bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs
Authors: Wadie Bishoy , Kleshchevnikov Vitalii , Sandaltzopoulou Elissavet , Benz Caroline , Petsalaki Evangelia 
Published: June 2021

AbstractLinear motifs have an integral role in dynamic cell functions including cell signalling, the cell cycle and others. However, due to their small size, low complexity, degenerate nature, and frequent mutations, identifying novel functional motifs is a challenging task. Viral proteins rely extensively on the molecular mimicry of cellular linear motifs for modifying cell signalling and other processes in ways that favour viral infection. This study aims to discover human linear motifs convergently evolved also in disordered regions of viral proteins, under the hypothesis that these will result in enrichment in functional motif instances. We systematically apply computational motif prediction, combined with implementation of several functional and structural filters to the most recent publicly available human-viral and human-human protein interaction network. By limiting the search space to the sequences of viral proteins, we observed an increase in the sensitivity of motif prediction, as well as improved enrichment in known instances compared to the same analysis using only human protein interactions. We identified > 8,400 motif instances at various confidence levels, 105 of which were supported by all functional and structural filters applied. Overall, we provide a pipeline to improve the identification of functional linear motifs from interactomics datasets and a comprehensive catalogue of putative human motifs that can contribute to our understanding of the human domain-linear motif code and the mechanisms of viral interference with this.
Cellular intelligence: dynamic specialization through non-equilibrium multi-scale compartmentalization
Authors: Tuyéras Rémy , Agudelo Leandro Z. , Ram Soumya P. , Loon Anjanet , Kutlu Burak , Grove Kevin , Kellis Manolis 
Published: June 2021

AbstractIntelligence is usually associated with the ability to perceive, retain and use information to adapt to changes in one’s environment. In this context, systems of living cells can be thought of as intelligent entities. Here, we show that the concepts of non-equilibrium tuning and compartmentalization are sufficient to model manifestations of cellular intelligence such as specialization, division, fusion and communication using the language of operads. We implement our framework as an unsupervised learning algorithm, IntCyt, which we show is able to memorize, organize and abstract reference machine-learning datasets through generative and self-supervised tasks. Overall, our learning framework captures emergent properties programmed in living systems, and provides a powerful new approach for data mining.Structured abstractBackgroundAlthough intelligence has been given many definitions, we can associate it with the ability to perceive, retain, and use information to adapt to changes in one’s environment. In this context, systems of living cells can be thought of as intelligent entities. While one can reasonably describe their adaptive abilities within the realm of homeostatic mechanisms, it is challenging to comprehend the principles governing their metabolic intelligence. In each organism, cells have indeed developed as many ways to adapt as there are cell types, and elucidating the impetus of their evolutionary behaviors could be the key to understanding life processes and likely diseases.AdvancesThe goal of this article is to propose principles for understanding cellular intelligence. Specifically, we show that the concepts of non-equilibrium tuning and compartmentalization are enough to recover cellular adaptive behaviors such as specialization, division, fusion, and communication. Our model has the advantage to encompass all scales of life, from organelles to organisms through systems of organs and cell assemblies. We achieve this flexibility using the language of operads, which provides an elegant framework for reasoning about nested systems and, as an emergent behavior, non-equilibrium compartmentalization.To demonstrate the validity and the practical utility of our model, we implement it in the form of an unsupervised learning algorithm, IntCyt, and apply it to reference machine learning datasets through generative and self-supervised tasks. We find that IntCyt’s interpretability, plasticity and accuracy surpass that of a wide range of machine learning algorithms, thus providing a powerful approach for data mining.OutlookOur results indicate that the nested hierarchical language of operads captures the emergent properties of programmed cellular metabolism in the development of living systems, and provide a new biologically-inspired, yet practical and lightweight, computational paradigm for memorizing, organizing and abstracting datasets.
Age-related change in adult chimpanzee social network integration
Authors: González Nicole Thompson , Machanda Zarin , Otali Emily , Muller Martin N. , Enigk Drew K. , Wrangham Richard , Thompson Melissa Emery 
Published: June 2021

AbstractBackgroundSocial isolation is a key risk factor for the onset and progression of age-related disease and mortality in humans, yet older people commonly have narrowing social networks. Few models explain why human networks shrink with age, despite the risk that small networks and isolation pose. We evaluate models grounded in a life history perspective by studying social aging in wild chimpanzees, which are long-lived and show physical decline with age.MethodologyWe applied social network analysis to examine age-related changes in social integration in a 7+ year mixed-longitudinal dataset comprised of 38 wild adult chimpanzees (22 F, 16 M) in the Kanyawara community in the Kibale National Park, Uganda. Metrics of social integration included social attractivity and overt effort (directed degree and strength), gregariousness (undirected strength), social roles (betweenness and local transitivity), and embeddedness (eigenvector centrality) in grooming and spatial association networks.ResultsMales reduced overt social effort yet increased in attractivity, roles in cliques, and embeddedness. Females were overall less integrated than males, and their decreased integration with age suggested social avoidance. Effects of age were largely independent of rank. Both sexes maintained highly repeatable inter-individual differences in several aspects of integration, particularly among mixed-sex partners.Conclusions and implicationsAs in humans, chimpanzees experience age-related declines in social effort. However, important facets of integration aged more similarly to humans in non-industrialized vs. industrialized societies, suggesting an evolutionary social mismatch between conserved declines in effort and dynamics of industrialized society. Lastly, individual and sex differences have the potential to be important mediators of successful social aging in chimpanzees, as in humans.
Structural determinants of Acid-sensing ion channel potentiation by single chain lipids
Authors: Klipp Robert C. , Bankston John R. 
Published: June 2021

AbstractAcid-sensing ion channels (ASICs) are sensitized to activation by inflammatory mediators like the polyunsaturated fatty acid (PUFA) arachidonic acid (AA). Previous work has shown that AA can potentiate ASIC currents at subsaturating proton concentrations, but the structural mechanisms of this change in gating are not understood. Here we show that PUFAs cause multiple gating changes in ASIC3 including shifting the pH dependence of activation, slowing the rate of desensitization, and increasing the current even at a saturating pH. The impact on gating depends on the nature of both the head and tail of the lipid with the head group structure primarily determining the magnitude of the effect on the channel. An N-acyl amino acid (NAAA), arachidonoyl glycine (AG), is such a strong regulator that it can act as a ligand at neutral pH. Mutation of an arginine in the outer segment of TM1 (R64) eliminated the effect of docosahexaenoic acid (DHA) even at high concentrations suggesting a potential interaction site for the lipid on the channel. Our results suggest a model where PUFAs bind to ASICs both via their tail group as well as an electrostatic interaction between the negatively charged PUFA head group and the positively charged arginine side chain. These data provide the first look at the structural features of lipids that are important for modulating ASICs and suggest a potential binding site for PUFAs on the channel.Short SummaryArachidonic acid (AA) is a known modulator of ASICs. Bankston and Klipp examine the structural requirements for ASIC modulation by a number of lipids related to AA. Negatively charged head groups are stronger potentiators and may interact with an arginine in TM1 near the outer leaflet of the plasma membrane.
Woman Authorship in Pre-print Versus Peer-Reviewed Oral Health-Related Publications: A Two-Year Observational Study
Authors: Rajendran Lavanya , Khandelwal Namita , Feine Jocelyne , Ioannidou Effie 
Published: June 2021

AbstractObjectivesWomen in oral health science face similar societal issues and challenges as those in other STEMM careers, and gender disparities continue to exist as evidenced by fewer women represented as first and last authors in scientific publications. Pre-prints may serve as a conduit to immediately disseminating one’s work, bypassing the arduous peer review process and its associated inherent biases. Therefore, the purpose of this study was to 1] compare the gender of first and last authors in pre-print versus peer reviewed publications, 2] examine the composition of first and last author pairs as stratified by publication type, and 3] examine the correlation between woman authorship and institutional geographic location and publication metrics stratified by publication type.MethodsThe keyword “oral health” was used to search for publications in BioRxiv and Pubmed in the years 2018 and 2019. Gender of first and last authors were determined, and its frequency was considered as the primary outcome. Additionally, the geographic location of the author’s associated institution and publication metrics measured by Altmetrics score were extracted. Data was descriptively summarized by frequencies and percentages. Chi-square analysis was conducted for categorical variables which included the relationship between gender and publication type as well as gender and region of author’s associated institution. Binomial regression analysis was conducted to analyze the relationship between gender and Altmetrics.ResultsWoman first authors comprised 40.3% of pre-prints and 64.5% of peer reviewed publications [p<0.05]. Woman last authors comprised 31.3% of pre-prints and 61.5% of peer reviewed publications [p<0.05]. When analyzing the relationships between first and last author, the Man-Man pairing represented 47.7% of the pre-print publications and the Woman-Woman pairing comprised a majority of the of the peer review publications at 47.5%. All results were statistically significant with a p-value <0.05. No significant correlation was found between region of institution or Altmetrics and gender of first or last authors [p>0.05].ConclusionFor the first time in oral health science, it was found that women show higher representation as first and last author positions in peer reviewed publications versus pre-prints.
Dynamical transitions of the actomyosin cortex can trigger single cell morphogenesis
Authors: Zhu Hongkang , Alonso-Matilla Roberto , McDargh Zachary , O’Shaughnessy Ben 
Published: June 2021

AbstractMorphogenetic changes driven by actomyosin contractile forces are well-characterized at the tissue level. At the single cell level, shape changes steered by actomyosin contractile forces include mitotic rounding and cytokinetic furrow ingression. In some cases, more complex shape transitions associated with spatial patterning of the cortex were observed. The actomyosin cortex was widely studied using active gel frameworks, and stabilized contractile instabilities were shown to generate patterns, but whether complex shapes can emerge from these cortical patterns is not established. Here we show that complex morphogenetic changes at the single cell level can accompany cortical patterns, using a minimal active gel model. For sufficiently low membranecortex drag, an initially homogeneous cortex spontaneously develops stripes associated with stable furrows, similar to furrowing observed in cells. Our work suggests that controlled cortical instability can trigger morphogenesis at the cellular level.
Oxytocin receptors influence the development and maintenance of social behavior in zebrafish (Danio rerio)
Authors: Gemmer Anja , Mirkes Kristina , Anneser Lukas , Eilers Tim , Kibat Caroline , Mathuru Ajay , Ryu Soojin , Schuman Erin 
Published: June 2021

AbstractZebrafish are highly social teleost fish and an excellent model to study social behavior. The neuropeptide Oxytocin is associated different social behaviors as well as disorders resulting in social impairment like autism spectrum disorder. However, how Oxytocin receptor signaling affects the development and expression kinetics of social behavior is not known. In this study we investigated the role of the two oxytocin receptors, Oxtr and Oxtrl, in the development and maintenance of social preference and shoaling behavior in 2- to 8-week-old zebrafish. Using CRISPR/Cas9 mediated oxtr and oxtrl knock-out fish, we found that the development of social preference is accelerated if one of the Oxytocin receptors is knocked-out and that the knock-out fish reach significantly higher levels of social preference. Moreover, oxtr-/- fish showed impairments in the maintenance of social preference. Social isolation prior to testing led to impaired maintenance of social preference in both wild-type and oxtr and oxtrl knock-out fish. Knocking-out one of the Oxytocin receptors also led to increased group spacing and reduced polarization in a 20-fish shoal at 8 weeks post fertilization, but not at 4. These results show that the development and maintenance of social behavior is influenced by the Oxytocin receptors and that the effects are not just pro- or antisocial, but dependent on both the age and social context of the fish.
Enforced specialization fosters mutual cheating and not division of labour in the bacterium Pseudomonas aeruginosa
Authors: Mridha Subham , Kümmerli Rolf 
Published: June 2021

AbstractA common way for bacteria to cooperate is via the secretion of beneficial public goods (proteases, siderophores, biosurfactants) that can be shared among individuals in a group. Bacteria often simultaneously deploy multiple public goods with complementary functions. This raises the question whether natural selection could favour division of labour where subpopulations or species specialise in the production of a single public good, whilst sharing the complementary goods at the group level. Here we use an experimental system, where we genetically enforce specialization in the bacterium Pseudomonas aeruginosa with regard to the production of its two siderophores, pyochelin and pyoverdine, and explore the conditions under which specialization can lead to division of labour. When growing pyochelin and pyoverdine specialists at different mixing ratios in various iron limited environments, we found that specialists could only successfully complement each other in environments with moderate iron limitation and grow as good as the generalist wildtype but not better. Under more stringent iron limitation, the dynamics in specialist communities was characterized by mutual cheating and with higher proportions of pyochelin producers greatly compromising group productivity. Nonetheless, specialist communities remained stable through negative frequency-dependent selection. Our work shows that specialization in a bacterial community can be spurred by mutual cheating and does not necessarily result in beneficial division of labour. We propose that natural selection might favour fine-tuned regulatory mechanisms in generalists over division of labour because the former enables generalists to remain flexible and adequately adjust public good investments in fluctuating environments.
The performance and corporate risk-taking of firms: evidence from Malaysian agricultural firms
Authors: Ahmad Hanis Hazwani , Azhari Adilah 
Published: June 2021

PurposeThis study explores the effects of the performance and corporate risk-taking behaviour of agricultural firms. Despite its importance in mitigating climate change, the agricultural sector also faces global competition, market liberalisation, rapid technological advances and the starter of stricter quality and safety procedures, all of which require firms to take greater risks.Design/methodology/approachThis study explores this relationship by applying generalised least square (GLS), random effect methodologies (REM) and generalised method of moments (GMM).FindingsThe findings report a favourable relationship between firm performance and corporate risk-taking using a sample of firms from an emerging market.Research limitations/implicationsThe effects of these results for management practice and recommendations for further research were examined.Originality/valueWhile this empirical study used a sample focused on a single industry, most previous studies focused on multiple industries. The originality of this study is its analysis of how firm performance affects corporate risk-taking in the Malaysian agriculture sector.
Illicit enrichment: is reconciliation a prevention of or an invitation to corruption? (The Egyptian example)
Authors: Al Agha Samah 
Published: June 2021

Purpose
This paper aims to explore the offense of illicit enrichment by public officials. It examines whether “reconciliation” could be a preventive measure from corruption or a vehicle for corruption.

Design/methodology/approach
To obtain the data on identifying the illicit enrichment offense and on examining “reconciliation” as a legal tool that combats corruption, this study uses a combination of primary and secondary resources such as the assigned laws, precedents by the Egyptian Cassation Court, academic books, journal articles and reliable websites. Using the same resources, the study explores the adverse aspects associated with “reconciliation.”

Findings
The paper concludes that the Egyptian Illicit Gains Authority Law No.62 of 1975 jeopardizes the “presumption of innocence” because it shifts the burden of proof from the prosecution to the defendant, but the Egyptian Cassation Court decides differently in many cases, whereby it puts emphasis on the prosecution to present enough evidence on illicit enrichment. If the accused is unable to prove the legitimate source of the increased wealth, then there will not be any conviction of illicit enrichment offense due to the presumption of innocence.
Mainstreaming whistleblowing as a regulatory mechanism against fraud in Nigeria’s capital market
Authors: Nwosu Edith O. , Nwoke Uchechukwu , Ajibo Collins Chikodi , Nwodo Fochi , Okoli Ikenna 
Published: June 2021

Purpose
This paper aims to analyze the importance and application of whistleblowing in the fight against fraud in Nigeria’s capital market.

Design/methodology/approach
Drawing from existing legislation and literature in the area, the paper (by adopting a doctrinal approach), analyzes the application of whistleblowing in the Nigerian capital market.

Findings
As a result of an inadequate legislative framework (a structure consisting mainly of mere policy directives and voluntary codes), whistleblowing is seldom used in Nigeria’s capital market.

Originality/value
This paper extends the body of knowledge in the area of whistleblowing in Nigeria’s capital market by not only identifying the non-utilization of the concept but also offers creative suggestions, which will help it is to normalize as a regulatory tool for reducing fraud in this sector.
Gender differences in child nutrition status of Bangladesh: a multinomial modeling approach
Authors: Haq Iqramul , Hossain Md. Ismail , Parvin Mst. Moushumi , Saleheen Ahmed Abdus Saleh , Habib Md. Jakaria , Chowdhury Imru- Al-Quais 
Published: June 2021

PurposeMalnutrition is one of the serious public health problems especially for children and pregnant women in developing countries such as Bangladesh. This study aims to identify the risk factors associated with child nutrition for both male and female children in Bangladesh.Design/methodology/approachThis study was conducted among 23,099 mothers or caretakers of children under five years of age from a nationally representative survey named Bangladesh Multiple Indicator Cluster Survey, 2019. This study used chi-square test statistic for bivariate analysis and multinomial logistic regression was used to evaluate the adjusted effects of those covariates on child nutritional status.FindingsThe prevalence of severely malnourished, nourishment was higher for males than females (5.3% vs 5.1%, 77.4% vs 76.8%) while moderately malnourished were higher for females (18.1% vs 17.4%). The findings from the multinomial model insinuated that the mother’s education level, wealth index, region, early child development, mother’s functional difficulties, child disability, reading children's books and diarrhea had a highly significant effect on moderate and severe malnutrition for male children. For the female children model, factors such as mother’s education level, wealth index, fever, child disability, rural, diarrhea, early child development and reading less than three books were significant for moderate and severe malnutrition.Originality/valueThere is a solution to any kind of problem and malnutrition is not an exceptional health problem. So, to overcome this problem, policymakers should take effective measures to improve maternal education level, wealth status, child health.
The Egyptian revolution of January 25, 2011 as an anti-systemic movement
Authors: Osman Amany Abdellatif 
Published: June 2021

Purpose
This paper aims to analyze the Egyptian revolution as an anti-systemic movement. It illustrates how Egypt’s position in the world-economy has affected its political economy orientation and led to the marginalization of critical masses, who launched the revolution.

Design/methodology/approach
The paper follows Wallerstein’s world-system analysis focusing on the anti-systemic movement concept. The paper analyzes the Egyptian case based on Annales school’s longue durée concept, which is a perspective to study developments of social relations historically.

Findings
The Egyptian revolution was not only against the autocratic regime but also against the power structure resulting from the neoliberal economic policies, introduced as a response to the capitalism crisis. It represented the voice of the forgotten. The revolution was one of the anti-systemic movements resisting the manifestations of the capitalist world-economy.

Originality/value
This paper aims at proving that the Egyptian revolution was an anti-systemic movement; which will continue to spread as a rejection to the world-system and to aspire a more democratic and egalitarian world. The current COVID-19 pandemic is exacerbating the crisis of the world-system.