bluuebunny/crossref_metadata_2025 huggingface dataset:
An Exome-Seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants
Authors: Jia Shangang , Morton Kyla , Zhang Chi , Holding David
Published: February 2019

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 × Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-specific expression data to narrow down the list of candidate genes/mutations and identified deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identified in mutant 531, which occurs within a ∼200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4 (RdDM4) and AMP-binding protein, respectively. This study demonstrates the efficiency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection, providing a new option in mapping-by-sequencing for maize functional genomics studies.
Role of DAPK1 in neuronal cell death, survival and diseases in the nervous system
Authors: Sulaiman Alsaadi Maryam
Published: February 2019

DAPK (death‐associated protein kinase) is a calcium/calmodulin (Ca2+/CaM) regulated serine/threonine kinase. Structurally, it assumes a multi‐domain structure and participates in various apoptotic systems which imply that it may interact with a wide range of intracellular components to exert its action. DAPK plays vital roles in pro‐apoptotic, apoptotic and autophagic pathways. In addition, it plays important roles in many diseases such as cancer, Alzheimer's disease, cerebral ischemia and epilepsy. Although a novel protein, DAPK's various cellular signal transduction pathways proves that it can be a target for a potential future therapeutic effects. Specific role of DAPK in the development and maintenance of the nervous system needs to be further investigated as it is involved in neurodegeneration, traumatic brain injury and neuronal development or recovery from injury. This review summarizes DAPK signaling pathways in autophagy, apoptosis, and stresses the important role it might play in the nervous system.
The Sign Theory of Language and the form-meaning interface / La Théorie du langage basée sur le signe et l’interface forme-sens
Authors: Newmeyer Frederick J.
Published: February 2019

This article examines a key feature of Denis Bouchard's Sign Theory of Language, namely theSubstantive Hypothesis(SH), the idea that “the most explanatory linguistic theory is one that minimizes the elements (ideally to zero) that do not have an external motivation in the prior properties of the perceptual and conceptual substances of language”. The article argues that the strongest form of the SH is challenged by two widespread classes of phenomena: morphosyntactic generalizations that are not sign-based, and non-sign-based external pressures on grammars. It concludes with some speculative remarks on why, to a significant degree, grammatical patterning is not sign-based.
Persistent Hall rays for Lagrange spectra at cusps of Riemann surfaces
Authors: ARTIGIANI MAURO , MARCHESE LUCA , ULCIGRAI CORINNA
Published: February 2019

We study Lagrange spectra at cusps of finite area Riemann surfaces. These spectra are penetration spectra that describe the asymptotic depths of penetration of geodesics in the cusps. Their study is in particular motivated by Diophantine approximation on Fuchsian groups. In the classical case of the modular surface and classical Diophantine approximation, Hall proved in 1947 that the classical Lagrange spectrum contains a half-line, known as a Hall ray. We generalize this result to the context of Riemann surfaces with cusps and Diophantine approximation on Fuchsian groups. One can measure excursion into a cusp both with respect to a natural height function or, more generally, with respect to any proper function. We prove the existence of a Hall ray for the Lagrange spectrum of any non-cocompact, finite covolume Fuchsian group with respect to any given cusp, both when the penetration is measured by a height function induced by the imaginary part as well as by any proper function close to it with respect to the Lipschitz norm. This shows that Hall rays are stable under (Lipschitz) perturbations. As a main tool, we use the boundary expansion developed by Bowen and Series to code geodesics and produce a geometric continued fraction-like expansion and some of the ideas in Hall’s original argument. A key element in the proof of the results for proper functions is a generalization of Hall’s theorem on the sum of Cantor sets, where we consider functions which are small perturbations in the Lipschitz norm of the sum.
Shock-induced energy conversion of entropy in non-ideal fluids
Authors: Touber Emile , Alferez Nicolas
Published: February 2019

From shaping cosmic structures in space to producing intense sounds in aircraft engines, shock waves in fluids ineluctably convert entropy fluctuations into swirling motions and sound waves. Studies of the corresponding conversion from internal energy to kinetic energy have so far been restricted to ideal (or idealised) fluids. Yet, many substances do not obey the ideal-gas law (including those in the above two examples). The present work demonstrates that non-ideal thermodynamic properties provide a remarkable degree of control over the conversion to solenoidal and dilatational kinetic energies. Of particular interest is the ability to suppress much of the emitted acoustic field whilst promoting mixing downstream of the shock. This is made possible by exploiting the convexity (or lack thereof) of the shock adiabats. Whilst illustrated here using dense vapours near the thermodynamic critical point, this ability to design and control specific shock-induced energy transfers extends beyond near-critical-point phenomena; e.g. shocked mixtures (high-speed dusty flows on Mars, nanoparticle formation in supersonic expanders for drug manufacturing), reacting fronts (supersonic combustion, rocket propulsion), ionising shocks (reentry systems, inertial confinement fusion) or fronts in active fluids (bacterial and crowd flows). This theoretical work, which demonstrates the predictive capabilities of linear theory, lays the foundation for future experimental investigations ultimately aimed at delivering novel shock-based flow-control strategies exploiting the thermodynamic properties of the fluid.
Multi-point Monin–Obukhov similarity in the convective atmospheric surface layer using matched asymptotic expansions
Authors: Tong Chenning , Ding Mengjie
Published: February 2019

The multi-point Monin–Obukhov similarity (MMO) was recently proposed (Tong & Nguyen, J. Atmos. Sci., vol. 72, 2015, pp. 4337–4348) to address the issue of incomplete similarity in the framework of the original Monin–Obukhov similarity theory (MOST). MMO hypothesizes the following: (1) The surface-layer turbulence, defined to consist of eddies that are entirely inside the surface layer, has complete similarity, which however can only be represented by multi-point statistics, requiring a horizontal characteristic length scale (absent in MOST). (2) The Obukhov length $L$ is also the characteristic horizontal length scale; therefore, all surface-layer multi-point statistics, non-dimensionalized using the surface-layer parameters, depend only on the height and separations between the points, non-dimensionalized using $L$. However, similar to MOST, MMO was also proposed as a hypothesis based on phenomenology. In this work we derive MMO analytically for the case of the horizontal Fourier transforms of the velocity and potential temperature fluctuations, which are equivalent to the two-point horizontal differences of these variables, using the spectral forms of the Navier–Stokes and the potential temperature equations. We show that, for the large-scale motions (wavenumber $k<1/z$) in a convective surface layer, the solution is uniformly valid with respect to $z$ (i.e. as $z$ decreases from $z>-L$ to $z<-L$), where $z$ is the height from the surface. However, for $z<-L$ the solution is not uniformly valid with respective to $k$ as it increases from $k<-1/L$ to $k>-1/L$, resulting in a singular perturbation problem, which we analyse using the method of matched asymptotic expansions. We show that (1) $-L$ is the characteristic horizontal length scale, and (2) the Fourier transforms satisfy MMO with the non-dimensional wavenumber $-kL$ as the independent similarity variable. Two scaling ranges, the convective range and the dynamic range, discovered for $z\ll -L$ in Tong & Nguyen (2015) are obtained. We derive the leading-order spectral scaling exponents for the two scaling ranges and the corrections to the scaling ranges for finite ratios of the length scales. The analysis also reveals the dominant dynamics in each scaling range. The analytical derivations of the characteristic horizontal length scale ($L$) and the validity of MMO for the case of two-point horizontal separations provide strong support to MMO for general multi-point velocity and temperature differences.
Spatio-temporal proper orthogonal decomposition of turbulent channel flow
Authors: Derebail Muralidhar Srikanth , Podvin Bérengère , Mathelin Lionel , Fraigneau Yann
Published: February 2019

An extension of proper orthogonal decomposition is applied to the wall layer of a turbulent channel flow ($Re_{\unicode[STIX]{x1D70F}}=590$), so that empirical eigenfunctions are defined in both space and time. Due to the statistical symmetries of the flow, the eigenfunctions are associated with individual wavenumbers and frequencies. Self-similarity of the dominant eigenfunctions, consistent with wall-attached structures transferring energy into the core region, is established. The most energetic modes are characterized by a fundamental time scale in the range 200–300 viscous wall units. The full spatio-temporal decomposition provides a natural measure of the convection velocity of structures, with a characteristic value of 12$u_{\unicode[STIX]{x1D70F}}$in the wall layer. Finally, we show that the energy budget can be split into specific contributions for each mode, which provides a closed-form expression for nonlinear effects.
Source counts and confusion at 72–231 MHz in the MWA GLEAM survey
Authors: Franzen T. M. O. , Vernstrom T. , Jackson C. A. , Hurley-Walker N. , Ekers R. D. , Heald G. , Seymour N. , White S. V.
Published: February 2019

The GaLactic and Extragalactic All-sky Murchison Widefield Array survey is a radio continuum survey at 72–231 MHz of the whole sky south of declination +30º, carried out with the Murchison Widefield Array. In this paper, we derive source counts from the GaLactic and Extragalactic All-sky Murchison data at 200, 154, 118, and 88 MHz, to a flux density limit of 50, 80, 120, and 290 mJy respectively, correcting for ionospheric smearing, incompleteness and source blending. These counts are more accurate than other counts in the literature at similar frequencies as a result of the large area of sky covered and this survey’s sensitivity to extended emission missed by other surveys. At S154 MHz > 0.5 Jy, there is no evidence of flattening in the average spectral index (α ≈ −0.8 where S ∝ vα) towards the lower frequencies. We demonstrate that the Square Kilometre Array Design Study model by Wilman et al. significantly underpredicts the observed 154-MHz GaLactic and Extragalactic All-sky Murchison counts, particularly at the bright end. Using deeper Low-Frequency Array counts and the Square Kilometre Array Design Study model, we find that sidelobe confusion dominates the thermal noise and classical confusion at v ≳ 100 MHz due to both the limited CLEANing depth and the undeconvolved sources outside the field-of-view. We show that we can approach the theoretical noise limit using a more efficient and automated CLEAN algorithm.
Non-destructive detection and classification of in-shell insect-infested almonds based on multispectral imaging technology
Authors: Yu J. , Ren S. , Liu C. , Wei B. , Zhang L. , Younas S. , Zheng L.
Published: February 2019

The feasibility of non-destructive detection and classification of in-shell insect-infested almonds was examined by using multispectral imaging (MSI) technology combined with chemometrics. Differentiation of reflectance spectral data between intact and insect-infested almonds was attempted by using analytical approaches based on principal component analysis and support vector machines, classification accuracy rates as high as 99.1% in the calibration set and 97.5% in the prediction set were achieved. Meanwhile, the in-shell almonds were categorized into three classes (intact, slightly infested and severely infested) based on the degree of damage caused by insect infestation and were characterized quantitatively by the analysis of shell/kernel weight ratio. A three-class model for the identification of intact, slightly infested and severely infested almonds yielded acceptable classification performance (95.6% accuracy in the calibration set and 93.3% in the prediction set). These results revealed that MSI technology combined with chemometrics may be a promising approach for the non-destructive detection of hidden insect damage in almonds and could be used for industrial applications.
A Simple Method to Solve the Instantaneous Kinematics of the 5-RUR Parallel Manipulator
Authors: Gallardo-Alvarado Jaime , Abedinnasab Mohammad H. , Islam Md. Nazrul
Published: February 2019

In this work a simple method to solve the kinematics of the 5-R$\underbar{P}$UR parallel manipulator is introduced. Dealing with the displacement analysis, the kinematic constraint equations required to address the forward–inverse displacement analysis are established according to linear combinations of two vectors attached to the moving platform. Then, besides the solution of the inverse displacement analysis two strategies are proposed in order to solve the forward position analysis. Finally, the input–output equations of velocity and acceleration are systematically obtained by resorting to reciprocal-screw theory. Numerical examples are provided with the purpose to illustrate the proposed method. Furthermore, the numerical results obtained by means of screw theory are confirmed with the aid of commercially available software.
Barriers to Staff Involvement in End-of-Life Decision-Making for Long-Term Care Residents with Dementia
Authors: Sutherland Nisha , Wiersma Elaine , Vangel Paula
Published: February 2019

Bien que le personnel infirmier (autorisé et auxiliaire) et de soutien à la personne des centres de soins de longue durée (CSLD) fournisse des soins directs aux résidents atteints de démence, son implication est rarement considérée dans la prise de décisions en fin de vie. L’objectif de cette étude était d’examiner les obstacles et les facilitateurs à la participation du personnel des CSLD dans la prise de décisions liées à la fin de vie chez les personnes atteintes de démence sévère. Nous présentons les obstacles rencontrés en matière de participation à cette prise de décision pour ces travailleurs. Un design descriptif interprétatif a permis de mettre en évidence quatre principaux obstacles liés à la participation du personnel dans la prise de décisions : a) la prédominance d’un modèle de soins biomédical, b) les divergences dans la compréhension de l’approche palliative, c) la complexité des relations avec les familles, et d) le malaise associé aux discussions concernant le décès. Les résultats suggèrent que le modèle biomédical, qui est important et prédominant dans les CSLD, devrait s’inspirer d’une approche philosophique mettant davantage l’accent sur les relations entre les résidents atteints de démence, leur famille et le personnel.
William Johnson's Hypothesis: A Free Black Man and the Problem of Legal Knowledge in the Antebellum United States South
Authors: Welch Kimberly
Published: February 2019

This essay uses the diary of free black barber and Natchez, Mississippi, businessman William T. Johnson as a means to explore the extent to which one black man in the antebellum U.S. South knew the law; how he came to know it; and what role he saw it play in his life and community. In recent years, scholars have paid increasing attention to black Americans' engagement with the legal system in the pre-Civil War U.S. South and have undermined the notion that black people were legal outsiders. In particular, they have shown that African Americans in the slave South were legal actors in their own right and were legally savvy. Yet what does it mean when scholars say that free blacks and slaves knew how to use the law? This essay uses Johnson's diary to demystify the phrase “to know the law” and shows that we speak of “knowing the law,” we speak of a remarkably complex and uneven phenomenon, one best mapped on a case-to-case basis. Understanding what it meant “to know the law” sometimes requires examining an individual's personal theory or hypothesis of what law does for them.
High burden of co-morbidity and mortality among severely malnourished children admitted to outpatient therapeutic programme facilities in the conflict setting of Borno, Nigeria: a retrospective review
Authors: Chamla Dick , Oladeji Olusola , Maduanusi Ifeanyi , Mele Sule , Mshelia Helni , Safi Naqibullah
Published: February 2019

Objective

To present evidence on the burden and outcomes of co-morbidities among severely malnourished (SAM) children admitted to outpatient therapeutic programme (OTP) facilities in the conflict setting of Borno, Nigeria.

Design

Retrospective medical chart review.

Setting

Facility-based study.

Participants

Children aged 6–59 months with SAM enrolled in OTP between June and November 2016 whose medical records were analysed. Only pneumonia and diarrhoea were examined due to data limitations. Stata software was used for descriptive, multivariate and survival analyses.

Results

Records of 396 children with median age of 15 months were identified and analysed from the date of enrolment to exit from OTP. Mean length of stay in OTP was 61d, with co-infected SAM children having shorter stay (P=0·006). Of the total, 148 (37·4 %) had at least one co-morbidity (pneumonia or diarrhoea), of which thirty-nine (26·4 %) had both. Cumulative rate of mortality during follow-up time was 9·5 (95 % CI 6·0, 15·1) per 10 000 child-days; SAM children with co-morbidities were ten times more likely to die than those without (hazard ratio=10·2; 95 % CI 3·4, 31·0). In multivariable analysis, co-morbidity (P=0·01), oedema (P=0·003), dehydration (P=0·02) and weight on admission (P=0·01) were associated with mortality. Both recovery and defaulter rates (57·8 and 36·1 %, respectively) did not meet SPHERE standards.

Conclusions

Children with SAM and co-morbidities are less likely to survive, presenting a significant barrier in improving child survival. The findings call for integrated OTP models that incorporate clinical algorithms and ensure prompt referral for SAM children with co-morbidity.
E-Commerce in South Korean FTAs: Policy Priorities and Provisional Inconsistencies
Authors: KIM EVAN Y.
Published: February 2019

The e-commerce chapters in South Korea's Free Trade Agreements (FTAs) cover a wide range of issues, ranging from non-discrimination to electronic signatures. Across the agreements, the country's provisions on consumer protection, paperless trading, and data protection are uniquely consistent, while those on other issues are not. With the aid of a framework (Framer v. Follower) that captures the dynamics of bilateral negotiations, this paper argues that in Korea's case, the more consistent a particular set of provisions is portfolio-wide, the more likely it was for Korea to have prioritized the relevant issue and actively pushed its preferred terms in the FTAs.
Social security and retirement timing: evidence from a national sample of teachers
Authors: Morrill Melinda Sandler , Westall John
Published: February 2019

This study documents an important role for Social Security income in workers’ retirement timing. About 40% of public school teachers are not covered by Social Security. This provides an opportunity to analyze the causal impact of Social Security on retirement timing by comparing covered and non-covered teachers. Using individual-level data from the American Community Survey, we find robust evidence of higher rates of retirement among covered teachers at Social Security eligibility ages. This pattern is confirmed using an alternative regression model of participation in the teacher labor force. These estimates suggest that, should the federal government mandate full inclusion in Social Security for all public sector workers, the retirement timing patterns of newly covered teachers and other public sector workers would likely change.
Distress and self-care among chaplains working in palliative care
Authors: White Kelsey B. , Murphy Patricia E. , Jeuland Jane , Fitchett George
Published: February 2019

Background

The prevalence of burnout and distress among palliative care professionals has received much attention since research suggests it negatively impacts the quality of care. Although limited, research suggests low levels of burnout or distress among healthcare chaplains; however, there has been no research among chaplains working in specific clinical contexts, including palliative care.

Objective

This study explored the distress, self-care, and debriefing practices of chaplains working in palliative care.

Method

Exploratory, cross-sectional survey of professional chaplains. Electronic surveys were sent to members of four professional chaplaincy organizations between February and April 2015. Primary measures of interest included Professional Distress, Distress from Theodicy, Informal Self-care, Formal Self-care, and debriefing practices.

Result

More than 60% of chaplains working in palliative care reported feeling worn out in the past 3 months because of their work as a helper; at least 33% practice Informal Self-care weekly. Bivariate analysis suggested significant associations between Informal Self-care and both Professional Distress and Distress from Theodicy. Multivariate analysis also identified that distress decreased as Informal and Formal Self-care increased.

Significance of results

Chaplains working in palliative care appear moderately distressed, possibly more so than chaplains working in other clinical areas. These chaplains also use debriefing, with non-chaplain palliative colleagues, to process clinical experiences. Further research is needed about the role of religious or spiritual beliefs and practices in protecting against stress associated with care for people at the end of life.
Actigraphy as an assessment of performance status in patients with advanced lung cancer
Authors: Fujisawa Daisuke , Temel Jennifer S. , Greer Joseph A. , El-Jawahri Areej , Traeger Lara , Jacobs Jamie M. , Cutrono Stacy , Pirl William F.
Published: February 2019

Objective

Wearable devices such as a wrist actigraph may have a potential to objectively estimate patients’ functioning and may supplement performance status (PS). This proof-of-concept study aimed to evaluate whether actigraphy data are significantly associated with patients’ functioning and are predictive of their survival in patients with metastatic non-small cell lung cancer.

Method

We collected actigraphy data for a three-day period in ambulatory patients with stage IV non-small cell lung cancer. We computed correlations between actigraphy data (specifically, proportion of time spent immobile while awake) and clinician-rated PS, subjective report of physical activities, quality of life (the Functional Assessment of Cancer Therapy – Trial Outcome Index), and survival.

Result

Actigraphy data (the proportion of time awake spent immobile) were significantly correlated with Functional Assessment of Cancer Therapy – Trial Outcome Index (r= −0.53,p< 0.001) and with the Eastern Cooperative Oncology Group PS (ECOG PS) (r= 0.37,p< 0.001). The proportion of time awake spent immobile was significantly associated with worse survival. For each 10% increase in this measure, the hazard ratio (HR) was 1.48 (95% confidence interval [CI95%] = 1.06, 2.06) for overall mortality, and odds ratio was 2.99 (CI95%= 1.27, 7.05) for six-month mortality. ECOG PS was also associated with worse survival (HR = 2.80,CI95%= 1.34, 5.86). Among patients with ECOG PS 0-1, the percentage of time awake spent immobile was significantly associated with worse survival, HR = 1.93 (CI95%= 1.10, 3.42), whereas ECOG PS did not predict survival.

Significance of Results

Actigraphy may have potential to predict important clinical outcomes, such as quality of life and survival, and may serve to supplement PS. Further validation study is warranted.
CONFESSIONAL MODERNITY: NICOLA SPEDALIERI, THE CATHOLIC CHURCH AND THE FRENCH REVOLUTION,C.1775–1800
Authors: SCHETTINI GLAUCO
Published: February 2019

This article reconsiders the Catholic reaction to the French Revolution, focusing on Nicola Spedalieri'sOn the Rights of Man(1791) and on the debate that its publication sparked in Italy and beyond. The outbreak of the Revolution and the polarization of public opinion between the supporters of the new regime and its relentless opponents convinced Spedalieri, a well-reputed Catholic theologian, of the need to find a via media between these two extremes. Assuming the re-Christianization of the postrevolutionary world as his goal, Spedalieri argued that some aspects of revolutionary political culture were acceptable from a Catholic standpoint as long as the revolutionaries, in turn, agreed to abandon secularization and to uphold the traditional confessional organization of the state. It was not modernity itself, he claimed, that should be rejected, but secularization, for a different modernity from that conceived by the revolutionaries—a confessional modernity, combining revolutionary politics and confessional states—was possible. Far from gaining immediate acceptance, Spedalieri's ideas were harshly criticized during the 1790s and then set aside by the triumph of reactionary Catholicism during the Restoration. However, they resurfaced later in the nineteenth century and ultimately played a decisive role in the development of the church's attitudes toward modern culture, for they carved a path for Catholics to fight secularization from within and to reshape modernity accordingly.
Performing Together: Monozygotic Twin Comedians/Twin research: Mirror-Image Cleft Lip and Palate; Dental Caries; Noninvasive Prenatal testing; Capgras Syndrome with Folie à Deux/In the News: Athletic Twins; Transgendered Twins; Crib-Sharing; Common Careers
Authors: Segal Nancy L.
Published: February 2019

Twin studies have shown that our sense of humor has an underlying genetic component, but less investigation of the origins of stand-up comedy has been undertaken. This article briefly reviews twin research findings on humor, then describes the working partnership and social affiliation of a pair of monozygotic male twins who perform together as stand-up comedians. The abilities, personalities and temperaments of these twins suggest future avenues for research in this interesting area. Next, findings from twin studies and case reports of twins with cleft lip and palate, dental caries, noninvasive prenatal testing and Capgras syndrome (with folie à deux) are summarized. In conclusion, recent news about athletic twins, transgendered twins, crib-sharing and career choice are presented.
Excitation of Highly Oblique Lower Band and Upper Band Chorus by a Loss Cone Feature and Temperature Anisotropy Distribution
Authors: Zhou Qinghua , Yang Chang , He Yihua , Liu Si , Gao Zhonglei , Xiao Fuliang
Published: February 2019

Recent studies have indicated that highly oblique lower band chorus could be excited by temperature anisotropy with a low‐energy electron plateau. Here we present another excitation mechanism of highly oblique lower and upper band chorus by using the simultaneous observations and numerical modeling. During 23:00–24:00 UT on 3 July 2016, Van Allen probe A observed chorus with the wave normal angle close to the resonance cone both in the lower and upper bands around L = 5.0 and MLT = 3. Enhanced flux and pitch angle anisotropy of energetic electrons were observed in the same spatial region. Calculations of chorus growth rates show that highly oblique chorus waves can be excited by the energetic electrons with a loss cone feature and distinct temperature anisotropy, particularly more efficient in the presence of a low‐energy plateau. The temperature anisotropy for the oblique upper band is higher than that for the lower band.
Stress Field in the 2016 Kumamoto Earthquake (M 7.3) Area
Authors: Yu Zhiteng , Zhao Dapeng , Li Jiabiao , Huang Zhouchuan , Nishizono Yukihisa , Inakura Hirohito
Published: February 2019

We used 1‐D and 3‐D velocity models to determine focal mechanism solutions (FMSs) of 349 crustal earthquakes (M 2.7–7.3) and stress tensors in the source area of the 2016 Kumamoto earthquake (M 7.3) that occurred on the Futagawa‐Hinagu fault zone in Kyushu, Southwest Japan. There are some differences in the FMSs determined with the 1‐D and 3‐D velocity models. The use of the 3‐D velocity model leads to better results of stress tensors, which are determined by inverting the FMSs. The orientation of the minimum stress (σ3) axis is more accurately determined, which trends NNW‐SSE to N‐S nearly horizontally. In contrast, the axes of the maximum and intermediate stresses (σ1 and σ2) trend WSW‐ENE to E‐W with wide ranges. Significant spatiotemporal variations of the stress field are revealed in the Kumamoto source zone, indicating a small magnitude of deviatoric stress. The friction coefficient of the faults is estimated to be relatively small (~0.4), indicating that the seismogenic faults in central Kyushu are weak. The fault weakening may be caused by fluids beneath the source area and arc magma under the nearby Aso active volcano.
Whether the Rock Fragment Content Should Be Considered When Investigating Nitrogen Cycle in Stony Soils?
Authors: Liao Kaihua , Lai Xiaoming , Zhou Zhiwen , Zeng Xiankui , Xie Wenyi , Castellano Michael J. , Zhu Qing
Published: February 2019

This study was conducted on a stony‐soil hillslope that severely eroded due to land use change from bamboo to tea. First, three approaches were used to extract soil hydraulic properties and then inputted into the Denitrification–Decomposition model for simulations. The Denitrification–Decomposition model defaults and ROSETTA pedotransfer function were traditional approaches without considering the rock fragment impacts on soil hydraulic properties, while the dual‐porosity function considered rock fragment impacts since it was calibrated with observed soil water retention data. Results showed that dual‐porosity functions gave the most accurate or physically sound results in simulating the nitrous oxide (N2O) emissions and leachate nitrate nitrogen (NO3−‐N) concentrations, with the root‐mean‐square errors as 0.0043–0.0107 kg N/ha and 4.39–9.09 mg/L, respectively. This suggested that rock fragments could impact the soil N cycle by affecting soil hydraulic properties. Second, the model simulations in the first step were further corrected by the volumetric rock fragment contents. This correction significantly reduced the N2O emissions and NO3−‐N leaching by 25–43% and improved the simulations. This suggested that high rock fragment contents could reduce the N emission and leaching by decreasing the volume of soils participated in N cycle. Last, under the climate change, the NO3−‐N leaching were overestimated without considering the rock fragments, while simulation using regular sets of Denitrification–Decomposition was coincide to the real N2O emissions without physical meanings. Our findings suggested that rock fragments should be considered in soil N cycling studies in the stony‐soil areas.
Estimation of Spatial Gradients and Temporal Variations of the Total Electron Content Using Ground‐Based GNSS Measurements
Authors: Jakowski N. , Hoque M. M.
Published: February 2019

Precision and safety of life applications of Global Navigation Satellite Systems require key information on space weather conditions in particular on the perturbation degree of the ionosphere. Such systems are particularly vulnerable against severe spatial gradients and rapid changes of the total electron content (TEC) measured along different satellite‐receiver links. To estimate spatial gradients and rapid temporal variations of ionospheric TEC, two approaches are discussed. The Gradient Ionosphere indeX (GIX) and the Sudden Ionospheric Disturbance indeX are able to estimate the perturbation degree of the ionosphere instantaneously without taking into account previous measurements. The capabilities and accuracy of the index approaches are demonstrated by simulations using a 3‐D electron density model of the ionosphere and plasmasphere in conjunction with realistic Global Navigation Satellite Signal constellations. Real data tests confirm the applicability of GIX and the related standard deviation GIX Sigma to monitor spatial gradients. Sudden Ionospheric Disturbance indeX is able to monitor rapid temporal variations of TEC as exemplified by using Global Navigation Satellite Signal measurements carried out during solar flare events. Both approaches could identify enhanced space weather impacts on precise point positioning and the European Geostationary Navigation Overlay Service. More comprehensive studies analyzing ionospheric storms in close dialogue with potential customers are needed to fully utilize the potential of these approaches to serve as objective ionospheric indices for scaling horizontal TEC gradients and rapid TEC variations in space weather services.
Graphene oxide nanosheets coupled with paper microfluidics for enhanced on-site airborne trace metal detection
Authors: Sun Hao , Jia Yuan , Dong Hui , Fan Longxiang
Published: February 2019

Rapid on-site analysis of airborne trace metals has been heavily favored over traditional methodologies because air pollutants can be altered by environmental, behavioral, and social patterns at any given time and location. However, existing portable approaches are either not capable of performing integrated on-site analysis or not yet practically applicable. Exploiting graphene oxide (GO) in enhancing the analytical performance of paper-based colorimetric detection, for the first time, this paper reports the development of a practically useful portable system for accurate, sensitive on-site characterization of trace metals in ambient particulate matter (PM). The system consists of GO-nanosheet-coated paper devices, unmanned aerial vehicle multiaxial sampling, and cellphone-based colorimetric detection. The increased specific surface area and the homogeneity of color distribution from the coating of GO improves the accuracy and sensitivity of the assays. Additionally, by leveraging a Wi-Fi camera, a self-developed app and a sample pretreatment cartridge, metal in PM samples can be readily processed and characterized on-site within 30 min. The effects of chip geometric design, pH, reaction volume, and metal interference on detection results have been studied. The detection limits of the system were calibrated to be 16.6, 5.1, and 9.9 ng for metals Fe, Cu, and Ni, respectively, which are comparable to the detection limits of commercial inductively coupled plasma (ICP) instruments, thus making our portable system practically useful. Finally, the system was used for airborne trace-metal study at 6 locations in Fuzhou City (China), and the results obtained using our system demonstrated good agreement with those obtained by the ICP. The significance of our system in supplementing air pollution study and furthering research on rapid, accurate, on-site air toxicity assessment was demonstrated.
Multimodel inference for biomarker development: an application to schizophrenia
Authors: Cooper Jason D. , Han Sung Yeon Sarah , Tomasik Jakub , Ozcan Sureyya , Rustogi Nitin , van Beveren Nico J. M. , Leweke F. Markus , Bahn Sabine
Published: February 2019

In the present study, to improve the predictive performance of a model and its reproducibility when applied to an independent data set, we investigated the use of multimodel inference to predict the probability of having a complex psychiatric disorder. We formed training and test sets using proteomic data (147 peptides from 77 proteins) from two-independent collections of first-onset drug-naive schizophrenia patients and controls. A set of prediction models was produced by applying lasso regression with repeated tenfold cross-validation to the training set. We used feature extraction and model averaging across the set of models to form two prediction models. The resulting models clearly demonstrated the utility of a multimodel based approach to make good (training set AUC > 0.80) and reproducible predictions (test set AUC > 0.80) for the probability of having schizophrenia. Moreover, we identified four proteins (five peptides) whose effect on the probability of having schizophrenia was modified by sex, one of which was a novel potential biomarker of schizophrenia, foetal haemoglobin. The evidence of effect modification suggests that future schizophrenia studies should be conducted in males and females separately. Future biomarker studies should consider adopting a multimodel approach and going beyond the main effects of features.
Flavones hydroxylated at 5, 7, 3′ and 4′ ameliorate skin fibrosis via inhibiting activin receptor-like kinase 5 kinase activity
Authors: Zhang Yifan , Wang Jing , Zhou Sizheng , Xie Zhibo , Wang Chuandong , Gao Ya , Zhou Jia , Zhang Xiaoling , Li Qingfeng
Published: February 2019

Skin fibrosis is mainly characterized by excessive collagen deposition. Studies have recently identified a number of flavonoids with variable structures that have the potency of inhibiting collagen synthesis and thus attenuating organ fibrosis. In this study, we found that flavones with 5, 7, 3′, 4′ hydroxy substitution reduced collagen expression most efficiently. Among those flavones, luteolin, quercetin, and myricetin were selected for follow-up. In vivo, the three compounds ameliorated skin fibrosis and reduced collagen deposition. Further analysis showed the compounds had significant inhibition on the proliferation, activation and contractile ability of dermal fibroblasts in vitro and in vivo. More importantly, we revealed that luteolin, quercetin, and myricetin selectively downregulated the phosphorylation of Smad2/3 in TGF-β/Smads signaling via binding to activin receptor-like kinase 5 (ALK5) and impairing its catalytic activity. We also found flavones with 5, 7, 3′, 4′ hydroxy substitution showed stronger affinity with ALK5 compared with other flavonoids. Herein, we identified at least in part the underlying molecular basis as well as the critical structures that contribute to the antifibrotic bioactivity of flavones, which might benefit drug design and modification.
Redundant and receptor-specific activities of TRADD, RIPK1 and FADD in death receptor signaling
Authors: Füllsack Simone , Rosenthal Alevtina , Wajant Harald , Siegmund Daniela
Published: February 2019

We evaluated redundant and receptor-specific activities of TRADD, RIPK1, and FADD in RIPK3-expressing HeLa cells lacking expression of these proteins or any combination of two of these factors. We confirmed the opposing role of FADD in TNF- and TRAIL-induced necroptosis and observed an anti-necroptotic function of TRADD. RIPK1 and TRADD act in a redundant manner in TNF- but not TRAIL-induced apoptosis. Complementary, FADD proved to be sufficient for TRAIL- but not for TNF-induced apoptosis. TRADD and RIPK1, however, redundantly mediated proinflammatory signaling in response to TNF and TRAIL. FADD deficiency sensitized more efficiently for TNFR1-mediated necroptosis than caspase-8 deficiency pointing to a caspase-8 independent inhibitory activity of FADD on TNF-induced necroptosis. Based on these characteristics, we propose a model in which the death receptor-specific activities of TRADD, RIPK1, and FADD are traced back to their hierarchically different position in TNFR1- and TRAIL death receptor signaling.
Altered mitochondrial quality control in Atg7-deficient VSMCs promotes enhanced apoptosis and is linked to unstable atherosclerotic plaque phenotype
Authors: Nahapetyan Hripsimé , Moulis Manon , Grousset Elisa , Faccini Julien , Grazide Marie-Hélène , Mucher Elodie , Elbaz Meyer , Martinet Wim , Vindis Cécile
Published: February 2019

Vascular smooth muscle cells (VSMCs) are one of the main cellular determinants in arterial pathology. A large body of evidence indicates that death of VSMCs is associated with features of high-risk/vulnerable atherosclerotic plaques. Mitochondrial turnover is an essential aspect of the mitochondrial quality control in which dysfunctional mitochondria are selectively eliminated through autophagy and replaced through expansion of preexisting mitochondria. Even though successful autophagy promotes VSMC survival, it is unclear whether reduced autophagic flux affects mitochondrial quality control of VSMCs in atherosclerotic plaques. By using apolipoprotein E-deficient (ApoE−/−) mice carrying a VSMC-specific deletion of the essential autophagy gene Atg7, we show in the present study that impaired VSMC autophagy promotes an unstable plaque phenotype, as well as the accumulation of fragmented mitochondria with reduced bioenergetic efficiency and more oxidative stress. Furthermore, we demonstrate that disrupted autophagic flux is linked to defective mitophagy and biogenesis of mitochondria, which exacerbate VSMC apoptosis and in turn plaque vulnerability. Overall, our data indicate that mitochondrial quality control is a promising therapeutic target to stabilize atherosclerotic plaques.
Tomonaga–Luttinger liquid behavior and spinon confinement in YbAlO3
Authors: Wu L. S. , Nikitin S. E. , Wang Z. , Zhu W. , Batista C. D. , Tsvelik A. M. , Samarakoon A. M. , Tennant D. A. , Brando M. , Vasylechko L. , Frontzek M. , Savici A. T. , Sala G. , Ehlers G. , Christianson A. D. , Lumsden M. D. , Podlesnyak A.
Published: February 2019

Low dimensional quantum magnets are interesting because of the emerging collective behavior arising from strong quantum fluctuations. The one-dimensional (1D) S = 1/2 Heisenberg antiferromagnet is a paradigmatic example, whose low-energy excitations, known as spinons, carry fractional spin S = 1/2. These fractional modes can be reconfined by the application of a staggered magnetic field. Even though considerable progress has been made in the theoretical understanding of such magnets, experimental realizations of this low-dimensional physics are relatively rare. This is particularly true for rare-earth-based magnets because of the large effective spin anisotropy induced by the combination of strong spin–orbit coupling and crystal field splitting. Here, we demonstrate that the rare-earth perovskite YbAlO3 provides a realization of a quantum spin S = 1/2 chain material exhibiting both quantum critical Tomonaga–Luttinger liquid behavior and spinon confinement–deconfinement transitions in different regions of magnetic field–temperature phase diagram.
A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation
Authors: Hadzhiev Yavor , Qureshi Haseeb K. , Wheatley Lucy , Cooper Ledean , Jasiulewicz Aleksandra , Van Nguyen Huy , Wragg Joseph W. , Poovathumkadavil Divyasree , Conic Sascha , Bajan Sarah , Sik Attila , Hutvàgner György , Tora Làszlò , Gambus Agnieszka , Fossey John S. , Müller Ferenc
Published: February 2019

Most metazoan embryos commence development with rapid, transcriptionally silent cell divisions, with genome activation delayed until the mid-blastula transition (MBT). However, a set of genes escapes global repression and gets activated before MBT. Here we describe the formation and the spatio-temporal dynamics of a pair of distinct transcription compartments, which encompasses the earliest gene expression in zebrafish. 4D imaging of pri-miR430and zinc-finger-gene activities by a novel, native transcription imaging approach reveals transcriptional sharing of nuclear compartments, which are regulated by homologous chromosome organisation. These compartments carry the majority of nascent-RNAs and active Polymerase II, are chromatin-depleted and represent the main sites of detectable transcription before MBT. Transcription occurs during the S-phase of increasingly permissive cleavage cycles. It is proposed, that the transcription compartment is part of the regulatory architecture of embryonic nuclei and offers a transcriptionally competent environment to facilitate early escape from repression before global genome activation.
NADP+ is an endogenous PARP inhibitor in DNA damage response and tumor suppression
Authors: Bian Chunjing , Zhang Chao , Luo Tao , Vyas Aditi , Chen Shih-Hsun , Liu Chao , Kassab Muzaffer Ahmad , Yang Ying , Kong Mei , Yu Xiaochun
Published: February 2019

ADP-ribosylation is a unique posttranslational modification catalyzed by poly(ADP-ribose) polymerases (PARPs) using NAD+ as ADP-ribose donor. PARPs play an indispensable role in DNA damage repair and small molecule PARP inhibitors have emerged as potent anticancer drugs. However, to date, PARP inhibitor treatment has been restricted to patients with BRCA1/2 mutation-associated breast and ovarian cancer. One of the major challenges to extend the therapeutic potential of PARP inhibitors to other cancer types is the absence of predictive biomarkers. Here, we show that ovarian cancer cells with higher level of NADP+, an NAD+ derivative, are more sensitive to PARP inhibitors. We demonstrate that NADP+ acts as a negative regulator and suppresses ADP-ribosylation both in vitro and in vivo. NADP+ impairs ADP-ribosylation-dependent DNA damage repair and sensitizes tumor cell to chemically synthesized PARP inhibitors. Taken together, our study identifies NADP+ as an endogenous PARP inhibitor that may have implications in cancer treatment.
eg occupancy as an effective descriptor for the catalytic activity of perovskite oxide-based peroxidase mimics
Authors: Wang Xiaoyu , Gao Xuejiao J. , Qin Li , Wang Changda , Song Li , Zhou Yong-Ning , Zhu Guoyin , Cao Wen , Lin Shichao , Zhou Liqi , Wang Kang , Zhang Huigang , Jin Zhong , Wang Peng , Gao Xingfa , Wei Hui
Published: February 2019

A peroxidase catalyzes the oxidation of a substrate with a peroxide. The search for peroxidase-like and other enzyme-like nanomaterials (called nanozymes) mainly relies on trial-and-error strategies, due to the lack of predictive descriptors. To fill this gap, here we investigate the occupancy of eg orbitals as a possible descriptor for the peroxidase-like activity of transition metal oxide (including perovskite oxide) nanozymes. Both experimental measurements and density functional theory calculations reveal a volcano relationship between the eg occupancy and nanozymes’ activity, with the highest peroxidase-like activities corresponding to eg occupancies of ~1.2. LaNiO3-δ, optimized based on the eg occupancy, exhibits an activity one to two orders of magnitude higher than that of other representative peroxidase-like nanozymes. This study shows that the eg occupancy is a predictive descriptor to guide the design of peroxidase-like nanozymes; in addition, it provides detailed insight into the catalytic mechanism of peroxidase-like nanozymes.