bluuebunny/crossref_metadata_2025 huggingface dataset:
Primary Productivity in Estuary Mangrove Kurau, Bangka Tengah
Authors: Utami E , Mahardika R G
Published: October 2019

Ocean primary production is an important factor for determining the ocean’s role in global carbon cycle. Primary production is the process whereby inorganic carbon is fixed in the sunlit (euphotic) zone of the upper ocean and forms the base of the marine food pyramid. It occurs when marine phytoplankton use sunlight energy and dissolved nutrients to convert inorganic carbon to organic material, thereby releasing oxygen. The objective of this study was to analyze primary productivity in estuary mangrove area in Kurau, Bangka Tengah, Indonesia. The study area was carried out in mangrove area, specifically in Kurau mangrove, Bangka Tengah, Indonesia. The physicochemical sea water parameters were recorded for all stations. The area was divided into four research stations. Based on the data, value of GPP was between 98.95 mg/L – 114.58 mg/L, NPP between 10.42 - 72.92 mg/L, R between 41.67 - 104.17 mg/L. In general, the mean value of temperature, pH, salinity, sea water current, brightness, phosphate were 29.5 ± 0.5 °C; 6.75 ± 0.83; 15 ± 12.74 ppm; 0.075 ± 0.032 m/second; 0.21 ± 0.15 m; 0.74 ± 0.52 mg/L. GPP rates still in typical state range for estuary of equator. Based on nitrate data, the sampling area was eutrophic, so that respiration rates was higher than NPP rates. Moreover, it is because higher recycling of labeled organic matter in brackish part of the estuary as well.
The determining of an environmentally oriented mining direction using the ordinary kriging method
Authors: Amelia R , Guskarnali  , Mardiah
Published: October 2019

Cassiterite (SnO2) is a mineral carrying element of tin (Sn) and other associated minerals of economic value. Mining activities need to go through several analyze including those related to environmental impacts regardless of primary and secondary sediment conditions. In this reseacrh, twenty-six data samples were took around Sambunggiri Hill, Jurung Village, Merawang District, Bangka Regency. The data were test using X-Ray Fluorescence (XRF) in a laboratory. There are two types of elements will be taken, they are Tin, (Sn) and Zircon (Zr), as well as one other type of related mineral is Hematite (Fe2O3). In this research, we use spatial analysis to estimate patterns of distribution of mineral content. The spherical model can apply to describe the spatial relationship between location pairs based on Hematite, Tin and Zircon. The pattern of minerals distribution mostly found to the east of Sambunggiri Hill. The estimated distribution pattern of Cassiterite minerals can provide an overview of mining activities that can prevent environmental damage. So that environmental damage caused by mining activities can be minimized and raise awareness to maintain a sustainable environment. A good mining concept will have a positive impact on the surrounding environment.
School infrastructure green environment
Authors: Sucipto  , Safitri R
Published: October 2019

School infrastructure that reflects environmental management efforts really needs attention. This study aims to analyze the importance of green environm entally friendly school infrastructure development in supporting the learning process in schools. The object of this research is Junior High School at Salatiga. This research is descriptive qualitative research. The parameters in this study are implementation and strategy in creating an environmentally friendly school environment. Data collection is done through interviews, documents, and observations. The results of this study indicate that green school infrastructure must have clean water, rubbish (the provision of separate bins, composters), feces, wastewater/drainage, green open space (RTH), noise/vibration/radiation. The realization of a green environment also needs to be maintained by planting trees, contest, strict sanctions, slogan, galactic activities that are fostering a love for the environment, and defend grass fields.
Technical Evaluation of Associated Tin Minerals Processing at Bidang Pengolahan Mineral (BPM) Unit Metalurgi Muntok, PT Timah Tbk
Authors: Virgiawan M R , Pitulima J
Published: October 2019

Since 2017 PT Timah Tbk has been processing residual ore (SHP) with low tin content of ± 10-30% wt. In order to increase tin grade and associated mineral products to be high grade (> 70% wt), an evaluation and optimization process is needed on High Tension Roll Separator processing equipment. The evaluation and optimization process was carried out on conductor products, especially index of separation efficiency of cassiterite. Sampling of the feed and the product based on the parameter settings. The feed rate is set at 250, 630 and 2100 gr/10s. The splitter opening is set at 13, 16, 20 cm of magnetic rollers. While the electric current is set at 1, 2 and 3 miliamperes. Mass and grade data are then analyzed by regression and variance statistical methods and optimized by the response surface method. The evaluation results show that only the splitter opening parameters and electric current strength are significant in explaining the product results obtained with a level of hypothesis error of 5%. The results of HTRS optimization show that the best parameter conditions are in the <1.5 ampere of electric current and <14 cm of splitter openings with schulz’s efficiency capable of >90% in second order of central composite design.
Being open to the unexpected
Authors: Murphy Coleen T.
Published: October 2019

I am grateful to have received the 2019 Women in Cell Biology Mid-Career Award from the American Society for Cell Biology. My lab has been studying aging and longevity regulation since 2005, but along the way we have had some surprises. These unexpected findings have morphed from detours to main directions, changing how I view biology. As I look back I’ve come to appreciate the importance and joy that can come from being open to these surprise interests and rigorously pursuing them.
I am an American scientist of the world
Authors: Li Rong
Published: October 2019

The ongoing trade war between the United States and China has led to questions about the loyalty and intent of Chinese American scientists. In this essay, I use my own small stories to recall the history of my generation of Chinese American scientists and our journey in this country to build career and life, all in fewer than 1000 words. It intends to be a tribute to the generosity of the American spirit and its openness to strangers, which is the very reason behind the inexhaustible creativity and world-leading research of this country.
How to run an academic lab based on a basketball strategy
Authors: Petry Sabine
Published: October 2019

It is a huge honor to receive the WICB Junior Award for Excellence in Research. In this essay, I first describe what we have discovered in my lab so far. Then, I summarize the strategies that helped transition my lab from its infant shoes to a mature research environment where discoveries are being made.
Drug–target prediction utilizing heterogeneous bio-linked network embeddings
Authors: Zong Nansu , Wong Rachael Sze Nga , Yu Yue , Wen Andrew , Huang Ming , Li Ning
Published: November 2019

To enable modularization for network-based prediction, we conducted a review of known methods conducting the various subtasks corresponding to the creation of a drug–target prediction framework and associated benchmarking to determine the highest-performing approaches. Accordingly, our contributions are as follows: (i) from a network perspective, we benchmarked the association-mining performance of 32 distinct subnetwork permutations, arranging based on a comprehensive heterogeneous biomedical network derived from 12 repositories; (ii) from a methodological perspective, we identified the best prediction strategy based on a review of combinations of the components with off-the-shelf classification, inference methods and graph embedding methods. Our benchmarking strategy consisted of two series of experiments, totaling six distinct tasks from the two perspectives, to determine the best prediction. We demonstrated that the proposed method outperformed the existing network-based methods as well as how combinatorial networks and methodologies can influence the prediction. In addition, we conducted disease-specific prediction tasks for 20 distinct diseases and showed the reliability of the strategy in predicting 75 novel drug–target associations as shown by a validation utilizing DrugBank 5.1.0. In particular, we revealed a connection of the network topology with the biological explanations for predicting the diseases, ‘Asthma’ ‘Hypertension’, and ‘Dementia’. The results of our benchmarking produced knowledge on a network-based prediction framework with the modularization of the feature selection and association prediction, which can be easily adapted and extended to other feature sources or machine learning algorithms as well as a performed baseline to comprehensively evaluate the utility of incorporating varying data sources.
BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study
Authors: Dong Jie , Zhu Min-Feng , Yun Yong-Huan , Lu Ai-Ping , Hou Ting-Jun , Cao Dong-Sheng
Published: October 2019

Background

With the increasing development of biotechnology and information technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these resources needs to be extracted and then transformed to useful knowledge by various data mining methods. However, a main computational challenge is how to effectively represent or encode molecular objects under investigation such as chemicals, proteins, DNAs and even complicated interactions when data mining methods are employed. To further explore these complicated data, an integrated toolkit to represent different types of molecular objects and support various data mining algorithms is urgently needed.

Results

We developed a freely available R/CRAN package, called BioMedR, for molecular representations of chemicals, proteins, DNAs and pairwise samples of their interactions. The current version of BioMedR could calculate 293 molecular descriptors and 13 kinds of molecular fingerprints for small molecules, 9920 protein descriptors based on protein sequences and six types of generalized scale-based descriptors for proteochemometric modeling, more than 6000 DNA descriptors from nucleotide sequences and six types of interaction descriptors using three different combining strategies. Moreover, this package realized five similarity calculation methods and four powerful clustering algorithms as well as several useful auxiliary tools, which aims at building an integrated analysis pipeline for data acquisition, data checking, descriptor calculation and data modeling.

Conclusion

BioMedR provides a comprehensive and uniform R package to link up different representations of molecular objects with each other and will benefit cheminformatics/bioinformatics and other biomedical users. It is available at: https://CRAN.R-project.org/package=BioMedR and https://github.com/wind22zhu/BioMedR/.
Is the Eurozone disintegrating? Macroeconomic divergence, structural polarisation, trade and fragility
Authors: Gräbner Claudius , Heimberger Philipp , Kapeller Jakob , Schütz Bernhard
Published: October 2019

This paper analyses macroeconomic developments in the Eurozone since its inception in 1999. In doing so, we document a process of divergence and polarisation among those countries that joined the Eurozone during its first two years. We find evidence for a ‘core–periphery’ pattern among Eurozone countries, that is, however, marked by substantial heterogeneity within these two clusters. We show how the polarisation process underlying this pattern first manifested in increasing current account imbalances, before it translated unto the level of general macroeconomic development when the crisis hit. Empirically, we demonstrate how this macroeconomic divergence is tied to a ‘structural polarisation’ in terms of the sectoral composition of Eurozone countries; specifically, the emergence of export-driven growth in core countries and debt-driven growth in the Eurozone periphery can be traced back to differences in technological capabilities and firm performance. Pushing for convergence within Europe requires the implementation of industrial policies aiming at a technological catch-up process in periphery countries in combination with public investment and progressive redistributional policies to sustain adequate levels of aggregate demand in all Eurozone countries.
Hierarchical Categorization and Review of Recent Techniques on Image Forgery Detection
Authors: Vinolin V , Sucharitha M
Published: November 2019

Information in the form of the image conveys more details than any other form of information. Several software packages are available to manipulate the images so that the authenticity of the images is being questioned. Several image processing approaches are available to create fake images without leaving any visual clue about the forging operation. So, proper image forgery detection tools are required to detect such forgery images. Over the past few years, several research papers were published in the digital image forensics domain for detecting fake images, thus escalating the legitimacy of the images. This survey paper attempts to review the recent approaches proposed for detecting image forgery. Accordingly, several research papers related to image forgery detection are reviewed and analyzed. The taxonomy of image forgery detection techniques is presented, and the algorithms related to each technique are discussed. The comprehensive analysis is carried out based on the dataset used, software used for the implementation and the performance achievement. Besides, the research issues associated with every approach were scrutinized together with the recommendation for future work.
Multi-Swarm Cuckoo Search Algorithm with Q-Learning Model
Authors: Li Juan , Xiao Dan-dan , Zhang Ting , Liu Chun , Li Yuan-xiang , Wang Gai-ge
Published: October 2019

As a novel swarm intelligence optimization algorithm, cuckoo search (CS) has been successfully applied to solve diverse problems in the real world. Despite its efficiency and wide use, CS has some disadvantages, such as premature convergence, easy to fall into local optimum and poor balance between exploitation and exploration. In order to improve the optimization performance of the CS algorithm, a new CS extension with multi-swarms and Q-Learning namely MP-QL-CS is proposed. The step size strategy of the CS algorithm is that an individual fitness value is examined based on a one-step evolution effect of an individual instead of evaluating the step size from the multi-step evolution effect. In the MP-QL-CS algorithm, a step size control strategy is considered as action, which is used to examine the individual multi-stepping evolution effect and learn the individual optimal step size by calculating the Q function value. In this way, the MP-QL-CS algorithm can increase the adaptability of individual evolution, and a good balance between diversity and intensification can be achieved. Comparing the MP-QL-CS algorithm with various CS algorithms, variants of differential evolution (DE) and improved particle swarm optimization (PSO) algorithms, the results demonstrate that the MP-QL-CS algorithm is a competitive swarm algorithm.
Qualitative insights into the opioid prescribing practices of Australian GP
Authors: Prathivadi Pallavi , Barton Chris , Mazza Danielle
Published: October 2019

Background

Over the last three decades, Australian opioid-prescribing rates and related morbidity and mortality have dramatically increased. Opioids are frequently prescribed by general practitioners (GPs) to manage chronic non-cancer pain, despite evidence-based recommendations from the Centre for Disease Control, National Institute for Health and Care Excellence and World Health Organization widely cautioning their use. Little is known about the factors influencing the opioid prescribing decisions of Australian GPs, especially when not evidence based.

Objective

To explore the opioid prescribing knowledge, attitudes and practices of Australian GPs.

Methods

Semi-structured interviews with 20 GPs recruited from the Monash University practice-based research network in metropolitan, southeastern Melbourne. Thematic analysis was used to identify emergent themes. Data were managed using QSR NVivo. Ethics approval was granted by Monash University.

Results

Three key themes emerged. GP attitudes towards opioid use for chronic pain varied by age of patient and goals for therapy. Use of opioids for elderly patients was positively perceived. GPs were reluctant to use opioids in younger patients due to fears of addiction and difficulty weaning. GPs felt obliged to prescribe opioids recommended by specialists, even if they believed the opioids were unsafe.

Conclusion

This study identified and described the patient-centred nature of GP opioid prescribing decisions. Patient age and perceived age-related opioid harm were important factors influencing prescribing decisions. Future work should inform interventions that value GP autonomy while still encouraging a collaborative inter-speciality approach to managing chronic pain patients with opioids.
Inversion of marine controlled source electromagnetic data using a parallel non-dominated sorting genetic algorithm
Authors: Ayani Mohit , MacGregor Lucy , Mallick Subhashis
Published: October 2019

We developed a multi-objective optimization method for inverting marine controlled source electromagnetic data using a fast-non-dominated sorting genetic algorithm. Deterministic methods for inverting electromagnetic data rely on selecting weighting parameters to balance the data misfit with the model roughness and result in a single solution which do not provide means to assess the non-uniqueness associated with the inversion. Here, we propose a robust stochastic global search method that considers the objective as a two-component vector and simultaneously minimizes both components: data misfit and model roughness. By providing an estimate of the entire set of the Pareto-optimal solutions, the method allows a better assessment of non-uniqueness than deterministic methods. Since the computational expense of the method increases as the number of objectives and model parameters increase, we parallelized our algorithm to speed up the forward modelling calculations. Applying our inversion to noisy synthetic data sets generated from horizontally stratified earth models for both isotropic and anisotropic assumptions and for different measurement configurations, we demonstrate the accuracy of our method. By comparing the results of our inversion with the regularized genetic algorithm, we also demonstrate the necessity of casting this problem as a multi-objective optimization for a better assessment of uncertainty as compared to a scalar objective optimization method.
Dining With Inflammatory Bowel Disease: A Review of the Literature on Diet in the Pathogenesis and Management of IBD
Authors: Gu Phillip , Feagins Linda A
Published: October 2019

Inflammatory bowel diseases (IBDs) are chronic immune-related diseases hypothesized to be a sequela of an interplay of genetic predisposition and environmental exposures. The global incidence of IBD is increasing, and more patients are exploring diet as a means to explain and treat their IBD. In fact, many patients strongly believe diet plays a fundamental role in the onset and management of their IBD. However, a significant proportion of patients report limited nutritional education from their provider, and providers report limited nutritional resources to aid in discussions with patients. This imbalance between supply and demand likely reflects the previous paucity of available literature characterizing the influence of diet in IBD. To address this gap in knowledge, we review the available literature to characterize the role of diet in the pathogenesis, exacerbation, and treatment of IBD. We aim to provide patients and providers with resources to better understand and discuss the role of diet in IBD, with the overall goal of improving patient care and satisfaction.
Distribution and Antifungal Susceptibility of Candida Species Causing Candidemia in China: An Update From the CHIF-NET Study
Authors: Xiao Meng , Chen Sharon C-A , Kong Fanrong , Xu Xiu-Li , Yan Li , Kong Hai-Shen , Fan Xin , Hou Xin , Cheng Jing-Wei , Zhou Meng-Lan , Li Ying , Yu Shu-Ying , Huang Jing-Jing , Zhang Ge , Yang Yang , Zhang Jing-Jia , Duan Si-Meng , Kang Wei , Wang He , Xu Ying-Chun
Published: November 2019

Background

Candidemia is the most common, serious fungal infection and Candida antifungal resistance is a challenge. We report recent surveillance of candidemia in China.

Methods

The study encompassed 77 Chinese hospitals over 3 years. Identification of Candida species was by mass spectrometry and DNA sequencing. Antifungal susceptibility was determined using the Clinical and Laboratory Standards Institute broth microdilution method.

Results

In total, 4010 isolates were collected from candidemia patients. Although C. albicans was the most common species, non-albicans Candida species accounted for over two-thirds of isolates, predominated C. parapsilosis complex (27.1%), C. tropicalis (18.7%), and C. glabrata complex (12.0%). Most C. albicans and C. parapsilosis complex isolates were susceptible to all antifungal agents (resistance rate <5%). However, there was a decrease in voriconazole susceptibility to C. glabrata sensu stricto over the 3 years and fluconazole resistance rate in C. tropicalis tripled. Amongst less common Candida species, over one-third of C. pelliculosa isolates were coresistant to fluconazole and 5-flucytocine, and >56% of C. haemulonii isolates were multidrug resistance.

Conclusions

Non-albicans Candida species are the predominant cause of candidemia in China. Azole resistance is notable amongst C. tropicalis and C. glabrata. Coresistance and multidrug resistance has emerged in less common Candida species.
The Race to the Water for Offshore Renewable Energy: Assessing Cumulative and In-combination Impacts for Offshore Renewable Energy Developments
Authors: Caine Catherine Ann
Published: October 2019

Wind, wave and tidal energy are widely regarded as being the ‘good guys’ in energy production for their carbon neutral qualities. However, lurking in the shadow of this good reputation is the uncertainty about the impacts that this new technology will have on the marine environment. It could cause a potential conflict between carbon-neutral energy production and the protection of habitats, and the prevention of biodiversity loss. This article presents empirical data collected from three case studies in England and Scotland. This research indicates that the disjointed nature of the consenting processes for offshore renewables does not encourage full assessment of the cumulative impacts of offshore renewable developments as required by European Union environmental impact assessment legislation. The article identifies elements of the consenting processes, which fail to provide a full assessment of cumulative and in-combination impacts, and recommends changes to these processes in England and Scotland.
The impact of lymphadenectomy on prognosis and survival of clinically apparent early-stage malignant ovarian germ cell tumors
Authors: Qin Beijiao , Xu Wenyan , Li Yanfang
Published: October 2019

Objective

To determine the impact of lymphadenectomy (LND) on survival of clinically apparent early-stage malignant ovarian germ cell tumors (MOGCTs).

Methods

We retrospectively analyzed the survival of patients who were diagnosed with the three most common histopathology types of malignant ovarian germ cell tumors (yolk sac tumor, dysgerminoma and immature teratoma) and with clinical stage I and II disease, and treated at Sun Yat-sen University Cancer Center between 1 January 1970 and 30 September 2018.

Results

There were 227 stage I, 28 stage II and one stage IIIA cases after surgery. One hundred and twenty-six patients underwent lymphadenectomy and 130 did not. Only one lymph node metastasis (0.8%) was found in the lymphadenectomy group. Two hundred and twenty-four out of 256 patients (87.5%) received postoperative chemotherapy. There were five relapses (4.0%) in the lymphadenectomy group and four (3.1%) in the non-lymphadenectomy group. Median follow-up was 68 months (range, 1–388). The 10-year disease-free survival rate in the lymphadenectomy group and non-lymphadenectomy group were 88.2 and 96.4%, respectively (P = 0.412); the 10-year overall survival rate in the two groups were 95.7 and 98.2%; respectively (P = 0.798). The results showed that lymphadenectomy did not improve patient survival.

Conclusions

Lymphadenectomy may have little impact on survival in patients with clinically apparent early-stage malignant ovarian germ cell tumors and may be omitted in the surgical treatment.
Design of a Repellent Against Aedes aegypti (Diptera: Culicidae) Using in silico Simulations With AaegOBP1 Protein
Authors: Portilla-Pulido Johan Sebastián , Castillo-Morales Ruth Mariela , Barón-Rodríguez Mario Alberto , Duque Jonny Edward , Mendez-Sanchez Stelia Carolina
Published: October 2019

Skin irritation has been reported to be the main adverse effect of excessive use of N,N-diethyl-m-toluamide (DEET) and ethyl 3-acetyl(butyl)amino (IR3535) commercial repellents. Therefore, there is an interest in alternatives of natural origin such as essential oils (EOs) and major compounds, which have repellent effects but have no contraindications. The main purpose of the present study was to identify the repellent effect of selected terpenes on Aedes aegypti Linnaeus, 1762 (Diptera: Culicidae) by in silico analysis based on their affinity with the odorant protein AaegOBP1. The protein-metabolite interactions in 20 terpenes were analyzed using the SwissDock tool. Terpenes presenting the highest affinity compared with commercial repellents were selected to evaluate repellent activity at concentrations 0.1, 10, and 25% against Ae. aegypti. Different periods (0–2, 2–15, 15–60 min) were evaluated with DEET as a positive control. The toxicity of terpenes was verified through Osiris and Molinspiration Cheminformatics Software, and cytotoxicity assays in Vero and HepaRG cells were performed using the MTT method. Two formulations were prepared with polyethylene glycol to evaluate skin long-lasting in vivo assay. The results showed four terpenes: geranyl acetate, nerolidol, α-bisabolol, and nerol, with affinity to AaegOBP1 comparable with DEET and IR3535. Geranyl acetate, nerolidol, and their mixtures showed no cytotoxicity and protection percentages close to 100% during the test at concentrations 10 and 25%. Long-lasting assays with geranyl acetate and nerolidol formulate showed 3 h as maximum protection time with 100% protection percentage. These metabolites and their mixtures are candidates to repellent formulations with times and protection percentages similar to DEET.
HIV RNA, CD4+ Percentage, and Risk of Hepatocellular Carcinoma by Cirrhosis Status
Authors: Torgersen Jessie , Kallan Michael J , Carbonari Dena M , Park Lesley S , Mehta Rajni L , D’Addeo Kathryn , Tate Janet P , Lim Joseph K , Goetz Matthew Bidwell , Rodriguez-Barradas Maria C , Gibert Cynthia L , Bräu Norbert , Brown Sheldon T , Roy Jason A , Taddei Tamar H , Justice Amy C , Lo Re Vincent
Published: October 2019

Background

Despite increasing incidence of hepatocellular carcinoma (HCC) among HIV-infected patients, it remains unclear if HIV-related factors contribute to development of HCC. We examined if higher or prolonged HIV viremia and lower CD4+ cell percentage were associated with HCC.

Methods

We conducted a cohort study of HIV-infected individuals who had HIV RNA, CD4+, and CD8+ cell counts and percentages assessed in the Veterans Aging Cohort Study (1999–2015). HCC was ascertained using Veterans Health Administration cancer registries and electronic records. Cox regression was used to determine hazard ratios (HR, 95% confidence interval [CI]) of HCC associated with higher current HIV RNA, longer duration of detectable HIV viremia (≥500 copies/mL), and current CD4+ cell percentage less than 14%, adjusting for traditional HCC risk factors. Analyses were stratified by previously validated diagnoses of cirrhosis prior to start of follow-up.

Results

Among 35 659 HIV-infected patients, 302 (0.8%) developed HCC over 281 441 person-years (incidence rate = 107.3 per 100 000 person-years). Among patients without baseline cirrhosis, higher HIV RNA (HR = 1.25, 95% CI = 1.12 to 1.40, per 1.0 log10 copies/mL) and 12 or more months of detectable HIV (HR = 1.47, 95% CI = 1.02 to 2.11) were independently associated with higher risk of HCC. CD4+ percentage less than 14% was not associated with HCC in any model. Hepatitis C coinfection was a statistically significant predictor of HCC regardless of baseline cirrhosis status.

Conclusion

Among HIV-infected patients without baseline cirrhosis, higher HIV RNA and longer duration of HIV viremia increased risk of HCC, independent of traditional HCC risk factors. This is the strongest evidence to date that HIV viremia contributes to risk of HCC in this group.
(-)-Loliolide, the most ubiquitous lactone, is involved in barnyardgrass-induced rice allelopathy
Authors: Li Lei-Lei , Zhao Huan-Huan , Kong Chui-Hua
Published: November 2019

Neighbor detection and allelochemical response are important mediators in plant-plant interactions. Despite increasing knowledge of plant allelochemicals in response to the presence of competitors involved in the neighbor-derived signaling chemicals, less is known about which signaling chemicals are responsible for the neighbor-induced allelochemical response. Here, we experimentally demonstrated (-)-loliolide, a carotenoid metabolite, as a signaling chemical in barnyardgrass-rice allelopathic interactions. The production of rice allelochemicals momilactone B and tricin was increased in the presence of five biotypes of barnyardgrass. (-)-Loliolide was found in all biotypes of barnyardgrass and their root exudates and rhizosphere soils. There were significant positive relationships between rice allelechemicals and (-)-loliolide concentrations across biotypes of barnyardgrass. Furthermore, (-)-loliolide elicited the production of momilactone B and tricin. Comparative transcriptome analysis showed regulation of (-)-loliolide on diterpenoid and flavonoid biosynthesis pathway. The expression of key genes involved in the biosynthesis of momilactone B (CPS4, KSL4 and MAS) and tricin (CYP75B3 and CYP75B4) was up-regulated by (-)-loliolide. These findings suggest that (-)-loliolide as a signaling chemical participates in barnyardgrass-rice allelopathic interactions. Through the signaling chemical, allelopathic rice plants can detect competing barnyardgrass and respond by increasing allelochemical levels to provide an advantage for their own growth.
Determining the origin of the building blocks of the Ice Giants based on analogue measurements from comets
Authors: Mandt K E , Mousis O , Treat S
Published: November 2019

The abundances of the heavy elements and isotopic ratios in the present atmospheres of the giant planets can be used to trace the composition of volatiles that were present in the icy solid material that contributed to their formation. The first definitive measurements of noble gas abundances and isotope ratios at comet 67P/Churyumov–Gerasimenko (67P/C–G) were recently published by Marty et al. (2017) and Rubin et al. (2018, 2019). The implications of these abundances for the formation conditions of the 67P/C–G building blocks were then evaluated by Mousis et al. (2018a). We add here an analysis of the implications of these results for understanding the formation conditions of the building blocks of the Ice Giants and discuss how future measurements of Ice Giant atmospheric composition can be interpreted. We first evaluate the best approach for comparing comet observations with giant planet composition, and then determine what would be the current composition of the Ice Giant atmospheres based on four potential sources for their building blocks. We provide four scenarios for the origin of the Ice Giants building blocks based on four primary constraints for building block composition: (1) the bulk abundance of carbon relative to nitrogen, (2) noble gas abundances relative to carbon and nitrogen, (3) abundance ratios Kr/Ar and Xe/Ar, and (4) Xe isotopic ratios. In situ measurements of these quantities by a Galileo-like entry probe in the atmosphere(s) of Uranus and/or Neptune should place important constraints on the formation conditions of the Ice Giants.
Beyond two-point statistics: using the minimum spanning tree as a tool for cosmology
Authors: Naidoo Krishna , Whiteway Lorne , Massara Elena , Gualdi Davide , Lahav Ofer , Viel Matteo , Gil-Marín Héctor , Font-Ribera Andreu
Published: October 2019

Cosmological studies of large-scale structure have relied on two-point statistics, not fully exploiting the rich structure of the cosmic web. In this paper we show how to capture some of this cosmic web information by using the minimum spanning tree (MST), for the first time using it to estimate cosmological parameters in simulations. Discrete tracers of dark matter such as galaxies, N-body particles or haloes are used as nodes to construct a unique graph, the MST, that traces skeletal structure. We study the dependence of the MST on cosmological parameters using haloes from a suite of COmoving Lagrangian Acceleration (COLA) simulations with a box size of $250\ h^{-1}\, {\rm Mpc}$, varying the amplitude of scalar fluctuations (As), matter density (Ωm), and neutrino mass (∑mν). The power spectrum P and bispectrum B are measured for wavenumbers between 0.125 and 0.5 $h\, {\rm Mpc}^{-1}$, while a corresponding lower cut of ∼12.6 $h^{-1}\, {\rm Mpc}$ is applied to the MST. The constraints from the individual methods are fairly similar but when combined we see improved 1σ constraints of $\sim 17{{\ \rm per\ cent}}$ ($\sim 12{{\ \rm per\ cent}}$) on Ωm and $\sim 12{{\ \rm per\ cent}}$ ($\sim 10{{\ \rm per\ cent}}$) on As with respect to P (P + B) thus showing the MST is providing additional information. The MST can be applied to current and future spectroscopic surveys (BOSS, DESI, Euclid, PSF, WFIRST, and 4MOST) in 3D and photometric surveys (DES and LSST) in tomographic shells to constrain parameters and/or test systematics.
Light curve variation caused by accretion column switching stellar hemispheres
Authors: Čemeljić Miljenko , Siwak Michał
Published: October 2019

We investigate switching of the accretion column between the stellar hemispheres in the magnetosphere of a star with the dipole magnetic field aligned with the stellar rotation axis. We show that such switching can produce “hiccups” in the observed lightcurves. The intensity of emitted radiation from the stellar surface as seen by distant observers is computed from our two dimensional axisymmetric viscous and resistive magnetohydrodynamic numerical simulations. This result is used to construct a three-dimensional model of a star with the ring-shaped hot spots from the accretion columns at the stellar surface. We compute the intensity from such hot spots. To obtain a non-axisymmetric model with arc-shaped hot spots, we remove a ring section in the azimuthal direction from the hot-spots and compute the intensity of the radiated emission. Such models can be used to relate physical parameters in the simulations to the observations. We show an example with the intensity computed from our model compared to observational light curve.
Genotyping and De Novo Discovery of Allelic Variants at the Brassicaceae Self-Incompatibility Locus from Short-Read Sequencing Data
Authors: Genete Mathieu , Castric Vincent , Vekemans Xavier
Published: October 2019

Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinarily high levels of polymorphism, both in terms of the number of functionally distinct S-alleles that segregate in SI species and in terms of their nucleotide sequence divergence. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological challenges that have so far largely prevented the comprehensive analysis of complete allelic series in natural populations, and also precluded the obtention of complete genic sequences for many S-alleles. Here, we develop a powerful methodological approach based on a computationally optimized comparison of short Illumina sequencing reads from genomic DNA to a database of known nucleotide sequences of the extracellular domain of SRK (eSRK). By examining mapping patterns along the reference sequences, we obtain highly reliable predictions of S-genotypes from individuals collected from natural populations of Arabidopsis halleri. Furthermore, using a de novo assembly approach of the filtered short reads, we obtain full-length sequences of eSRK even when the initial sequence in the database was only partial, and we discover putative new SRK alleles that were not initially present in the database. When including those new alleles in the reference database, we were able to resolve the complete diploid SI genotypes of all individuals. Beyond the specific case of Brassicaceae S-alleles, our approach can be readily applied to other polymorphic loci, given reference allelic sequences are available.
Structural transitions in the RNA 7SK 5′ hairpin and their effect on HEXIM binding
Authors: Röder Konstantin , Stirnemann Guillaume , Dock-Bregeon Anne-Catherine , Wales David J , Pasquali Samuela
Published: October 2019

7SK RNA, as part of the 7SK ribonucleoprotein complex, is crucial to the regulation of transcription by RNA-polymerase II, via its interaction with the positive transcription elongation factor P-TEFb. The interaction is induced by binding of the protein HEXIM to the 5′ hairpin (HP1) of 7SK RNA. Four distinct structural models have been obtained experimentally for HP1. Here, we employ computational methods to investigate the relative stability of these structures, transitions between them, and the effects of mutations on the observed structural ensembles. We further analyse the results with respect to mutational binding assays, and hypothesize a mechanism for HEXIM binding. Our results indicate that the dominant structure in the wild type exhibits a triplet involving the unpaired nucleotide U40 and the base pair A43-U66 in the GAUC/GAUC repeat. This conformation leads to an open major groove with enough potential binding sites for peptide recognition. Sequence mutations of the RNA change the relative stability of the different structural ensembles. Binding affinity is consequently lost if these changes alter the dominant structure.
A unique internal ribosome entry site representing a dynamic equilibrium state of RNA tertiary structure in the 5′-UTR of Wheat yellow mosaic virus RNA1
Authors: Geng Guowei , Yu Chengming , Li Xiangdong , Yuan Xuefeng
Published: October 2019

Internal ribosome entry sites (IRESes) were first reported in RNA viruses and subsequently identified in cellular mRNAs. In this study, IRES activity of the 5′-UTR in Wheat yellow mosaic virus (WYMV) RNA1 was identified, and the 3′-UTR synergistically enhanced this IRES activity via long-distance RNA–RNA interaction between C80U81and A7574G7575. Within the 5′-UTR, the hairpin 1(H1), flexible hairpin 2 (H2) and linker region (LR1) between H1 and H2 played an essential role in cap-independent translation, which is associated with the structural stability of H1, length of discontinuous stems and nucleotide specificity of the H2 upper loop and the long-distance RNA–RNA interaction sites in LR1. The H2 upper loop is a target region of the eIF4E. Cytosines (C55, C66, C105 and C108) in H1 and H2 and guanines (G73, G79 and G85) in LR1 form discontinuous and alternative base pairing to maintain the dynamic equilibrium state, which is used to elaborately regulate translation at a suitable level. The WYMV RNA1 5′-UTR contains a novel IRES, which is different from reported IRESes because of the dynamic equilibrium state. It is also suggested that robustness not at the maximum level of translation is the selection target during evolution of WYMV RNA1.
Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster
Authors: Ellison Christopher E , Cao Weihuan
Published: November 2019

Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which has provided important insight into the population dynamics of TEs. However, such approaches are not able to identify insertions of uncharacterized TEs, nor can they assemble the full sequence of inserted elements. Here, we use nanopore sequencing and Hi-C scaffolding to produce de novo genome assemblies for two wild strains of Drosophila melanogaster from the Drosophila Genetic Reference Panel (DGRP). Ovarian piRNA populations and Illumina split-read TE insertion profiles have been previously produced for both strains. We find that nanopore sequencing with Hi-C scaffolding produces highly contiguous, chromosome-length scaffolds, and we identify hundreds of TE insertions that were missed by Illumina-based methods, including a novel micropia-like element that has recently invaded the DGRP population. We also find hundreds of piRNA-producing loci that are specific to each strain. Some of these loci are created by strain-specific TE insertions, while others appear to be epigenetically controlled. Our results suggest that Illumina approaches reveal only a portion of the repetitive sequence landscape of eukaryotic genomes and that population-level resequencing using long reads is likely to provide novel insight into the evolutionary dynamics of repetitive elements.
A DNA aptamer for binding and inhibition of DNA methyltransferase 1
Authors: Wang Linlin , Lee Ju Yong , Gao Linfeng , Yin Jiekai , Duan Yaokai , Jimenez Luis A , Adkins Gary Brent , Ren Wendan , Li Linhui , Fang Jian , Wang Yinsheng , Song Jikui , Zhong Wenwan
Published: November 2019

DNA methyltransferases (DNMTs) are enzymes responsible for establishing and maintaining DNA methylation in cells. DNMT inhibition is actively pursued in cancer treatment, dominantly through the formation of irreversible covalent complexes between small molecular compounds and DNMTs that suffers from low efficacy and high cytotoxicity, as well as no selectivity towards different DNMTs. Herein, we discover aptamers against the maintenance DNA methyltransferase, DNMT1, by coupling Asymmetrical Flow Field-Flow Fractionation (AF4) with Systematic Evolution of Ligands by EXponential enrichment (SELEX). One of the identified aptamers, Apt. #9, contains a stem-loop structure, and can displace the hemi-methylated DNA duplex, the native substrate of DNMT1, off the protein on sub-micromolar scale, leading for effective enzymatic inhibition. Apt. #9 shows no inhibition nor binding activity towards two de novo DNMTs, DNMT3A and DNMT3B. Intriguingly, it can enter cancer cells with over-expression of DNMT1, colocalize with DNMT1 inside the nuclei, and inhibit the activity of DNMT1 in cells. This study opens the possibility of exploring the aptameric DNMT inhibitors being a new cancer therapeutic approach, by modulating DNMT activity selectively through reversible interaction. The aptamers could also be valuable tools for study of the functions of DNMTs and the related epigenetic mechanisms.
DSR-GUP, maximally localized state, and black hole thermodynamics
Authors: Chung Won Sang , Hassanabadi Hassan
Published: October 2019

We consider a new type of doubly special relativity transformation which gives a new types of generalized uncertainty principle. This model is known to have invariant Planck energy (or Planck momentum) and minimal length. For this model we discuss the generalized uncertainty relation and compute the minimal length and momentum upper bound. We also compute the corresponding maximally localized state explicitly. Finally, we use the generalized uncertainty relation compatible with doubly special relativity to discuss black hole thermodynamics.
Factors associated with long-term wearable physical activity monitor user engagement
Authors: Friel Ciarán P , Cornelius Talea , Diaz Keith M
Published: October 2019

Wearable physical activity monitors (PAMs) have potential to positively influence physical activity. However, high rates of disengagement have been reported, which dampens enthusiasm, as these devices are unlikely to impact habitual physical activity if they are not worn for a sustained period of time. The purpose of this study was to identify demographic and device-use characteristics (e.g., data sharing) associated with sustained device engagement. Current PAM users (n = 418; mean age: 35.0 ± 12.5; 78% female) from across the USA were recruited online and completed a baseline web-based survey in 2015–2016 comprising questions about demographics and device use. Participants were followed-up again in 2017, at which time they reported whether or not they still used a PAM. Sustained PAM engagement was defined as those who continued use at follow-up. The median follow-up time was 15.5 (±3.7) months. In fully adjusted models, the following were significantly associated with long-term engagement: age (odds ratio [OR]: 1.03; 95% confidence interval [CI]: 1.01–1.05, p = .014), Hispanic ethnicity (OR: 3.67; 95% CI: 1.20–11.26, p = .023), running as a preferred exercise (OR: 1.82; 95% CI: 1.02–3.24, p = .043), wanting to monitor health variables as a reason for choosing to use a PAM (OR: 1.73; 95% CI: 1.02–2.92, p = .042), and sharing data from the PAM publicly on social media (e.g., Facebook and Twitter; OR: 5.11; 95% CI: 1.64–15.93, p = .005). A number of sociodemographic and use characteristics were associated with sustained device use over a median follow-up of 1.3 years. One modifiable factor that may lead to longer device engagement is encouraging users to share data publicly.