bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visibility Graph Based Community Detection for Biological Time Series
Authors: Zheng Minzhang , Domanskyi Sergii , Piermarocchi Carlo , Mias George I. 
Published: March 2020

AbstractMotivationTemporal behavior is an essential aspect of all biological systems. Time series have been previously represented as networks. Such representations must address two fundamental problems: (i) How to create the appropriate network to reflect the characteristics of biological time series. (ii) How to detect characteristic temporal patterns or events as network communities. General methods to detect communities have used metrics to compare the connectivity within a community to the connectivity one would expect in a random model, or assumed a known number of communities, or are based on the betweenness centrality of edges or nodes. However, such methods were not specifically designed for network representations of time series. We introduce a visibility-graph-based method to build networks from different kinds of biological time series and detect temporal communities within these networks.ResultsTo characterize the uneven sampling of typical experimentally obtained biological time series, and simultaneously capture events associated to peaks and troughs, we introduce the Weighted Dual-Perspective Visibility Graph (WDPVG) for time series. To detect communities, we first find the shortest path of the network between start and end nodes to identify nodes which have high intensities. This identifies the main stem of our community detection algorithm. Then, we aggregate nodes outside the shortest path to the nodes found on the main stem based on the closest path length. Through simulation, we demonstrate the validity of our method in detecting community structures on various networks derived from simulated time series. We also confirm its effectiveness in revealing temporal communities in experimental biological time series. Our results suggest our method of visibility graph based community detection can be effective in detecting temporal biological patterns.AvailabilityThe methods of building WDPVG and visibility graph based community detection are available as a module of the open source Python package PyIOmica (https://doi.org/10.5281/zenodo.3691912) with documentation athttps://pyiomica.readthedocs.io/en/latest/. The dataset and codes we used in this manuscript are publicly available athttps://doi.org/10.5281/zenodo.3693984.Contactgmias@msu.edu
Plant origin determines seed mass, seed nutrients and germination behavior of a dominant grass species
Authors: Veselá Andrea , Duongová Lien , Münzbergová Zuzana 
Published: March 2020

AbstractAlthough number of studies exploring effects of climate change on plants is increasing, only few studies pay attention to germination. Understanding of germination behaviour is complicated by impact of climate on seed mass and possibly also seed nutrients, which play irreplaceable role in nourishing the sprout. The germination behaviour of species may also depend on trade-off between generative and vegetative reproduction.We studied Festuca rubra originating from localities situated along a natural climatic grid. Seeds of different origin were germinated in two temperature and two moisture regimes, simulating the extremes of the grid. To study relationship between generative and vegetative reproduction we used data on vegetative traits originating from the same study system.Seed mass and nutrient concentrations (nitrogen and phosphorus) were significantly affected by original climate, while carbohydrates not. Higher seed mass and warm temperature of origin caused higher and faster germination. Warm and dry condition during germination caused the lowest germination but the highest seed viability. Total germination and proportion of viable seeds negatively correlated with plant performance variables contributing to vegetative reproduction. Despite this, the patterns detected using datasets of germination and plant performance, did not provide fully comparable results.Simulated changes in climatic condition can modify seed mass and seed nutrients and these changes translate into changes in species germination behavior. After accounting for seed mass, both original and target conditions determine species germination indicating that both genetic differentiation as well as actual conditions drive the germination patterns. As the patterns detected at the level of seed germination do not fully match those detected for the vegetative traits, we urge that future studies should focus on multiple stages of plant life to understand species responses to future climates.
Molecular determinants and heterogeneity of tissue-resident memory CD8+T lymphocytes revealed by single-cell RNA sequencing
Authors: Kurd Nadia S. , He Zhaoren , Milner J. Justin , Omilusik Kyla D. , Louis Tiani L. , Tsai Matthew S. , Widjaja Christella E. , Kanbar Jad N. , Olvera Jocelyn G. , Tysl Tiffani , Quezada Lauren K. , Boland Brigid S. , Huang Wendy J. , Murre Cornelis , Goldrath Ananda W. , Yeo Gene W. , Chang John T. 
Published: March 2020

AbstractDuring an immune response to microbial infection, CD8+T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of non-circulating tissue-resident memory (TRM) cells that mediate potent protection within non-lymphoid tissues. Here, we utilized single-cell RNA-sequencing to examine the gene expression patterns of individual CD8+T cells in the spleen and small intestine intraepithelial lymphocyte (siIEL) compartment throughout the course of their differentiation in response to viral infection. These analyses revealed previously unknown transcriptional heterogeneity within the siIEL CD8+T cell population at several states of differentiation, representing functionally distinct TRMcell subsets as well as a subset of TRMcell precursors within the tissue early in infection. Taken together, these findings may inform strategies to optimize CD8+T cell responses to protect against microbial infection and cancer.One sentence summaryHere, we applied single-cell RNA-sequencing to elucidate the gene expression patterns of individual CD8+T cells differentiating throughout the course of infection in the spleen and small intestinal epithelium, which revealed previously unidentified molecular determinants of tissue-resident T cell differentiation as well as functional heterogeneity within the tissue-resident CD8+T cell population.
Differential neural plasticity of individual fingers revealed by fMRI neurofeedback
Authors: Oblak Ethan , Lewis-Peacock Jarrod , Sulzer James 
Published: March 2020

AbstractPrevious work has shown that fMRI activity patterns associated with individual fingers can be shifted by temporary impairment of the hand. Here, we investigated whether these neural activity patterns could be modulated endogenously and whether any behavioral changes result from this modulation. We used decoded neurofeedback in healthy individuals to encourage participants to shift the neural activity pattern in sensorimotor cortex of the middle finger towards the index finger, and the ring finger towards the little finger. We first mapped the neural activity patterns for all fingers of the right hand in an fMRI pattern localizer session. Then, in three subsequent neurofeedback sessions, participants were rewarded after middle/ring finger presses according to their activity pattern overlap during each trial. A force-sensitive keyboard was used to ensure that participants were not altering their physical finger coordination patterns. We found evidence that participants could learn to shift the activity pattern of the ring finger but not of the middle finger. Increased variability of these activity patterns during the localizer session was associated with the ability of participants to modulate them using neurofeedback. Participants also showed an increased preference for the ring finger but not for the middle finger in a post-neurofeedback motor task. Our results show that neural activity and behaviors associated with the ring finger are more readily modulated than those associated with the middle finger. These results have broader implications for rehabilitation of individual finger movements, which may be limited or enhanced by individual finger plasticity after neurological injury.
Speed and strength of an epidemic intervention
Authors: Dushoff Jonathan , Park Sang Woo 
Published: March 2020

AbstractAn epidemic can be characterized by its speed (i.e., the exponential growth rater) and strength (i.e., the reproductive number ℛ). Disease modelers have historically placed much more emphasis on strength, in part because the effectiveness of an intervention strategy is typically evaluated on this scale. Here, we develop a mathematical framework for this classic, strength-based paradigm and show that there is a corresponding speed-based paradigm which can provide complementary insights. In particular, we note thatr= 0 is a threshold for disease spread, just like ℛ = 1, and show that we can measure the speed and strength of an intervention on the same scale as the speed and strength of an epidemic, respectively. We argue that, just as the strength-based paradigm provides the clearest insight into certain questions, the speed-based paradigm provides the clearest view in other cases. As an example, we show that evaluating the prospects of “test-and-treat” interventions against the human immunodeficiency virus (HIV) can be done more clearly on the speed than strength scale, given uncertainty in the proportion of HIV spread that happens early in the course of infection. We suggest that disease modelers should avoid over-emphasizing the reproductive number at the expense of the exponential growth rate, but instead look at these as complementary measures.
iHyd-ProSite: A novel Computational Approach for Identifying Hydroxylation Sites in Proline Via Mathematical Modeling
Authors: Mahmood Muhammad Khalid , Ehsan Asma , Khan Yaser Daanial 
Published: March 2020

AbstractIn various cellular functions, post translational modifications (PTM) of protein play a vital role. The addition of certain functional group through a covalent bond to the protein induces PTM. The number of PTMs are identified which are closely linked with diseases for example cancer and neurological disorder. Hydroxylation is one of the PTM, modified proline residue within a polypeptide sequence. The defective hydroxylation of proline causes absences of ascorbic acid in human which produce scurvy, and many other dominant health issues. Undoubtedly, the prediction of hydroxylation sites in proline residues is of challenging frontier. The experimental identification of hydroxyproline site is quite difficult, high-priced and time-consuming. The diversity in protein sequences instigates to develop a computational tool to identify hydroxylated site within short time with excellent prediction accuracy to handle such proteomics problems. In this work a novel in silico predictor is developed through rigorous mathematical modeling to identify which site of proline is hydroxylated and which site is not? Then performance of the predictor was verified using three validations tests, namely self-consistency test, cross-validation test and jackknife test over the benchmark dataset. A comparison was established for jackknife test with the previous methods. In comparison with previous predictors the proposed tool is more accurate than the existing techniques. Hence this scheme is highly useful and inspiring in contrast to all previous predictors.
Regulation of gene expression by repression condensates during development
Authors: Treen Nicholas , Shimobayashi Shunsuke F. , Eeftens Jorine , Brangwynne Clifford P. , Levine Michael S. 
Published: March 2020

AbstractThere is emerging evidence for transcription condensates in the activation of gene expression1–3. However, there is considerably less information regarding transcriptional repression, despite its pervasive importance in regulating gene expression in development and disease. Here, we explore the role of liquid-liquid phase separation (LLPS) in the organization of the Groucho/TLE (Gro) family of transcriptional corepressors, which interact with a variety of sequence-specific repressors such as Hes/Hairy4. Gro-dependent repressors have been implicated in a variety of developmental processes, including segmentation of theDrosophilaembryo and somitogenesis in vertebrates. These repressors bind to specific recognition sequences, but instead of interacting with coactivators (e.g., Mediator) they recruit Gro corepressors5. Gro contains a series of WD40 repeats that are thought to mediate oligomerization6. How putative Hes/Gro oligomers repress transcription has been the subject of numerous studies5, 6. Here we show that Hes/Gro complexes form discrete puncta within nuclei of livingCionaembryos. These puncta rapidly dissolve during the onset of mitosis and reappear in the ensuing cell cycle. Modified Hes/Gro complexes that are unable to bind DNA exhibit the properties of viscous liquid droplets, similar to those underlying the biogenesis of P-granules inC. elegans7and nucleoli inXenopusoocytes8. These observations provide vivid evidence for LLPS in the control of gene expression and suggest a simple physical exclusion mechanism for transcriptional repression. WD40 repeats have been implicated in a wide variety of cellular processes in addition to transcriptional repression9. We suggest that protein interactions using WD40 motifs might be a common feature of processes reliant on LLPS.
Examining user experience of eLearning systems implemented in two universities in Tanzania
Authors: Mtebe Joel S. 
Published: March 2020

Purpose
This study aims to investigate the factors that influence user experience (UX) of eLearning systems implemented in two institutions in Tanzania.

Design/methodology/approach
The study adopted questionnaire consisting of Nielsen’s heuristics and didactic metrics as pragmatic metrics and hedonic metrics followed by focus group discussions with students.

Findings
The study found that the eLearning system of University of Dar es Salaam had 43 UX problems related to Nielsen’s heuristics and 54 UX problems related to didactic heuristics. The eLearning system of the Open University of Tanzania had 50 UX problems related to Nielsen’s heuristics and 59 UX problems related to didactic heuristics. Moreover, the two systems provided positive UX hedonic quality on identification and evocation dimensions while stimulation was perceived to be neutral.

Research limitations/implications
The study has used learners as evaluators rather than expert evaluators. Learners are not particularly experienced in the learning domain, and therefore, it is difficult for them to identify many didactic violations of the eLearning systems.

Originality/value
The study contributes toward finding the underlying factors for non-use or underuse of the installed eLearning systems in various universities in sub-Saharan Africa.
Sustainability of the rice-shrimp farming system in Mekong Delta, Vietnam: a climate adaptive model
Authors: Dang Huy Duc 
Published: March 2020

PurposeAgricultural systems in Mekong Delta have transformed to cope with climate change. Various researches pointed out that integrated agriculture-aquaculture (IAA) farming systems (i.e., rice-shrimp, rice-fish…) emerged as potential climate adaptive practices. However, limited studies are attempting to assess the sustainability of these agricultural practices. Therefore, it is essential to assess whether or not these systems will be sustainable in the context of climate change and what can be done to make it sustainable. The present study conducted the sustainability assessment of the rice-shrimp system to identify potential areas for improvement as well as policy implication to increase resilience and adaptation of coastal IAA system which could contribute to the understanding of other coastal agricultural deltas around the globe.Design/methodology/approachThis study used a quantitative approach including the assessment protocol of van Asselt et al. (2014), the assessment framework of Vanloon et al. (2005), and the MCA methodology to flexibly and holistically assess the sustainability level of agricultural systems.FindingsResults concluded that rice-shrimp systems have the potential to improve livelihood, food security, and adaptation of coastal farmers. Major improvements should be considered for productivity, efficiency, and equity themes, while minor improvements can be made for stability, durability, and compatibility themes.Originality/valueThis research could be used as a guideline for sustainability assessment in a context-specific case study of IAA, which showed a potential for the application of other climate-smart IAAs in similar contexts around the globe.
Economic growth and quality of institutions in 27 postsocialist economies
Authors: Alexiou Constantinos , Vogiazas Sofoklis , Solovev Nikita 
Published: March 2020

PurposeThe relationship between institutional quality and economic growth is revisited.Design/methodology/approachA panel cointegration methodology and causality analysis are applied to 27 postsocialist economies over the period from 1996 to 2016.FindingsUtilizing the Worldwide Governance Indicators as a means of assessing the quality of institutions, it is found that in the long run, economic growth is positively associated with the rule of law and voice and accountability. In the short run, regulatory quality retains a positive effect, but voice and accountability demonstrate a puzzling negative effect on economic growth that merits further analysis. In exploring the causal dimension of our variables, supporting evidence of the strong links between the quality of institutions and economic growth is provided, hence rendering robust results.Originality/valueTo the best of the authors’ knowledge, it is the first time that an ARDL methodological framework, which addresses potential endogeneity issues, is used to investigate the relationship between institutional quality and growth in the context of postsocialist economies.
A PCA-DEA method for organizational performance evaluation based on intellectual capital and employee loyalty
Authors: Rahimpour Khojasteh , Shirouyehzad Hadi , Asadpour Milad , Karbasian Mehdi 
Published: March 2020

Purpose
The purpose of this study is to propose a model to evaluate the performance of organizational units considering intellectual capital (IC) and employee loyalty approach applying principal component analysis and data envelopment analysis (PCA-DEA) method.

Design/methodology/approach
Organization units are considered as decision-making units, IC components including human capital (HC), structural capital (SC) and customer capital are inputs and employee loyalty is output. The principal component analysis was used to converts inputs and outputs into the independent variables. As a return to scale is variable, a modified envelopment input-oriented BCC model applied to obtain the efficiency of organization units. Also, all units of organization are ranked. Eventually, sensitivity analysis performed to show how input variables influence on output variable.

Findings
Operation, design and construction, production planning, internal affairs, quality control and security were recognized as efficient units. Also, units of operation, internal affairs and quality control ranked first to third, and the human resource unit earned the last rank. In addition, results of sensitivity analysis on input variables showed that the order of impact intensity is: customer capital, HC and SC, respectively.

Originality/value
Existence a framework for the development of human resource strategies and prioritization in the allocation of organizational resources to improve the performance of the organization considering human resources is vital. Most of the previous studies, just have examined the impact of IC on different dimensions of organizational performance. Meanwhile, evaluating the performance of IC with employee loyalty approach, using PCA-DEA simultaneously can evaluate and measure the impact of IC on the performance of the organization and its units regarding employee loyalty, which has a significant impact on improving the organization’s level of IC and human resource management.
Innovation and intellectual capital as intermediary variables among transformational leadership, transactional leadership, and organizational performance
Authors: Alrowwad Ala'aldin , Abualoush Shadi Habis , Masa'deh Ra'ed 
Published: March 2020

PurposeThe purpose of this paper is to examine the mediating effect of intellectual capital and innovation on the relationship between transformational and transactional leadership and organizational performance in Jordanian banks located in Irbid city.Design/methodology/approachA questionnaire that targeted 350 respondents resulted in 298 usable ones with a response rate of 85.14 percent. To test the research hypotheses, a structural equation model was conducted, in addition to descriptive statistics that provided background on the respondents.FindingsThe findings indicate that transformational and transactional leadership relate positively to organizational performance. The results also support the argument that intellectual capital and innovation played mediating roles in transformational and transactional leadership and organizational performance.Practical implicationsThe present study provides managers with empirical proof that possessing strong intellectual capital in its three dimensions seems to help the banking sector in Jordan to reinforce their ability to generate both radical and incremental innovation. Also, applying an effective leadership style will motivate and lead to superior performance.Originality/valueAlthough papers have shown that leadership style is an important factor influencing employees' performance and outcomes, this is one of the few studies that investigates the interrelationships between leadership styles, intellectual capital, and innovation on organization performance. Furthermore, it is the first to test the model on the banking sector in Jordan.
Vanillin-based thiol-ene systems as photoresins for optical 3D printing
Authors: Navaruckiene Aukse , Kasetaite Sigita , Ostrauskaite Jolita 
Published: March 2020

Purpose
This study aims to present a design and investigation of novel vanillin-based thiol-ene photocurable systems as candidate materials for optical three-dimensional printing.

Design/methodology/approach
Two vanillin acrylates, vanillin dimethacrylate and vanillin diacrylate, were tested in thiol-ene photocurable systems with 1,3-benzenedithiol. The kinetics of photocross-linking was investigated by real-time photorheometry using two photoinitiators, diphenyl (2,4,6-trimethylbenzoyl)phosphine oxide or ethyl (2,4,6-trimethylbenzoyl)phenylphosphinate in different quantities. The dependencies of rheological properties of resins on the used vanillin derivative, photoinitiator, and the presence of a solvent, as well as structure, thermal and mechanical properties of the selected polymers were investigated.

Findings
The most rigid polymers were obtained from vanillin diacrylate-based resins without any solvent. The vanillin diacrylate-based polymer possessed higher values of cross-linking density, the yield of insoluble fraction, thermal stability and better mechanical properties in comparison to the vanillin dimethacrylate-based polymer.

Originality/value
The kinetics of photocross-linking of vanillin-based thiol-ene systems was investigated by real-time photorheometry for the first time. The designed novel photocurable systems based on vanillin acrylates and 1,3-benzenedithiol are promising renewable photoresins for optical three-dimensional printing on demand.