bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learned protein embeddings for machine learning
Authors: Yang Kevin K , Wu Zachary , Bedbrook Claire N , Arnold Frances H 
Published: March 2018

Abstract

Motivation
Machine-learning models trained on protein sequences and their measured functions can infer biological properties of unseen sequences without requiring an understanding of the underlying physical or biological mechanisms. Such models enable the prediction and discovery of sequences with optimal properties. Machine-learning models generally require that their inputs be vectors, and the conversion from a protein sequence to a vector representation affects the model’s ability to learn. We propose to learn embedded representations of protein sequences that take advantage of the vast quantity of unmeasured protein sequence data available. These embeddings are low-dimensional and can greatly simplify downstream modeling.

Results
The predictive power of Gaussian process models trained using embeddings is comparable to those trained on existing representations, which suggests that embeddings enable accurate predictions despite having orders of magnitude fewer dimensions. Moreover, embeddings are simpler to obtain because they do not require alignments, structural data, or selection of informative amino-acid properties. Visualizing the embedding vectors shows meaningful relationships between the embedded proteins are captured.

Availability and implementation
The embedding vectors and code to reproduce the results are available at https://github.com/fhalab/embeddings_reproduction/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Identification of miR-9-5p as direct regulator of ABCA1 and HDL-driven reverse cholesterol transport in circulating CD14+ cells of patients with metabolic syndrome
Authors: D’Amore Simona , Härdfeldt Jennifer , Cariello Marica , Graziano Giusi , Copetti Massimiliano , Di Tullio Giuseppe , Piglionica Marilidia , Scialpi Natasha , Sabbà Carlo , Palasciano Giuseppe , Vacca Michele , Moschetta Antonio 
Published: March 2018

Abstract

Aims
Metabolic syndrome (MS) is a cluster of cardio-metabolic risk factors associated with atherosclerosis and low-grade inflammation. Using unbiased expression screenings in peripheral blood mononuclear cells, we depict here a novel expression chart of 678 genes and 84 microRNAs (miRNAs) controlling inflammatory, immune and metabolic responses. In order to further elucidate the link between inflammation and the HDL cholesterol pathway in MS, we focussed on the regulation of the ATP-binding cassette transporter A1 (ABCA1), a key player in cholesterol efflux (CE).

Methods and results
ABCA1 mRNA levels are suppressed in CD14+ cells of MS patients and are negatively correlated to body mass index (BMI), insulin-resistance (HOMA-IR) and cardiovascular risk, and positively to HDL cholesterol and CE. miRNA target in silico prediction identified a putative modulatory role of ABCA1 for the nuclear factor kappa-light-chain-enhancer of activated B cell (NF-κB) target miR-9-5p, whose expression pattern was up-regulated in CD14+ cells of MS patients, positively correlated to BMI, HOMA-IR, and triglycerides, and negatively to ABCA1 mRNA levels, HDL cholesterol and CE. Ectopic gain and loss of miR-9-5p function in macrophages modulated ABCA1 mRNA and protein levels, ABCA1 miRNA 3’-untranslated region target sequence reporter assay, and CE into HDL, thus confirming ABCA1 as a target of miR-9-5p.

Conclusions
We identified the NF-κB target miR-9-5p as a negative regulator of ABCA1 adding a novel target pathway in the relationship between inflammation and HDL-driven reverse cholesterol transport for prevention or treatment of atherosclerosis in MS.
Blunted nitric oxide regulation in Tibetans under high-altitude hypoxia
Authors: He Yaoxi , Qi Xuebin , Ouzhuluobu  , Liu Shiming , Li Jun , Zhang Hui , Baimakangzhuo  , Bai Caijuan , Zheng Wangshan , Guo Yongbo , Duojizhuoma  , Baimayangji  , Dejiquzong  , Bianba  , Gonggalanzi  , Pan Yongyue , Qula  , Kangmin  , Cirenyangji  , Guo Wei , Yangla  , Peng Yi , Zhang Xiaoming , Xiang Kun , Yang Zhaohui , Wang Liangbang , Gengdeng  , Zhang Yanfeng , Wu Tianyi , Su Bing , Cui Chaoying 
Published: March 2018

ABSTRACT
Nitric oxide (NO) is an important molecule for vasomotor tone, and elevated NO signaling was previously hypothesized as a unique and adaptive physiological change in highland Tibetans. However, there has been lack of NO data from Tibetans living at low altitude and lowlander immigrants living at high altitude, which is crucial to test this hypothesis. Here, through cross-altitude (1990–5018 m) and cross-population (Tibetans and Han Chinese) analyses of serum NO metabolites (NOx) of 2086 individuals, we demonstrate that although Tibetans have a higher serum NOx level compared to lowlanders, Han Chinese immigrants living at high altitude show an even higher level than Tibetans. Consequently, our data contradict the previous proposal of increased NO signaling as the unique adaptive strategy in Tibetans. Instead, Tibetans have a relatively lower circulating NOx level at high altitude. This observation is further supported by data from the hypoxic experiments using human umbilical vein endothelial cells and gene knockout mice. No difference is detected between Tibetans and Han Chinese for endothelial nitric oxide synthase (eNOS), the key enzyme for circulating NO synthesis, suggesting that eNOS itself is unlikely to be the cause. We show that other NO synthesis-related genes (e.g. GCH1) carry Tibetan-enriched mutations significantly associated with the level of circulating NOx in Tibetans. Furthermore, gene network analysis revealed that the downregulation and upregulation of NOx is possibly achieved through distinct pathways. Collectively, our findings provide novel insights into the physiological and genetic mechanisms of the evolutionary adaptation of Tibetans to high-altitude hypoxia.
Inner Sound
Authors: Weinel Jonathan 
Published: March 2018

Abstract
Inner Sound explores how altered states of consciousness have shaped the design of electronic music and audio-visual media. The book begins by discussing consciousness, and how this may change during states such as dreaming, psychedelic experience, meditation, and trance. Next, a variety of shamanic traditions are reviewed, in order to explore how indigenous societies have reflected visionary experiences through visual art and music. This provides the necessary background from which to consider how analogue and digital audio technologies enable specific capabilities for representing or inducing altered states of consciousness in psychedelic rock, electronic dance music, and electroacoustic music. Developing the discussion to consider sound in the context of audio-visual media, the role of altered states of consciousness in films, visual music, VJ performances, interactive video games, and virtual reality applications is also discussed. Through the analysis of these examples, the author uncovers common mechanisms, and ultimately proposes a conceptual model for ‘Altered States of Consciousness Simulations’. This theoretical model describes how sound can be used to simulate various subjective states of consciousness from a first-person perspective, in an interactive context. Throughout the book, the ethical issues regarding altered states of consciousness in electronic music and audio-visual media are also explored, ultimately allowing the reader to consider not only the design of Altered States of Consciousness Simulations, but also the implications of their use for digital society. In this way, Inner Sound explores the limits of technology for representing and manipulating consciousness, at the frontiers of electronic music and art.
Introduction
Authors: Weinel Jonathan 
Published: March 2018

Abstract
This introduction to Inner Sound: Altered States of Consciousness in Electronic Music and Audio-Visual Media outlines the background, aims, and scope of the book. The chapter begins by introducing altered states of consciousness through a description of visual hallucinations, which may have provided a basis for some of the oldest-known artworks. Next, a brief historical overview of altered states is given, from ancient shamanic traditions and cults, to modern-day use of psychedelic drugs such as LSD. The use of altered states in these contexts has resulted in a variety of associated art, literature, music, films, and video games, which in recent years have been rendered with the aid of new sound and audio-visual technologies. These works provide the main focus of Inner Sound, which explores the relationship of altered states of consciousness with electronic music and audio-visual media, in order to develop a conceptual theory of ‘Altered States of Consciousness Simulations’.
Abstractions
Authors: Weinel Jonathan 
Published: March 2018

Abstract
The concluding chapter of Inner Sound: Altered States of Consciousness in Electronic Music and Audio-Visual Media consolidates the main arguments of the book. The journey taken is recapitulated, from shamanic rituals to psychedelic rock shows and raves; and from outdoor electroacoustic concerts to synaesthetic films and hallucinatory video games. Across these examples, similar underlying principles can be identified, revealing a continuity from ancient shamanism to modern ‘technoshamanism’. Yet while some imperatives have remained consistent, the technologies have evolved, yielding ever-more accurate and sophisticated representations of altered states in electronic music and audio-visual media. This finds us on the brink of ‘Altered States of Consciousness Simulations’, which replicate the sensory experience of altered states using immersive technologies such as fulldomes and virtual reality headsets. Looking forwards, the possible uses and ethical implications of these simulations are explored, at the frontiers of electronic music and art.
Judgment
Authors: Kershner Jon R. 
Published: March 2018

Abstract
The chapter argues that Woolman believed God intervened in human history and natural events to accomplish the divine will. Woolman felt that he was capable of interpreting historical events for his fellow colonists so that they could understand the spiritual meaning God intended them to learn from disease, war, and pestilence. Woolman held to two forms of divine judgment. One form he called “chastisements,” which were divine attempts to get humanity’s attention and to call humanity back to obedience. The second type of divine judgment was a retributive wrath, in which God destroyed all forces opposed to the divine will. Woolman’s theology of divine judgment gave him assurance that the vision for colonial America he proclaimed would come to pass, because God could not be thwarted. This theology convinced him that God was already intervening in human affairs, and so provided theological meaning to the events of his day.
Enoch’s Roles in Human Society
Authors: Reeves John C. , Reed Annette Yoshiko 
Published: March 2018

AbstractThis chapter brings together testimonies about the diverse social roles and vocations which Enoch allegedly exercised among his contemporaries during the antediluvian era. These include descriptions of Enoch functioning as a teacher, a prophet, an expert on proper religious behaviors, a ruler or lawgiver, a builder, a warrior, a hermit, a funeral director, a sorcerer’s apprentice, and as the designated heir or legatee of his father Yared.
Reference databases
Authors: Taberlet Pierre , Bonin Aurélie , Zinger Lucie , Coissac Eric 
Published: March 2018

Abstract
DNA references databases are a prerequisite to identify sequences obtained from a metabarcoding experiments. Chapter 3 “Reference databases” gives a brief description of the content and structure of existing generalistic resources and proposes guidelines to construct reference databases specific to the metabarcode of interest, when no specific databases are available. The method presented consists in capturing all sequences corresponding to the metabarcode in generalistic international repositories by using the program ecoPCR. Second, existing resources specific to rRNAs or classical barcodes are presented. Finally, this chapter develops strategies relying on either on polymerase chain reaction (PCR), or on genome skimming, to enrich existing databases with new species from fresh specimens or collections in museums. This chapter does not deal with taxonomic assignment per se, which is discussed in Chapter 8.
Reconstructing Republican Oratory in Cassius Dio’s Roman History
Authors: Burden-Strevens Christopher 
Published: March 2018

AbstractThis chapter explores the way in which Cassius Dio—a third-century Greek historian of the Roman Republic—used published oratory of the late Republic as a basis for his own historiographical speeches. It argues that, far from belonging in a sophistic thought-world divorced from their depicted historical context, Cassius Dio’s historiographical speeches display a marked attention for preserving not only specific arguments, but also the rhetorical strategies and turns of phrase used to make those arguments in the oratory of the first century ad. While Cicero inevitably appears to predominate in Dio’s register of sources for Roman oratory, this chapter nevertheless demonstrates Dio’s awareness of non-Ciceronian oratory—such as the speeches of Catulus, Hortensius, and M. Antonius—preserved in quoted material and testimonies of these orators in Ciceronian texts, which the historian reproduced accordingly.
Oratorum Romanarum Fragmenta Liberae Rei Publicae
Authors: Hallett Judith P. 
Published: March 2018

AbstractThis chapter explores the boundaries of female public speech at Rome through an analysis of a letter, preserved by Nepos, which was sent to the tribune Gaius Gracchus by his mother Cornelia. It argues that Cornelia’s words should be studied alongside fragments of spoken oratory because of the intertextual relations between this fragment and the attested oratory of both her father Scipio Africanus and her son Gaius Gracchus and because of its characteristics as a contribution to a political debate. In addition, the probable oral circumstances of the letter’s composition and its use of oratorical sound effects further decrease the distance between it and the fragmentary remains of Republican speeches.
Double Photoionisation Spectra of Molecules
Authors: Eland John , Feifel Raimund 
Published: March 2018

Abstract
This book contains spectra of the doubly charged positive ions (dications) of some 75 molecules, including the major constituents of terrestrial and planetary atmospheres and prototypes of major chemical groups. It is intended to be a new resource for research in all areas of molecular spectroscopy involving high energy environments, both terrestrial and extra-terrestrial. All the spectra have been produced by photoionisation using laboratory lamps or synchrotron radiation and have been measured using the magnetic bottle time-of-flight technique by coincidence detection of correlated electron pairs. Full references to published work on the same species are given, though for several molecules these are the first published spectra. Double ionisation energies are listed and discussed in relation to the molecular electronic structure of the molecules. A full introduction to the field of molecular double ionisation is included and the mechanisms by which double photoionisation can occur are examined in detail. A preliminary chapter covers double photoionisation of an atom in order to explain the basic principles of the technique, then five chapters present spectra of molecules of increasing size. A seventh chapter on the new fields of core–core and core–valence double ionisations, with selected examples, completes the main body of the book. Appendices explain the detailed mechanisms of double photoionisation, the calibration of the electron spectrometers, and give a brief summary of the methods by which double ionisation energies are calculated theoretically.
Molecules with four, five or seven atoms
Authors: Eland John H.
                            D. , Feifel Raimund 
Published: March 2018

Abstract
Double photoionisation spectra of NH3, C2H2, HCHO, C2N2, PCl3, CH4, the methyl halides CH3F, CH3Cl, CH3I, the methylene halides CH2Cl2, CH2Br2, CH2I2, the carbon tetrahalides CF4, CCl4, CBr4, germanium tetrahalides GeCl4, GeBr4, and SF6 are presented with analysis to identify the electronic states of the doubly charged ions. The effects of indirect double ionisation pathways are discussed. There are relatively few important molecules with just four atoms, but most of the ones included here are present and sometimes abundant in planetary and astrophysical environments. The range of five-atom molecules includes methane and all its simple derivatives. Where possible closely related molecules are grouped together in this chapter, as much of the discussion of their electronic structure is the same for all members of a group. This chapter also includes SF6 as a closely related molecule, even though its atom count goes beyond those of some molecules in later chapters.
Europe's Growth Champion
Authors: Piatkowski Marcin 
Published: March 2018

Abstract
The book is about one of the biggest economic success stories that one has hardly ever heard about. It is about a perennially backward, poor, and peripheral country, which over the last twenty-five years has unexpectedly become Europe’s and a global growth champion and joined the ranks of high-income countries during the life of just one generation. It is about the lessons learned from its remarkable experience for other countries in the world, the conditions that keep countries poor, and challenges that countries need face to grow and become high-income. It is also about a new growth model that this country—Poland—and its peers in Central and Eastern Europe and elsewhere need to adopt to continue to grow and catch up with the West for the first time ever. The book emphasizes the importance of the fundamental sources of growth—institutions, culture, ideas, and leaders—in economic development. It argues that a shift from an extractive society, where the few rule for the benefit of the few, to an inclusive society, where many rule for the benefit of many, was the key to Poland’s success. It asserts that a newly emerged inclusive society will support further convergence of Poland and Central and Eastern Europe with the West and help sustain the region’s Golden Age, but moving to the core of the European economy will require further reforms and changes in Poland’s developmental DNA.
From Black Death to Black Hole
Authors: Piatkowski Marcin 
Published: March 2018

Abstract
In this chapter I explain why Poland and most countries in Eastern Europe have always lagged behind Western Europe in economic development. I discuss why in the past the European continent split into two parts and how Western and Eastern Europe followed starkly different developmental paths. I then demonstrate how Polish oligarchic elites built extractive institutions and how they adopted ideologies, cultures, and values, which undermined development from the late sixteenth century to 1939. I also describe how the elites created a libertarian country without taxes, state capacity, and rule of law, and how this ‘golden freedom’ led to Poland’s collapse and disappearance from the map of Europe in 1795. I argue that Polish extractive society was so well established that it could not reform itself from the inside. It was like a black hole, where the force of gravity is so strong that the light could not come out.
The New Growth Model for Central and Eastern Europe
Authors: Piatkowski Marcin 
Published: March 2018

Abstract
In this chapter, I argue that although the existing growth model has worked well so far, Poland and the rest of the region needs to re-adjust it to sustain a high growth rate. I then introduce the concept of the ‘Warsaw Consensus’, a set of ten policy prescriptions that should guide further convergence of Poland and CEE with the West. The ‘Warsaw Consensus’ upgrades, corrects, and enhances the ‘Washington Consensus’ and embeds it in the specific context of CEE. It deals with the key challenges to the region’s growth and offers policy solutions. I argue that implementation of the ‘Warsaw Consensus’ should be based on a new policy approach of experimenting, evaluating, and pragmaticizing (being pragmatic), and be assessed against its impact on economic growth, well-being, and happiness. Countries should also ensure that they minimize the risks of crises and become anti-fragile.
Hume, Defeat, and Miracle Reports
Authors: Anderson Charity 
Published: March 2018

Abstract
No one believes every miracle report they hear. At least, no one I know. For religious and non-religious alike, it is common to disbelieve testimony to the miraculous; it is also common to dismiss such testimony outright. This chapter investigates the rationality of failing to believe miracle reports. Hume famously argued that it is irrational to believe that a miracle has occurred on the basis of testimony alone. While certain aspects of Hume’s argument have received extensive discussion, other features of his argument have been largely overlooked. After offering a reconstruction of Hume’s argument, I will argue that epistemic defeat plays a central role in the argument and explore the aptness of as well as some limitations to Hume’s reasoning.
A Theological Critique of the Fine-Tuning Argument
Authors: Halvorson Hans 
Published: March 2018

Abstract
The fine-tuning argument attempts to use data from contemporary physics as evidence for God’s existence. In particular, contemporary physics suggests that—in absence of any divine intervention—there was little chance that a universe like ours would come into existence. The chapter points out a theological problem with the fine-tuning argument: since God can choose the laws of nature, God can set the chances that a universe like ours would come into existence. It argues, however, that if God could be expected to create a nice universe, then God could also be expected to set favourable chances for a nice universe. Therefore, the fine-tuning argument defeats itself.
Testimony amidst Diversity
Authors: Baker-Hytch Max 
Published: March 2018

Abstract
This chapter takes up the question of what (if anything) might be wrong with religious beliefs that are held primarily on the basis of testimony, in light of the facts of religious diversity. The chapter first considers whether religious diversity entails that a religious believer’s testimony-based beliefs are not formed in a suitably epistemically reliable manner even conditional upon the truth of her religion. After casting doubt on this thought the chapter turns to look at the idea that testimony-based beliefs are subject to defeaters in light of awareness of religious diversity, and suggests that many such beliefs are not obviously so. According to the author’s diagnosis the problem, rather, is that believers who base their religious beliefs just on testimony will be very unlikely to have reflective (that is, second-order) knowledge even if they possess first-order knowledge, and the author explains why this is a notable shortcoming.
Delusions of Knowledge Concerning God’s Existence
Authors: DeRose Keith 
Published: March 2018

Abstract
The author suspects that hardly anyone, if anyone at all, knows whether God exists. In this chapter he explains, and to some extent defends, this suspicion. His focus is limited to exploring what seems to be the most promising proposal as to how it might be that at least some people could know whether God exists—which turns out to be a way by which some theists might know that God does indeed exist: by means of religious experience. The author explains why it looks to him as if, at least in almost all cases, even if these people are right about God’s existence, the way in question fails to be a way by which they know that God exists.