bluuebunny/crossref_metadata_2025 huggingface dataset:
Matrix crosslinking enhances macrophage adhesion, migration, and inflammatory activation
Authors: Hsieh Jessica Y. , Keating Mark T. , Smith Tim D. , Meli Vijaykumar S. , Botvinick Elliot L. , Liu Wendy F.
Published: March 2019

Macrophages are versatile cells of the innate immune system that can adopt a variety of functional phenotypes depending on signals in their environment. In previous work, we found that culture of macrophages on fibrin, the provisional extracellular matrix protein, inhibits their inflammatory activation when compared to cells cultured on polystyrene surfaces. Here, we sought to investigate the role of matrix stiffness in the regulation of macrophage activity by manipulating the mechanical properties of fibrin. We utilize a photo-initiated crosslinking method to introduce dityrosine crosslinks to a fibrin gel and confirm an increase in gel stiffness through active microrheology. We observe that matrix crosslinking elicits distinct changes in macrophage morphology, integrin expression, migration, and inflammatory activation. Macrophages cultured on a stiffer substrate exhibit greater cell spreading and expression of αM integrin. Furthermore, macrophages cultured on crosslinked fibrin exhibit increased motility. Finally, culture of macrophages on photo-crosslinked fibrin enhances their inflammatory activation compared to unmodified fibrin, suggesting that matrix crosslinking regulates the functional activation of macrophages. These findings provide insight into how the physical properties of the extracellular matrix might control macrophage behavior during inflammation and wound healing.
Multireference Rayleigh–Schrödinger perturbation theory and its application
Authors: Yi Jiang , Chen Feiwu
Published: March 2019

Based on the complete active space multireference wavefunction, multireference Rayleigh–Schrödinger perturbation theory (MRSPT) is derived with the assumption that the orbital energies of active orbitals are the same as ε¯, an unknown parameter. In this work, ε¯ is optimized at the MRSPT2 level. The second and third order perturbation theories are shown numerically to be size extensive. The second order perturbation theory is exploited to compute the ground state energies of F2, AlH, HCl, and P2 and to optimize the equilibrium bond lengths and harmonic vibrational frequencies of BH, BF, P2, HF, and F2. The dissociation behaviors of NH3 and OH− have also been investigated. Comparisons with other theoretical models as well as the experimental data have been made to show advantages of the present theory.
A theoretical study of Ar8+-acetylene collisions at 1.2 MeV: Ionization and dissociation dynamics
Authors: Yu W. , Gao C.-Z. , Jiang T. , Zou Y. , Wang J.-G. , Wu Y. , Wei B.
Published: March 2019

We theoretically study Ar8+-induced dissociation of C2H2 molecule at 1.2 MeV using the time-dependent density-functional theory non-adiabatically coupled to nuclear dynamics. We find that molecular dissociation depends strongly on the ionization at the initial stage and the collision configuration. A detailed analysis shows a correspondence between the charge state of [C2H2]q+ and the final fragments. A remarkable impact parameter effect provides deep insights of bond breakup and electronic transport. We analyze two typical sequential dissociation channels reported in experiments by tracking structural and electronic dynamics in real time. Our results provide better understanding of experiments. Moreover, the comparison between various exchange-correlation functionals reveals that electrons’ correlation and self-interaction do not significantly impact the initial ionization and fragment distribution in the present study.
Microwave metamaterial absorber based on aqueous electrolyte solution for X-band application
Authors: Gogoi Dhruba Jyoti , Bhattacharyya Nidhi Saxena
Published: March 2019

Metamaterial absorber is investigated by using an aqueous electrolyte solution as a meta-“atom.” For the first time, an aqueous electrolyte solution of Aluminum Chloride (AlCl3) is used as a fluid filler for a periodic rectangular metastructure. Aqueous solutions of varying molarity (0.5, 1.0, 1.5, 2.0, and 2.5M) are encapsulated inside a flexible silicone rubber sheet to develop a meta-“atom” and realized as a resonating microwave metamaterial absorber backed with copper. The complex material permittivities of the electrolyte solutions are measured at an X-band (8.2–12.4 GHz) frequency region. A unit cell is designed and its parameters are optimized in a computer simulation software microwave studio suite to enhance a wide absorption bandwidth with 90% absorption efficiency throughout the X-band region. Additionally, the proposed absorber shows a polarization insensitive absorption along with a wide-incident angle absorption for both TM and TE waves. The resonance and absorption mechanisms are investigated with the help of electric field, magnetic field, current density and penetration depth of microwave into the electrolyte solution. The experimental absorption performance is carried out in an ideal waveguide environment.
Quantitative quantum mechanical approach to SABRE hyperpolarization at high magnetic fields
Authors: Knecht Stephan , Ivanov Konstantin L.
Published: March 2019

A theoretical approach is proposed for quantitative modeling of SABRE (Signal Amplification by Reversible Exchange) experiments performed using an NMR spectrometer at a high magnetic field. SABRE is a method that exploits the spin order of parahydrogen (the H2 molecule in its nuclear singlet state) for hyper-polarizing the spins of various substrates to enhance their NMR signals. An important feature of SABRE is that the substrate is not modified chemically; instead, spin order transfer takes place in a transient complex with parahydrogen. In high-field SABRE experiments, such a transfer is achieved by using suitable NMR excitation schemes. The approach presented here can explicitly treat the spin dynamics in the SABRE complex as well as the kinetics of substrate exchange (between the free and bound form) and complex interplay of spin evolution and chemical processes. One more important effect included in the model is the alteration of the spin state of parahydrogen giving rise to the formation of anti-phase spin order from the initial singlet order. Such a treatment enables a detailed analysis of known high-field SABRE schemes, quantitative comparison with experiments, and elucidation of the key factors that limit the resulting NMR signal enhancement.
The effect of polymorphism on the structural, dynamic and dielectric properties of plastic crystal water: A molecular dynamics simulation perspective
Authors: Skarmoutsos Ioannis , Mossa Stefano , Guardia Elvira
Published: March 2019

We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, particularly in the face-centered-cubic phase. The calculated hydrogen bond statistics and dynamics provide further indications of the existence of a strongly heterogeneous and rapidly interconverting local orientational structural network in both polymorphs. We have observed a hindered molecular rotation, much more pronounced in the body-centered-cubic phase, which is reflected by the decay of the fourth-order Legendre reorientational correlation functions and angular Van Hove functions. Molecular rotation, however, is additionally hindered in the high-pressure liquid compared to the plastic crystal phase. The results obtained also reveal significant differences in the dielectric properties of the polymorphs due to the different dipolar orientational correlation characterizing each phase.
Enhanced imbibition from the cooperation between wetting and inertia via pulsatile forcing
Authors: Flores Gerónimo J. , Hernández-Machado A. , Corvera Poiré E.
Published: March 2019

We study the dynamics of microfluidic interfaces driven by pulsatile pressures in the presence of neutral and hydrophilic walls. For this, we propose a new phase field model that takes inertia into account. For neutral wetting, the interface dynamics is characterized by a response function that depends on a non-dimensional frequency, which involves the time scale associated with inertia. We have found a regime, for large values of this non-dimensional frequency, in which inertia is relevant, and our model is necessary for a correct description of the dynamics. For hydrophilic walls, the dynamics of the contact line with pulsatile forcing is basically undistinguishable to the dynamics of imbibition solely due to wetting. However, we observe that the presence of inertia causes the interface to advance faster than in the absence of pulsatile forcing. This is because pulsatile forcing induces inertia at the bulk to cooperate with wetting creating an enhancement of the imbibition process. We characterize this complex dynamics with transitory exponents that, at early times, are larger than the Washburn ones, and tend to the Washburn exponent at long times, when the interface feels less and less the driving force applied at the entrance of the microchannel, and the dynamics is dominated solely by wetting.
Harmonic linearized Navier-Stokes equation on describing the effect of surface roughness on hypersonic boundary-layer transition
Authors: Zhao Lei , Dong Ming , Yang Yanguang
Published: March 2019

Laminar-turbulent transition is crucially influenced by wall roughness. This paper develops a numerical approach based on the harmonic linearized Navier-Stokes (HLNS) equations to accommodate the scattering effect of the rapidly distorted mean flow induced by a two-dimensional hump or indentation at the wall on the oncoming instability modes (including the Mack first and second modes) in a hypersonic boundary layer. Due to the ellipticity of the scattering system when the roughness width is comparable with the instability wavelength, the traditional linear stability theory and the linear parabolized stability equation do not apply, and therefore, the HLNS approach has advantages in both accuracy and efficiency. The impact of a roughness is characterized by a transmission coefficient, which is the ratio of the asymptotic amplitude downstream of the roughness to that upstream. At a Mach number of 5.92, the dependence of the transmission coefficient on the frequency and the oblique angle of the oncoming mode and the size and location of the hump/indentation is studied systematically. It is confirmed that the synchronization frequency appears as a critical frequency, above and below which the oncoming instability modes are suppressed and enhanced by the roughness, respectively, which provides fundamental basis to the laminar-flow control in hypersonic boundary layers.
Importance of van der Waals effects on the hydration of metal ions from the Hofmeister series
Authors: Zhou Liying , Xu Jianhang , Xu Limei , Wu Xifan
Published: March 2019

The van der Waals (vdW) interaction plays a crucial role in the description of liquid water. Based on ab initio molecular dynamics simulations, including the non-local and fully self-consistent density-dependent implementation of the Tkatchenko-Scheffler dispersion correction, we systematically studied the aqueous solutions of metal ions (K+, Na+, and Ca2+) from the Hofmeister series. Similar to liquid water, the vdW interactions strengthen the attractions among water molecules in the long-range, leading to the hydrogen bond networks softened in all the ion solutions. However, the degree that the hydration structure is revised by the vdW interactions is distinct for different ions, depending on the strength of short-range interactions between the hydrated ion and surrounding water molecules. Such revisions by the vdW interactions are important for the understanding of biological functionalities of ion channels.
Gyrokinetic investigations on entropy modes in dipole magnetic field confined plasmas with an anisotropic temperature
Authors: Qian Liang , Wang Zhibin , Wang Xiaogang
Published: March 2019

Entropy modes are typical instabilities particularly seen in dipole field confined plasmas. In this paper, linear gyrokinetic calculations, together with the integral dispersion relation method, are applied to study the electrostatic entropy mode in such plasmas with an anisotropic temperature. The numerical approach is verified for certain typical conditions with previous studies. We then further focus on the anisotropic temperature effect on the entropy mode. Basic characteristics of the entropy mode are obtained with the effect. The results show that the entropy mode has a peak growth rate at kρi ∼ 1, and the mode is shifted from the ion to the electron diamagnetic regimes at small k⊥ρi. This work can be applied for various dipole magnetic field confined plasmas as well as certain other configurations, such as Z-pinch and field reversed configurations.
Effects of strontium doping on the morphological, structural, and photophysical properties of FASnI3 perovskite thin films
Authors: Adjokatse Sampson , Kahmann Simon , Duim Herman , Loi Maria Antonietta
Published: March 2019

Doping engineering has been an effective technique applied extensively to enrich semiconductors and modulate their fundamental properties for electronic and optoelectronic applications. In this work, we report the influence of strontium (Sr) doping on solution-processed formamidinium tin iodide (FASnI3) perovskite thin films. We show that the addition of the Sr2+ dopant to the host perovskite drastically changes the morphology of the material but has no significant effect on the structural phase for doping concentrations lower than 10%. Using photoluminescence spectroscopy, we showed that for doping contents below 15%, the film is heterogeneously doped and strontium predominantly resides at the surface of the film. Above 15% of Sr, the bulk of the material is significantly doped. Our results show that Sr doping into FASnI3 perovskite can be a route for the attainment of new perovskites with interesting physical properties.
Single-crystalline Cu2O thin films of optical quality as obtained by the oxidation of single-crystal Cu thin films at low temperature
Authors: Ha Taewoo , Park Inhee , Sim Kyung Ik , Lee Howon , Bae Jong-Sung , Kim Su Jae , Kim Jong Phil , Kim Teun-Teun , Kim Jae Hoon , Jang Joon Ik , Jeong Se-Young
Published: March 2019

High-quality, single-crystal-like Cu2O thin films of various thicknesses (10 nm–45 nm) were prepared at a low temperature (150 °C) by controlling layer-by-layer oxidation of wafer-scale Cu thin films sputtered along the (111) direction using a pure single-crystal Cu target. The cross-sectional images of the thin films reveal high crystallinity of Cu2O layers except for 60° twinning in the sequential stacking order as evidenced by high-resolution transmission electron microscopy, which is consistent with the absence of the photoluminescence (PL) signals arising from atomic-scale vacancies. The optical properties of our Cu2O films were investigated using temperature-dependent PL and Raman spectroscopy. All of the Cu2O thin films exhibit characteristic band-to-band transitions together with the series of yellow excitonic transitions slightly below the fundamental bandgap. The spectral locations for the PL are approximately consistent with those for the bulk counterpart. The excellent optical quality of our Cu2O was further demonstrated by significantly reduced quasi-direct transition that occurs at symmetry-breaking crystal imperfection, which relaxes the stringent momentum conservation rule. We identified the three main Raman scattering modes of the Cu2O thin films, where the two forbidden modes of Γ15(1) and Γ12−+Γ25− are resonantly allowed by the proximity of the incident photon energy to the green bandgap. We believe that our synthesis technique can be utilized for the preparation of single-crystal-like metal oxide thin films at low production temperatures with precise thickness control for the development of novel optoelectronic devices and for the exploration of the nanoscale light-matter interaction as well.
Challenges and opportunities in exosome research—Perspectives from biology, engineering, and cancer therapy
Authors: Li Xia , Corbett Alexander L. , Taatizadeh Erfan , Tasnim Nishat , Little Jonathan P. , Garnis Cathie , Daugaard Mads , Guns Emma , Hoorfar Mina , Li Isaac T. S.
Published: March 2019

Exosomes are small (∼30–140 nm) lipid bilayer-enclosed particles of endosomal origin. They are a subset of extracellular vesicles (EVs) that are secreted by most cell types. There has been growing interest in exosome research in the last decade due to their emerging role as intercellular messengers and their potential in disease diagnosis. Indeed, exosomes contain proteins, lipids, and RNAs that are specific to their cell origin and could deliver cargo to both nearby and distant cells. As a result, investigation of exosome cargo contents could offer opportunities for disease detection and treatment. Moreover, exosomes have been explored as natural drug delivery vehicles since they can travel safely in extracellular fluids and deliver cargo to destined cells with high specificity and efficiency. Despite significant efforts made in this relatively new field of research, progress has been held back by challenges such as inefficient separation methods, difficulties in characterization, and lack of specific biomarkers. In this review, we summarize the current knowledge in exosome biogenesis, their roles in disease progression, and therapeutic applications and opportunities in bioengineering. Furthermore, we highlight the established and emerging technological developments in exosome isolation and characterization. We aim to consider critical challenges in exosome research and provide directions for future studies.
Design of BCP buffer layer for inverted perovskite solar cells using ideal factor
Authors: Shibayama Naoyuki , Kanda Hiroyuki , Kim Tae Woong , Segawa Hiroshi , Ito Seigo
Published: March 2019

In the inverted structure perovskite solar cells, a buffer layer is generally used at the interface between the n-type semiconductor layer and the metal electrode, but its design guidelines have not yet been established. Here, a series of inverted perovskite solar cells have been fabricated with the controlled thickness of bathocuproine (BCP) buffer layers deposited by thermal evaporation and validated the BCP buffer layer evaluation tool. The ideal factor was calculated from the gradient in the plot of Voc against the log of Jsc, and the effect of the BCP buffer layer on charge recombination was verified. Since the ideal factor greatly decreased from 5 to 1.4 by introducing the BCP buffer layer, it was confirmed that the interface between the n-type semiconductor layer and the metal electrode gradually changed from a Schottky barrier diode to an ohmic contact. On the other hand, it was found that an excessive BCP film thickness causes the series resistance to increase and induced recombination. Finally, as a result of optimizing the perovskite layer and the BCP buffer layer, respectively, the performance exceeding 17% was obtained. This study provides insight into the improvements in the conversion efficiency of perovskite solar cells by optimizing the thickness of the buffer layer using the ideal factor.
On the inherent bias of swirling strength in defining vortical structure
Authors: Bernard Peter S.
Published: March 2019

The traditional practice of using rotational motion as the principal attribute of coherent vortical structures in the buffer region of near-wall turbulent flow is shown to create a biased accounting of the role of vorticity within the structures. Vorticity associated with rotation is given a favored consideration against vorticity that is equally strong but not associated with rotation. Using data from a highly resolved direct numerical simulation of channel flow, it is shown that describing the structures based on the properties of the rotational field leads to a distorted view of the actual structures that are present. As a practical matter, this means that where hairpins are typically considered to be the flow structures, a more accurate description of the coherent events is that they are elongated mushroom-shaped vortical objects ejecting over low speed streaks. In this, hairpin-shaped rotational regions are embedded in the lobes of the mushrooms.
The effects of post-fire forest management on soil erosion rates 3 and 4 years after a wildfire, demonstrated on the 2010 Mount Carmel fire
Authors: Zituni Rami , Wittenberg Lea , Malkinson Dan
Published: March 2019

During 2–5 December 2010, an area of 2500ha in the Carmel forests was consumed by a severe wildfire, causing soil erosion from the exposed slopes. Whereas most studies show that post-fire erosion rates tend to decline after the second year, in this case, we aim to address the ongoing consequences that different management practices had on soil erosion 3 and 4 years after a fire. Three management operations were applied: (a) preservation management (PM) – mulching wood chips on the burned area; (b) tree-clearing management (TCM) – burned trees were cut and removed; and (c) skid-trail formation (ST) – provisional pathways were formed while trees were dragged outside. Consequently, the objectives of the study were: (1) to monitor the effects of these post-fire practices 3 and 4 years after fire; and (2) to characterise the physical features of the eroded soil. The sediments were collected after every effective rain event over two rainy seasons (2013–14, 2014–15). TCM and ST practices resulted in significantly elevated soil-erosion yields compared to PM. The sediments following PM had a high percentage of fine material. Furthermore, PM had an evident positive effect on the soil, whereas all other practices inhibited vegetation renewal and system rehabilitation.
LGR4 is essential for R-spondin1-mediated suppression of food intake via pro-opiomelanocortin
Authors: Otsuka Ayano , Jinguji Ayana , Maejima Yuko , Kasahara Yoshiyuki , Shimomura Kenju , Hidema Shizu , Nishimori Katsuhiko
Published: March 2019

Leucine-rich repeat-containing G-protein coupled receptor 4 (LGR4) suppresses food intake after its activation by binding of its ligands, R-spondins. We investigated the mechanism of food intake suppression by R-spondin1 in a region-specific Lgr4 gene knockout (LGR4 cKO) mouse model, generated by deletion of the Lgr4 gene in arcuate nucleus (ARC) using Lgr4fx/fx mice combined with infection of an AAV-Cre vector. After R-spondin1 administration, LGR4 cKO mice didn’t exhibit a suppressed appetite, compared to that in control mice, which received a vehicle. In ARC of LGR4 cKO mice, Pomc mRNA expression was reduced, leading to suppressed food intake. On the other hand, neurons-specific LGR4 KO mice exhibited no differences in Pomc expression, and no structural differences were observed in the ARC of mutant mice. These results suggest that LGR4 is an essential part of the mechanism, inducing Pomc gene expression with R-spondin1 in ARC neurons in mice, thereby regulating feeding behavior.

Abbreviations: LGR4: Leucine-rich repeat-containing G-protein coupled receptor 4; RSPOs: roof plate-specific spondins; ARC: arcuate nucleus; AAV: adeno associated virus; POMC: pro-opiomelanocortin; CART: cocaine and amphetamine-regulated transcript; NPY: neuropeptide Y; AgRP: agouti-related peptide; Axin2: axis inhibition protein 2; Lef1: lymphoid enhancer binding factor 1; ccnd1: cyclin D1
Identification of the targets of HbEIN3/EILs in genomic wide in Hevea brasiliensis
Authors: Wang Qichao , Xu Gang , Zhai Jinling , Yuan Hongmei , Huang Xi
Published: March 2019

EIN3/EILs are key regulators in ET signaling pathway. In this work, 4 members of EIN3/EILs of Hevea brasiliensis (HbEIN3/EILs) showed interaction with two F box proteins, HbEBF1 and HbEBF2. HbEIN3 located in nucleus and exhibited strong transcriptional activity. HbEIN3 was induced by ET treatment in C-serum, but not in B-serum of latex. HbEIN3/EILs bound to G-box cis-element. To globally search the potential targets of HbEIN3/EILs, genomic sequences of H. brasiliensis was re-annotated and an HCES (Hevea Cis-Elements Scanning) program was developed (www.h-brasiliensis.com). HCES scanning results showed that ET- and JA- responsive cis-elements distribute overlapping in gene promoters. 3146 genes containing G-box in promoters are potential targets of HbEIN3, including 41 genes involved in biosynthesis and drainage of latex, of which 7 rate-limiting genes of latex production were regulated by both ET and JA, suggesting that ET and JA signaling pathways coordinated the latex biosynthesis and drainage in H. brasiliensis.

Abbreviations: ABRE: ABA responsive elements; bHLH: basic helix-loop-helix; COG: Orthologous Groups; DRE: dehydration response element; ERE: ethylene responsive element; ET: Ethylene; GO: Gene Ontology; HCES: Hevea Cis-Elements Scanning; JA: jasmonates; JRE: Jasmonate-responsive element; KEGG: Kyoto Encyclopedia of Genes and Genomes; NR: non-redundant database; PLACE: Plant Cis-acting Regulatory DNA Elements; qRT-PCR: quantitative real-time RT-PCR.
The financialisation of transnational family care: a study of UK-based senders of remittances to Ghana and Nigeria
Authors: Yeates Nicola , Owusu-Sekyere Freda
Published: March 2019

Transnational families occupy centre-stage in literatures on transformations in the social organisation and relations of care and welfare because they express how social bonds are sustained despite geographical separation. This paper examines some key themes arising from a research study into remittance-sending practices of UK-based Ghanaians and Nigerians in the light of research literatures on transnational family care and development finance. The data comprises qualitative interviews with 20 UK-based Ghanaian and Nigerian people who regularly send remittances to their families ‘back home’. This paper discusses a social issue that arises from the transnationalisation of family structures and relations, when migrant family members are positioned within family networks as ‘absent providers’, and familial relations eventually become financialised. The findings show the complexities of transnational living, the hardships endured by remittance-senders and the particular strains of remittance-mediated family relationships. The financialisation of family relations affects the social subjectivity and positioning of remittance-senders within the family. Strain and privation are integral to participants’ experiences of transnational family life, while themes of deception, betrayal, and expatriation also feature. The suppression of emotion is a feature of the significant labour inputs participants make in sustaining relationships within transnational families. The paper considers UK social policy implications of the findings.
Assessment of 3D motion modeling performance for dose accumulation mapping on the MR-linac by simultaneous multislice MRI
Authors: Borman P T S , Bos C , Stemkens B , Moonen C T W , Raaymakers B W , Tijssen R H N
Published: March 2019

Hybrid MR-linac systems enable intrafraction motion monitoring during radiation therapy. Since time-resolved 3D MRI is still challenging, various motion models have been developed that rely on time-resolved 2D imaging. Continuous validation of these models is important for accurate dose accumulation mapping. In this study we used 2D simultaneous multislice (SMS) imaging to improve the PCA-based motion modeling method developed previously (Stemkens et al 2016 Phys. Med. Biol. 61 5335–55). From the additional simultaneously acquired slices, several independent motion models could be generated, which allowed for an assessment of the sensitivity of the motion model to the location of the time-resolved 2D slices. Additionally, the best model could be chosen at every time-point, increasing the method’s robustness.

Imaging experiments were performed in six healthy volunteers using three simultaneous slices, which generated three independent models per volunteer. For each model the motion traces of the liver tip and both kidneys were estimated. We found that the location of the 2D slices influenced the model’s error in five volunteers significantly with a p -value  <0.05, and that selecting the best model at every time-point can improve the method. This allows for more accurate and robust motion characterization in MR-guided radiotherapy.
Community-based monitoring of Indigenous food security in a changing climate: global trends and future directions
Authors: Lam Steven , Dodd Warren , Skinner Kelly , Papadopoulos Andrew , Zivot Chloe , Ford James , Garcia Patricia J , Harper Sherilee L
Published: March 2019

Climate change is expected to exacerbate existing food security challenges, especially in Indigenous communities worldwide. Community-based monitoring (CBM) is considered a promising strategy to improve monitoring of, and local adaptation to climatic and environmental change. Yet, it is unclear how this approach can be applied in food security or Indigenous contexts. The objectives of this paper are to: (1) review and synthesize the published literature on CBM of Indigenous food security; and, (2) identify gaps and trends in these monitoring efforts in the context of climate change. Using a systematic search and screening process, we identified 86 published articles. To be included, articles had to be published in a journal, describe a CBM system, describe any aspect of food security, and explicitly mention an Indigenous community. Relevant articles were thematically analyzed to characterize elements of CBM in the context of climate change. Results show that the number of articles published over time was steady and increased more than two-fold within the last five years. The reviewed articles reported on monitoring mainly in North America (37%) and South America (28%). In general, monitoring was either collaborative (51%) or externally-driven (37%), and focused primarily on tracking wildlife (29%), followed by natural resources (16%), environmental change (15%), fisheries (13%), climate change (9%), or some combination of these topics (18%). This review provides an evidence-base on the uses, characteristics, and opportunities of CBM, to guide future food security monitoring efforts in the context of climate change.
PIV measurement of internal flow in mini centrifugal pump
Authors: Shigemitsu T , Ogawa Y , Nakaishi E
Published: March 2019

The diameter of the ventricular assist pump and cooling pump for electrical devices like servers is about a dozen millimetres and these kinds of pumps belong to the mini pump. The internal flow condition of the mini centrifugal pump has to be clarified because there are so many types of mini pumps according to special specifications and shapes. Therefore, in this research, an open impeller was adopted as a mini centrifugal pump with 55mm impeller diameter in consideration of reduction in impeller manufacturing cost and its internal flow was investigated. Since the outlet angle of the test impeller is large, the maximum efficiency flow rate moves to a large flow rate and the relatively high head and efficiency were obtained in large flow rate region. In the present paper, the velocity and vorticity distribution near the volute tongue are shown and the internal flow in the mini centrifugal pump is clarified based on the PIV measurement results.
Symmetry of the KP-type solitary waves
Authors: Esfahani Amin , Levandosky Steve
Published: March 2019

In this paper, we study the behavior of the solitary waves of the rotation-modified Kadomtsev-Petviashvili equation. By knowing the symmetry of solitary waves in the transverse direction, we improve the previous results and show that these solutions are also symmetric with respect to the direction of propagation.
On the local time process of a skew Brownian motion
Authors: Borodin Andrei , Salminen Paavo
Published: March 2019

We derive a Ray–Knight type theorem for the local time process (in the space variable) of a skew Brownian motion up to an independent exponential time. It is known that the local time seen as a density of the occupation measure and taken with respect to the Lebesgue measure has a discontinuity at the skew point (in our case at zero), but the local time taken with respect to the speed measure is continuous. In this paper we discuss this discrepancy by characterizing the dynamics of the local time process in both of these cases. The Ray–Knight type theorem is applied to study integral functionals of the local time process of the skew Brownian motion. In particular, we determine the distribution of the maximum of the local time process up to a fixed time, which can be seen as the main new result of the paper.
Pinetree: a step-wise gene expression simulator with codon-specific translation rates
Authors: Jack Benjamin R , Wilke Claus O
Published: March 2019

Motivation

Stochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programing interfaces, which limit their utility.

Results

We present Pinetree, a step-wise gene expression simulator with codon-specific translation rates. Pinetree models both transcription and translation in a stochastic framework with individual polymerase and ribosome-level detail. Written in C++ with a Python front-end, any user familiar with Python can specify a genome and simulate gene expression. Pinetree was designed to be efficient and scale to simulate large plasmids or viral genomes.

Availability and implementation

Pinetree is available on GitHub (https://github.com/benjaminjack/pinetree) and the Python Package Index (https://pypi.org/project/pinetree/).
Determining parameters for non-linear models of multi-loop free energy change
Authors: Ward Max , Sun Hongying , Datta Amitava , Wise Michael , Mathews David H
Published: March 2019

Motivation

Predicting the secondary structure of RNA is a fundamental task in bioinformatics. Algorithms that predict secondary structure given only the primary sequence, and a model to evaluate the quality of a structure, are an integral part of this. These algorithms have been updated as our model of RNA thermodynamics changed and expanded. An exception to this has been the treatment of multi-loops. Although more advanced models of multi-loop free energy change have been suggested, a simple, linear model has been used since the 1980s. However, recently, new dynamic programing algorithms for secondary structure prediction that could incorporate these models were presented. Unfortunately, these models appear to have lower accuracy for secondary structure prediction.

Results

We apply linear regression and a new parameter optimization algorithm to find better parameters for the existing linear model and advanced non-linear multi-loop models. These include the Jacobson-Stockmayer and Aalberts & Nandagopal models. We find that the current linear model parameters may be near optimal for the linear model, and that no advanced model performs better than the existing linear model parameters even after parameter optimization.

Availability and implementation

Source code and data is available at https://github.com/maxhwardg/advanced_multiloops.

Supplementary information

Supplementary data are available at Bioinformatics online.
RTNsurvival: an R/Bioconductor package for regulatory network survival analysis
Authors: Groeneveld Clarice S , Chagas Vinicius S , Jones Steven J M , Robertson A Gordon , Ponder Bruce A J , Meyer Kerstin B , Castro Mauro A A
Published: March 2019

Motivation

Transcriptional networks are models that allow the biological state of cells or tumours to be described. Such networks consist of connected regulatory units known as regulons, each comprised of a regulator and its targets. Inferring a transcriptional network can be a helpful initial step in characterizing the different phenotypes within a cohort. While the network itself provides no information on molecular differences between samples, the per-sample state of each regulon, i.e. the regulon activity, can be used for describing subtypes in a cohort. Integrating regulon activities with clinical data and outcomes would extend this characterization of differences between subtypes.

Results

We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles using transcriptional networks reconstructed by the RTN package, gene expression data, and a two-tailed Gene Set Enrichment Analysis. Given regulon activity profiles across a cohort, RTNsurvival can perform Kaplan-Meier analyses and Cox Proportional Hazards regressions, while also considering confounding variables. The Supplementary Information provides two case studies that use data from breast and liver cancer cohorts and features uni- and multivariate regulon survival analysis.

Availability and implementation

RTNsurvival is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNsurvival/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Molecular profiling demonstrates modulation of immune cell function and matrix remodeling during luteal rescue†
Authors: Hughes Camilla K , Maalouf Samar W , Liu Wan-Sheng , Pate Joy L
Published: March 2019

The corpus luteum (CL) is essential for maintenance of pregnancy in all mammals and luteal rescue, which occurs around day 16–19 in the cow, is necessary to maintain luteal progesterone production. Transcriptomic and proteomic profiling were performed to compare the day 17 bovine CL of the estrous cycle and pregnancy. Among mRNA and proteins measured, 140 differentially abundant mRNA and 24 differentially abundant proteins were identified. Pathway analysis was performed using four programs. Modulated pathways included T cell receptor signaling, vascular stability, cytokine signaling, and extracellular matrix remodeling. Two mRNA that were less in pregnancy were regulated by prostaglandin F2A in culture, while two mRNA that were greater in pregnancy were regulated by interferon tau. To identify mRNA that could be critical regulators of luteal fate, the mRNA that were differentially abundant during early pregnancy were compared to mRNA that were differentially abundant during luteal regression. Eight mRNA were common to both datasets, including mRNA related to regulation of steroidogenesis and gene transcription. A subset of differentially abundant mRNA and proteins, including those associated with extracellular matrix functions, were predicted targets of differentially abundant microRNA (miRNA). Integration of miRNA and protein data, using miRPath, revealed pathways such as extracellular matrix–receptor interactions, abundance of glutathione, and cellular metabolism and energy balance. Overall, this study has provided a comprehensive profile of molecular changes in the corpus luteum during maternal recognition of pregnancy and has indicated that some of these functions may be miRNA-regulated.
MiR-664-2 impacts pubertal development in a precocious-puberty rat model through targeting the NMDA receptor-1†
Authors: Ju Minda , Yang Liu , Zhu Jing , Chen Zhejun , Zhang Mizhen , Yu Jin , Tian Zhanzhuang
Published: March 2019

Precocious puberty (PP) commonly results from premature activation of the hypothalamic–pituitary–gonadal axis (HPGA). Gonadotropin-releasing hormone (GnRH) is the initial trigger for HPGA activation and plays an important role in puberty onset. N-methyl-D-aspartate (NMDA) can promote pulsatile GnRH secretion and accelerates puberty onset. However, the mechanism of N-methyl-D-aspartate receptors (NMDARs) in PP pathogenesis remains obscure. We found that serum GnRH, luteinizing hormone (LH), follicle-stimulating hormone (FSH), estrogen (E2) levels, hypothalamic NMDAR1, and GnRH mRNA expression peaked at the vaginal opening (VO) day. Next, the hypothalamic NMDAR1 mRNA and protein levels in rats treated with danazol, a chemical commonly effecting on the reproductive system, were significantly increased at the VO day (postnatal day 24) compared to controls, accompanied by enhanced serum GnRH, LH, FSH, and E2 levels. Further, microRNA-664-2 (miR-664-2) was selected after bioinformatics analysis and approved in primary hypothalamic neurons, which binds to the 3′-untranslated regions of NMDAR1. Consistently, the miR-664-2 expression in hypothalamus of the Danazol group was decreased compared to Vehicle. Our results suggested that attenuated miR-664-2 might participate in PP pathogenesis through enhancing the NMDAR1 signaling.
Comparison of different algorithms for the assessment of cardiovascular risk after kidney transplantation by the time of entering waiting list
Authors: Herzog Anna Laura , Kalogirou Charis , Wanner Christoph , Lopau Kai
Published: March 2019

Background

The prevalence of cardiovascular disease is high among patients with chronic kidney disease and cardiovascular events (CVE) remain the leading cause of death after kidney transplantation (KT). We performed a retrospective analysis of 389 KT recipients to assess if the European Society of Cardiology Score (ESC-Score), Framingham Heart Study Score (FRAMINGHAM), Prospective Cardiovascular Munster Study Score (PROCAM-Score) or Assessing cardiovascular risk using Scottish Intercollegiate Guidelines Network Score (ASSIGN-Score) algorithms can predict cardiovascular risk after KT at the time of entering the waiting list.

Methods

389 KT candidates were scored by the time of entering the waiting list. Pearsons chi-square test, cox regression analysis and survival estimates were performed to evaluate the reliability of the cardiovascular scoring models after successful KT.

Results

During a follow-up of 8 ± 5.8 years, 96 patients (30%) died due to cardiovascular problems, whereas 13.9% suffered non-fatal CVE. Graft loss occurred in 84 patients (21.6%). Predictors of CVE, survival and graft loss were age and the length of end-stage kidney disease. All scores performed well in assessing the risk for CVE (P < 0.01). Receiver-operating characteristic analysis using the ESC-SCORE, as an example, suggested a cut-off for risk stratification and clinical decisions.

Conclusions

We found all tested scores were reliable for cardiovascular assessment. We suggest using cardiac scores for risk assessment before KT and then taking further steps according to current guidelines.
Propensity-matched comparison of the long-term outcome of the Nunn and two-patch techniques for the repair of complete atrioventricular septal defects
Authors: Bell Douglas , Thakeria Priyanka , Betts Kim , Justo Robert , Jalali Homayoun , Wijesekera Vishva , Venugopal Prem , Karl Tom , Alphonso Nelson
Published: March 2019

OBJECTIVES

To compare the long-term performance of the Nunn and 2-patch techniques for the repair of complete atrioventricular septal defects.

METHODS

Between January 1995 and December 2015, a total of 188 patients (Nunn n = 41; 2-patch n = 147) were identified from hospital databases. Univariable Cox regression was performed to calculate the risk of reintervention in each group. Propensity score matching was used to balance the Nunn group and the 2-patch group.

RESULTS

Baseline characteristics including age at surgery, weight, trisomy 21, other cardiac anomalies, previous operations and preoperative atrioventricular valve regurgitation did not differ between the 2 groups. Overall, there was no difference in mortality between the 2 groups (P = 0.43). Duration of cardiopulmonary bypass (CPB) and myocardial ischaemia time were 29 min (P < 0.001) and 28 min (P < 0.001) longer, respectively, in the 2-patch group. Median follow-up was 10.8 years (2–21 years). Unadjusted Cox regression did not reveal a significant difference in the risk of reoperation for either group 9 years after initial surgery [hazard ratio (HR) (Nunn) 0.512, 95% confidence interval 0.176–1.49; Nunn 89%; 2-patch 82%]. This finding was reiterated from Cox regression performed on the propensity-matched sample (31 pairs). The probability of freedom from moderate or worse left atrioventricular valve regurgitation or left ventricular outflow obstruction was similar in the 2 groups.

CONCLUSIONS

The Nunn and 2-patch techniques are comparable in terms of the long-term mortality and probability of freedom from reoperation, moderate or severe left atrioventricular valve regurgitation and left ventricular outflow obstruction. However, the duration of CPB and myocardial ischaemia is longer in the 2-patch group.
Income Mobility and Moving to a Better Neighbourhood: An Enquiry into Ethnic Differences in Finland
Authors: Vaalavuo Maria , van Ham Maarten , Kauppinen Timo M
Published: March 2019

The spatial concentration of immigrants in disadvantaged neighbourhoods may hinder their opportunities for social and economic integration. It is therefore important that immigrants can translate their available economic resources into mobility to less disadvantaged neighbourhoods. This study adds to existing research on the relationship between socioeconomic and spatial integration by focusing on the effects of income mobility on residential mobility. We analyse intra-urban residential mobility from low-income neighbourhoods into non-low-income neighbourhoods among immigrants and native-born residents in three urban regions in Finland. We use longitudinal register data for the 2004–2014 period for the full population, allowing a dynamic analysis of changes in income and neighbourhood of residence. Based on fixed-effects multinomial logit modelling of residential outcomes, we found that upward income mobility is connected to exit from low-income areas, but the effect is stronger among the native-born Finns than among those with an immigrant background. This stronger effect for natives is in contrast to findings of previous European studies, suggesting that these might have been influenced by unobserved individual-level heterogeneity. Our findings imply that both policies improving labour market opportunities of immigrants and policies reducing constraints for spatial integration are needed if the aim is to decrease ethnic residential segregation.
Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome
Authors: Bergman Alexandra , Vitay Dóra , Hellgren John , Chen Yun , Nielsen Jens , Siewers Verena
Published: March 2019

Microbial conversion of biomass to fatty acids (FA) and products derived thereof is an attractive alternative to the traditional oleochemical production route from animal and plant lipids. This study examined if NADPH-costly FA biosynthesis could be enhanced by overexpressing the transcription factor Stb5 in Saccharomyces cerevisiae. Stb5 activates expression of multiple genes encoding enzymes within the pentose phosphate pathway (PPP) and other NADPH-producing reactions. Overexpression of STB5 led to a decreased growth rate and an increased free fatty acid (FFA) production during growth on glucose. The improved FFA synthetic ability in the glucose phase was shown to be independent of flux through the oxidative PPP. RNAseq analysis revealed that STB5 overexpression had wide-ranging effects on the transcriptome in the batch phase, and appeared to cause a counterintuitive phenotype with reduced flux through the oxidative PPP. During glucose limitation, when an increased NADPH supply is likely less harmful, an overall induction of the proposed target genes of Stb5 (eg. GND1/2, TAL1, ALD6, YEF1) was observed. Taken together, the strategy of utilizing STB5 overexpression to increase NADPH supply for reductive biosynthesis is suggested to have potential in strains engineered to have strong ability to consume excess NADPH, alleviating a potential redox imbalance.