bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylome combined with chromosome cluster-oriented analysis provides an early signature for cutaneous melanoma aggressiveness
Authors: Carrier Arnaud , Desjobert Cécile , Ponger Loïc , Lamant Laurence , Bustos Matias , Torres-Ferreira Jorge , Henrique Rui , Jeronimo Carmen , Lanfrancone Luisa , Delmas Audrey , Favre Gilles , Daunay Antoine , Busato Florence , Hoon Dave S.B. , Tost Jörg , Etievant Chantal , Riond Joëlle , Arimondo Paola B. 
Published: April 2022

ABSTRACTAberrant DNA methylation is a well-known feature of tumours and has been associated with metastatic melanoma. However, since melanoma cells are highly heterogeneous, it has been challenging to use affected genes to predict tumour aggressiveness, metastatic evolution, and patients’ outcomes. We hypothesized that common aggressive hypermethylation signatures should emerge early in tumorigenesis and should be shared in aggressive cells, independent of the physiological context under which this trait arises.We compared paired melanoma cell lines with the following properties:(i)each pair comprises one aggressive counterpart and its parental cell line, and(ii)the aggressive cell lines were each obtained from different host and their environment (human, rat, and mouse), though starting from the same parent cell line. Next, we developed a multi-step genomic pipeline that combines the DNA methylome profile with a chromosome cluster-oriented analysis.A total of 229 differentially hypermethylated genes were commonly found in the aggressive cell lines. Genome localization analysis revealed hypermethylation peaks and clusters, identifying eight hypermethylated gene promoters for validation in tissues from melanoma patients.Five CpG identified in primary melanoma tissues were transformed into a DNA methylation score that can predict survival (Log-rank test,p=0.0008). This strategy is potentially universally applicable to other diseases involving DNA methylation alterations.
Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex
Authors: Çiftçi Ozan , Alverson Andrew J. , van Bodegom Peter , Roberts Wade R. , Mertens Adrienne , Van de Vijver Bart , Trobajo Rosa , Mann David G. , Pirovano Walter , van Eijk Iris , Gravendeel Barbara 
Published: April 2022

AbstractIn contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea, a widespread species complex with several morphologically based taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear-lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Subsequent gene-tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies and a resulting putative recent hybrid. Our study shows that phylogenomic analyses of many unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.
Hierarchical Computational Modeling and Dynamic Network Analysis of Allosteric Regulation in the SARS-CoV-2 Spike Omicron Trimer Structures: Omicron Mutations Cooperate to Allosterically Control Balance of Protein Stability and Conformational Adaptability
Authors: Verkhivker Gennady M. , Agajanian Steve , Kassab Ryan , Krishnan Keerthi 
Published: April 2022

AbstractStructural and computational studies of the Omicron spike protein in various functional states and complexes provided important insights into molecular mechanisms underlying binding, high transmissibility, and escaping immune defense. However, the regulatory roles and functional coordination of the Omicron mutations are poorly understood and often ignored in the proposed mechanisms. In this work, we explored the hypothesis that the SARS-CoV-2 spike protein can function as a robust allosterically regulated machinery in which Omicron mutational sites are dynamically coupled and form a central engine of the allosteric network that regulates the balance between conformational plasticity, protein stability, and functional adaptability. In this study, we employed coarse-grained dynamics simulations of multiple full-length SARS-CoV-2 spike Omicron trimers structures in the closed and open states with the local energetic frustration analysis and collective dynamics mapping to understand the determinants and key hotspots driving the balance of protein stability and conformational adaptability. We have found that the Omicron mutational sites at the inter-protomer regions form regulatory clusters that control functional transitions between the closed and open states. Through perturbation-based modeling of allosteric interaction networks and diffusion analysis of communications in the closed and open spike states, we quantify the allosterically regulated activation mechanism and uncover specific regulatory roles of the Omicron mutations. The network modeling demonstrated that Omicron mutations form the inter-protomer electrostatic bridges that connect local stable communities and function as allosteric switches of signal transmission. The results of this study are consistent with the experiments, revealing distinct and yet complementary role of the Omicron mutational sites as a network of hotspots that enable allosteric modulation of structural stability and conformational changes which are central for spike activation and virus transmissibility.
Bayesian Parameter Estimation for Dynamical Models in Systems Biology
Authors: Linden Nathaniel J. , Kramer Boris , Rangamani Padmini 
Published: April 2022

AbstractDynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent advances in experimental measurements, including sensor development and ‘-omics’ studies that have helped populate protein-protein interaction networks in great detail, systems biology modeling lacks systematic methods to estimate kinetic parameters and quantify associated uncertainties. This is because of multiple reasons, including sparse and noisy experimental measurements, lack of detailed molecular mechanisms underlying the reactions, and missing biochemical interactions. Additionally, the inherent nonlinearities with respect to the states and parameters associated with the system of differential equations further compound the challenges of parameter estimation. In this study, we propose a comprehensive framework for Bayesian parameter estimation and complete quantification of the effects of uncertainties in the data and models. We apply these methods to a series of signaling models of increasing mathematical complexity. Systematic analysis of these dynamical systems showed that parameter estimation depends on data sparsity, noise level, and model structure, including the existence of multiple steady states. These results highlight how focused uncertainty quantification can enrich systems biology modeling and enable additional quantitative analyses for parameter estimation.
Sensory conflict disrupts circadian rhythms in the sea anemone Nematostella vectensis
Authors: Berger Cory A. , Tarrant Ann M. 
Published: April 2022

AbstractCircadian clocks infer time of day by integrating information from cyclic environmental factors called zeitgebers, including light and temperature. Single zeitgebers entrain circadian rhythms, but few studies have addressed how multiple, simultaneous zeitgeber cycles interact to affect clock behavior. Misalignment between zeitgebers (“sensory conflict”) can disrupt circadian rhythms, or alternatively clocks may privilege information from one zeitgeber over another. Existing studies are limited in the range of tested zeitgeber relationships, and also in their taxonomic breadth, which is restricted to insects and vertebrates among animals. Here, we show that temperature cycles entrain circadian locomotor rhythms in Nematostella vectensis, a model system for cnidarian circadian biology. We then conduct behavioral experiments across a comprehensive range of light and temperature cycles. Nematostella’s circadian behavior is disrupted by chronic sensory conflict, including disruption of the endogenous clock itself rather than a simple masking effect. Sensory conflict also disrupts the rhythmic transcriptome, with numerous genes losing rhythmic expression. However, many metabolic genes remained rhythmic and in-phase with temperature, and other genes even gained rhythmicity, implying that some rhythmic metabolic processes persist even when behavior is disrupted. Our results show that a cnidarian clock relies on information from light and temperature, rather than prioritizing one zeitgeber over the other. Although we identify limits to the clock’s ability to integrate conflicting sensory information, there is also a surprising robustness of behavioral and transcriptional rhythmicity.
Remarkable lives: Khia Stacey in conversation with Robert Hurst
Authors: Stacey Khia , Hurst Robert 
Published: April 2022

Purpose
The purpose of this paper is to share Khia Stacey’s story.

Design/methodology/approach
Khia Stacey wrote a short piece detailing her journey, and she was then interviewed by Robert Hurst.

Findings
Khia Stacey spoke about experiencing trauma, facing difficulties within child and adolescent mental health services and how she chose to fight on.

Research limitations/implications
Recovery narratives such as the current one give the readers an overview of only a single person’s experiences. However, they allow the person with lived experience to explore their story in depth.

Practical implications
Khia Stacey stresses the importance of listening to service users and gives advice on how mental health professionals can better support those in services.

Social implications
There is so much to learn from a story such as Khia’s – for those who have had similar experiences and for those who work in mental health services.

Originality/value
This is the first time that Khia has chosen to share her unique story. Its value is apparent immediately upon reading it.
Bridging the marketing-finance divide: use of customer voice in managerial decision-making
Authors: Saxena Deepak , Brady Mairead , Lamest Markus , Fellenz Martin 
Published: April 2022

PurposeThis study aims to provide more insight into how customer voice is captured and used in managerial decision-making at the marketing-finance interface. This study’s focus is on understanding how the customer voice, often communicated through online and social media platforms, is used in high-performing hotels.Design/methodology/approachThis research is based on a case study of four high-performing Irish hotels. For each case, multiple informants, including marketing managers, general managers and finance managers, were interviewed and shadowed. Twenty seven decisions across the four cases were analysed to assess the use of customer voice in managerial decision-making.FindingsSocial media provides a stage that has empowered the customer voice because of the public nature of the interaction and the network effect. Customer voice is incorporated in managerial decision-making in three distinct ways – symbolically as part of an early warning system, for action-oriented operational decisions and to some extent in the knowledge-enhancing role for tactical decisions. While there is a greater appreciation among senior managers and the finance and accounting managers of the importance of customer voice, this study finds clear limits in its utilisation and more reliance on traditional finance and accounting data, especially in strategic decision-making.Research limitations/implicationsThe cases belong to a highly visible open environment of hotels in an industry where customer voice has immediate and strong effects. The findings may not directly apply to industries characterised by a relatively more closed context such as banking or insurance. Moreover, the findings reflect the practices of high-performing hotels and do not necessarily capture the practices used in less successfully operating hotels.Practical implicationsWhile marketers need to enhance their ability to create a narrative that links the customer voice to revenue generation, finance managers also need to develop a skillset and adopt a mindset that appropriately reflects the influential role for customer voice in managerial decision-making.Originality/valueDespite the linkage of marketing performance to business performance, there is limited research on the impact of customer information on managerial decision-making. This research provides insight into how customer voice is considered at the critical marketing-finance interface.
Diversity and ecology of Radiolaria in modern oceans
Authors: Biard Tristan 
Published: April 2022

SummaryAmong the many inhabitants of planktonic communities, several lineages have biomineralized intricate skeletons. These have existed for millions of years and include the Radiolaria, a group of marine protists, many of which bear delicate mineral skeletons of different natures. Radiolaria are well known for their paleontological signatures, but little is known about the ecology of modern assemblages. They are found from polar to tropical regions, in the sunlit layers of the ocean down to the deep and cold bathypelagic. They are closely involved in the biogeochemical cycles of silica, carbon and strontium sulfate, carrying important amounts of such elements to the deep ocean. However, relatively little is known on the actual extent of genetic diversity or biogeographic patterns. The rapid emergence and acceptance of molecular approaches have nevertheless led to major advances in our understanding of diversity within and evolutionary relationships between major radiolarian groups. Here, we review the state of knowledge relating to the classification, diversity and ecology of extant radiolarian orders, highlighting the substantial gaps in our understanding of the extent of their contribution to marine biodiversity and their role in marine food webs.
The impact and policy relevance of street lighting for crime prevention: A systematic review based on a half‐century of evaluation research
Authors: Welsh Brandon C. , Farrington David P. , Douglas Stephen 
Published: April 2022

AbstractResearch SummaryThis article reports on an updated systematic review and meta‐analysis of the effects of street lighting interventions on crime in public places. Following Campbell Collaboration guidelines, it uses robust criteria for inclusion of studies, comprehensive search strategies to identify eligible studies, a detailed protocol for coding key study characteristics, and rigorous methods for analyzing studies. A total of 21 studies met the inclusion criteria, originating in four countries (United States, United Kingdom, Brazil, and South Korea) and covering almost 50 years (1974–2021). The review finds that street lighting interventions are associated with a significant desirable effect on total crime (14% reduction in treatment areas compared with comparable control areas); desirable effects are greater in studies that measured both night and day crimes than in studies that only measured night crimes; and street lighting is followed by a significant reduction in property crimes, but not in violent crimes.Policy ImplicationsCompared to past years, it would seem that an even stronger case can be made today for street lighting interventions to be part of crime‐prevention policy. A larger body of high‐quality evaluation research, implemented in a range of high‐crime public places, some evidence of value for money, and a continued desirable impact on crime, especially property crime, all point to the policy relevance of street lighting interventions.
Rheological and tribological nature of flaxseed gum influenced by concentration and temperature and its application as a coating agent for potato chips
Authors: Safdar Bushra , Pang Zhihua , Liu Xinqi , Jatoi Mushtaque Ahmad , Rashid Muhammad Tayyab 
Published: April 2022

AbstractInfluence of different concentrations (0.5, 1.0, 2.0, and 3.0% w/v) and temperatures (4, 25, 50, and 75°C) on particle size distribution (PSD) and rheological and tribological characteristics of flaxseed gum (FSG) solutions was investigated. Besides, FSG dispersions (0.5, 1.0, and 2.0% w/v) were used as edible coating and their influence on the quality parameters (oil uptake, moisture loss, texture, and sensory properties) of fried potato chips was studied. All FSG dispersions revealed shear‐thinning nature and viscous properties (as G″ > G′) that were more dominant at higher concentrations and lower temperatures. The power–law model presented a good fit in demonstrating the flow behavior of FSG dispersions. Concentration was the variable that affected the tribology of FSG dispersions, while temperature had little effect on the tribology. Particle size distribution was increased with the increasing concentration of FSG. FSG dispersions as an edible coating effectively reduced the moisture loss, oil uptake, and hardness properties of potato chips.Practical ApplicationProfiling the influence of concentration and temperature on the rheology and tribology of flaxseed gum is particularly valuable during food processing. The results predict the physical properties of coated potato chips that can support the potential application of flaxseed gum as a coating agent. Today's consumers prefer healthier food products with low caloric, higher fiber content, functional properties, and sensory qualities. Food industries can use FSG as a low‐cost natural coating material in terms of economic benefits, consumer acceptance, and providing an inordinate potential both for its protective effect and carrying functional compounds such as antioxidants in their coating matrix.
Prognostic value of preoperative plasma fibrinogen levels in resected stage I non‐small cell lung cancer
Authors: Mitsui Suguru , Tanaka Yugo , Doi Takefumi , Hokka Daisuke , Maniwa Yoshimasa 
Published: April 2022

AbstractBackgroundThe number of surgical procedures has increased among patients with early‐stage lung cancer. If the poor prognostic factors for stage I non‐small cell lung cancer (NSCLC) can be simply validated preoperatively, appropriate treatment will be provided. The current study aimed to evaluate the prognostic value of preoperative plasma fibrinogen levels in patients with resected stage I NSCLC.MethodsWe retrospectively analyzed the clinicopathological information of patients (n = 149) who underwent lobectomy for stage I NSCLC between May 2014 and July 2016. Data about peripheral blood analysis, histopathological finding, and follow‐up assessment results were collected from the databases. Patients were divided into the low and high fibrinogen groups. Univariate and multivariate analyses were performed to evaluate the predictors of recurrence and survival.ResultsCompared with the low fibrinogen group (<377 mg/dl), the high fibrinogen group (≥377 mg/dl) had a significantly greater number of male participants (p = 0.04), smokers (p < 0.001), and those with elevated cytokeratin antigen levels (p = 0.04), lymphatic invasion (p = 0.007), and squamous cell carcinoma (p < 0.001). Plasma fibrinogen level was considered a significant independent factor for recurrence and overall survival on both the univariate and multivariate analyses (p < 0.001 and p = 0.010) and the multivariate analysis alone (p = 0.020 and p < 0.012).ConclusionPreoperative plasma fibrinogen level might be a useful predictor of recurrence and survival in patients with stage I NSCLC. The treatment strategy for patients with high fibrinogen levels could be cautiously considered preoperatively.
Audit Risk Evaluation Using Data Envelopment Analysis with Ordinal Data
Authors: Amin Gholam R. , El‐Temtamy Osama , Garas Samy 
Published: April 2022

This study examines the data envelopment analysis (DEA) model for audit risk evaluation which was initially developed by Bradbury and Rouse (2002) and reinterpreted by Davutyan and Kavut (2005). Bradbury and Rouse (2002) apply the standard DEA model for audit risk factors, including judgemental (ordinal) measures. In the presence of ordinal data, efficiency analysis in DEA requires appropriate models to be applied instead of the standard DEA model. Accordingly, audit risk evaluation based on the standard DEA model is not assessed appropriately because the risk factors are qualitative and ordinal measures. Hence, we employ an appropriate DEA model to accurately evaluate audit risk in the presence of ordinal data. In light of the prior two studies, our results demonstrate the appropriateness of the ordinal DEA model.
The use of digital footprints in the US mortgage market
Authors: Jayasuriya D Dulani , Ayaz Mohamed , Williams Michael 
Published: April 2022

AbstractWe study the rise of digital footprint (DF) users in the U.S. residential mortgage market. The proportion of lenders that use a borrower's DF has witnessed remarkable growth from 6% in 2013 to 34% in 2018 in a short span – according to our analysis. We show that the use of DFs can significantly reduce a lender's overall risk and that the use of DFs can result in considerable societal benefits, by reducing the overall discriminatory forces. In sum, we provide evidence that the informational advantage associated with using a borrower's DF far outweighs that of existing traditional lending methods.
Can B cell‐deficient patients rely on COVID‐19 vaccine‐induced T‐cell immunity?
Authors: Shree Tanaya 
Published: April 2022

SummaryAnti‐CD20 antibody treatments prevent humoral responses to vaccines against severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) vaccines, but the nature of T‐cell responses in this setting is less well understood. Riise et al. assess vaccine‐induced epitope‐specific CD8 T cell responses in patients with lymphoma recently treated with rituximab and find a wide range of responses, with the most recently treated patients frequently failing to respond, while others exhibit responses stronger than healthy controls. They suggest these epitopes among others could be used in a T cell‐targeted vaccine, and such strategies are indeed in clinical trials now.Commentary on: Riise J, et al. Rituximab‐treated patients with lymphoma develop strong CD8 T‐cell responses following COVID‐19 vaccination. Br J Haematol. 2022;197:697‐708