still remain, although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings.

Results

In this review, we first briefly introduce some of the major challenges faced by NGS sequence assembly. Then, we analyze the characteristics of various sequencing platforms and their impact on assembly results. After that, we classify de novo assemblers according to their frameworks (overlap graph‐based, de Bruijn graph‐based and string graph‐based), and introduce the characteristics of each assembly tool and their adaptation scene. Next, we introduce in detail the solutions to the main challenges of de novo assembly of next generation sequencing data, single‐cell sequencing data and single molecule sequencing data. At last, we discuss the application of SMS long reads in solving problems encountered in NGS assembly.

Conclusions

This review not only gives an overview of the latest methods and developments in assembly algorithms, but also provides guidelines to determine the optimal assembly algorithm for a given input sequencing data type.
Quantifying blood‐brain barrier leakage in small vessel disease: Review and consensus recommendations
Authors: Thrippleton Michael J. , Backes Walter H. , Sourbron Steven , Ingrisch Michael , van Osch Matthias J.P. , Dichgans Martin , Fazekas Franz , Ropele Stefan , Frayne Richard , van Oostenbrugge Robert J. , Smith Eric E. , Wardlaw Joanna M.
Published: April 2019

Cerebral small vessel disease (cSVD) comprises pathological processes of the small vessels in the brain that may manifest clinically as stroke, cognitive impairment, dementia, or gait disturbance. It is generally accepted that endothelial dysfunction, including blood‐brain barrier (BBB) failure, is pivotal in the pathophysiology. Recent years have seen increasing use of imaging, primarily dynamic contrast‐enhanced magnetic resonance imaging, to assess BBB leakage, but there is considerable variability in the approaches and findings reported in the literature. Although dynamic contrast‐enhanced magnetic resonance imaging is well established, challenges emerge in cSVD because of the subtle nature of BBB impairment. The purpose of this work, authored by members of the HARNESS Initiative, is to provide an in‐depth review and position statement on magnetic resonance imaging measurement of subtle BBB leakage in clinical research studies, with aspects requiring further research identified. We further aim to provide information and consensus recommendations for new investigators wishing to study BBB failure in cSVD and dementia.
Crack wave resonances within the basal water layer
Authors: Gräff Dominik , Walter Fabian , Lipovsky Bradley P.
Published: April 2019

Hydraulic processes within and beneath glacial bodies exert a far-reaching control on ice flow through their influence on basal sliding. Within the subglacial system, rapid changes in these processes may excite resonances whose interpretation requires an understanding of the underlying wave mechanics. Here, we explore these mechanics using observations from a kHz-sampled pressure sensor installed in a borehole directly above the hard granite bedrock of a temperate mountain glacier in Switzerland. We apply a previously established theory of wave propagation along thin, water-filled structures such as water-filled voids, basal water layers, or hydraulic fractures. Within such structures, short-wavelength waves experience restoring forces due to compressibility and are composed of sound waves. Long-wavelength resonances, in contrast, experience restoring forces due to elasticity and are composed of anomalously dispersed crack waves or Krauklis waves. Our borehole observations confirm the occurrence of both sound and crack waves within the basal water layer. Using both the resonance frequencies and attenuation of recorded crack waves we estimate thickness, aperture and length of the resonating basal water layer patch into which we drilled. We demonstrate that high-frequency observations of subglacial hydraulic processes provide new insights into this evolving dynamic system.
The transnational drivers of populist backlash in Europe: The role of courts
Authors: Pin Andrea
Published: April 2019

This Article explores whether and how contemporary constitutionalism may have triggered or facilitated populism and its illiberal agenda. In particular, it focuses on some of the legal doctrines that have characterized the growth of transnational and supranational judicial fora, contrasting them with populism in Europe. The Article first sketches the role of courts in shaping contemporary transnationalism and supranationalism in Europe. Then, it analyzes the role that the ideals of progress and equality have played in the judicialization of pan-European legal culture. Finally, it ponders the consequences of the constitutionalization process of European law for the role of democratically accountable institutions.
The two faces of populism: Between authoritarian and democratic populism
Authors: Bugaric Bojan
Published: April 2019

Populism is Janus-faced; simultaneously facing different directions. There is not a single form of populism, but rather a variety of different forms, each with profoundly different political consequences. Despite the current hegemony of authoritarian populism, a much different sort of populism is also possible: Democratic and anti-establishment populism, which combines elements of liberal and democratic convictions. Without understanding the political economy of the populist revolt, it is difficult to understand the true roots of populism, and consequently, to devise an appropriate democratic alternative to populism.
The role of electronic health record and “add-on” clinical decision support systems to enhance antimicrobial stewardship programs
Authors: Kuper Kristi M. , Nagel Jerod L. , Kile Jarrod W. , May Larissa S. , Lee Francesca M.
Published: April 2019

Increasingly, demands are placed on healthcare systems to meet antimicrobial stewardship standards and reporting requirements. This trend, combined with reduced financial and personnel resources, has created a need to adopt information technology (IT) to help ease these burdens and facilitate action. The incorporation of IT into an antimicrobial stewardship program can help improve stewardship intervention efficiencies and facilitate the tracking and reporting of key metrics, including outcomes. This paper provides a review of the stewardship-related functionality within these IT systems, describes how these platforms can be used to improve antimicrobial use, and identifies how they can support current and potential future antimicrobial stewardship regulatory and accreditation standards. Finally, recommendations to help close the gaps in existing systems are provided and suggestions for future areas of development within these programs are delineated.
Subharmonic resonant interaction of a gravity–capillary progressive axially symmetric wave with a radial cross-wave
Authors: Shen Meng , Liu Yuming
Published: April 2019

We theoretically investigate the problem of subharmonic resonant interaction of a progressive (axially symmetric) ring wave with a radial cross-wave in the context of the potential-flow formulation for gravity-capillary waves. The objective is to understand the nonlinear mechanism governing energy transfer from a progressive ring wave to its subharmonic cross-waves through triadic resonant interactions. We first show that for an arbitrary three-dimensional body floating in an unbounded free surface, there exists a set of homogeneous solutions at any frequency in the gravity-capillary wave context. The homogeneous solution depends solely on the mean free-surface slope at the waterline of the body and physically represents a progressive radial cross-wave. Unlike standing cross-waves, a progressive cross-wave loses energy during propagation by overcoming the work done by surface tension at the waterline and through wave radiation. We then consider the subharmonic interaction of a progressive ring wave, which is forced by a radial swelling–contraction deformation of a vertical circular cylinder, with subharmonic cross-waves. We derive the nonlinear spatial–temporal evolution equation governing the motion of the cross-wave by use of the average Lagrangian method. In addition to energy-input terms from the interaction with the forced ring wave, the evolution equation contains a damping term associated with energy loss in cross-wave propagation. We show that the presence of the damping term leads to a non-trivial threshold value of the ring wave steepness (or amplitude) beyond which the cross-wave becomes unstable and grows with time by taking energy from the ring wave. Finally, we extend this analysis to the experimental case of Tatsuno et al. (Rep. Res. Inst. Appl. Mech. Kyushu University, vol. 17, 1969, pp. 195–215) in which asymmetric wave patterns are observed during high-frequency vertical oscillations of a surface-piercing sphere. The theoretical prediction of the threshold value of oscillation amplitude and characteristic features of generated radial cross-waves agrees reasonably well with experimental observations.
Multicores-periphery structure in networks
Authors: Yan Bowen , Luo Jianxi
Published: April 2019

Many real-world networks exhibit a multicores-periphery structure, with densely connected vertices in multiple cores surrounded by a general periphery of sparsely connected vertices. Identification of the multicores-periphery structure can provide a new lens to understand the structures and functions of various real-world networks. This paper defines the multicores-periphery structure and introduces an algorithm to identify the optimal partition of multiple cores and the periphery in general networks. We demonstrate the performance of our algorithm by applying it to a well-known social network and a patent technology network, which are best characterized by the multicores-periphery structure. The analyses also reveal the differences between our multicores-periphery detection algorithm and two state-of-the-art algorithms for detecting the single core-periphery structure and community structure.
Randomized optimal transport on a graph: framework and new distance measures
Authors: Guex Guillaume , Kivimäki Ilkka , Saerens Marco
Published: April 2019

The recently developed bag-of-paths (BoP) framework consists in setting a Gibbs–Boltzmann distribution on all feasible paths of a graph. This probability distribution favors short paths over long ones, with a free parameter (the temperatureT) controlling the entropic level of the distribution. This formalism enables the computation of new distances or dissimilarities, interpolating between the shortest-path and the resistance distance, which have been shown to perform well in clustering and classification tasks. In this work, the bag-of-paths formalism is extended by adding two independent equality constraints fixing starting and ending nodes distributions of paths (margins).When the temperature is low, this formalism is shown to be equivalent to a relaxation of the optimal transport problem on a network where paths carry a flow between two discrete distributions on nodes. The randomization is achieved by considering free energy minimization instead of traditional cost minimization. Algorithms computing the optimal free energy solution are developed for two types of paths: hitting (or absorbing) paths and non-hitting, regular, paths and require the inversion of ann×nmatrix withnbeing the number of nodes. Interestingly, for regular paths on an undirected graph, the resulting optimal policy interpolates between the deterministic optimal transport policy (T→ 0+) and the solution to the corresponding electrical circuit (T→ ∞). Two distance measures between nodes and a dissimilarity between groups of nodes, both integrating weights on nodes, are derived from this framework.
Party Constituency Associations and the Service, Policy and Symbolic Responsiveness of Canadian Members of Parliament
Authors: Koop Royce
Published: April 2019

Abstract.Effective representation requires that representatives learn of the needs and preferences of their constituents and communicate their representative accomplishments back to those constituents. This article demonstrates how Canadian political parties, specifically their constituency associations in the ridings, assist MPs in their representative functions by facilitating communication between MPs and constituents. Representatives of local “sectors” on constituency association executives provide a means for focused communication between MPs and constituents. The result is that constituency associations enhance the service, policy and symbolic responsiveness of many MPs in their ridings. This article therefore elucidates the largely unrecognized role of Canadian parties' constituency organizations as important democratic and representational actors in the ridings.

Résumé.Pour être efficace, il faut que les élus (1) comprennent les besoins et les préférences de leurs électeurs et (2) communiquent leurs activités en tant que parlementaires. Cet article montre à quel point les partis politiques canadiens, surtout les comités au niveau des comtés individuels, sont importants comme instrument pour réaliser ces tâches. Les comités organisent la communication entre un député et les groupes locaux qui s'intéressent au sujet en question. Pour résumer, les comités de militants fournit un element crucial au succès d'un politicien dans son comté. C'est une dimension de l'activité que les politiologues ont tendance à ignorer.
Earlier age at menarche as a transdiagnostic mechanism linking childhood trauma with multiple forms of psychopathology in adolescent girls
Authors: Colich Natalie L. , Platt Jonathan M. , Keyes Katherine M. , Sumner Jennifer A. , Allen Nicholas B. , McLaughlin Katie A.
Published: April 2019

Background

Although early life adversity (ELA) increases risk for psychopathology, mechanisms linking ELA with the onset of psychopathology remain poorly understood. Conceptual models have argued that ELA accelerates development. It is unknown whether all forms of ELA are associated with accelerated development or whether early maturation is a potential mechanism linking ELA with psychopathology. We examine whether two distinct dimensions of ELA – threat and deprivation – have differential associations with pubertal timing in girls, and evaluate whether accelerated pubertal timing is a mechanism linking ELA with the onset of adolescent psychopathology.

Methods

Data were drawn from a large, nationally representative sample of 4937 adolescent girls. Multiple forms of ELA characterized by threat and deprivation were assessed along with age at menarche (AAM) and the onset of DSM-IV fear, distress, externalizing, and eating disorders.

Results

Greater exposure to threat was associated with earlier AAM (B = −0.1, p = 0.001). Each 1-year increase in AAM was associated with reduced odds of fear, distress, and externalizing disorders post-menarche (ORs = 0.74–0.85). Earlier AAM significantly mediated the association between exposure to threat and post-menarche onset of distress (proportion mediated = 6.2%), fear (proportion mediated = 16.3%), and externalizing disorders (proportion mediated = 2.9%).

Conclusions

Accelerated pubertal development in girls may be one transdiagnostic pathway through which threat-related experiences confer risk for the adolescent onset of mental disorders. Early pubertal maturation is a marker that could be used in both medical and mental health settings to identify trauma-exposed youth that are at risk for developing a mental disorder during adolescence in order to better target early interventions.
The intrusive hyphen is everywhere
Authors: Booth John E.
Published: April 2019

When can a hyphen be described as ‘intrusive’? As with many other ‘rules’ of grammar and of punctuation, use of the hyphen is limited to a specific syntactical context. Hence, to use a hyphen where it should not be used makes it intrusive. Just like the apostrophe, it cannot be used arbitrarily. There is, for instance, a tattooist parlour in the English town of Oldham whose shopfront advertises Inkcredible Tatoo's (sic) and, with it, both the owner's or owners’ ability to play on words in writing and their inability to sign a plural form correctly – the rule being that apostrophes are not used to mark the plural of either common or proper nouns in written English.
Oxidation State of Arc Mantle Revealed by Partitioning of V, Sc, and Ti Between Mantle Minerals and Basaltic Melts
Authors: Wang Jintuan , Xiong Xiaolin , Takahashi Eiichi , Zhang Le , Li Li , Liu Xingcheng
Published: April 2019

Whether arc mantle is more oxidized than oceanic mantle is persistently debated. The behavior of multivalent vanadium (V) is oxygen fugacity (fO2) sensitive, and the ratios of V to a homovalent element (e.g., Sc, Ti, or Yb) in basalts were commonly used as fO2 proxies. Similar ratios, such as V/Sc, between arc basalts and mid‐ocean ridge basalts were previously taken as evidence for similar fO2s in their mantle sources. However, this claim may be problematic because elemental ratios are primarily controlled by partition coefficients (D values), which are further affected by various factors. Here we determined D values of V and other transition elements between mantle minerals and basaltic melts at typical arc T–P‐H2O conditions and variable fO2s. Combining experimental results with published data, the effects of fO2, T, P, and phase compositions on DV, DSc, and DTi for olivine, orthopyroxene (opx), clinopyroxene (cpx), and spinel were evaluated using multiple linear regressions. The results show that DV values for these four minerals all increase with decreasing fO2 and temperature, leading to higher DV/DSc and DV/DTi ratios at low temperatures than those at high temperatures given a certain fO2. Thus, similar V/Sc and V/Ti ratios between arc basalts and mid‐ocean ridge basalts reflect a relatively oxidized arc mantle due to its lower melting temperatures. In light of the highly incompatible behavior of Ti during mantle melting, V‐Ti systematics are regarded to be more superior than V‐Sc systematics in the fO2 estimation. Partial melting modelling results using V‐Ti systematics reveal that arc mantle is, on average, ~0.9 log units higher in fO2 than oceanic mantle.
Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution
Authors: Ren Minglei , Feng Xiaoyuan , Huang Yongjie , Wang Hui , Hu Zhong , Clingenpeel Scott , Swan Brandon K , Fonseca Miguel M , Posada David , Stepanauskas Ramunas , Hollibaugh James T , Foster Peter G , Woyke Tanja , Luo Haiwei
Published: April 2019

Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports three sequential events: origin of AOA from terrestrial non-AOA ancestors, colonization of the shallow ocean, and expansion to the deep ocean. Careful molecular dating suggests that these events coincided with the Great Oxygenation Event around 2300 million years ago (Mya), and oxygenation of the shallow and deep ocean around 800 and 635–560 Mya, respectively. The first transition was likely enabled by the gain of an aerobic pathway for energy production by ammonia oxidation and biosynthetic pathways for cobalamin and biotin that act as cofactors in aerobic metabolism. The first transition was also accompanied by the loss of dissimilatory nitrate and sulfate reduction, loss of oxygen-sensitive pyruvate oxidoreductase, which reduces pyruvate to acetyl-CoA, and loss of the Wood–Ljungdahl pathway for anaerobic carbon fixation. The second transition involved gain of a K+ transporter and of the biosynthetic pathway for ectoine, which may function as an osmoprotectant. The third transition was accompanied by the loss of the uvr system for repairing ultraviolet light-induced DNA lesions. We conclude that oxygen availability drove the terrestrial origin of AOA and their expansion to the photic and dark oceans, and that the stressors encountered during these events were partially overcome by gene acquisitions from Euryarchaeota and Bacteria, among other sources.
A new widespread subclass of carbonic anhydrase in marine phytoplankton
Authors: Jensen Erik L , Clement Romain , Kosta Artemis , Maberly Stephen C , Gontero Brigitte
Published: April 2019

Most aquatic photoautotrophs depend on CO2-concentrating mechanisms (CCMs) to maintain productivity at ambient concentrations of CO2, and carbonic anhydrase (CA) plays a key role in these processes. Here we present different lines of evidence showing that the protein LCIP63, identified in the marine diatom Thalassiosira pseudonana, is a CA. However, sequence analysis showed that it has a low identity with any known CA and therefore belongs to a new subclass that we designate as iota-CA. Moreover, LCIP63 unusually prefers Mn2+ to Zn2+ as a cofactor, which is potentially of ecological relevance since Mn2+ is more abundant than Zn2+ in the ocean. LCIP63 is located in the chloroplast and only expressed at low concentrations of CO2. When overexpressed using biolistic transformation, the rate of photosynthesis at limiting concentrations of dissolved inorganic carbon increased, confirming its role in the CCM. LCIP63 homologs are present in the five other sequenced diatoms and in other algae, bacteria, and archaea. Thus LCIP63 is phylogenetically widespread but overlooked. Analysis of the Tara Oceans database confirmed this and showed that LCIP63 is widely distributed in marine environments and is therefore likely to play an important role in global biogeochemical carbon cycling.
UHRF genes regulate programmed interdigital tissue regression and chondrogenesis in the embryonic limb
Authors: Sanchez-Fernandez Cristina , Lorda-Diez Carlos I. , García-Porrero Juan A. , Montero Juan A. , Hurlé Juan M.
Published: April 2019

The primordium of the limb contains a number of progenitors far superior to those necessary to form the skeletal components of this appendage. During the course of development, precursors that do not follow the skeletogenic program are removed by cell senescence and apoptosis. The formation of the digits provides the most representative example of embryonic remodeling via cell degeneration. In the hand/foot regions of the embryonic vertebrate limb (autopod), the interdigital tissue and the zones of interphalangeal joint formation undergo massive degeneration that accounts for jointed and free digit morphology. Developmental senescence and caspase-dependent apoptosis are considered responsible for these remodeling processes. Our study uncovers a new upstream level of regulation of remodeling by the epigenetic regulators Uhrf1 and Uhrf2 genes. These genes are spatially and temporally expressed in the pre-apoptotic regions. UHRF1 and UHRF2 showed a nuclear localization associated with foci of methylated cytosine. Interestingly, nuclear labeling increased in cells progressing through the stages of degeneration prior to TUNEL positivity. Functional analysis in cultured limb skeletal progenitors via the overexpression of either UHRF1 or UHRF2 inhibited chondrogenesis and induced cell senescence and apoptosis accompanied with changes in global and regional DNA methylation. Uhrfs modulated canonical cell differentiation factors, such as Sox9 and Scleraxis, promoted apoptosis via up-regulation of Bak1, and induced cell senescence, by arresting progenitors at the S phase and upregulating the expression of p21. Expression of Uhrf genes in vivo was positively modulated by FGF signaling. In the micromass culture assay Uhrf1 was down-regulated as the progenitors lost stemness and differentiated into cartilage. Together, our findings emphasize the importance of tuning the balance between cell differentiation and cell stemness as a central step in the initiation of the so-called “embryonic programmed cell death” and suggest that the structural organization of the chromatin, via epigenetic modifications, may be a precocious and critical factor in these regulatory events.
MIReAD, a minimum information standard for reporting arthropod abundance data
Authors: Rund Samuel S. C. , Braak Kyle , Cator Lauren , Copas Kyle , Emrich Scott J. , Giraldo-Calderón Gloria I. , Johansson Michael A. , Heydari Naveed , Hobern Donald , Kelly Sarah A. , Lawson Daniel , Lord Cynthia , MacCallum Robert M. , Roche Dominique G. , Ryan Sadie J. , Schigel Dmitry , Vandegrift Kurt , Watts Matthew , Zaspel Jennifer M. , Pawar Samraat
Published: April 2019

Arthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the “FAIR,” (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests.
Solid-phase microextraction and on-fiber derivatization for assessment of mammalian and vegetable milks with emphasis on the content of major phytoestrogens
Authors: Aresta Antonella , Cotugno Pietro , Zambonin Carlo
Published: April 2019

A new solvent-free method for the simultaneous determination of some major phytoestrogens (equol, enterodiol, daidzein, genistein, glycitein) in different commercial milks (cow, goat and soy-rice) was developed. After solid phase microextraction, performed by direct immersion of a 65 μm-polydimethylsiloxane–divinylbenzene fiber in diluted (1:100 with 0.2% formic acid - 30% sodium chloride) milk samples (18 °C for 20 min under stirring), a direct on-fiber silylation with N,O-bis (trimethylsilyl)trifluoroacetamide) containing 1% trimethylchlorosilane (70 °C for 20 min) was performed prior to gas chromatography–mass spectrometry analysis. Since the target compounds were determined as aglycones, the hydrolytic removal of the aglycone from the glycosides was performed. The method permitted the determination of the target analytes in all the considered milk samples as well as the detection of some major amphipathic fats indicating that the approach could potentially be applied in the future for further applications, such as milk profiling.
Early Synaptic Alterations and Selective Adhesion Signaling in Hippocampal Dendritic Zones Following Organophosphate Exposure
Authors: Farizatto Karen L. G. , Almeida Michael F. , Long Ronald T. , Bahr Ben A.
Published: April 2019

Organophosphates account for many of the world’s deadliest poisons. They inhibit acetylcholinesterase causing cholinergic crises that lead to seizures and death, while survivors commonly experience long-term neurological problems. Here, we treated brain explants with the organophosphate compound paraoxon and uncovered a unique mechanism of neurotoxicity. Paraoxon-exposed hippocampal slice cultures exhibited progressive declines in synaptophysin, synapsin II, and PSD-95, whereas reduction in GluR1 was slower and NeuN and Nissl staining showed no indications of neuronal damage. The distinctive synaptotoxicity was observed in dendritic zones of CA1 and dentate gyrus. Interestingly, declines in synapsin II dendritic labeling correlated with increased staining for β1 integrin, a component of adhesion receptors that regulate synapse maintenance and plasticity. The paraoxon-induced β1 integrin response was targeted to synapses, and the two-fold increase in β1 integrin was selective as other synaptic adhesion molecules were unchanged. Additionally, β1 integrin–cofilin signaling was triggered by the exposure and correlations were found between the extent of synaptic decline and the level of β1 integrin responses. These findings identified organophosphate-mediated early and lasting synaptotoxicity which can explain delayed neurological dysfunction later in life. They also suggest that the interplay between synaptotoxic events and compensatory adhesion responses influences neuronal fate in exposed individuals.
Integration of lodging resistance QTL in soybean
Authors: Hwang Sadal , Lee Tong Geon
Published: April 2019

Poor lodging resistance could limit increases in soybean yield. Previously, a considerable number of observations of quantitative trait loci (QTL) for lodging resistance have been reported by independent studies. The integration of these QTL into a consensus map will provide further evidence of their usefulness in soybean improvement. To improve informative QTL in soybean, a mapping population from a cross between the Harosoy and Clark cultivars, which inherit major U.S. soybean genetic backgrounds, was used along with previous mapping populations to identify QTL for lodging resistance. Together with 78 QTL for lodging collected from eighteen independent studies, a total of 88 QTL were projected onto the soybean consensus map. A total of 16 significant QTL clusters were observed; fourteen of them were confirmed in either two or more mapping populations or a single population subjected to different environmental conditions. Four QTL (one on chromosome 7 and three on 10) were newly identified in the present study. Further, meta-analysis was used to integrate QTL across different studies, resulting in two significant meta-QTL each on chromosomes 6 and 19. Our results provide deeper knowledge of valuable lodging resistance QTL in soybean, and these QTL could be used to increase lodging resistance.
Differential impacts of pesticides on Euschistus heros (Hem.: Pentatomidae) and its parasitoid Telenomus podisi (Hym.: Platygastridae)
Authors: Pazini Juliano de Bastos , Padilha Aline Costa , Cagliari Deise , Bueno Flávio Amaral , Rakes Matheus , Zotti Moisés João , Martins José Francisco da Silva , Grützmacher Anderson Dionei
Published: April 2019

Euschistus heros (Fabricius) (Hemiptera: Pentatomidae) primarily attack the pods and seeds of soybean plants, causing severe economic losses in Neotropical Region, and chemical control is essential to avoid these losses. Thus, insecticides more effective against this pest and less toxic to Telenomus podisi Ashmead (Hymenoptera: Platygastridae) - the main biological control agent of E. heros - should be used. In this report, we studied the differential acute impacts of pesticides used in Brazilian soybean against E. heros and T. podisi and evaluated their sublethal effects on the parasitoid to identify effective pesticides towards the pest with less harmful effect to the natural enemy. The LC50 of the insecticides to E. heros ranged from 1.20 to 533.74 ng a.i./cm2; the order of toxicity was thiamethoxam + lambda-cyhalothrin > acetamiprid + fenpropathrin > zeta-cypermethrin > acephate > imidacloprid. All pesticides were classified as slightly to moderately toxic to T. podisi based on the risk quotient. The exposure of T. podisi females to imidacloprid and the insecticide pre-formulated mixtures reduced the emergence of the offspring parasitoids by up to 40% whereas zeta-cypermethrin and the insecticides pre-formulated mixtures reduced offspring survival. The preferred order of choice of insecticides for the management of E. heros according to agronomic, toxicological, and environmental feasibility was the following: thiamethoxam + lambda-cyhalothrin > zeta-cypermethrin > acetamiprid + fenpropathrin > acephate > imidacloprid. Our study provides important and pioneer information to select insecticides for effective control of E. heros with lower impacts on T. podisi.
Reference genes for gene expression studies by RT-qPCR in Brevipalpus yothersi (Acari: Tenuipalpidae), the mite vector of citrus leprosis virus
Authors: Rogerio Luana Aparecida , Galdeano Diogo Manzano , Arena Gabriella Dias , Nunes Maria Andreia , Machado Marcos Antonio , Novelli Valdenice Moreira
Published: April 2019

Quantitative reverse transcription PCR (RT-qPCR) is a high-throughput method to analyze the transcriptional expression of genes. Currently, no reference genes have been described for evaluating gene expression in Brevipalpus yothersi, the false spider mite, a polyphagous that act as vector of the citrus leprosis virus C (CiLV-C), an important citrus disease. This study aimed to identify the most stable reference genes in B. yothersi. The RT-qPCR expression data for selected genes were evaluated from three conditions: different developmental stages, plant hosts and acquisition of CiLV-C. To analyze the stability of the candidate reference genes we used ΔCq method, GeNorm, NormFinder, BestKeeper and RefFinder. Ubiq and GAPDH are best suited for normalizing gene expression data in viruliferous and non-viruliferous mites. Ubiq, EF1α and GAPDH are the most stable for different developmental stages. RPL13 and RPL32 are the best reference genes for approaches to B. yothersi in different host plants. Considering all the experimental conditions, Ubiq, EF1α, and GAPDH were the most stable genes. Here we developed an accurate and comprehensive RT-qPCR strategy for use in B. yothersi gene expression analysis. These results will improve the understanding of the biology of the false spider mites and their role as virus vectors.
Vitamin K2 cannot substitute Coenzyme Q10 as electron carrier in the mitochondrial respiratory chain of mammalian cells
Authors: Cerqua Cristina , Casarin Alberto , Pierrel Fabien , Vazquez Fonseca Luis , Viola Giampiero , Salviati Leonardo , Trevisson Eva
Published: April 2019

Coenzyme Q10 (CoQ10) deficiencies are a group of heterogeneous conditions that respond to ubiquinone administration if treated soon after the onset of symptoms. However, this treatment is only partially effective due to its poor bioavailability. We tested whether vitamin K2, which was reported to act as a mitochondrial electron carrier in D. melanogaster, could mimic ubiquinone function in human CoQ10 deficient cell lines, and in yeast carrying mutations in genes required for coenzyme Q6 (CoQ6) biosynthesis. We found that vitamin K2, despite entering into mitochondria, restored neither electron flow in the respiratory chain, nor ATP synthesis. Conversely, coenzyme Q4 (CoQ4), an analog of CoQ10 with a shorter isoprenoid side chain, could efficiently substitute its function. Given its better solubility, CoQ4 could represent an alternative to CoQ10 in patients with both primary and secondary CoQ10 deficiencies.
Associated Factors and Clinical Implication of Cutaneous Allodynia in Patients with Cluster Headache: A Prospective Multicentre Study
Authors: Kim Byung-Su , Park Jeong Wook , Sohn Jong-Hee , Lee Mi Ji , Kim Byung-Kun , Chu Min Kyung , Ahn Jin-Young , Choi Yun-Ju , Song Tae-Jin , Chung Pil-Wook , Oh Kyungmi , Lee Kwang-Soo , Kim Soo-Kyoung , Park Kwang-Yeol , Chung Jae Myun , Moon Heui-Soo , Chung Chin-Sang , Cho Soo-Jin
Published: April 2019

Cutaneous allodynia (CA) is an abnormal pain in response to non-painful stimuli. In the present study, we sought to investigate the presence of CA, its associated factors, and its clinical implications in patients with cluster headache (CH). In this cross-sectional study, we analysed data from a prospective multicentre registry enrolling consecutive patients with CH. We identified CA during and between headache attacks using the 12-item Allodynia Symptom Checklist (ASC) administered during the CH bout period. Comorbid depression and anxiety were ascertained using the Patient Health Questionnaire (PHQ-9) and the Generalized Anxiety Disorder (GAD-7) scales. Headache impact was evaluated using the Headache Impact Test-6 (HIT-6). Of 119 eligible patients, 48 and two (40.3% and 1.7%) had CA during and between headache attacks, respectively. In univariable analyses, total CH duration, major depressive disorder (MDD), and generalized anxiety disorder (GAD) were associated with CA during headache attack. They remained significantly associated with CA during headache attack in multivariable analyses. Patients with CA during headache attack had higher headache impact (P = 0.002). A “50% responder” analysis showed no difference in outcome of acute and preventive treatment between patients with and without CA during headache attack. Patients with CH commonly experienced CA during headache attack, but not between headache attacks. CA during headache attack was associated with disease duration, depression, and anxiety.
Effects of boat noise on fish fast-start escape response depend on engine type
Authors: McCormick Mark I. , Fakan Eric P. , Nedelec Sophie L. , Allan Bridie J. M.
Published: April 2019

Vessel noise represents a relatively recent but rapidly increasing form of pollution, which affects the many organisms that use sound to inform their behavioural decisions. Recent research shows that anthropogenic noise can lead to reduced responsiveness to risk and higher mortality. The current laboratory experiment determined whether the playback of noise from motorboats powered by two- or four-stroke outboard engines affected the kinematics of the fast-start response in a juvenile coral reef fish, and the time scale over which the effects may occur. Results show that the two engine types produce slightly different sound spectra, which influence fish differently. Playback of 2-stroke engines had the greatest effect on activity, but only for a brief period (45 s). While noise from 4-stroke outboard engines affected fast-start kinematics, they had half the impact of noise from 2-stroke engines. Two-stroke engine noise affected routine swimming more than 4-stroke engines, while 4-stroke noise had a greater effect on the speed at which fish responded to a startle. Evidence suggests that the source of the noise pollution will have a major influence on the way marine organisms will respond, and this gives managers an important tool whereby they may reduce the effects of noise pollution on protected communities.
Ring-opening metathesis polymerization-induced self-assembly (ROMPISA) of a cisplatin analogue for high drug-loaded nanoparticles
Authors: Wright Daniel B. , Proetto Maria T. , Touve Mollie A. , Gianneschi Nathan C.
Published: April 2019

We report the one-pot aqueous phase synthesis of cisplatin drug loaded micellar nanoparticles using Ring-Opening Metathesis Polymerization-Induced Self-Assembly (ROMPISA).
Size control of SSZ-13 crystals with APAM and its influence on the coking behaviour during MTO reaction
Authors: Xu Zhiqiang , Li Jianwen , Huang Yuxuan , Ma Hongfang , Qian Weixin , Zhang Haitao , Ying Weiyong
Published: April 2019

Crystal size reduction of SSZ-13 with APAM activates more naphthalene in the CHA cages.
(Di)triazolylidene manganese complexes in catalytic oxidation of alcohols to ketones and aldehydes
Authors: Pinto Mara F. , Olivares Marta , Vivancos Ángela , Guisado-Barrios Gregorio , Albrecht Martin , Royo Beatriz
Published: April 2019

A robust bimetallic manganese complex with a mesoionic 1,2,3,-triazolylidene ligand for efficient oxidation of alcohols with tert-butylhydroperoxide.
Synthesis, ribosomal selectivity, and antibacterial activity of netilmicin 4′-derivatives
Authors: Sonousi Amr , Shcherbakov Dimitri , Vasella Andrea , Böttger Erik C. , Crich David
Published: April 2019

We describe the synthesis and evaluation of 4′-subsituted netilmicin derivatives by selective functionalization at the 4′-position of the endocyclic enolether function.