bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nematodes Versus White Grubs: Long But Challenging Association
Authors: Haji Allahverdipour Hana , Karimi Javad 
Published: April 2021

AbstractSoil as a shared habitat of white grubs and entomopathogenic nematodes (EPNs) is a double-edged sword from the biological control point of view. Soil encompasses a diverse array of EPNs that could be exploited in grub microbial control; on the other hand, soil promotes the natural resistance of grubs to EPNs via the battle between both sides within the soil matrix. White grubs and EPNs have been armed in this battle by a multifaceted range of mechanisms, namely grub structural and physiological barriers, antagonism of grub gut microbiota toward the nematode bacterial symbionts, EPN excreted/secreted proteins, surface coat proteins, ascaroside pheromones produced by EPNs, and evolution of EPN resistance to herbivore self-defense. From the evolutionary point of view, EPN–grub interactions, the most advanced (sophisticated) association among others, could have evolved from other types of associations. Entomophilic nematode (e.g., Pristionchus spp.), the cognate bacterium and scarab associations along with the formation of dauer juveniles, are proof of preadaptation to entomopathogeny in a continual evolution. Here, we delve into the salient features of each component of EPN-white grub–host plant tripartite interactions as well as hints to improved exploitation of EPNs for grub management. Also, evolutionary associations between nematodes and scarabs will be reviewed, in short.
Ecotypic differentiation of a circumpolar Arctic-alpine species at mid-latitudes: variations in the ploidy level and reproductive system of Vaccinium vitis-idaea
Authors: Wakui Akimi , Kudo Gaku 
Published: April 2021

Abstract
Although plant species originated from Arctic regions commonly grow in alpine habitats at mid-latitudes, some populations of these species exist also in some specific habitats below the treeline. Local populations at lower elevations may have different origins, ploidy levels, mating systems and/or morphological traits from alpine populations, but comparative studies between alpine and low-elevation populations are scarce. We aimed to reveal the ecological and genetic differentiations between higher and lower populations of Vaccinium vitis-idaea in Hokkaido, northern Japan by comparing 22 populations growing in diverse environments. We analysed the ploidy level of individual populations using flow cytometry. Genetic differentiation among populations, and genetic diversity within populations were calculated using microsatellite markers. Fruit and seed production were recorded under natural conditions, and a pollination experiment was conducted to reveal the variations in mating system across populations. Furthermore, we compared shoot growth and leaf characteristics among populations. Most of the low-elevation populations were tetraploid, whereas all but one of the alpine populations were diploid. Tetraploid populations were clearly differentiated from diploid populations. Some tetraploid populations formed huge clonal patches but genetic diversity was higher in tetraploids than in diploids. Alpine diploids were self-incompatible and produced more seeds per fruit than tetraploid populations. In contrast, tetraploids showed high self-compatibility. Leaf size and foliar production were greater in tetraploid populations. Our results indicate that the genetic compositions of low-elevation tetraploid populations are different from those of alpine diploid populations. Most populations at lower elevations contained unique ecotypes suited to persistence in isolated situations. Local, low-elevation populations of typical alpine species maintain ecologically and genetically specific characteristics and could be valuable in terms of evolutionary and conservation biology. The present study demonstrates the biological importance of small and isolated populations at the edges of species distribution.
CoCoNet: an efficient deep learning tool for viral metagenome binning
Authors: Arisdakessian Cédric G , Nigro Olivia D , Steward Grieg F , Poisson Guylaine , Belcaid Mahdi 
Published: April 2021

Abstract

Motivation
Metagenomic approaches hold the potential to characterize microbial communities and unravel the intricate link between the microbiome and biological processes. Assembly is one of the most critical steps in metagenomics experiments. It consists of transforming overlapping DNA sequencing reads into sufficiently accurate representations of the community’s genomes. This process is computationally difficult and commonly results in genomes fragmented across many contigs. Computational binning methods are used to mitigate fragmentation by partitioning contigs based on their sequence composition, abundance or chromosome organization into bins representing the community’s genomes. Existing binning methods have been principally tuned for bacterial genomes and do not perform favorably on viral metagenomes.

Results
We propose Composition and Coverage Network (CoCoNet), a new binning method for viral metagenomes that leverages the flexibility and the effectiveness of deep learning to model the co-occurrence of contigs belonging to the same viral genome and provide a rigorous framework for binning viral contigs. Our results show that CoCoNet substantially outperforms existing binning methods on viral datasets.

Availability and implementation
CoCoNet was implemented in Python and is available for download on PyPi (https://pypi.org/). The source code is hosted on GitHub at https://github.com/Puumanamana/CoCoNet and the documentation is available at https://coconet.readthedocs.io/en/latest/index.html. CoCoNet does not require extensive resources to run. For example, binning 100k contigs took about 4 h on 10 Intel CPU Cores (2.4 GHz), with a memory peak at 27 GB (see Supplementary Fig. S9). To process a large dataset, CoCoNet may need to be run on a high RAM capacity server. Such servers are typically available in high-performance or cloud computing settings.

Supplementary information
Supplementary data are available at Bioinformatics online.
Optimal Bayesian supervised domain adaptation for RNA sequencing data
Authors: Boluki Shahin , Qian Xiaoning , Dougherty Edward R 
Published: April 2021

Abstract

Motivation
When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks.

Results
In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance.

Availability and implementation
The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Feasible TLC-Spectro-Densitometry Technique for Simultaneous Determination of Two Hepatitis C Antiviral Drugs, Sofosbuvir and Simeprevir: Application to Combined Pharmaceutical Dosage Forms and Human Plasma
Authors: Mohammed Bassam Shaaban , Derayea Sayed M , Hamad Amal E 
Published: April 2021

Abstract
A high-performance thin-layer chromatographic method was developed and validated for the concurrent determination of simeprevir (SMV) and sofosbuvir (SOF). The chromatographic separation was attained on silica gel 60 F254 as stationary phase and ethyl acetate–hexane–methanol (5.0:4.0:1.0, v/v/v) as developing solvent with UV detection at 273 nm. The RF values were 0.67±0.02 and 0.43±0.02 for SMV and SOF, respectively. The method has been validated in respect to the guidelines of the International Conference on Harmonization. Linearity was maintained between 60–1,000 and 70–1,200 ng/band for SMV and SOF, respectively, with good correlation coefficients (0.9993–0.9997) for both drugs. The suggested method was highly sensitive as the calculated detection limits were 15 and 22 ng/band, while the quantitation limits were 44 and 66 ng/ band for SMV and SOF, respectively. The suggested methodology has been effectively employed for the determination of the mentioned drugs in their pure forms and their pharmaceutical dosage forms as well as human plasma without significant interference of the pharmaceutical excipients or plasma components.
eCK-Secure Authenticated Key Exchange against Auxiliary Input Leakage
Authors: Li Sujuan , Zhang Futai 
Published: April 2021

Abstract
Authenticated key exchange protocols are quite important primitives for practical applications, since they enable two parties to generate a shared high entropy secret key. In this paper we mainly focus on the authenticated key exchange (AKE) against auxiliary input leakage. As the major contribution of this work, we present a generic framework for the construction of AKE protocols that are secure against auxiliary input leakage. An instantiation based on the generalized decisional Diffie-Hellman (GDDH) assumption in the standard model is also given to demonstrate the feasibility of our proposed framework. We also give a comparison among the existing leakage resilient AKE protocols with auxiliary inputs.
Young adults’ coping strategies against loneliness during the COVID-19-related quarantine in Greece
Authors: Golemis Adrianos , Voitsidis Panteleimon , Parlapani Eleni , Nikopoulou Vasiliki A , Tsipropoulou Virginia , Karamouzi Panayiota , Giazkoulidou Aikaterini , Dimitriadou Aikaterini , Kafetzopoulou Christina , Holeva Vasiliki , Diakogiannis Ioannis 
Published: April 2021

SummaryCOVID-19 and the related quarantine disrupted young adults’ academic and professional life, daily routine and socio-emotional well-being. This cross-sectional study focused on the emotional and behavioural responses of a young adult population during the COVID-19-related quarantine in April 2020, in Greece. The study was conducted through an online survey. A total of 1559 young adults, aged 18−30 years, completed Steele’s Social Responsibility Motivation Scale and the De Jong Gierveld Loneliness Scale, and answered questions about compliance with instructions, quarantine-related behaviours and coping strategies. According to the results, participants displayed a relatively high sense of social responsibility (M = 16.09, SD = 2.13) and a trend towards moderate feeling of loneliness (M = 2.65, SD = 1.62); young women reported significantly higher levels of loneliness than men. The majority complied with instructions often (46.4%) or always (44.8%). Significantly more women created a new social media account and used the social media longer than 5 h/day, compared with men. Resorting to religion, practicing sports and sharing thoughts and feelings about COVID-19 with others predicted higher levels of social responsibility; humour, practicing sports and sharing thoughts and feelings about COVID-19 with others predicted lower levels of loneliness. Conclusively, COVID-19 is expected to have a significant psychological impact on young adults. Currently, Greece is going through the second quarantine period. This study raises awareness about loneliness in young adults during the COVID-19-related quarantine and highlights the importance of developing online programmes, attractive to younger people, to nurture adaptive coping strategies against loneliness.
Proteomic analysis of aged and OPTN E50K retina in the development of normal tension glaucoma
Authors: Liu Xinna , Wang Qi , Shao Zhengbo , Zhang Shiqi , Hou Mingying , Jiang Menglu , Du Mengxian , Li Jing , Yuan Huiping 
Published: April 2021

Abstract
Progressive degeneration of retinal ganglion cells (RGCs) is a major characteristic of glaucoma, whose underlying mechanisms are still largely unknown. An E50K mutation in the Optineurin (OPTN) gene is a leading cause of normal tension glaucoma (NTG), directly affecting RGCs without high intraocular pressure and causing severe glaucomatous symptoms in clinical settings. A systematic analysis of the NTG mouse model is crucial for better understanding of the underlying pathological mechanisms for glaucoma. To elucidate proteomic and biochemical pathway alterations during NTG development, we established an OPTN E50K mutant mouse model through CRISPR/Cas9. Retinal proteins from resulting mice exhibiting glaucomatous phenotypes were subject to tandem mass tag-labeled quantitative proteomics and then analyzed through bioinformatics methods to characterize the molecular and functional signatures of NTG. We identified 6364 quantitative proteins in our proteomic analysis. Bioinformatics analysis revealed that OPTN E50K mice experienced protein synthesis dysregulation, age-dependent energy defects and autophagy-lysosome pathway dysfunction. Certain biological features, including amyloid deposition, RNA splicing, microglia activation and reduction of crystallin production, were similar to Alzheimer’s disease. Our study is the first to describe proteomic and biochemical pathway alterations in NTG pathogenesis during disease advancement. Several proteomic signatures overlapped with retinal changes found in the ad mice model, suggesting the presence of common mechanisms between age-related degenerative disorders, as well as prospective new targets for diagnostic and therapeutic strategies.
Perspective on integration of concentrated solar power plants
Authors: Yousef Bashria A A , Hachicha Ahmed A , Rodriguez Ivette , Abdelkareem Mohammad Ali , Inyaat Abrar 
Published: April 2021

Abstract
Integration concept of energy resources can complement between the competing energy technologies. This manuscript presents a comprehensive review on the state-of-the-art of concentrated solar power (CSP) integration technology with various energy sources. Compared to CSP alone, integration of CSP and fossil fuel provides promising solution to solar energy intermittence, emissions and installation cost reduction, with 25% increase in electric power generation. On the other hand, integration of CSP with other sources such as geothermal and biomass can supply dispatchable power with almost zero emissions. The electricity produced via integrated CSP and photovoltaic (PV) has better power quality and less cost compared to that produced by PV alone or CSP alone, respectively. Integration of CSP and wind energy can meet peak demand, reduce power fluctuation and provide electrical power at a high capacity factor. However, the lack of reliable biomass, geothermal and wind data with the solar availability at specific locations is the main obstacle for the acceptance and further deployment of hybridization systems. The advantages and limitations of the hybrid technologies presented in this paper according to the literature are reviewed. Moreover, future directions of CSP such as production of hydrogen, solid particles receivers and the integration of supercritical carbon dioxide cycle are also discussed.
Development of the perceptions of preventable adverse events assessment tool (PPAEAT): measurement properties and patients’ mental health status
Authors: Keller Franziska Maria , Derksen Christina , Kötting Lukas , Schmiedhofer Martina , Lippke Sonia 
Published: April 2021

Abstract

Background
Patient-centered care and patient involvement have been increasingly recognized as crucial elements of patient safety. However, patient safety has rarely been evaluated from the patient perspective with a quantitative approach aiming at making patient safety and preventable adverse events measurable.

Objectives
The objectives of this study were to develop and evaluate the psychometric properties of a questionnaire assessing patient safety by perceived triggers of preventable adverse events among patients in primary health-care settings while considering mental health.

Methods
Two hundred and ten participants were recruited through various digital and print channels and asked to complete an online survey between November 2019 and April 2020. Exploratory factor analysis was performed to identify domains of triggers of preventable adverse events affecting patient safety. Furthermore, a multi-trait scaling analysis was performed to evaluate internal reliability as well as item-scale convergent–discriminant validity. A multivariate analysis of covariance evaluated whether individuals below and above the symptom threshold for depression and generalized anxiety perceive triggers of preventable adverse events differently.

Results
The five factors determined were information and communication with patients, time constraints of health-care professionals, diagnosis and treatment, hygiene and communication among health-care professionals, and knowledge and operational procedures. The questionnaire demonstrated a good total and subscale internal consistency (α = 0.90, range = 0.75–0.88), good item-scale convergent validity with significant correlations between 0.57 and 0.78 (P &lt; 0.05; P &lt; 0.01) for all items with their associated subscales, and satisfactory item-scale discriminant validity between 0.14 and 0.55 (P &gt; 0.05) with no significant correlations between the items and their competing subscales. The questionnaire further revealed to be a generic measure irrespective of patients’ mental health status. Patients older than 50 years of age perceived a significantly greater threat to their own safety compared to patients below that age.

Conclusion
The developed Perceptions of Preventable Adverse Events Assessment Tool (PPAEAT) exhibits good psychometric properties, which supports its use in future research and primary health-care practice. Further validation of the PPAEAT in different settings, languages and larger samples is needed. The results of this study need to be considered when assessing patient safety in the context of health-care research.
The Looping Structure of Buddhist Thought (Or, How Chan Buddhism Resolves the Quantum Measurement Problem)
Authors: Sharf Robert H 
Published: April 2021

AbstractIs there a world out there when nobody is looking? This is a question that medieval Buddhist scholiasts struggled with over many centuries, giving rise to a variety of competing positions. In this article, I identify a loop that runs through and structures seemingly antithetical positions—some realist, some antirealist—in these debates. My claim is that the loop is a feature of our lifeworld, and thus any serious reflection on the mind/world relationship is bound to get entangled in it. Even modern physics has come up against it, such that rival positions advanced by quantum theorists are structurally analogous to positions proffered in medieval Buddhist writings. I conclude by turning to the Chan Buddhist tradition, which is often mischaracterized as hostile to philosophical analysis. Chan is among the few Buddhist schools that recognize, foreground, and celebrate the manner in which mind and world enfold each other. As such, this paper foregrounds the decidedly philosophical insights of the Chan tradition.
Robot-assisted thoracoscopic surgery using a narrow-profile vascular stapler through an 8-mm robotic port
Authors: Shidei Hiroaki , Mitsuboshi Shota , Akihiro Koen , Aoshima Hiroe , Isaka Tamami , Kanzaki Masato 
Published: April 2021

Abstract
The number of robot-assisted thoracoscopic surgery (RATS) procedures performed for thoracic disease has been increasing. Recently, a narrow-profile vascular stapler (Signia small-diameter reload, Covidien Japan, Tokyo, Japan) has been developed to provide superior access and precise staple placement in video-assisted thoracoscopic surgery (VATS) procedures. A 70-year-old man who was an exsmoker visited our hospital with a complaint of coughing. Chest computed tomography revealed a tumor with a cavity, ~55 mm in diameter, in the right-middle lobe. A 4-arm RATS right-middle lobectomy was performed with a 4-cm utility thoracotomy with da Vinci Xi (Intuitive Surgical, Sunnyvale, CA, USA). The pulmonary vessels were divided using a narrow-profile vascular stapler through an 8-mm port. No complications occurred in the postoperative course. With a narrow-profile vascular stapler, portal RATS can be performed after VATS lung biopsy using 8-mm ports.
Involvement of the R2R3-MYB transcription factor MYB21 and its homologs in regulating flavonol accumulation in Arabidopsis stamen
Authors: Zhang Xueying , He Yuqing , Li Linying , Liu Hongru , Hong Gaojie 
Published: April 2021

Abstract
Commonly found flavonols in plants are synthesized from dihydroflavonols by flavonol synthase (FLS). The genome of Arabidopsis thaliana contains six FLS genes, among which FLS1 encodes a functional enzyme. Previous work has demonstrated that the R2R3-MYB subgroup 7 transcription factors MYB11, MYB12, and MYB111 redundantly regulate flavonol biosynthesis. However, flavonol accumulation in pollen grains was unaffected in the myb11myb12myb111 triple mutant. Here we show that MYB21 and its homologs MYB24 and MYB57, which belong to subgroup 19, promote flavonol biosynthesis through regulation of FLS1 gene expression. We used a combination of genetic and metabolite analysis to identify the role of MYB21 in regulating flavonol biosynthesis through direct binding to the GARE cis-element in the FLS1 promoter. Treatment with kaempferol or overexpression of FLS1 rescued stamen defects in the myb21 mutant. We also observed that excess reactive oxygen species (ROS) accumulated in the myb21 stamen, and that treatment with the ROS inhibitor diphenyleneiodonium chloride partly rescued the reduced fertility of the myb21 mutant. Furthermore, drought increased ROS abundance and impaired fertility in myb21, myb21myb24myb57, and chs, but not in the wild type or myb11myb12myb111, suggesting that pollen-specific flavonol accumulation contributes to drought-induced male fertility by ROS scavenging in Arabidopsis.