bluuebunny/crossref_metadata_2025_split huggingface dataset:
The making of the oral microbiome in Agta hunter-gatherers
Authors: Dobon Begoña , Musciotto Federico , Mira Alex , Greenacre Michael , Schlaepfer Rodolph , Aguileta Gabriela , Astete Leonora H. , Ngales Marilyn , Latora Vito , Battiston Federico , Vinicius Lucio , Migliano Andrea B. , Bertranpetit Jaume 
Published: May 2022

AbstractEcological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analyzed the oral microbiota of the Agta, a hunter-gatherer population where part of its members is adopting an agricultural diet. We show that age is the strongest factor modulating the microbiome, likely through immunosenescence as there is an increase of pathogenicity with age. Biological and cultural processes generate sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggests that shifting from a fish/meat to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial, and shaped by various ecological and social factors that modify the oral environment.
AI inspired discovery of new biomarkers for clinical prognosis of liver cancer
Authors: Liang Junhao , Zhang Weisheng , Yang Jianghui , Wu Meilong , Dai Qionghai , Yin Hongfang , Xiao Ying , Kong Lingjie 
Published: May 2022

AbstractTissue biomarkers are crucial for cancer diagnosis, prognosis assessment, and treatment planning. However, few of current biomarkers used in clinics are robust enough to show a true analytical and clinical value. Thus the search for additional tissue biomarkers, including the strategies to identify them, is imperative. Recently, the capabilities of deep learning (DL)-based computational pathology in cancer diagnosis and prognosis have been explored, but the limited interpretability and generalizability make the results difficult to be accepted in clinical practice. Here we present an interpretable human-centric DL-guided framework—PathFinder (Pathological-biomarker-finder)— that can inspire pathologists to discover new tissue biomarkers from well-performing DL models, which bridges the gap between DL and clinical prognosis. By combining sparse multi-class tissue spatial distribution information of whole slide images (WSIs) with attribution methods, PathFinder can achieve localization, characterization, and verification of potential biomarkers, while guaranteeing state-of-the-art prognostic performance. With the inspiration of PathFinder, we discovered that tumor necrosis in liver cancer, a long-neglected factor, has a strong relationship with patient prognosis. Thus we proposed two clinically independent indicators, including necrosis area fraction and tumor necrosis distribution, for practical prognosis, and verified their potentials in clinical prognosis according to Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK)-derived criteria. Our work demonstrates a successful example of introducing artificial intelligence (AI) into clinical practice in a knowledge discovery way, which can be adopted in identifying biomarkers in various cancer types and modalities.
Insights into the microbial strain mediated impact on pest insect development
Authors: Gurung Kiran , Salles Joana Falcão , Wertheim Bregje 
Published: May 2022

AbstractMolecular analyses of host-associated microorganisms have demonstrated the essential role that the microbiome plays in host development. Approaches targeting the sequencing of ribosomal genes have successfully identified key species of the host-associated microbiome. However, it remains unclear to what extent the strain-specific characteristics influence the outcome of the host-microbiome interactions. This is particularly important for insect pests, where microbial species might be used as targets for biocontrol purposes. Understanding strain-level variation represents thus a crucial step in determining the microbial impact on hosts. To investigate the microbial strain-level effects on an invasive insect pest, Drosophila suzukii, we compared the impact of monocultures and cocultures of different bacterial and yeast strains. We investigated whether different strains of Gluconobacter and Pichia differentially influenced the larval development of the pest. Fly trait measurements demonstrated beneficial, although variable, impact of these microbial strains on the fitness of suzukii. Using cocultures of microbial strains, we found that in some combinations, the beneficial effects were intermediate between those of the respective monocultures. In contrast, in other cases, strong inhibitory effects were observed. Hence, our study reports that strain-level effects within species are present in D. suzukii, reinforcing the importance of assessing the impact of associated microbiota on pest insects at the strain level.HighlightsMicrobial strains make up an essential part of the diversity of an insect host’sCharacterizing and accounting for strain-specific impact on a pest’s life-history traits and different combinations of strains constitute an important step in our understanding of the pest management strategies.We investigated whether there was any strain-specific impact of bacteria and yeasts on the larval development of a frugivorous pest.We observed that strains varied in their impact, both as monocultures and cocultures, indicating their importance in modifying the host ecology.Our study adds to the growing literature on the importance of strains in pest insects.
Genome-wide DNA methylation patterns harbor signatures of hatchling sex and past incubation temperature in a species with environmental sex determination
Authors: Bock Samantha L. , Smaga Christopher R. , McCoy Jessica A. , Parrott Benjamin B. 
Published: May 2022

AbstractConservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic datasets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulfite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligator (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life-stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy and past incubation temperature with a mean absolute error of 1.2°C based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as non-lethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity.
Metacognitive domains are not aligned along a dimension of internal-external information source
Authors: Arbuzova Polina , Maurer Lisa K. , Filevich Elisa 
Published: May 2022

AbstractIt is still debated whether metacognition, or the ability to monitor our own mental states, relies on mechanisms that are ‘domain-general’ (a single mechanism can account for the monitoring of any mental process) or ‘domain-specific’ (metacognition is accomplished by a collection of multiple monitoring modules, one for each cognitive domain). It has been speculated that two broad categories of metacognitive mechanisms may exist: those that monitor primarily externally-generated vs. those that monitor primarily internally-generated information.To test this proposed division, we measured metacognitive performance (using m-ratio, a signal detection theoretical measure) in four tasks that could be ranked along an internal-external axis of the source of information, namely memory, motor, visuomotor and visual tasks. We found correlations between m-ratios in visuomotor and motor tasks only; but no correlations between m-ratios in visual and visuomotor tasks, or between motor and memory tasks.While we found no correlation in metacognitive ability between visual and memory tasks, and a positive correlation between visuomotor and motor tasks, we found no evidence for a correlation between motor and memory tasks. This pattern of correlations does not support the grouping of domains based on whether the source of information is primarily internal or external. We suggest that other groupings could be more reflective of the nature of metacognition and discuss the need to consider other non-domain task-features when using correlations as a way to test the underlying shared mechanisms between domains.
Critical Mechanistic Features of HIV-1 Viral Capsid Assembly
Authors: Gupta Manish , Pak Alexander J. , Voth Gregory A. 
Published: May 2022

AbstractThe maturation of HIV-1 capsid protein (CA) into a cone-shaped lattice encasing the condensed RNA genome is critical for viral infectivity. During HIV-1 maturation, CA can self-assemble into a wide range of capsid morphologies made of ~175-250 hexamers and 12 pentamers. Most recently, the cellular polyanion inositol hexakisphosphate (IP6) has been demonstrated to facilitate conical capsid formation by coordinating a ring of arginine residues within the central cavity of capsid hexamers and pentamers. However, the precise kinetic interplay of events during IP6 and CA co-assembly is unclear. In this work, we use Coarse-grained Molecular Dynamics (CGMD) simulations to elucidate the underlying molecular mechanism of capsid formation, including the crucial role played by IP6. We show that IP6, in relatively small quantities at first, promotes curvature generation by trapping pentameric defects in the growing lattice and shifts assembly behavior towards kinetically favored outcomes. Our analysis also suggests that IP6 can stabilize metastable capsid intermediates and can induce structural pleomorphism in mature capsids.TeaserComputer simulations reveal that IP6 promotes fullerene-like capsid formation by stabilizing high curvature regions of the capsid.
Beyond Pairwise Interactions: Higher-Order Dynamics in Protein Interaction Networks
Authors: Murgas Kevin A. , Saucan Emil , Sandhu Romeil 
Published: May 2022

AbstractProtein interactions form a complex dynamic system that shapes cell phenotype and function; in this regard, network analysis is a powerful tool for studying the dynamics of cellular processes. Graph-based models are limited, however, in that these models consider only pairwise relationships. Higher-order interactions are well-characterized in biology, including protein complex formation and feedback or feedforward loops. These higher-order relationships are better represented by a hypergraph as a generalized network model. Here, we present an approach to analyzing dynamic gene expression data using a hypergraph model and quantify network heterogeneity via Forman-Ricci curvature. We observe, on a global level, increased network curvature in pluripotent stem cells and cancer cells. Further, we use local curvature to conduct pathway analysis in a melanoma dataset, finding increased curvature in several oncogenic pathways and decreased curvature in tumor suppressor pathways. We compare this approach to a graph-based model and a differential gene expression approach.
Repulsive Sema3E-Plexin-D1 signaling coordinates both axonal extension and steering via activating an autoregulatory factor, Mtss1
Authors: Kim Namsuk , Li Yan , Yu Ri , Kwon Hyo-Shin , Song Anji , Jun Mi-Hee , Jeong Jin-Young , Lee Ji Hyun , Lim Hyun-Ho , Kim Mi-Jin , Kim Jung-Woong , Oh Won-Jong 
Published: May 2022

AbstractAxon guidance molecules are critical for neuronal pathfinding because they regulate directionality and growth pace during nervous system development. However, the molecular mechanisms coordinating proper axonal extension and turning are poorly understood. Here, Metastasis Suppressor 1 (Mtss1), a membrane protrusion protein, ensured axonal extension while sensitizing axons to the Semaphorin 3E (Sema3E)-Plexin-D1 repulsive cue. Sema3E-Plexin-D1 signaling enhanced Mtss1 expression in projecting striatonigral neurons. Mtss1 localized to the neurite axonal side and regulated neurite outgrowth in cultured neurons. Mtss1 also aided Plexin-D1 trafficking to the growth cone, where it signaled a repulsive cue to Sema3E. Mtss1 ablation reduced neurite extension and growth cone collapse in cultured neurons.Mtss1-knockout mice exhibited fewer striatonigral projections and irregular axonal routes and these defects were recapitulated inPlxnd1- orSema3e-knockout mice. These findings demonstrate that repulsive axon guidance activates an exquisite autoregulatory program coordinating both axonal extension and steering during neuronal pathfinding.
Past as prologue: Taylorism, the new scientific management and managing human capital
Authors: Birnbaum Dee , Somers Mark 
Published: May 2022

Purpose
The purpose of this paper is to explore parallels between scientific management and the new scientific management to gain insight into applications of machine learning and artificial intelligence (AI) to human resource management and employee assessment.

Design/methodology/approach
Analysis of Taylor’s work and its interpretation by scholars is contrasted with modern analysis of human resource analytics to demonstrate conceptual and methodological commonalities between the old and the new forms of scientific management.

Findings
The analysis demonstrates how the epistemology, ethos and cultural trajectory of scientific management has resulted in a mindset that has influenced the implementation and objectives of the new scientific management with respect to human resources analytics.

Social implications
This paper offers an alternative to the view that machine learning and AI as applied to work and employees are beneficial and points out why important challenges have been overlooked and how they can be addressed.

Originality/value
Commonalties between Taylorism and the new scientific management have been overlooked so that attempts to gain an understanding of how machine learning is likely to influence work, employees and work organizations are incomplete. This paper provides a new perspective that can be used to address challenges associated with applications of machine learning to work design and employee rights.
Winning the innovation game in emerging markets
Authors: Hensmans Manuel 
Published: May 2022

Purpose
This paper aims to provide advanced market managers in Europe, the USA or Japan with a long-term framework to prepare for and seize emerging market innovation opportunities.

Design/methodology/approach
This paper is based on eight years of studying emerging market innovation opportunities, how to prepare for them and how to seize them. This study mainly draws on experiential learning in the automotive sector, particularly in China.

Findings
The framework details the strategic co-evolution of advanced market firms, emerging market governments, customers and competitors through four stages of innovation. Emerging markets such as China and India at different stages, depending on the national context of development as well as the particular market context.

Research limitations/implications
This research is primarily based on cases in the automotive sector. Challenging the ongoing assumption of superior advanced market innovation, this paper contributes to insights on the new innovation world order and how to invest in emerging market innovation opportunities.

Practical implications
The framework helps advanced market managers identify the strategic stage they are in, depending on the emerging market context. It provides them with long-term strategic insights, helping them anticipate moves and countermoves by emerging market governments and competitors, as well as anticipate the rapidly shifting needs of emerging market customers.

Originality/value
The four-stage framework brings together advanced market firms, emerging market governments, customers and competitors in a clear big picture. It conditions emerging market success in the even bigger picture of advanced market firms drawing on their learning in emerging markets in stages 3 and 4 to accelerate the renewal of their core business.
Intellectual capital between measurement and reporting: a structured literature review
Authors: Paoloni Paola , Modaffari Giuseppe , Ricci Federica , Della Corte Gaetano 
Published: May 2022

PurposeIn the past decade, intellectual capital (IC) measurement and reporting have been feeding scientific debate; however, only few studies address these issues together. The present research aims to provide an integrated view of the topics covered by the existing literature and to highlight the emerging research trends and set the agenda for future research.Design/methodology/approachThis study develops a structured literature review (SLR) of the extant research concerned with IC measurement and reporting, using a comprehensive sample of 1,021 articles extracted from the Scopus database.FindingsThe findings of the SLR show that the existing literature focuses on seven research areas: IC and public sector; IC university and education; IC evaluation method; internal and external IC disclosure; IC and CSR; management of IC in organizations; other. Overall, findings indicate that IC measurement and reporting are highly researched topics that continue to attract the interests of scholars. Finally, the SLR analysis has allowed outlining a future research agenda, with particular reference to the IC evaluation method and internal and external IC disclosure research areas.Research limitations/implicationsThe main limitation of this research lies in the manual screening of relevant studies, which entails some degree of subjectivity. Furthermore, another limitation research could be considered the use of a single database (Scopus).Originality/valueThe present study brings potential contributions for scholars and practitioners. From a scholarly perspective, the paper provides a systematization of scientific contributions that have dealt with IC measurement and reporting. In particular, it contributes to the scholarly debate bringing into focus various IC measurement and reporting issues in the landscape of private and public organizations. Referring to practical implications, our research supports the strategic use of IC measurement and reporting as a key lever for improving the management of firms. Using an analytical framework that combines insights from the agency, stakeholder and legitimacy theories, this study highlights that IC reporting activity should be used strategically as a means to engage with all firm's stakeholders, in particular with a view to reducing information asymmetry and improving firm reputation.
Studying abroad: the role of consumer cosmopolitanism in the enrolment decisions
Authors: Salomão Miriam Taís , Silva Susana Costa , Côto José Ricardo 
Published: May 2022

Purpose
Cosmopolitans transcend their local boundaries by interacting and actively seeking other cultures, and the applications of these characteristics to consumption behaviour is called consumer cosmopolitanism. To outline inferences on what school leavers would experience, consider or do when planning to study abroad, this paper aims to examine people who have experienced Erasmus concerning the relationship between their level and type of consumer cosmopolitanism and the decisions related to enrolling in the Erasmus programme, which include the decision itself, motivations, choice of destination, pursuing cultural differences and search for different levels of globalisation.

Design/methodology/approach
After proposing a conceptual model, data were collected by surveying undergraduate or postgraduate students. Then a set of multivariate analyses were developed to validate the hypotheses.

Findings
Contrarily to what could be expected, results indicate that consumer cosmopolitanism decreases the likelihood for students to enrol on the programme. Additionally, three types of consumer cosmopolitanism were found: low, cultural and high cosmopolitans. According to results, low cosmopolitans display lower likelihoods of enrolment than the other two types. This evidence supports that intention to enrol is not always a good predictor of behaviour and that a gap is proven here as well. This study also suggests that cosmopolitan consumers do not reveal a preference for countries with similar/different cultures or levels of globalization to that of their own country, but, conversely, experiencing a different culture remains one of the leading motivations for these consumers.

Originality/value
Although cosmopolitanism has been extensively studied in different research fields, its link with the decisions on studying abroad has barely been explored.
Ligilactobacillus salivarius PS11610 exerts an effect on the microbial and immunological profile of couples suffering unknown infertility
Authors: Iniesta Silvia , Esteban Sergio , Armijo Ónica , Lobo Sonia , Manzano Susana , Espinosa Irene , Cárdenas Nivia , Bartha José Luis , Jiménez Esther 
Published: May 2022

AbstractProblemUnknown or idiopathic infertility has been associated with urogenital tract dysbiosis, reducing pregnancy and delivery ratios during assisted reproductive treatments (ART). The Ligilactobacillus salivarius PS11610 strain has shown extraordinary antimicrobial activity in vitro against urogenital pathogens as well as other probiotic characteristics. Therefore, an intervention study was performed to evaluate the effect of L. salivarius PS11610 on the microbial composition of urogenital tract in infertile couples with bacterial dysbiosis.Method of studySeventeen couples undergoing ART diagnosed with unknown infertility were selected. After confirming urogenital dysbiosis, they started a 6‐month treatment with L. salivarius PS11610 (1 dose/12 h for female and 1 dose/24 h for male). Vaginal, seminal, glans, uterine and plasma samples were collected for determination of the microbiome and immune profile at the beginning and the end of the treatment.ResultsSupplementation with L. salivarius PS11610 significantly modified the urogenital microbiome composition in male and female samples, solving dysbiosis of 67% of the couples. Pathogens disappeared from the vaginal samples whereas Lactobacilli percentage increased after 3 and 6 months of treatment. Moreover, L. salivarius PS11610 changed the uterine microbiome that could be associated with a change of the uterine immune profile. Additionally, the probiotic intake could be associated with the observed change in the systemic immunological profile of couples. Finally, the pregnant and delivery ratio were improved.ConclusionsProbiotic supplementation with L. salivarius PS11610 improved the male and female urogenital tract microbiome, modulating the immune system and increasing pregnancy success in couples undergoing ART.