bluuebunny/crossref_metadata_2025_split huggingface dataset:
Looking for God
Authors: Williams Thomas 
Published: November 2022

Abstract
With this detailed sketch of the divine nature before us, Chapter 3 turns to Anselm’s most famous argument for the claim that the original of our sketch must exist outside the mind—in other words, to his ontological argument for the existence of God. Anselm summarizes his account of the divine nature by describing God as ‘that than which a greater cannot be thought’. That is, God—if there is a God—is a being so great, so perfect, as to be unsurpassable in greatness and perfection. Anselm argues that there are features of ‘that than which a greater cannot be thought’ that guarantee its existence: it is strictly impossible to conceive of the nonexistence of this being of unsurpassable greatness. Anselm’s argument met with immediate pushback. An otherwise unknown monk named Gaunilo argued that if Anselm’s form of argument worked, it would prove not only the existence of a greatest possible being but the existence of a greatest possible island, which is clearly absurd. Anselm’s response to Gaunilo’s ‘Lost Island counterexample’—perhaps the most celebrated counterexample in the history of philosophy—extends and clarifies his original reasoning. Anselm explains that there are certain features of the greatest possible being that cannot belong to something that is possible but nonexistent. Since a perfect being is indeed possible, it must exist, and it must have all the attributes laid out in Chapter 2.
How to get and keep a microbiome
Authors: Douglas Angela E. 
Published: November 2022

Abstract
This chapter focuses on the ways that animal and plant hosts acquire microorganisms from the external environment and other hosts, including the mother. Hosts are challenged to facilitate the colonization of beneficial microorganisms while simultaneously deterring pathogens. In humans, birth indicates the transition from a microbe-free existence to a world filled with microorganisms, while diet and social contacts could promote or resist change in the gut microbiome, which had been regarded as unique as a fingerprint. The processes involved in retaining a microbiome are complex and involve host factors (including the immune system), among-microbe interactions (such as competition and mutualisms), and chance events that result in the loss or gain of particular microbial taxa.
Building Peace From the Ground Up
Authors: Miller-Graff Laura E. , Moeschberger Scott L. , Maloney Catherine A. 
Published: November 2022

Abstract
Violence against children (VAC) is one of the most significant, widespread, and preventable threats to human development in our world today. This chapter, which introduces the broader volume, argues that to promote just and sustainable responses to VAC, scholars and practitioners must develop a robust understanding of how direct, structural, and cultural forms of violence interact across social systems to coproduce and compound VAC and its negative effects. This understanding of VAC motivates a multisectoral response that seeks to promote intergenerational health and well-being through addressing violence in all its forms. With chapters highlighting diverse methodological approaches, context-specific case studies, and approaches to redress violence through practice and policy, this volume is designed to be a resource for researchers, practitioners, and policymakers working to prevent VAC.
Child Sex and Labor Trafficking
Authors: Kinnish Kelly , Perry Elizabeth W. , Reuben Katherine , O’Hara Kathryn , Self-Brown Shannon 
Published: November 2022

Abstract
This chapter explores the trafficking of children for sex and labor globally, with particular emphasis on experiences of trauma and violence prior to and while being trafficked. Complex, intersecting, and compounding vulnerabilities are reviewed, including individual violence exposure and maltreatment, parent and caregiving factors, systems involvement, vulnerability of youth from marginalized populations, and poverty and economic factors. The impacts of trafficking are often severe. In particular, trafficked children experience very high rates of trauma, significant posttraumatic stress symptoms, and other deleterious mental health outcomes. These impacts and emerging effective interventions are reviewed and implications for public policy and directions for future research are discussed.
Education in Crisis
Authors: Boothby Neil , Mills Abigail L. , Sharon Ygal , Salvatory Shukrani 
Published: November 2022

Abstract
This chapter provides preliminary findings on a group of war-affected children and youth who attempted to restart their schooling by enrolling in accelerated education programs (AEPs) in insecure, rural communities in the Democratic Republic of the Congo and in an internationally subsidized refugee camp in Tanzania. Two cohorts of learners in AEPs (cohort 1, N = 841; cohort 2, N = 633), aged 10 to 17 years, were randomly selected from a list of eligible children. Over the course of 4 years, the educational outcomes and academic progress of students enrolled in the AEPs were examined. The present study found significant progress in reading, comprehension, and math skills among students who were able to complete one or more years of the AEPs. The overall reach and impact of the AEPs were diminished due to high attrition rates from the AEPs. Recommendations for future research are discussed.
Dignity in Care
Authors: Chochinov Harvey Max 
Published: November 2022

AbstractThis chapter is a culmination of insights and approaches based on a program of research that engaged hundreds of patients exploring what supports, or undermines, their sense of dignity. Innovations such as the Patient Dignity Inventory and Dignity Therapy describe approaches that are well supported by research and that can inform anyone in healthcare on how to be attentive to patient dignity, whatever the current healthcare challenges may be. This chapter also provides a very detailed description of the Dignity Model, with case illustrations demostrating how each element of the model informs ways of achieving dignity in care.
On the origin and evolution of microbial mercury methylation
Authors: Lin Heyu , Moody Edmund R. R. , Williams Tom A. , Moreau John W. 
Published: November 2022

AbstractThe origin of microbial mercury methylation has long been a mystery. Here we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury methylating gene,hgcAB, constrain the ancestral origin of thehgcoperon, and explain the distribution ofhgcin Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded bymerB) reduced a selective advantage for mercury methylators and resulted in widespread loss ofhgcin Bacteria and Archaea.SignificanceNeurotoxic methylmercury (MeHg+(aq)) is synthesized from HgII(aq)in the environment by microorganisms possessing the gene pairhgcAB. Our phylogenetic analyses elucidate the origin and evolution of thehgcoperon, and support a hypothesis that mercury methylation evolved as an antimicrobial production mechanism, possibly from competition for limited resources on the early Earth. We infer from our analyses thathgchas been primarily vertically inherited in Bacteria and Archaea, with extensive parallel loss, and note that few taxa possessinghgcalso possess the gene encoding for MeHg+demethylation,merB. Our findings support the interpretation thatmerBevolved as a defense mechanism against the evolution of microbial HgII(aq)methylation.
Boost the resilience of Protected Areas to shocks by reducing their dependency on tourism
Authors: Andrianambinina F. Ollier D. , Schuurman Derek , Rakotoarijaona Mamy A. , Razanajovy Chantal N. , Ramparany Honorath M. , Rafanoharana Serge C. , Rasamuel H. Andry , Faragher Kevin D. , Waeber Patrick O. , Wilmé Lucienne 
Published: November 2022

AbstractNature-based or ecotourism is widely considered a strong mechanism for the sustainable funding of protected areas (PAs). Implemented during the 1990s in Madagascar, nature-based tourism experienced positive growth over the last 30 years with increasing numbers of visits to the parks and reserve safeguarding the endemic biodiversity. Revenue earned from entrance fees to the network of PAs managed by Madagascar National Parks has never been sufficient to finance their management. Political crises and the COVID-19 pandemic in particular, have highlighted the risks for park managers of relying on such earnings when they covered just 1 % of the funding required in 2021. Alternative mechanisms of funding are analysed for all Madagascar’s PAs in order to facilitate sustainable conservation of the localities and protection of the island’s biodiversity.
Expanding large-scale mechanistic models with machine learned associations and big datasets
Authors: Erdem Cemal , Birtwistle Marc R. 
Published: November 2022

AbstractComputational models that can explain and predict complex sub-cellular, cellular, and tissue level drug response mechanisms could speed drug discovery and prioritize patient-specific treatments (i.e., precision medicine). Some models are mechanistic: detailed equations describing known (or supposed) physicochemical processes, while some models are statistical/machine learning-based: descriptive correlations that explain datasets but have no mechanistic or causal guarantees. These two types of modeling are rarely combined, missing the opportunity to explore possibly causal but data-driven new knowledge while explaining what is already known. Here, we explore a combination of machine learning with mechanistic modeling methods to develop computational models that could more fully represent cell-line-specific drug responses. In this proposed framework, machine learning/statistical models built using omics datasets provide high confidence predictions for new interactions between genes and proteins where there is physicochemical uncertainty. These possibly new interactions are used as new connections (edges) in a large-scale mechanistic model (called SPARCED) to better recapitulate the recently released NIH LINCS Consortium large-scale MCF10A dataset. As a test case, we focused on incorporating novel IFNγ/PD-L1 related associations into the SPARCED model to enable description of the cellular response to checkpoint inhibitor immunotherapies. This work is a template for combining big data, machine-learning-inferred interactions with mechanistic models, which could be more broadly applicable towards building multi-scale precision medicine and whole cell models.
Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue
Authors: Engblom Camilla , Thrane Kim , Lin Qirong , Andersson Alma , Toosi Hosein , Chen Xinsong , Steiner Embla , Mantovani Giulia , Hagemann-Jensen Michael , Saarenpää Sami , Jangard Mattias , Michaëlsson Jakob , Hartman Johan , Lagergren Jens , Mold Jeff , Lundeberg Joakim , Frisén Jonas 
Published: November 2022

AbstractThe spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed Spatial Transcriptomics of VDJ sequences (Spatial VDJ), which maps immunoglobulin and TR antigen receptors in human tissue sections. Spatial VDJ captures lymphocyte clones matching canonical T, B, and plasma cell distributions in tissues and amplifies clonal sequences confirmed by orthogonal methods. We confirm spatial congruency between paired receptor chains, develop a computational framework to predict receptor pairs, and link the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity, class switch recombination, and lineage trajectories within their spatial context. Taken together, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, which could have important therapeutic implications.One-Sentence SummarySpatial transcriptomics-based technology co-captures T and B cell receptors within their anatomical niche in human tissue.
Characterization of caffeine response regulatory variants in vascular endothelial cells
Authors: Boye Carly , Kalita Cynthia , Findley Anthony , Alazizi Adnan , Wei Julong , Wen Xiaoquan , Pique-Regi Roger , Luca Francesca 
Published: November 2022

AbstractGenetic variants in gene regulatory sequences can modify gene expression and mediate the molecular response to environmental stimuli. In addition, genotype-environment interactions (GxE) contribute to complex traits such as cardiovascular disease. Caffeine is the most widely consumed stimulant and is known to produce a vascular response. To investigate GxE for caffeine, we treated vascular endothelial cells with caffeine and used a massively parallel reporter assay to measure allelic effects on gene regulation for over 43,000 genetic variants. We identified 665 variants with allelic effects on gene regulation and 29 variants that regulate the gene expression response to caffeine (GxE, FDR<10%). When overlapping our GxE results with eQTLs colocalized with CAD and hypertension, we dissected their regulatory mechanisms and showed a modulatory role for caffeine. Our results demonstrate that massively parallel reporter assay is a powerful approach to identify and molecularly characterize GxE in the specific context of caffeine consumption.
Yeast nicotinate-nucleotide pyrophosphorylase in complex with its ligand: Crystallization and Preliminary structural approaches
Authors: Kim Tae Gyun , Kwon Taek Hun , Choi Hyo Jung , Park Min Kyung , Park Jungbae , Chae Inkyung , An Hyun-Jung 
Published: November 2022

ABSTRACTPyridine-2,3-dicarboxylic acid which is a biologically potent molecule implicated in neurodegenerative environment is catalyzed by nicotinate-nucleotide pyrophosphorylase (NMnPP) to produce a precursor molecule, nicotinate mononucleotide (NMn), ofde novobiosynthesis of the coenzyme nicotinamide adenine dinucleotide (NAD+). The protein preparation, crystallization, and preliminary structural features of full-length enzyme in complex with product reactant suggest that yeast NMnPP acts as stable hexamer formation.S. cerevisiaeNMnPP was obtained and diffracted to a resolution of 1.74 Å and 1.99 Å for apo and complex forms, belonged to the trigonal symmetry groupR32 in the unit-cell parameters of a=b=155.313, c=67.507 and a=b=155.091, c=69.204, respectively. Based on our comparison of eukaryotic NMnPP structures in the apo and complex forms, we propose functional and structural investigation for the product binding and hexamer stabilization.
Individual identity and environmental conditions explain different aspects of sleep behaviour in wild boar
Authors: Mortlock Euan , Silovský Václav , Güldenpfennig Justine , Faltusová Monika , Olejarz Astrid , Börger Luca , Ježek Miloš , Jennings Dómhnall J , Capellini Isabella 
Published: November 2022

AbstractSleep is a fundamental behaviour as it serves vital physiological functions, yet how the sleep of wild animals is constrained by environmental conditions is poorly understood. Using non-invasive multi-sensor high-resolution biologgers and a robust classification approach, we quantified multiple dimensions of sleep in wild boar (Sus scrofa), a nocturnally active mammal, monitored for up to a full annual cycle. In support of the hypothesis that environmental conditions determining thermoregulatory challenges regulate sleep, we show that on warmer, longer, and more humid days sleep quality and quantity are reduced, whilst greater snow cover and rainfall promote sleep quality. Importantly, our study reveals large inter-and intra-individual variation in sleep durations, suggestive of pace-of-life syndromes. Given the major role that sleep plays in health, our results suggest that global warming and the associated increase in extreme climatic events are likely to negatively impact sleep, and consequently health in wildlife, particularly in nocturnal animals.
Quantification of surface tension effects and nucleation-and-growth rates during self-assembly of biological condensates
Authors: Sárkány Zsuzsa , Rocha Fernando , Bratek-Skicki Anna , Tompa Peter , Macedo-Ribeiro Sandra , Martins Pedro M. 
Published: November 2022

AbstractLiquid-solid and liquid-liquid phase separation (PS) drives the formation of functional and disease-associated biological assemblies. Principles of phase equilibrium are here employed to derive a general kinetic solution that predicts the evolution of the mass and size of biological assemblies. Thermodynamically, protein PS is determined by two measurable concentration limits: the saturation concentration and the critical solubility. Due to surface tension effects, the critical solubility can be higher than the saturation concentration for small, curved nuclei. Kinetically, PS is characterized by the primary nucleation rate constant and a combined rate constant accounting for growth and secondary nucleation. It is demonstrated that the formation of a few number of large condensates is possible without active mechanisms of size control and in the absence of coalescence phenomena. Our exact analytical solution can be used to interrogate how the elementary steps of PS are affected by candidate drugs.
Predictive coordination of breathing during speaking and listening
Authors: Abbasi Omid , Kluger Daniel S. , Chalas Nikos , Steingräber Nadine , Meyer Lars , Gross Joachim 
Published: November 2022

AbstractIt has long been known that human breathing is altered during listening and speaking compared to rest. Theoretical models of human communication suggest two distinct phenomena during speaking and listening: During speaking, inhalation depth is adjusted to the air volume required for the upcoming utterance. During listening, inhalation is temporally aligned to inhalation of the speaker. While evidence for the former is relatively strong, it is virtually absent for the latter. We address both questions using recordings of speech envelope and respiration in 30 participants during 14 minutes of speaking and listening. We extend existing evidence for the first phenomenon by using the speech envelope to show that inhalation depth is positively correlated with the total power of the speech envelope in the following utterance. Pertaining to the second phenomenon, we provide first evidence that inhalation during listening to your own speech is significantly more likely at time points of inhalation during speaking. These findings are compatible with models that postulate alignment of internal forward models of interlocutors with the aim to facilitate communication.
The structural basis of the multi-step allosteric activation of Aurora B kinase
Authors: Segura-Peña Dario , Hovet Oda , Gogoi Hemanga , Dawicki-McKenna Jennine M. , Hansen Wøien Stine Malene , Carrer Manuel , Black Ben E. , Cascella Michele , Sekulić Nikolina 
Published: November 2022

AbstractAurora B, together with IN-box, the C-terminal part of INCENP, forms an enzymatic complex that ensures faithful cell division. The [Aurora B/IN-box] complex is activated by autophosphorylation in the Aurora B activation loop and in IN-box, but it is not clear how these phosphorylations activate the enzyme. We used a combination of experimental and computational studies to investigate the effects of phosphorylation on the molecular dynamics and structure of [Aurora B/IN-box]. In addition, we generated partially phosphorylated intermediates to analyze the contribution of each phosphorylation independently. We found that the dynamics of Aurora and IN-box are interconnected, and IN-box plays both positive and negative regulatory roles depending on the phosphorylation status of the enzyme complex. Phosphorylation in the activation loop of Aurora B occurs intramolecularly and prepares the enzyme complex for activation, but two phosphorylated sites are synergistically responsible for full enzyme activity.
Development of a new faecal DNA extraction method (HV-CTAB-PCI) for amplification of mitochondrial and nuclear markers used in genetic analyses of dugongs (Dugong dugon)
Authors: Ooi Vicky , McMichael Lee , Hunter Margaret E. , Kamla Aristide Takoukam , Lanyon Janet M. 
Published: November 2022

AbstractNon-invasively collected faecal samples are an alternative source of DNA to tissues, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to develop a new tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, amplification success of genetic markers from dugong faeces was compared between an established QIAamp and a newly developed DNA extraction method. Faecal DNA extracted using a new ‘High Volume-CTAB-PCI’ (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of dugong skin DNA. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified mtDNA and nDNA better than eroded scats. Using the HV-CTAB-PCI method, nDNA was successfully amplified for the first time from dugong faeces. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.