bluuebunny/crossref_metadata_2025_split huggingface dataset:
Present and future trends
Authors: Steger Manfred B. 
Published: September 2023

Abstract
This chapter reflects on the present and future trends of globalization. It explains how the COVID-19 pandemic served as a particularly significant marker of unsettled time after global interconnectivity and mobilities of various kinds faced major pandemic-related obstacles caused by repeated national lockdowns. However, the rapid global spread of COVID-19 and the ensuing global efforts to develop vaccines indicate that certain forms of globalization accelerated and intensified during times of worldwide COVID-19-related disruption and paralysis. The chapter then explains ‘disjunctive globalization’ which refers to acceleration of digital and other manifestations of disembodied globalization formations at the expense of the other three major globalization formations. The chapter ends with a discussion of how necessary transformative social processes should be guided by an ethical commitment to advance global social justice.
Understanding the world
Authors: Taub Liba 
Published: September 2023

Abstract
‘Understanding the World’ introduces attempts to comprehend the natural world, rather than strategies to control it. It focuses on Greece and Rome, covering a broad sweep of time from the 8th century bce to the 6th century ce. For many early Greek philosophers, the study of nature focused on explaining what can be seen (phenomena), while for some, nature included the human body and disease. This chapter discusses conceptions of ‘nature’ among ancient Greeks and Romans; the investigation of nature was part of a larger culture of enquiry. The meaning of the Greek word kosmos is examined, meaning ‘order’ or ‘adornment’. For some ancient thinkers, not only animals, humans, and plants but the cosmos itself was understood to be alive. The chapter considers modern accounts of ancient science that emphasize certain perceived features, which are implicitly approved of or disparaged, such as the emphasis on mathematics and the lack of experimentation.
Let no one unskilled in geometry enter
Authors: Taub Liba 
Published: September 2023

Abstract
This chapter explores the ideas credited to Pythagoras and his followers regarding the importance of number in explaining the world. It also considers the origin of the idea of the harmony of the spheres that is usually traced to early Pythagoreans. The Greek word harmonia refers to joining together or fastening. Plato highlighted the Pythagorean idea of the mathematical structure of the cosmos and of cosmic harmony. Plato also emphasized the value of mathematics in education. Astronomy was a branch of mathematics for the ancient Greeks and was used by Plato, Eudoxus, and others to describe the motions of astronomical bodies.
Chapter 12 Beyond antiquity
Authors: Taub Liba 
Published: September 2023

Abstract
‘Beyond Antiquity’ traces the legacies of ancient Greek and Roman science that endured through the Middle Ages, Renaissance, and into the modern period. The longevity of some concepts and concerns, such as those relating to matter, atoms, and chaos, points to a degree of continuity among scientific practitioners and communities. The influence of some ancient thinkers remained strong throughout the medieval and early modern periods. A division of labour between mathematicians and philosophers continued in formalized ways through the organization of education. The universities that were founded in the Middle Ages followed an Aristotelian curriculum, prevailing throughout the Renaissance until the 18th century. This chapter explores the specific interests of several Nobel prize-winning physicists in ancient Greek science, and the publication of the fragments of the Presocratic philosophers by Hermann Diels.
Interactions in ecosystems
Authors: Lockwood Julie L. , Welbourne Dustin J. 
Published: September 2023

Abstract
This chapter explains how interactions between invasive species and their ecosystems underpin impacts. It defines an ecosystem as the community of organisms that exist within a given area that interact with one another and the physical environment. The major types of interactions that invasive species have in the ecosystem range from eating native species, competing with native species, and increasing infections of native species with parasites and pathogens. The chapter considers the ecological interactions between the invasive species and their physical environment, which can affect the niche space of native species. It emphasizes that ecological interactions do not occur in isolation.
It is never simple
Authors: Lockwood Julie L. , Welbourne Dustin J. 
Published: September 2023

Abstract
This chapter expounds on the complexities of understanding and managing invasive species, grouping them into three broad areas. First, the chapter looks at how different people weigh the desirability of impacts since a single non-native species might produce both desirable and undesirable impacts, depending on who evaluates the desirability. Second, the chapter highlights the difficulties when invasive species positively affect endangered species, or when the invasive species is itself endangered. Finally, the chapter concludes by examining how climate change adds a new dimension to understanding biological invasions.
A deliberate future
Authors: Lockwood Julie L. , Welbourne Dustin J. 
Published: September 2023

Abstract
This concluding chapter considers the future of invasive species. It acknowledges that invasive species have had enormous impacts on economic and human health, recognizing that they are one of the greatest global threats to other species and ecosystems. In the future, more invasive species are expected to arise due to climate change, economic demand, and international trade. However, breakthroughs in policy, technology, or understanding may mitigate the future number of invasive species and their associated impacts. The chapter points out that our actions with respect to invasive species will either be lambasted or praised by future generations, since society is a patchwork of cultural, institutional, and philosophical paradigms.
The pulse of the past
Authors: Dixon Thomas 
Published: September 2023

Abstract
This chapter introduces the role of emotions in history. Narrative histories often attribute key decisions of protagonists to emotional states from jealousy or vengeance to empathy and compassion. Moreover, historians have always written about the lives of people in the past in order to move people in the present. The chapter begins by looking at the debates among historians regarding the French Revolution to introduce the emergence of the history of emotions as a discipline. It then discusses French historian Lucien Febvre’s Annales school of history, before discussing historically ancient beliefs around emotions’ correlation with dichotomies of gender.
A multitude of states of matter
Authors: McKenzie Ross H. 
Published: September 2023

Abstract
There are ‘a multitude of states of matter’. Materials composed of just one or two types of atoms can form many different states of matter. Each state has qualitatively different physical properties. Transitions between distinct states are tipping points and are defined by abrupt changes in properties. Dramatic examples include superconductivity and superfluidity. Phase diagrams encode which state of a material is stable under specific conditions defined by variables such as temperature and pressure. The phase diagrams of water, carbon dioxide, and carbon are discussed to illustrate key ideas in condensed matter physics and its industrial relevance. At the critical point there is no distinction between liquid and gas. Sublimation involves a direct transition between solid and gas states. Topics discussed are relevant to making artificial diamonds, freeze-dried food, decaffeinated coffee, and dry ice.
The critical point
Authors: McKenzie Ross H. 
Published: September 2023

Abstract
‘The critical point’ in a phase diagram denotes the conditions under which a continuous transition between two states of matter occurs. Surprisingly, near the critical point diverse systems can have the same dependence of physical properties on parameters such as temperature. The only details that determine the critical exponents are the symmetry of the order parameter and the spatial dimensionality of the system. This independence from chemical and structural details, known as universality, presented a major challenge to theoretical physics for decades. Theory must deal with the large fluctuations in the amount of order that occurs close to the critical point. The successful theory developed by Ken Wilson exploits the fact that different states of a system and different systems can be related to one another by mathematically rescaling the length scales in the system. The mathematics involved can be made tractable by considering the abstract idea of a system with a variable number of spatial dimensions. The idea of rescaling is illustrated with the results of computer simulations of an Ising model and with images of fractals.
Quantum matter
Authors: McKenzie Ross H. 
Published: September 2023

Abstract
‘Quantum matter’ describes how superconductors and superfluids can have properties like those found in the strange quantum world of atoms, electrons, and photons. In quantum theory, properties such as energy cannot have any possible value, but are quantized. Energy comes in discrete lumps. Particles can act like waves, be in more than one place at the same time, and interfere with themselves. The weirdness of quantum theory is captured in the paradox of Schrödinger’s cat, where quantum effects occur on the macroscopic scale. This is realized in a superconductor, where magnetic flux is quantized. Brian Josephson proposed an electrical circuit that is the basis for a Superconducting Quantum Interference Device (SQUID). These devices are of technological significance as they are used in quantum computing, and to make precise measurements of fundamental physical constants and of magnetic field strengths. SQUIDs are now used in metrology, the science of precise measurements, being the basis for the international standard for the volt, the unit of electrical voltage, and are used in quantum computing.
I’ll name that tune in…
Authors: Earl Richard 
Published: September 2023

Abstract
A piano string can vibrate to create a single, pure note, but generally a vibration is made up of infinite such pure contributions or ‘harmonics’. Fourier analysis—named after Joseph Fourier—is the idea of expressing general vibrations as an infinite sum of harmonics. ‘I’ll name that tune in…’ describes Fourier’s work, which has wider significance, for example in quantum theory. It would take the development of an infinite-dimensional analysis, called ‘functional analysis’, in the 20th century to describe all these applications rigorously. The chapter also discusses the related question: can you hear the shape of a drum? That is, can differently shaped drums produce the same frequencies of harmonics?
But there’s more…
Authors: Earl Richard 
Published: September 2023

Abstract
‘But there’s more…’ describes other topics of 20th-century analysis that didn’t make it into earlier chapters. This includes: Lebesgue’s generalization of the rather limited Riemann integral; the foundational grounding of probability theory using analysis; hyperreals, a way to treat infinities and infinitesimals rigorously; and, finally, Dirichlet’s introduction of analytical methods to number theory, including the Prime Number Theorem, which describes the long-term distribution of prime numbers.
What is biodiversity, and why does it matter?
Authors: Macdonald David W. 
Published: September 2023

Abstract
This chapter discusses the concept of biodiversity, the diversity of life at different scales. Biodiversity is crucial to safeguarding human well-being, as well as the well-being of nature and all its moving parts. The chapter begins by providing an overview of the astonishing range of life on Earth, before explaining how biodiversity is assembled into communities. Biomes are the regions of Earth that can be distinguished by their climate, fauna, and flora, with the organisms that live in each biome adapted to its circumstances. The five major types of biome include aquatic, grassland, forest, desert, and tundra. The chapter then considers biodiversity hotspots and the ecosystem services underpinned by biodiversity.
The Tale of Genji
Authors: Tansman Alan 
Published: September 2023

Abstract
In the first decade of the eleventh century, Murasaki Shikibu, a lady-in-waiting at the imperial court, began writing what was to become the most influential work in the Japanese tradition. The novelist Kawabata Yasunari, for example, looking back at the entire Japanese literary tradition, situated Murasaki Shikibu’s The Tale of Genji at its apex, a view that is widely shared. Genji may be the greatest achievement of all of Japanese literature, and has inspired a vast machinery of interpretation, translation into both modern Japanese and other languages, and adaptation in a range of media, throughout the centuries.
Prenatal Exposure to Opioids and Neurodevelopmental Disorders in Children: A Bayesian Mediation Analysis
Authors: Wang Shuang , Puggioni Gavino , Wu Jing , Meador Kimford J , Caffrey Aisling , Wyss Richard , Slaughter Jonathan L , Suzuki Etsuji , Ward Kristina E , Lewkowitz Adam K , Wen Xuerong 
Published: September 2023

Abstract
This study explores natural direct and joint natural indirect effects (JNIE) of prenatal opioid exposure on neurodevelopmental disorders (NDDs) in children mediated through pregnancy complications, major and minor congenital malformations, and adverse neonatal outcomes, using Medicaid claims linked to vital statistics in Rhode Island, United States, 2008–2018. A Bayesian mediation analysis with elastic net shrinkage prior was developed to estimate mean time to NDD diagnosis ratio using posterior mean and 95% credible intervals (CrIs) from Markov chain Monte Carlo algorithms. Simulation studies showed desirable model performance. Of 11,176 eligible pregnancies, 332 had ≥2 dispensations of prescription opioids anytime during pregnancy, including 200 (1.8%) having ≥1 dispensation in the first trimester (T1), 169 (1.5%) in the second (T2), and 153 (1.4%) in the third (T3). A significant JNIE of opioid exposure was observed in each trimester (T1, JNIE = 0.97, 95% CrI: 0.95, 0.99; T2, JNIE = 0.97, 95% CrI: 0.95, 0.99; T3, JNIE = 0.96, 95% CrI: 0.94, 0.99). The proportion of JNIE in each trimester was 17.9% (T1), 22.4% (T2), and 56.3% (T3). In conclusion, adverse pregnancy and birth outcomes jointly mediated the association between prenatal opioid exposure and accelerated time to NDD diagnosis. The proportion of JNIE increased as the timing of opioid exposure approached delivery.
Machine learning-based quantification for disease uncertainty increases the statistical power of genetic association studies
Authors: Park Jun Young , Lee Jang Jae , Lee Younghwa , Lee Dongsoo , Gim Jungsoo , Farrer Lindsay , Lee Kun Ho , Won Sungho 
Published: September 2023

AbstractMotivationAllowance for increasingly large samples is a key to identify the association of genetic variants with Alzheimer’s disease (AD) in genome-wide association studies (GWAS). Accordingly, we aimed to develop a method that incorporates patients with mild cognitive impairment and unknown cognitive status in GWAS using a machine learning-based AD prediction model.ResultsSimulation analyses showed that weighting imputed phenotypes method increased the statistical power compared to ordinary logistic regression using only AD cases and controls. Applied to real-world data, the penalized logistic method had the highest AUC (0.96) for AD prediction and weighting imputed phenotypes method performed well in terms of power. We identified an association (P&lt;5.0×10-8) of AD with several variants in the APOE region and rs143625563 in LMX1A. Our method, which allows the inclusion of individuals with mild cognitive impairment, improves the statistical power of GWAS for AD. We discovered a novel association with LMX1A.Availability and implementationSimulation codes can be accessed at https://github.com/Junkkkk/wGEE_GWAS.
Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach
Authors: Hu Yan , Keloth Vipina K , Raja Kalpana , Chen Yong , Xu Hua 
Published: September 2023

Abstract

Motivation
Automated extraction of population, intervention, comparison/control, and outcome (PICO) from the randomized controlled trial (RCT) abstracts is important for evidence synthesis. Previous studies have demonstrated the feasibility of applying natural language processing (NLP) for PICO extraction. However, the performance is not optimal due to the complexity of PICO information in RCT abstracts and the challenges involved in their annotation.

Results
We propose a two-step NLP pipeline to extract PICO elements from RCT abstracts: (i) sentence classification using a prompt-based learning model and (ii) PICO extraction using a named entity recognition (NER) model. First, the sentences in abstracts were categorized into four sections namely background, methods, results, and conclusions. Next, the NER model was applied to extract the PICO elements from the sentences within the title and methods sections that include &gt;96% of PICO information. We evaluated our proposed NLP pipeline on three datasets, the EBM-NLPmod dataset, a randomly selected and re-annotated dataset of 500 RCT abstracts from the EBM-NLP corpus, a dataset of 150 Coronavirus Disease 2019 (COVID-19) RCT abstracts, and a dataset of 150 Alzheimer’s disease (AD) RCT abstracts. The end-to-end evaluation reveals that our proposed approach achieved an overall micro F1 score of 0.833 on the EBM-NLPmod dataset, 0.928 on the COVID-19 dataset, and 0.899 on the AD dataset when measured at the token-level and an overall micro F1 score of 0.712 on EBM-NLPmod dataset, 0.850 on the COVID-19 dataset, and 0.805 on the AD dataset when measured at the entity-level.

Availability and implementation
Our codes and datasets are publicly available at https://github.com/BIDS-Xu-Lab/section_specific_annotation_of_PICO.
DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction
Authors: Qu Wei , You Ronghui , Mamitsuka Hiroshi , Zhu Shanfeng 
Published: September 2023

Abstract

Motivation
Computationally predicting major histocompatibility complex class I (MHC-I) peptide binding affinity is an important problem in immunological bioinformatics, which is also crucial for the identification of neoantigens for personalized therapeutic cancer vaccines. Recent cutting-edge deep learning-based methods for this problem cannot achieve satisfactory performance, especially for non-9-mer peptides. This is because such methods generate the input by simply concatenating the two given sequences: a peptide and (the pseudo sequence of) an MHC class I molecule, which cannot precisely capture the anchor positions of the MHC binding motif for the peptides with variable lengths. We thus developed an anchor position-aware and high-performance deep model, DeepMHCI, with a position-wise gated layer and a residual binding interaction convolution layer. This allows the model to control the information flow in peptides to be aware of anchor positions and model the interactions between peptides and the MHC pseudo (binding) sequence directly with multiple convolutional kernels.

Results
The performance of DeepMHCI has been thoroughly validated by extensive experiments on four benchmark datasets under various settings, such as 5-fold cross-validation, validation with the independent testing set, external HPV vaccine identification, and external CD8+ epitope identification. Experimental results with visualization of binding motifs demonstrate that DeepMHCI outperformed all competing methods, especially on non-9-mer peptides binding prediction.

Availability and implementation
DeepMHCI is publicly available at https://github.com/ZhuLab-Fudan/DeepMHCI.
Brain tumour genetic network signatures of survival
Authors: Ruffle James K , Mohinta Samia , Pombo Guilherme , Gray Robert , Kopanitsa Valeriya , Lee Faith , Brandner Sebastian , Hyare Harpreet , Nachev Parashkev 
Published: September 2023

Abstract
Tumour heterogeneity is increasingly recognized as a major obstacle to therapeutic success across neuro-oncology. Gliomas are characterized by distinct combinations of genetic and epigenetic alterations, resulting in complex interactions across multiple molecular pathways. Predicting disease evolution and prescribing individually optimal treatment requires statistical models complex enough to capture the intricate (epi)genetic structure underpinning oncogenesis.
Here, we formalize this task as the inference of distinct patterns of connectivity within hierarchical latent representations of genetic networks. Evaluating multi-institutional clinical, genetic and outcome data from 4023 glioma patients over 14 years, across 12 countries, we employ Bayesian generative stochastic block modelling to reveal a hierarchical network structure of tumour genetics spanning molecularly confirmed glioblastoma, IDH-wildtype; oligodendroglioma, IDH-mutant and 1p/19q codeleted; and astrocytoma, IDH-mutant.
Our findings illuminate the complex dependence between features across the genetic landscape of brain tumours and show that generative network models reveal distinct signatures of survival with better prognostic fidelity than current gold standard diagnostic categories.
SOCS1 acts as a ferroptosis driver to inhibit the progression and chemotherapy resistance of triple-negative breast cancer
Authors: Wang Yiding , Pang Xiaoling , Liu Yuexin , Mu Guiling , Wang Qian 
Published: September 2023

Abstract

Objectives
Ferroptosis is involved in many types of cancers, including triple-negative breast cancer (TNBC). Suppressor of cytokine signaling 1 (SOCS1) has recently been implicated as a regulator of ferroptosis. We aim to explore whether targeting SOCS1 is a potential therapeutic strategy for TNBC therapy.

Methods
Stable cell lines were constructed using lentivirus transfection. Cell viability was determined using CCK-8 and cell colony formation assays, respectively. Assays including lactate dehydrogenase release, lipid peroxidation and malondialdehyde assays were conducted to evaluate ferroptosis. Real-time quantitative polymerase chain reaction and western blotting were performed to evaluate mRNA and protein expression, respectively. A xenograft animal model was established by subcutaneous injection of cells into the flank.

Results
Our results showed that SOCS1 overexpression inhibited cell proliferation and induced ferroptosis in TNBC cells, while SOCS1 knockdown promoted cell proliferation and reduced ferroptosis. We also found that SOCS1 regulated ferroptosis by modulating GPX4 expression. Furthermore, SOCS1 regulated cisplatin resistance in TNBC cells by promoting ferroptosis. Our in vivo data suggested that SOCS1 regulated tumor growth and cisplatin resistance in vivo.

Conclusions
SOCS1 inhibits the progression and chemotherapy resistance of TNBC by regulating GPX4 expression.