bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic interaction patterns of monolingual and bilingual infants with their parents
Authors: GAMPE Anja , HARTMANN Leonie , DAUM Moritz M.
Published: December 2019

Bilingual children show a number of advantages in the domain of communication. The aim of the current study was to investigate whether differences in interactions are present before productive language skills emerge. For a duration of 5 minutes, 64 parents and their 14-month-old infants explored a decorated room together. The coordination of their behaviors in the modalities of action, language, and gesture was coded. The results showed no differences in interactions across different language statuses. In two additional analyses, we first compared monolinguals and bilinguals with caregivers who shared the same language and culture. Results showed the same pattern of non-difference. Second, we compared bilinguals with caregivers from different cultures. The rate and duration of coordination differed across infants with different cultural backgrounds. The findings suggest that exposure to two languages is not sufficient to explain the previously identified beneficial effects in the communicative interactions of bilingual children.
Examining effects of mother and father warmth and control on child externalizing and internalizing problems from age 8 to 13 in nine countries
Authors: Rothenberg W. Andrew , Lansford Jennifer E. , Alampay Liane Peña , Al-Hassan Suha M. , Bacchini Dario , Bornstein Marc H. , Chang Lei , Deater-Deckard Kirby , Di Giunta Laura , Dodge Kenneth A. , Malone Patrick S. , Oburu Paul , Pastorelli Concetta , Skinner Ann T. , Sorbring Emma , Steinberg Laurence , Tapanya Sombat , Tirado Liliana Maria Uribe , Yotanyamaneewong Saengduean
Published: December 2019

This study used data from 12 cultural groups in 9 countries (China, Colombia, Italy, Jordan, Kenya, Philippines, Sweden, Thailand, and United States;N= 1,315) to investigate bidirectional associations between parental warmth and control, and child externalizing and internalizing behaviors. In addition, the extent to which these associations held across mothers and fathers and across cultures with differing normative levels of parent warmth and control were examined. Mothers, fathers, and children completed measures when children were ages 8 to 13. Multiple-group autoregressive cross-lagged structural equation models revealed that evocative child-driven effects of externalizing and internalizing behavior on warmth and control are ubiquitous across development, cultures, mothers, and fathers. Results also reveal that parenting effects on child externalizing and internalizing behaviors, though rarer than child effects, extend into adolescence when examined separately in mothers and fathers. Father-based parent effects were more frequent than mother effects. Most parent- and child-driven effects appear to emerge consistently across cultures. The rare culture-specific parenting effects suggested that occasionally the effects of parenting behaviors that run counter to cultural norms may be delayed in rendering their protective effect against deleterious child outcomes.
ANN-STATE ENDOGENOUS MARKOV-SWITCHING MODEL WITH APPLICATIONS IN MACROECONOMICS AND FINANCE
Authors: Hwu Shih-Tang , Kim Chang-Jin , Piger Jeremy
Published: December 2019

We develop anN-regime Markov-switching model in which the latent state variable driving the regime switching is endogenously determined with the model disturbance term. The models structure captures a wide variety of patterns of endogeneity and yields a simple test of the null hypothesis of exogenous switching. We derive an iterative filter that generates objects of interest, including the model likelihood function and estimated regime probabilities. Using simulation experiments, we demonstrate that the maximum likelihood estimator performs well in finite samples and that a likelihood ratio test of exogenous switching has good size and power properties. We provide results from two applications of the endogenous switching model: a three-state model of US business cycle dynamics and a three-state volatility model of US equity returns. In both cases, we find statistically significant evidence in favor of endogenous switching.
Military, Authoritarianism and Islam: A Comparative Analysis of Bangladesh and Pakistan
Authors: Sheikh Md Ziaul Haque , Ahmed Zahid Shahab
Published: December 2019

The years 1975 and 1977 witnessed a wave of de facto military regimes in Bangladesh and Pakistan, respectively. In Pakistan, General Muhammad Zia-ul-Haq operationalized the country's preexisting Islamic identity from emblematic to substantive at both domestic and international levels. General Ziaur Rahman and General Ershad of Bangladesh revived the country's Islamic identity at the domestic and international levels and reopened the space for religious fractions that were banned from politics constitutionally in the previous regime. Focusing on military regimes in Bangladesh and Pakistan between 1975 and 1990, this paper aims to bridge that gap by specifically examining the use of Islam. This study argues that dictators in both countries used Islam to support their survival strategies of legitimacy, repression, and social control. Authoritarian rulers did not have to use Islam to maintain military coherence, because of the military's culture of subordination to superiors.
Data Localization and ASEAN Economic Community
Authors: WONG Benjamin
Published: December 2019

Data localization is a phenomenon that is of increasing global significance, as a growing number of countries impose data localization requirements on data controllers. This paper discusses data localization in the ASEAN context. It proposes a schema of data localization laws which comprises two categories of data localization requirements. This schema is used to examine data localization laws within ASEAN, and it will be shown that there is presently a moderate level of data localization among ASEAN Member States. The paper then discusses how data localization is dealt with in the EU and in ASEAN, addressing some recent developments in the two regimes. It concludes with recommendations for ASEAN's approach to data localization, drawing from the EU regime.
Perspectives on Correctness in Probabilistic Inference from Psychology
Authors: Pothos Emmanuel M. , Basieva Irina , Khrennikov Andrei , Yearsley James M.
Published: December 2019

Research into decision making has enabled us to appreciate that the notion of correctness is multifaceted. Different normative framework for correctness can lead to different insights about correct behavior. We illustrate the shifts for correctness insights with two tasks, the Wason selection task and the conjunction fallacy task; these tasks have had key roles in the development of logical reasoning and decision making research respectively. The Wason selection task arguably has played an important part in the transition from understanding correctness using classical logic to classical probability theory (and information theory). The conjunction fallacy has enabled a similar shift from baseline classical probability theory to quantum probability. The focus of this overview is the latter, as it represents a novel way for understanding probabilistic inference in psychology. We conclude with some of the current challenges concerning the application of quantum probability theory in psychology in general and specifically for the problem of understanding correctness in decision making.
Primer on quantum cognition
Authors: Busemeyer Jerome R. , Wang Zheng
Published: December 2019

Quantum cognition is a new field in psychology, which is characterized by the application of quantum probability theory to human judgment and decision making behavior. This article provides an introduction that presents several examples to illustrate in a simple and concrete manner how to apply these principles to interesting psychological phenomena. Following each simple example, we present the general mathematical derivations and new predictions related to these applications.
The Contribution of Moral Disengagement to Dating Violence and General Aggression: The Gender and Age Moderating Effects
Authors: Rubio-Garay Fernando , Amor Pedro J. , Carrasco Miguel A.
Published: December 2019

The main aims of this study were, first to analyze the partial effects of specific mechanisms of moral disengagement (MMD) on different manifestations of general aggression and dating violence (DV) in adolescents and youths; second, to explore the moderating effects of gender and age on these relations. Moral disengagement, and different forms of aggression and DV, were evaluated in a sample of 424 participants (61.1% women) aged 15 to 25 years (M = 18.80; SD = 2.69). Pearson correlations and different hierarchical multiple linear regression analyses were conducted. All regressions were controlled by social desirability
.
MMD contributed to physical aggression with a medium effect size (R2 = .22) and verbal aggression with a small effect size (R2 = .10). Conversely, MMD did not appear to clearly contribute to DV. In conclusion, depersonalization and rationalization were the most important MMD for physical aggression, rationalization for verbal aggression, and irresponsibility for verbal-emotional violence in dating relationships. Moreover, the relationships between physical aggression and rationalization mechanism were significantly moderated by gender: there appears to be a stronger relationship between rationalization and physical aggression in boys than in girls. Moderating effects of age on these relations were not found.
Challenges and Opportunities in Magnetospheric Space Weather Prediction
Authors: Morley S. K.
Published: December 2019

Space Weather is the study of the dynamics of the coupled Solar‐Terrestrial environment, as these dynamics impact technological systems and human activity. This paper reviews a selection of the advances, challenges, and new opportunities for magnetospheric space weather, and while the focus is on specific phenomena, many other aspects of space weather will have similar challenges and needs. As a scientific field with direct applications, the field of space weather is partly driven by imperatives from both policy and operations. We provide an introduction to some of the context in which the field exists and discuss how this might shape future developments and norms within the space weather enterprise. We briefly examine benchmarking, as a policy and operationally driven activity, as it provides immediate societal relevance and an opportunity to stretch scientific understanding. As numerical space weather prediction now becomes routine, and exascale computing is in the near future, we identify challenges relating to computational expense and big data, capturing and accounting for uncertainties, and specification of boundary conditions. Here, as with the observations supporting numerical space weather prediction, the key challenge lies in extending the lead time of predictions. We also discuss the role of data, particularly in regard to model validation and empirical modeling. Due to the growing societal impact of space weather, we also examine the relationships between space weather and its terrestrial counterpart and look at the importance of continuous evaluation, monitoring progress in predictive capability, and communication with researchers, forecasters, and end users.
Characterizing the temporal Dynamics of Melatonin and Cortisol Changes in Response to Nocturnal Light Exposure
Authors: Rahman Shadab A. , Wright Kenneth P. , Lockley Steven W. , Czeisler Charles A. , Gronfier Claude
Published: December 2019

We studied the dynamics of melatonin suppression and changes in cortisol levels in humans in response to light exposure at night using high-frequency blood sampling. Twenty-one young healthy participants were randomized to receive either intermittent bright (~9,500 lux) light (IBL), continuous bright light (CBL) or continuous dim (~1 lux) light (VDL) for 6.5 h during the biological night (n = 7 per condition). Melatonin suppression occurred rapidly within the first 5 min and continued until the end of each IBL stimuli (t1/2 = ~13 min). Melatonin recovery occurred more slowly between IBL stimuli (half-maximal recovery rate of ~46 min). Mean melatonin suppression (~40%) and recovery (~50%) were similar across IBL stimuli. Suppression dynamics under CBL were also rapid (t1/2 = ~18 min), with no recovery until the light exposure ended. There was a significant linear increase of cortisol levels between the start and end of each IBL stimulus. Under CBL conditions cortisol showed trimodal changes with an initial linear activating phase, followed by an exponential inhibitory phase, and a final exponential recovery phase. These results show that light exposure at night affects circadian driven hormones differently and that outcomes are influenced by the duration and pattern of light exposure.
Four hundred years of cork imaging: New advances in the characterization of the cork structure
Authors: Crouvisier-Urion Kevin , Chanut Julie , Lagorce Aurélie , Winckler Pascale , Wang Zi , Verboven Pieter , Nicolai Bart , Lherminier Jeannine , Ferret Eric , Gougeon Régis D. , Bellat Jean-Pierre , Karbowiak Thomas
Published: December 2019

In 1665, Robert Hooke was the first to observe cork cells and their characteristic hexagonal shape, using the first optical microscope, which was invented by him at that time. With the evolution of imaging techniques, the structure of cork has been analysed with greater accuracy over time. This work presents the latest advances in the characterization of this unique material through a multiscale approach. Such investigation brings new insight into the architecture of cork, particularly the differences between the cells of the phellem and those bordering the lenticels. In the latter case, cell differentiation from the lenticular phellogen was restricted to one cell layer, which leads to a cell wall that is 10 times thicker for lenticels. They also displayed a different chemical composition because of unsuberization and a high lignin content in lenticels. Such advances in the knowledge of the structure and composition of cork cells contributes to a better understanding of the macroporosity of cork, down to the nanoscale.
Tumor-suppressing potential of stingless bee propolis in in vitro and in vivo models of differentiated-type gastric adenocarcinoma
Authors: Desamero Mark Joseph , Kakuta Shigeru , Tang Yulan , Chambers James Kenn , Uchida Kazuyuki , Estacio Maria Amelita , Cervancia Cleofas , Kominami Yuri , Ushio Hideki , Nakayama Jun , Nakayama Hiroyuki , Kyuwa Shigeru
Published: December 2019

The protective property of propolis across a wide spectrum of diseases has long been realized, yet the anti-tumor efficacy of this bioactive substance from Philippine stingless bees has remained poorly understood. Here, we showed the tumor-suppressing potential of crude ethanolic extract of Philippine stingless bee propolis (EEP) in in vitro models of gastric cancer highlighting the first indication of remarkable subtype specificity towards differentiated-type human gastric cancer cell lines but not the diffuse-type. Mechanistically, this involved the profound modulation of several cell cycle related gene transcripts, which correlated with the prominent cell cycle arrest at the G0/G1 phase. To reinforce our data, a unique differentiated-type gastric cancer model, A4gnt KO mice, together with age-matched 60 week-old C57BL/6 J mice were randomly assigned to treatment groups receiving distilled water or EEP for 30 consecutive days. EEP treatment induced significant regression of gross and histological lesions of gastric pyloric tumors that consistently corresponded with specific transcriptional regulation of cell cycle components. Also, the considerable p21 protein expression coupled with a marked reduction in rapidly dividing BrdU-labeled S-phase cells unequivocally supported our observation. Altogether, these findings support the role of Philippine stingless bee propolis as a promising adjunct treatment option in differentiated-type gastric cancer.
Identification of clinical and urine biomarkers for uncomplicated urinary tract infection using machine learning algorithms
Authors: Gadalla Amal A. H. , Friberg Ida M. , Kift-Morgan Ann , Zhang Jingjing , Eberl Matthias , Topley Nicholas , Weeks Ian , Cuff Simone , Wootton Mandy , Gal Micaela , Parekh Gita , Davis Paul , Gregory Clive , Hood Kerenza , Hughes Kathryn , Butler Christopher , Francis Nick A.
Published: December 2019

Women with uncomplicated urinary tract infection (UTI) symptoms are commonly treated with empirical antibiotics, resulting in overuse of antibiotics, which promotes antimicrobial resistance. Available diagnostic tools are either not cost-effective or diagnostically sub-optimal. Here, we identified clinical and urinary immunological predictors for UTI diagnosis. We explored 17 clinical and 42 immunological potential predictors for bacterial culture among women with uncomplicated UTI symptoms using random forest or support vector machine coupled with recursive feature elimination. Urine cloudiness was the best performing clinical predictor to rule out (negative likelihood ratio [LR−] = 0.4) and rule in (LR+ = 2.6) UTI. Using a more discriminatory scale to assess cloudiness (turbidity) increased the accuracy of UTI prediction further (LR+ = 4.4). Urinary levels of MMP9, NGAL, CXCL8 and IL-1β together had a higher LR+ (6.1) and similar LR− (0.4), compared to cloudiness. Varying the bacterial count thresholds for urine culture positivity did not alter best clinical predictor selection, but did affect the number of immunological predictors required for reaching an optimal prediction. We conclude that urine cloudiness is particularly helpful in ruling out negative UTI cases. The identified urinary biomarkers could be used to develop a point of care test for UTI but require further validation.
Boundary integral equation method for resonances in gradient index cavities designed by conformal transformation optics
Authors: Ryu Jung-Wan , Cho Jinhang , Lee Soo-Young , Kim Yushin , Park Sang-Jun , Rim Sunghwan , Choi Muhan , Kim Inbo
Published: December 2019

In the case of two-dimensional gradient index cavities designed by the conformal transformation optics, we propose a boundary integral equation method for the calculation of resonant mode functions by employing a fictitious space which is reciprocally equivalent to the physical space. Using the Green’s function of the interior region of the uniform index cavity in the fictitious space, resonant mode functions and their far-field distributions in the physical space can be obtained. As a verification, resonant modes in limaçon-shaped transformation cavities were calculated and mode patterns and far-field intensity distributions were compared with those of the same modes obtained from the finite element method.
LEGO® Block Structures as a Sub-Kelvin Thermal Insulator
Authors: Chawner J. M. A. , Jones A. T. , Noble M. T. , Pickett G. R. , Tsepelin V. , Zmeev D. E.
Published: December 2019

We report measurements of the thermal conductance of a structure made from commercial Acrylonitrile Butadiene Styrene (ABS) modules, known as LEGO® blocks, in the temperature range from 70 mK to 1.8 K. A power law for the sample’s thermal conductivity κ = (8.7 ± 0.3) × 10−5T 1.75±0.02 WK−1 m−1 was determined. We conclude that this ABS/void compound material provides better thermal isolation than well-known bulk insulator materials in the explored temperature range, whilst maintaining solid support. LEGO blocks represent a cheap and superlative alternative to materials such as Macor or Vespel. In our setup, <400 nW of power can heat an experimental area of 5 cm2 to over 1 K, without any significant change to the base temperature of the dilution refrigerator. This work suggests that custom-built modular materials with even better thermal performance could be readily and cheaply produced by 3D printing.
A space division multiplexed free-space-optical communication system that can auto-locate and fully self align with a remote transceiver
Authors: Abadi Mojtaba Mansour , Cox Mitchell A. , Alsaigh Rakan E. , Viola Shaun , Forbes Andrew , Lavery Martin P. J.
Published: December 2019

Free-Space Optical (FSO) systems offer the ability to distribute high speed digital links into remote and rural communities where terrain, installation cost or infrastructure security pose critical hurdles to deployment. A challenge in any point-to-point FSO system is initiating and maintaining optical alignment from the sender to the receiver. In this paper we propose and demonstrate a low-complexity self-aligning FSO prototype that can completely self-align with no requirement for initial manual positioning and could therefore form the opto-mechanical basis for a mesh network of optical transceivers. The prototype utilises off-the-shelf consumer electrical components and a bespoke alignment algorithm. We demonstrate an eight fibre spatially multiplexed link with a loss of 15 dB over 210 m.
Sensory-cognitive associations are only weakly mediated or moderated by social factors in the Canadian Longitudinal Study on Aging
Authors: Hämäläinen Anni , Phillips Natalie , Wittich Walter , Pichora-Fuller M. Kathleen , Mick Paul
Published: December 2019

Sensory and cognitive function both tend to decline with increasing age. Sensory impairments are risk factors for age-related cognitive decline and dementia. One hypothesis about sensory-cognitive associations is that sensory loss results in social isolation which, in turn, is a risk factor for cognitive decline. We tested whether social factors are associated with cognitive and sensory function, and whether sensory-cognitive associations are mediated or moderated by social factors. We used cross-sectional data from 30,029 participants in the Canadian Longitudinal Study of Aging, aged 45–85 years, who had no reported cognitive impairment or diagnosis of dementia. We found strong independent associations of self-reported social variables with hearing (pure-tone audiometry), vision (pinhole-corrected visual acuity), and executive function and weaker associations with memory. The moderating and mediating effects of social variables on sensory-cognitive associations were weak and mostly non-significant, but social factors could be slightly more important for females and older people. Partial retirement (relative to full retirement or not being retired) may have protective effects on cognition in the presence of hearing loss. These findings confirm the association between social factors and sensory and cognitive measures. However, support is weak for the hypothesis that social factors shape sensory-cognitive associations.
Semi-quantized Spin Pumping and Spin-Orbit Torques in Topological Dirac Semimetals
Authors: Misawa Takahiro , Nomura Kentaro
Published: December 2019

We study the time-development processes of spin and charge transport phenomena in a topological Dirac semimetal attached to a ferromagnetic insulator with a precessing magnetization. Compared to conventional normal metals, topological Dirac semimetals manifest a large inverse spin Hall effect when a spin current is pumped from the attached ferromagnetic insulator. It is shown that the induced charge current is semi-quantized, i.e., it depends only on the distance between the two Dirac points in momentum space and hardly depends on the disorder strength when the system remains in the topological Dirac semimetal phase. As an inverse effect, we show that the electric field applied to the topological Dirac semimetal exerts a spin torque on the local magnetization in the ferromagnetic insulator via the exchange interaction and the semi-quantized spin Hall effect. Our study demonstrates that the topological Dirac semimetal offers a less-dissipative platform for spin-charge conversion and spin switching.
The in vivo mechanics of the magnetotactic backbone as revealed by correlative FLIM-FRET and STED microscopy
Authors: Günther Erika , Klauß André , Toro-Nahuelpan Mauricio , Schüler Dirk , Hille Carsten , Faivre Damien
Published: December 2019

Protein interaction and protein imaging strongly benefit from the advancements in time-resolved and superresolution fluorescence microscopic techniques. However, the techniques were typically applied separately and ex vivo because of technical challenges and the absence of suitable fluorescent protein pairs. Here, we show correlative in vivo fluorescence lifetime imaging microscopy Förster resonance energy transfer (FLIM-FRET) and stimulated emission depletion (STED) microscopy to unravel protein mechanics and structure in living cells. We use magnetotactic bacteria as a model system where two proteins, MamJ and MamK, are used to assemble magnetic particles called magnetosomes. The filament polymerizes out of MamK and the magnetosomes are connected via the linker MamJ. Our system reveals that bacterial filamentous structures are more fragile than the connection of biomineralized particles to this filament. More importantly, we anticipate the technique to find wide applicability for the study and quantification of biological processes in living cells and at high resolution.
Caveolin-1 gene therapy inhibits inflammasome activation to protect from bleomycin-induced pulmonary fibrosis
Authors: Lin Xin , Barravecchia Michael , Matthew Kottmann R. , Sime Patricia , Dean David A
Published: December 2019

Idiopathic pulmonary fibrosis (IPF) is a devastating and fatal disease and characterized by increased deposition of extracellular matrix proteins and scar formation in the lung, resulting from alveolar epithelial damage and accumulation of inflammatory cells. Evidence suggests that Caveolin-1 (Cav-1), a major component of caveolae which regulates cell signaling and endocytosis, is a potential target to treat fibrotic diseases, although the mechanisms and responsible cell types are unclear. We show that Cav-1 expression was downregulated both in alveolar epithelial type I cells in bleomycin-injured mouse lungs and in lung sections from IPF patients. Increased expression of IL-1β and caspase-1 has been observed in IPF patients, indicating inflammasome activation associated with IPF. Gene transfer of a plasmid expressing Cav-1 using transthoracic electroporation reduced infiltration of neutrophils and monocytes/macrophages and protected from subsequent bleomycin-induced pulmonary fibrosis. Overexpression of Cav-1 suppressed bleomycin- or silica-induced activation of caspase-1 and maturation of pro-IL-1β to secrete cleaved IL-1β both in mouse lungs and in primary type I cells. These results demonstrate that gene transfer of Cav-1 downregulates inflammasome activity and protects from subsequent bleomycin-mediated pulmonary fibrosis. This indicates a pivotal regulation of Cav-1 in inflammasome activity and suggests a novel therapeutic strategy for patients with IPF.
Genetic Analysis of High Protein Content in ‘AC Proteus’ Related Soybean Populations Using SSR, SNP, DArT and DArTseq Markers
Authors: Samanfar Bahram , Cober Elroy R. , Charette Martin , Tan Le Hoa , Bekele Wubishet A. , Morrison Malcolm J. , Kilian Andrzej , Belzile François , Molnar Stephen J.
Published: December 2019

Key message: Several AC Proteus derived genomic regions (QTLs, SNPs) have been identified which may prove useful for further development of high yielding high protein cultivars and allele-specific marker developments. High seed protein content is a trait which is typically difficult to introgress into soybean without an accompanying reduction in seed yield. In a previous study, ‘AC Proteus’ was used as a high protein source and was found to produce populations that did not exhibit the typical association between high protein and low yield. Five high x low protein RIL populations and a high x high protein RIL population were evaluated by either quantitative trait locus (QTL) analysis or bulk segregant analyses (BSA) following phenotyping in the field. QTL analysis in one population using SSR, DArT and DArTseq markers found two QTLs for seed protein content on chromosomes 15 and 20. The BSA analyses suggested multiple genomic regions are involved with high protein content across the five populations, including the two previously mentioned QTLs. In an alternative approach to identify high protein genes, pedigree analysis identified SNPs for which the allele associated with high protein was retained in seven high protein descendants of AC Proteus on chromosomes 2, 17 and 18. Aside from the two identified QTLs (five genomic regions in total considering the two with highly elevated test statistic, but below the statistical threshold and the one with epistatic interactions) which were some distance from Meta-QTL regions and which were also supported by our BSA analysis within five populations. These high protein regions may prove useful for further development of high yielding high protein cultivars.
Semi-automated Root Image Analysis (saRIA)
Authors: Narisetti Narendra , Henke Michael , Seiler Christiane , Shi Rongli , Junker Astrid , Altmann Thomas , Gladilin Evgeny
Published: December 2019

Quantitative characterization of root system architecture and its development is important for the assessment of a complete plant phenotype. To enable high-throughput phenotyping of plant roots efficient solutions for automated image analysis are required. Since plants naturally grow in an opaque soil environment, automated analysis of optically heterogeneous and noisy soil-root images represents a challenging task. Here, we present a user-friendly GUI-based tool for semi-automated analysis of soil-root images which allows to perform an efficient image segmentation using a combination of adaptive thresholding and morphological filtering and to derive various quantitative descriptors of the root system architecture including total length, local width, projection area, volume, spatial distribution and orientation. The results of our semi-automated root image segmentation are in good conformity with the reference ground-truth data (mean dice coefficient = 0.82) compared to IJ_Rhizo and GiAroots. Root biomass values calculated with our tool within a few seconds show a high correlation (Pearson coefficient = 0.8) with the results obtained using conventional, pure manual segmentation approaches. Equipped with a number of adjustable parameters and optional correction tools our software is capable of significantly accelerating quantitative analysis and phenotyping of soil-, agar- and washed root images.
Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals
Authors: Clarke C. L. , Edwards M. E. , Gielly L. , Ehrich D. , Hughes P. D. M. , Morozova L. M. , Haflidason H. , Mangerud J. , Svendsen J. I. , Alsos I. G.
Published: December 2019

Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could “run out of space” as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.
Semantic segmentation of synchrotron tomography of multiphase Al-Si alloys using a convolutional neural network with a pixel-wise weighted loss function
Authors: Strohmann Tobias , Bugelnig Katrin , Breitbarth Eric , Wilde Fabian , Steffens Thomas , Germann Holger , Requena Guillermo
Published: December 2019

Human-based segmentation of tomographic images can be a tedious time-consuming task. Deep learning algorithms and, particularly, convolutional neural networks have become state of the art techniques for pattern recognition in digital images that can replace human-based image segmentation. However, their use in materials science is beginning to be explored and their application needs to be adapted to the specific needs of this field. In the present work, a convolutional neural network is trained to segment the microstructural components of an Al-Si cast alloy imaged using synchrotron X-ray tomography. A pixel-wise weighted error function is implemented to account for microstructural features which are hard to identify in the tomographs and that play a relevant role for the correct description of the 3D architecture of the alloy investigated. The results show that the total operation time for the segmentation using the trained convolutional neural network was reduced to <1% of the time needed with human-based segmentation.
Transcriptome alteration spectrum in rat lung induced by radiotherapy
Authors: Zhang Tao , Cheng Guowei , Sun Li , Deng Lei , Wang Xin , Bi Nan
Published: December 2019

Radiation therapy is crucial for curative treatment of lung cancer, which frequently leads to lung injury. Long non-coding RNAs (lncRNAs) are a group of RNAs longer than 200 nucleotides and lack protein-coding capacity. Increasing evidences demonstrate the important roles of lncRNAs in biological processes. However, the mechanism underlying the association of ionizing radiation with alterations in mRNA and lncRNA expression and lung injury remains unclear. In our study, the male Sprague-Dawley (SD) rats were exposed to a dose of 18 Gy of 6 MV X-ray and the transcriptome spectrum was studied. To identify the differentially expressed mRNAs and lncRNAs induced by X-ray, the RNA sequencing data of lung tissues from irradiated and normal rats for 4, 8, and 16 weeks were analyzed, using |log2_ratio| ≥ 1 and q ≤ 0.05 as thresholds for significantly differential expression. The number of differentially expressed mRNAs was 1097 (686 up- and 411 down-) for 4-week radiotherapy group, 3006 (1935 up- and 1071 down-) for 8-week group and 1838 (1178 up- and 660 down-) for 16-week group. There were 606 (279 up- and 327 down-) differentially expressed lncRNAs in 4-week group, 1715 (831 up- and 884 down-) in 8-week group and 1043 (656 up- and 387 down-) in 16-week group. The differentially expressed mRNAs were mainly involved in cell cycle regulation and Fc receptor pathway, while the lncRNA target genes were significantly enriched in cellular stress response and regulation of cell migration. Moreover, compared with the control group, the irradiated group presented higher tissue specificity of lncRNAs. Radiation-induced lung injury, especially the dynamic network of lncRNAs and mRNAs, is worthy of study. Investigation on the regulatory details of related pathways is significant for the prevention of radiation-related lung injury, as well as the improvement of radiation therapy.
Long noncoding RNA AURKAPS1 potentiates malignant hepatocellular carcinoma progression by regulating miR-142, miR-155 and miR-182
Authors: Li Jianhua , Guo Wenzhi , Xue Wenping , Xu Pengfei , Deng Zhen , Zhang Danhua , Zheng Shouhua , Qiu Xinguang
Published: December 2019

The mitotic serine/threonine kinase aurora kinase-A (AURKA) has been identified as carcinogenic in hepatocellular carcinoma (HCC). AURKAPS1, a long non-coding RNA (lncRNA), is the pseudo-gene of AURKA, which play important roles in the cancer. Its underlying functions and mechanisms in liver cancer progression remain largely unknown. The mRNA expression of AURKAPS1 in HCC tumor tissues was significantly higher, which is associated with tumor size and TNM stage. The high expression of AURKAPS1 promotes cell movement, migration and invasion. AURKAPS1 can increases the protein expression of RAC1, promotes the activation of ERK, and enhance the formation of membrane ruffles by binding with miR-182, miR-155 and miR-142 competively. Thus, AURKAPS1 could be a useful marker, and the combination of AURKAPS1/miRNAs (miR-142, miR-155 and miR-182) may be a new theoretical basis for the treatment of HCC.
Land use affects lowland stream ecosystems through dissolved oxygen regimes
Authors: dos Reis Oliveira Paula C. , van der Geest Harm G. , Kraak Michiel H. S. , Verdonschot Piet F. M.
Published: December 2019

The aim of the present study was to assess the impact of surrounding land use on the structure and functioning of lowland stream ecosystems. To this end, five different land use types were selected (forest, extensive grassland, intensive grassland, cropland and wastewater treatment plant) each represented by four replicate streams, in which diel dissolved oxygen concentrations were recorded, sediment and water quality parameters were measured and macroinvertebrate community composition was determined. Chironomus sp., Oligochaeta and Gastropoda dominated the cropland and wastewater treatment plant (WWTP) streams, while Plecoptera and most Trichoptera only occurred in forest and extensive grassland streams. Forest streams communities were related to a high oxygen saturation, a high C/N ratio in the sediment and woody debris and coarse particulate organic matter (CPOM) substrate cover. Macroinvertebrate communities in cropland and WWTP streams were related to a low oxygen saturation in water and sediment and high concentrations of dissolved nitrogen, phosphorus and carbon. It is concluded that land use specific impacts on lowland streams are likely exerted via fine sediment accumulation in deposition zones, affecting oxygen regimes, sediment oxygen demand and stream metabolism, ultimately changing macroinvertebrate community composition. This study supports therefore the importance of including the catchment scale in ecological stream quality assessments, combining structural and functional endpoints.
Sulfur isotope analysis for representative regional background atmospheric aerosols collected at Mt. Lulin, Taiwan
Authors: Chung Chuan-Hsiung , You Chen-Feng , Hsu Shih-Chieh , Liang Mao-Chang
Published: December 2019

Air pollution resulted from fossil fuel burning has been an environmental issue in developing countries in Asia. Sulfur-bearing compounds, in particular, are species that are regulated and monitored routinely. To assess how the species affect at local and global scales, regional background level has to be defined. Here, we report analysis of sulfur isotopes in atmospheric sulfate, the oxidation end product of sulfur species, in particulate phase collected at the Lulin observatory located at 2862 m above mean sea level in 2010. The averaged sulfate concentration for 44 selected samples is 2.7 ± 2.3 (1-σ standard deviation) μg m−3, and the averaged δ34S is 2.2 ± 1.6‰, with respect to the international standard Vienna Canyon Diablo Troilite. Regardless of the origins of air masses, no noticeable difference between the low-altitude Pacific and high-altitude free troposphere sulfate aerosols is observed. Also, no identifiable seasonal cycle in seen. Correlation analysis with respect to coal burning tracers such as lead and oil industry tracers such as vanadium shows sulfate concentration is in better correlation with vanadium (R2 = 0.86, p-value < 0.001) than with lead (R2 = 0.45, p-value < 0.001) but no statistically significant correlation is found in δ34S with any of physical quantities measured. We suggest the sulfate collected at Lulin can best represent the regional background level in the Western Pacific, a quantity that is needed in order to quantitatively assess the budget of sulfur in local to country scales.
Metagenomic analysis of dental calculus in ancient Egyptian baboons
Authors: Ottoni Claudio , Guellil Meriam , Ozga Andrew T. , Stone Anne C. , Kersten Oliver , Bramanti Barbara , Porcier Stéphanie , Van Neer Wim
Published: December 2019

Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals’ oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th–6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons’ oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.
Electron Tomography Analysis of Thylakoid Assembly and Fission in Chloroplasts of a Single-Cell C4 plant, Bienertia sinuspersici
Authors: Mai Keith Ka Ki , Yeung Wai-Tsun , Han Sang-Yun , Cai Xiaohao , Hwang Inhwan , Kang Byung-Ho
Published: December 2019

Bienertia sinuspersici is a single-cell C4 plant species of which chlorenchyma cells have two distinct groups of chloroplasts spatially segregated in the cytoplasm. The central vacuole encloses most chloroplasts at the cell center and confines the rest of the chloroplasts near the plasma membrane. Young chlorenchyma cells, however, do not have large vacuoles and their chloroplasts are homogenous. Therefore, maturing Bienertia chlorenchyma cells provide a unique opportunity to investigate chloroplast proliferation in the central cluster and the remodeling of chloroplasts that have been displaced by the vacuole to the cell periphery. Chloroplast numbers and sizes increased, more notably, during later stages of maturation than the early stages. Electron tomography analyses indicated that chloroplast enlargement is sustained by thylakoid growth and that invaginations from the inner envelope membrane contributed to thylakoid assembly. Grana stacks acquired more layers, differentiating them from stroma thylakoids as central chloroplasts matured. In peripheral chloroplasts, however, grana stacks stretched out to a degree that the distinction between grana stacks and stroma thylakoids was obscured. In central chloroplasts undergoing division, thylakoids inside the cleavage furrow were kinked and severed. Grana stacks in the division zone were disrupted, and large complexes in their membranes were dislocated, suggesting the existence of a thylakoid fission machinery.
Reciprocal connectivity between secondary auditory cortical field and amygdala in mice
Authors: Tsukano Hiroaki , Hou Xubin , Horie Masao , Kitaura Hiroki , Nishio Nana , Hishida Ryuichi , Takahashi Kuniyuki , Kakita Akiyoshi , Takebayashi Hirohide , Sugiyama Sayaka , Shibuki Katsuei
Published: December 2019

Recent studies have examined the feedback pathway from the amygdala to the auditory cortex in conjunction with the feedforward pathway from the auditory cortex to the amygdala. However, these connections have not been fully characterized. Here, to visualize the comprehensive connectivity between the auditory cortex and amygdala, we injected cholera toxin subunit b (CTB), a bidirectional tracer, into multiple subfields in the mouse auditory cortex after identifying the location of these subfields using flavoprotein fluorescence imaging. After injecting CTB into the secondary auditory field (A2), we found densely innervated CTB-positive axon terminals that were mainly located in the lateral amygdala (La), and slight innervations in other divisions such as the basal amygdala. Moreover, we found a large number of retrogradely-stained CTB-positive neurons in La after injecting CTB into A2. When injecting CTB into the primary auditory cortex (A1), a small number of CTB-positive neurons and axons were visualized in the amygdala. Finally, we found a near complete absence of connections between the other auditory cortical fields and the amygdala. These data suggest that reciprocal connections between A2 and La are main conduits for communication between the auditory cortex and amygdala in mice.
Controllable symmetry breaking solutions for a nonlocal Boussinesq system
Authors: Fei Jinxi , Ma Zhengyi , Cao Weiping
Published: December 2019

The generalized Boussinesq equation is a useful model to describe the water wave. In this paper, with the coupled Alice-Bob (AB) systems, the nonlocal Boussinesq system can be obtained via the parity and time reversal symmetry reduction. By introducing an extended Bäcklund transformation, the symmetry breaking rogue wave, symmetry breaking soliton and symmetry breaking breather solutions for a nonlocal Boussinesq system are obtained through the derived Hirota bilinear form. The residual symmetry and finite symmetry transformation of the nonlocal AB-Boussinesq system are also studied.
Impact of iterative reconstruction with resolution recovery in myocardial perfusion SPECT: phantom and clinical studies
Authors: Okuda Koichi , Nakajima Kenichi , Yoneyama Hiroto , Shibutani Takayuki , Onoguchi Masahisa , Matsuo Shinro , Hashimoto Mitsumasa , Kinuya Seigo
Published: December 2019

The corrections of photon attenuation, scatter, and depth-dependent blurring improve image quality in myocardial perfusion single-photon emission computed tomography (SPECT) imaging; however, the combined corrections induce artifacts. Here, we present the single correction method of depth-dependent blurring and its impact for myocardial perfusion distribution in phantom and clinical studies. The phantom and clinical patient images were acquired with two conditions: circular and noncircular orbits of gamma cameras yielded constant and variable depth-dependent blurring, respectively. An iterative reconstruction with the correction method of depth-dependent was used to reconstruct the phantom and clinical patient images. We found that the single correction method improved the robustness of phantom images whether the images contained constant or variable depth-dependent blurring. The myocardial perfusion databases generated from 72 normal patients exhibited uniform perfusion distribution of whole myocardium. In summary, the single correction method of depth-dependent blurring with iterative reconstruction is helpful for myocardial perfusion SPECT.