bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of magnetization characteristics of variable flux PM based on a Fourier-fitting hysteresis model
Authors: Yang Hui , Jie Yufei , Guo Xuanjiang , Li Jinda , Wang Minghui
Published: September 2019

This paper investigates the magnetization characteristics of variable flux permanent magnet (VF-PM) by using a simplified C-core magnetizer device with AlNiCo PMs. A combined methodology with magnetic circuit model, finite element analysis and Fourier series fitting hysteresis model is proposed. By means of the magnetic circuit analysis, the basic sizing parameters of the device are designed for the prototype manufacturing. A simple experimental setup including a device prototype, a Gaussmeter and H-bridge-converter-based magnetizing circuit is established. Then several experimental schemes are conducted to research the magnetization characteristics. According to the experimental results, a new numerical hysteresis model of AlNiCo PMs is proposed based on Fourier-fitting functions, which can be employed to correct the hysteresis model parameters used in finite element (FE) simulation. Finally, the correctness of the proposed Fourier-fitting hysteresis model (FFHM) is experimentally verified by the test results.
A new approach to prioritising groundwater dependent vegetation communities to inform groundwater management in New South Wales, Australia
Authors: Dabovic Jodie , Dobbs Lucy , Byrne Glenn , Raine Allan
Published: September 2019

Groundwater dependent ecosystems (GDEs) require access to groundwater to meet all or some of their water requirements to maintain community structure and function. The increasing demand of surface and groundwater resources has seen the NSW Government put in place management mechanisms to enable the sharing of water between irrigators, the environment, industry, towns and communities via water sharing plans. The groundwater sharing plans aim to provide adaptive management of GDEs by prioritising for protection those that are considered the most ecologically valuable within each plan area. The High Ecological Value Aquatic Ecosystems (HEVAE) framework has already been adopted to prioritise riverine ecosystems for management in surface water sharing plans. Here, we provide a method developed using the HEVAE framework to prioritise vegetation GDEs for management. The GDE HEVAE methods provide a derived ecological value dataset for identified groundwater dependent vegetation that is used to inform the planning and policy decisions in NSW. These decisions are required to manage and mitigate current and future risks caused by groundwater extraction. This is achieved via the identification of ecologically valuable assets to then use as the consequence component in a risk assessment for the groundwater sources, to provide vegetation GDE locations for setback distances for new groundwater production bores, and for the assessment of impacts due to current and potential future groundwater extraction. The GDE HEVAE method uses recorded and predicted spatial data to provide weighted scores for each attribute associated with the four HEVAE criteria (distinctiveness, diversity, vital habitat and naturalness). The combined scores categorise the ecological value of each groundwater dependent vegetation community (depicted as geographic information system (GIS) polygon features) from very high to very low. We apply the GDE HEVAE method to three catchments in order to demonstrate the method’s applicability across the Murray–Darling Basin with varying elevation and climate characteristics. The ecological value outcomes derived from the methods have been used to inform planning and policy decisions by NSW Government processes to allow for protection in not only areas that are currently at risk but to also manage for potential future risks from groundwater extraction.
Remediation of antimony-contaminated tap water using granular TiO2 column
Authors: Jiang Yuxuan , Yan Li , Nie Xiao , Yan Wei
Published: September 2019

Environmental contextAntimony (Sb) contamination from mining is an emergent environmental issue, and there is an urgent need for the development of effective water treatment technology. This study reports a complete Sb remediation strategy using granular titanium dioxide as the adsorbent, and describes adsorbent manufacture, Sb adsorptive removal and regeneration of the adsorbent. The findings highlight a practical way for on-site remediation of Sb-contaminated water.
AbstractAntimony (Sb) mining endorses the development of Sb remediation technology to reduce its contamination level and protect public health. In this study, a treatment process based on granular TiO2 was proposed to remediate the Sb-contaminated tap water at mining sites. The Langmuir isotherms indicated that the maximum adsorption capacity on granular TiO2 was 142mgg−1 for SbIII and 43mgg−1 for SbV. The kinetics results suggested that Sb adsorption conformed to the Weber–Morris intraparticle diffusion model. The adsorption of SbV featured the anionic adsorption characteristics, which were significantly inhibited at pH>8. Approximately, 586 bed volumes of tap water with an average SbV concentration of 324µgL−1 were filtered before the effluent concentration exceeded 6µgL−1 using a granular TiO2 column. The PHREEQC program integrated with charge distribution multi-site complexation (CD-MUSIC) modelling and a one-dimensional transport block was performed to predict the SbV breakthrough curve. The results revealed that the existence of Ca2+ significantly promoted SbV adsorption. Furthermore, the breakthrough curves of SbV and Ca2+ were well simulated after considering the effects of Ca2+ adsorption and the Ca-Sb-TiO2 ternary surface complex. Granular TiO2 can be regenerated and reused, and the solid residue from regeneration can be recycled. The insights of this study help to further understand the environmental chemistry of Sb on metal oxides, which provides a practical solution for Sb removal.
Parallel transport for vector bundles on 𝑝-adic varieties
Authors: Deninger Christopher , Werner Annette
Published: September 2019

We develop a theory of étale parallel transport for vector bundles with numerically flat reduction on a

p
p

-adic variety. This construction is compatible with natural operations on vector bundles, Galois equivariant and functorial with respect to morphisms of varieties. In particular, it provides a continuous

p
p

-adic representation of the étale fundamental group for every vector bundle with numerically flat reduction. The results in the present paper generalize previous work by the authors on curves. They can be seen as a

p
p

-adic analog of higher-dimensional generalizations of the classical Narasimhan-Seshadri correspondence on complex varieties. Moreover, they provide new insights into Faltings’

p
p

-adic Simpson correspondence between small Higgs bundles and small generalized representations by establishing a class of vector bundles with vanishing Higgs field giving rise to actual (not only generalized) representations.
1. What is scepticism?
Authors: Pritchard Duncan
Published: September 2019

Scepticism concerns doubt, primarily doubt about what is true. So construed, the sceptic is not proposing that truth is just subjective opinion in the way that the relativist is. Indeed, what is motivating scepticism is rather the worry that our beliefs might not be true in an objective sense. However, scepticism can slide into relativism if the former becomes extensive enough. ‘What is scepticism?’ asks how we would differentiate between a healthy scepticism that targets only specific claims, and a more generalized radical scepticism that has pernicious consequences. It considers different types of knowledge—propositional, ability, and perceptual—and why it might matter to us that we do have the widespread knowledge that we take ourselves to have.
2. Literature
Authors: Gutting Gary
Published: September 2019

Foucault used his writing to escape from any pigeonholing of identity and to allow him to become someone else. Is being an author a matter of having an identity? ‘Literature’ considers this question and examines it from Foucault’s point of view. What did he see his role as? As an author, a person can assume a variety of roles, corresponding to a diversity of selves. Foucault was interested in the way that authors can relate to language, not as self-expression, but as a way to lose the self in language. This refers to the concept of the death of the author as self-expressive. The author is a vehicle for letting language reveal itself.
4. Archaeology
Authors: Gutting Gary
Published: September 2019

Foucault is mostly regarded as a philosopher, despite the fact that most of his books were histories. He characterized his historic works first as ‘archaeology’ of thought and then later as ‘genealogy’. ‘Archaeology’ considers why Foucault defined his writing in these terms and what it shows us about his ideas. His notion of an archaeology of thought is closely linked to the modernist literary idea of language as a source of thought rather than an instrument of expression. Foucault was interested in the idea that every mode of thinking implicitly involves rules that restrict the range of thought. Foucault’s archaeology aimed at history without the individual subject.
9. Modern sex
Authors: Gutting Gary
Published: September 2019

Foucault was as unwilling to accept an identity based on his sexuality as he was on any other area of his life. His interest was, as always, an academic one. He was interested in gay explorations of new forms of human community and identity. ‘Modern sex’ evaluates Foucault’s History of Sexuality and its treatment of issues of power, gender, repression, and sexuality. His project of a history of sexuality extended to a history of modern bio-power and it also led him to believe that his study of sexuality was part of an effort to understand the process by which individuals became subjects.
Emotion: A Very Short Introduction
Authors: Evans Dylan
Published: September 2019

Was love invented by European poets in the Middle Ages or is it part of human nature? Will winning the lottery really make you happy? Is it possible to build robots that have feelings? Emotion: A Very Short Introduction explores the latest thinking about emotions, drawing on a wide range of scientific research, from anthropology and psychology to neuroscience and artificial intelligence. It discusses the evolution of emotions and their biological basis, the science of happiness, and the role that emotions play in memory and decision-making. This new edition has been updated to incorporate new developments in our understanding of emotions, including the neural basis of empathy and the emotional impact of films.
1. What is an emotion?
Authors: Evans Dylan
Published: September 2019

The word ‘emotion’ is fairly recent. Before the 19th century, people talked instead about ‘passions’, ‘sentiments’, and ‘affections’. ‘What is an emotion?’ begins by outlining the complex history of these words before exploring the variety of emotional experience in different cultures. However, our common emotional heritage binds humanity together in a way that transcends cultural difference. It is now widely accepted among anthropologists and emotion researchers that some emotions, at least, are not learned, but innate. The universality of basic and higher cognitive emotions argues strongly for their biological nature, shaped by our common evolutionary history.
2. The evolution of emotion
Authors: Evans Dylan
Published: September 2019

‘The evolution of emotion’ argues that emotions were—and still are—vital for survival. Ever since Plato, many Western thinkers have tended to view emotions as obstacles to intelligent action. We are all familiar with cases in which an excess of emotion prevents people from acting intelligently. The opposite idea—the positive view of emotion—is that emotions are vital for intelligent action. Until recently, this idea had not been popular among philosophers and psychologists, but considerations drawn from evolutionary theory and neuroscience now argue in its favour. The evolution of emotions such as fear, anger, joy, disgust, guilt, love, and revenge are considered along with the relationship between emotions and morality.
1. Truths universally acknowledged
Authors: O'Donoghue Bernard
Published: September 2019

‘Truths universally acknowledged’ considers some of the ways poetry has been defined and regarded over the ages, and the various things that have been proposed as indispensable to it. A long-established argument is between two schools of belief about the nature of poetry and what it is for: whether its object is pleasure or something more practical. Formal definitions such as rhyme, metre, and kinds of language—verse as opposed to prose—are discussed before considering poetry’s connection to ritual and the importance of syntax in poetry in English. Poetics is particularly concerned with the way that poetry foregrounds the figurative and metaphorical activity in language.
5. Poets and readers
Authors: O'Donoghue Bernard
Published: September 2019

‘Poets and readers’ is concerned with the respective roles of poets and readers in the creation of meaning as well as the function of critics and readers: a function that has attained increasing prominence in the 20th century and since, with the emergence of theories of reader response and the reception of poetry. Is the term poet reserved for a kind of elect or is it a name anyone can aspire to? The whole question of authorship and authority is also considered: whether the poem generally—or ever—speaks in the voice of the poet, and how that voice may relate to its audience.
Survey of Global Health Education and Training in Pathology Residency Programs in the United States
Authors: Glynn Emily H , Guarner Jeannette , Hall Allison , Nelson Ann M , Andiric Linda R , Milner Dan A , Eichbaum Quentin
Published: September 2019

Objectives

This study assessed the prevalence, general interest, and barriers to implementing global health curricula in pathology residency programs.

Methods

We conducted a survey of 166 US pathology residency programs.

Results

Thirty-two (195) of 166 programs responded. Of these, 13% have a formalized global health program (n = 4), and the majority indicated at least some general interest in global health among trainees (88%, n = 28) and faculty (94%, n = 30), albeit at a low to moderate level. Funding limitations, regulatory constraints, and insufficient knowledge of global health were frequently cited barriers to developing a global health program.

Conclusions

Few US pathology departments incorporate global health education into postgraduate training. The importance of pathology in global health has been underappreciated, despite its critical role in the delivery of health care in resource-limited settings. One solution is for pathology departments to expand global health educational opportunities for trainees.
Low-Grade Ductal Carcinoma In Situ
Authors: Alghamdi Sarah A , Krishnamurthy Kritika , Garces Narvaez Sofia A , Algashaamy Khaled J , Aoun Jessica , Reis Isildinha M , Recine Monica A , Jorda Merce , Poppiti Robert J , Gomez-Fernandez Carmen R
Published: September 2019

Objectives

We aimed to determine the interobserver reproducibility in diagnosing low-grade ductal carcinoma in situ (DCIS). We also aimed to compare the interobserver variability using a proposed two-tiered grading system as opposed to the current three-tiered system.

Methods

Three expert breast pathologists and one junior pathologist identified low-grade DCIS from a set of 300 DCIS slides. Months later, participants were asked to grade the 300 cases using the standard three-tiered system.

Results

Using the two-tiered system, interobserver agreement among breast pathologists was considered moderate (κ = 0.575). The agreement was similar (κ = 0.532) with the junior pathologist included. Using the three-tiered system, pathologists’ agreement was poor (κ = 0.235).

Conclusions

Pathologists’ reproducibility on diagnosing low-grade DCIS showed moderate agreement. Experience does not seem to influence reproducibility. Our proposed two-tiered system of low vs nonlow grade, where the intermediate grade is grouped in the nonlow category has shown improved concordance.
EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes
Authors: Marcet-Houben Marina , Gabaldón Toni
Published: September 2019

Motivation

The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism.

Results

We present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons.

Availability and implementation

https://github.com/Gabaldonlab/EvolClust/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics
Authors: Goig Galo A , Torres-Puente Manuela , Mariner-Llicer Carla , Villamayor Luis M , Chiner-Oms Álvaro , Gil-Brusola Ana , Borrás Rafael , Comas Espadas Iñaki
Published: September 2019

Motivation

Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers.

Results

In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research.

Availability and implementation

The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377.

Supplementary information

Supplementary data are available at Bioinformatics online.
Evaluation of bottom-up and top-down mass spectrum identifications with different customized protein sequences databases
Authors: Li Ziwei , He Bo , Feng Weixing
Published: September 2019

Motivation

Generally, bottom-up and top-down are two complementary approaches for proteoforms identification. The inference of proteoforms relies on searching mass spectra against an accurate proteoform sequence database. A customized protein sequence database derived by RNA-Seq data can be used to better identify the proteoform existed in a studied species. However, the quality of sequences in customized databases which constructed by different strategies affect the performances of mass spectrometry (MS) identification. Additionally, performances of identifications between bottom-up and top-down using customized databases are also needed to be evaluated

Results

Three customized databases were constructed with different strategies separately. Two of them were based on translating assembled transcripts with or without genomic annotation, and the third one is a variant-extending protein database. By testing with bottom-up and top-down MS data separately, a variant-extending protein database could identify not only the most number of spectra but also the alleles expressed at the same time in diploid cells. An assembled database could identify the spectrum missed in reference database and amino acid (AA) alterations existed in studied species.

Availability and implementation

Experimental results demonstrated that the proteoform sequences in an annotated database are more suitable for identifying AA alterations and peptide sequences missed in reference database. An unannotated database instead of a reference proteome database gets an enough high sensitivity of identifying mass spectra. The variant-extending reference database is the most sensitive to identify mass spectra and single AA variants

Supplementary information

Supplementary data are available at Bioinformatics online.
simurg: simulate bacterial pangenomes in R
Authors: Ferrés Ignacio , Fresia Pablo , Iraola Gregorio
Published: September 2019

Motivation

The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models.

Results

We developed simurg, an R package that allows to simulate bacterial pangenomes using different combinations of evolutionary constraints such as gene gain, gene loss and mutation rates. Our tool allows the straightforward and reproducible simulation of bacterial pangenomes using real sequence data, providing a valuable tool for benchmarking of pangenome software or comparing evolutionary hypotheses.

Availability and implementation

The simurg package is released under the GPL-3 license, and is freely available for download from GitHub (https://github.com/iferres/simurg).

Supplementary information

Supplementary data are available at Bioinformatics online.
Meltos: multi-sample tumor phylogeny reconstruction for structural variants
Authors: Ricketts Camir , Seidman Daniel , Popic Victoria , Hormozdiari Fereydoun , Batzoglou Serafim , Hajirasouliha Iman
Published: September 2019

Motivation

We propose Meltos, a novel computational framework to address the challenging problem of building tumor phylogeny trees using somatic structural variants (SVs) among multiple samples. Meltos leverages the tumor phylogeny tree built on somatic single nucleotide variants (SNVs) to identify high confidence SVs and produce a comprehensive tumor lineage tree, using a novel optimization formulation. While we do not assume the evolutionary progression of SVs is necessarily the same as SNVs, we show that a tumor phylogeny tree using high-quality somatic SNVs can act as a guide for calling and assigning somatic SVs on a tree. Meltos utilizes multiple genomic read signals for potential SV breakpoints in whole genome sequencing data and proposes a probabilistic formulation for estimating variant allele fractions (VAFs) of SV events.

Results

In order to assess the ability of Meltos to correctly refine SNV trees with SV information, we tested Meltos on two simulated datasets with five genomes in both. We also assessed Meltos on two real cancer datasets. We tested Meltos on multiple samples from a liposarcoma tumor and on a multi-sample breast cancer data (Yates et al., 2015), where the authors provide validated structural variation events together with deep, targeted sequencing for a collection of somatic SNVs. We show Meltos has the ability to place high confidence validated SV calls on a refined tumor phylogeny tree. We also showed the flexibility of Meltos to either estimate VAFs directly from genomic data or to use copy number corrected estimates.

Availability and implementation

Meltos is available at https://github.com/ih-lab/Meltos.

Supplementary information

Supplementary data are available at Bioinformatics online.
Late Miocene origin and recent population collapse of the Malagasy savanna olive tree (Noronhia lowryi)
Authors: Salmona Jordi , Olofsson Jill K , Hong-Wa Cynthia , Razanatsoa Jacqueline , Rakotonasolo Franck , Ralimanana Hélène , Randriamboavonjy Tianjanahary , Suescun Uxue , Vorontsova Maria S , Besnard Guillaume
Published: September 2019

Debates regarding the origin of tropical savannas have attempted to disentangle the role of human, biotic and abiotic factors. Understanding the origins of savanna remains essential to identifying processes that gave rise to habitat mosaics, particularly those found in the Central Plateau of Madagascar. Documenting the evolutionary history and demography of native trees occurring in open habitats may reveal footprints left by past and recent environmental changes. We conducted a population genetic analysis of an endangered Malagasy shrub (Noronhia lowryi, Oleaceae) of the Central Plateau. Seventy-seven individuals were sampled from three sites and genotyped at 14 nuclear and 24 chloroplast microsatellites. We found a highly contrasting nuclear and plastid genetic structure, suggesting that pollen-mediated gene flow allows panmixia, while seed-based dispersal may rarely exceed tens of metres. From a phylogeny based on full plastomes, we dated the surprisingly old crown age of maternal lineages back to ~6.2 Mya, perhaps co-occurring with the global expansion of savanna. In contrast, recent demographic history inferred from nuclear data shows a bottleneck signature ~350 generations ago, probably reflecting an environmental shift during the Late Pleistocene or the Holocene. Ancient in situ adaptation and recent demographic collapse of an endangered woody plant highlight the unique value and vulnerability of the Malagasy savannas.
The History of Foreseeability
Authors: Scott Helen
Published: September 2019

The factual component of the duty of care inquiry—that harm to the claimant as a result of the defendant’s conduct was reasonably foreseeable by the defendant—has been entrenched in English law since Donoghue v Stevenson. Both indigenous and comparative (specifically South African) evidence suggests that Lord Atkin’s formulation of the duty of care test was influenced by a particular fragment contained in Title 9.2 of Justinian’s Digest, ‘On the lex Aquilia’. Interrogation of the foreseeability principle in its original setting shows, however, that its role there was rather circumscribed. Derived perhaps from the account of wrongdoing offered by Aristotle, for whom the fact that harm had occurred contrary to expectation (paralogos) served to demonstrate that it had been unintentionally inflicted, in the context of Roman culpa foreseeability functioned as a technique for determining the avoidability of the harm—essentially a causal inquiry. This historical insight serves to illuminate the limits of foreseeability in the context of the modern test for duty of care. As a principle which generates liability, it may be that reasonable foreseeability cannot bear the normative weight assigned to it. Thus the history of foreseeability furnishes the material for a further critique of the duty concept, adding an historical dimension to contemporary calls to abandon the factual component of the duty of care entirely.
The Value of Communication Practices for Comparative Law: Exploring the Relationship Between Scotland and England
Authors: Braun Alexandra
Published: September 2019

This article explores the relationship between the Scottish and the English legal traditions through the lens of communication practices. ‘Communication practices’ are conceived of as the multiple ways in which legal traditions interact with one another by a combination of the circulation of legal ideas and the activities of legal actors. The article argues that greater attention should be paid in comparative legal literature to communication practices as they evolve over time and space, being especially mindful of the language used and the labels employed. By exploring different shapes of temporality and space, this article demonstrates the importance of looking beyond both discrete events and moments of transplantation, and the immediate geographical space. It also shows that the focus on language and what is explicitly said, but also on what is not said, generates insights both into the various techniques and practices involved in communication, as well as the factors that play a role. By examining concrete examples of communication involving both judges and legislatures, drawn from across different areas of law and different time periods, this article argues that contrary to the prevailing narrative, communication practices between Scotland and England are much richer and more dynamic than we tend to assume. Ultimately, the article questions the narrative and construction of the Scottish legal tradition, and of mixed legal systems more generally, as systems that primarily adopt ideas from abroad, rather than generating ideas capable of stimulating and shaping developments elsewhere.
Associations of six common functional polymorphisms in interleukins with tuberculosis: evidence from a meta-analysis
Authors: Yu Zhen , Wit Wichaidit , Xiong Lifen , Cheng Ying
Published: September 2019

Background

Associations of polymorphisms in interleukin-6 (IL-6), IL-8 and IL-10 with tuberculosis (TB) susceptibility were already reported by many publications. The aim of this meta-analysis was to more precisely clarify associations between polymorphisms in IL-6/IL-8/IL-10 and TB by combing the results of all relevant publications.

Methods

Eligible publications were searched from PubMed, Embase, Web of Science and CNKI. We used Review Manager to combine the results of individual studies.

Results

A total of 47 publications were included in this study. IL-6 rs1800795 (1750 cases and 2335 controls, dominant, recessive and allele comparisons), IL-8 rs4073 (1125 cases and 1188 controls, dominant, recessive and allele comparisons), IL-10 rs1800871 (5528 cases and 7671 controls, dominant, recessive and allele comparisons), IL-10 rs1800872 (5269 cases and 7013 controls, dominant and allele comparisons) and IL-10 rs1800896 (7564 cases and 8952 controls, recessive comparison) polymorphisms were all significantly associated with TB in overall combined analyses. In subgroup analyses, we found that the positive results were mainly driven by the pulmonary tuberculosis and Asian subgroups.

Conclusions

Collectively, this meta-analysis proved that IL-6 rs1800795, IL-8 rs4073, IL-10 rs1800871, IL-10 rs1800872 and IL-10 rs1800896 may confer susceptibility to TB.
Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents
Authors: Kogay Roman , Neely Taylor B , Birnbaum Daniel P , Hankel Camille R , Shakya Migun , Zhaxybayeva Olga
Published: September 2019

Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that are now maintained in genomes of some bacteria and archaea and are hypothesized to enable exchange of DNA within bacterial populations. In Alphaproteobacteria, genes homologous to the “head–tail” gene cluster that encodes structural components of the Rhodobacter capsulatus GTA (RcGTA) are found in many taxa, even if they are only distantly related to Rhodobacter capsulatus. Yet, in most genomes available in GenBank RcGTA-like genes have annotations of typical viral proteins, and therefore are not easily distinguished from their viral homologs without additional analyses. Here, we report a “support vector machine” classifier that quickly and accurately distinguishes RcGTA-like genes from their viral homologs by capturing the differences in the amino acid composition of the encoded proteins. Our open-source classifier is implemented in Python and can be used to scan homologs of the RcGTA genes in newly sequenced genomes. The classifier can also be trained to identify other types of GTAs, or even to detect other elements of viral ancestry. Using the classifier trained on a manually curated set of homologous viruses and GTAs, we detected RcGTA-like “head–tail” gene clusters in 57.5% of the 1,423 examined alphaproteobacterial genomes. We also demonstrated that more than half of the in silico prophage predictions are instead likely to be GTAs, suggesting that in many alphaproteobacterial genomes the RcGTA-like elements remain unrecognized.
Concentrate Questions and Answers Tort Law
Authors: Dyer Dr Karen
Published: September 2019

Each Concentrate revision guide is packed with essential information, key cases, revision tips, exam Q&As, and more. Concentrates show you what to expect in a law exam, what examiners are looking for, and how to achieve extra marks. Concentrate Questions and Answers Tort Law aims to provide the skills for success in exams in this area of law. It starts off by looking at negligence in terms of duty of care, breach of duty and causation and remoteness of damage. It then looks at employers' liability and vicarious liability. It also considers product and occupiers liabilities. It examines intentional torts. It looks at the case Rylands v Fletcher. General defences and damages are also considered. Finally, it provides mix topic questions and looks at coursework assessments.
13. Mixed-topic Questions
Authors: Dyer Dr Karen
Published: September 2019

Each Concentrate revision guide is packed with essential information, key cases, revision tips, exam Q&As, and more. Concentrates show you what to expect in a law exam, what examiners are looking for, and how to achieve extra marks. This chapter presents mixed-topic questions on tort law. In order to answer them fully, students are required to blend their knowledge of the law of tort. They will be able to assess their knowledge on: the purpose of the law of tort; negligence — duty of care, breach, causation, economic loss; remedies; and vicarious liability. Each question is accompanied by a diagram answer plan and suggested answers. Tips for getting extra marks and online resources are also provided.
Markesinis & Deakin's Tort Law
Authors: Deakin Simon , Adams Zoe
Published: September 2019

Markesinis and Deakin’s Tort Law, now in its 8th edition, provides a general overview of the law and discussion of the academic debates on all major topics, highlighting the relationship between the common law, legislation, and judicial policy. In addition, the book provides a variety of comparative and economic perspectives on the law of tort and its likely development, always placing the subject in its socio-economic context, thereby giving students a deep understanding of tort law. The book is composed of eight parts. Part I starts by setting the scene, Part II looks at the tort of negligence. Part III turns to special forms of negligence. This is followed by Part IV which examines interference with the person. Part V turns to intentional interferences with economic interests. The next part looks at stricter forms of liability. Part VII examines the protection of human dignity which includes looking at defamation and injurious falsehood, and human privacy. The last part looks at defences and remedies.
1. Introduction
Authors: Deakin Simon , Adams Zoe
Published: September 2019

This introductory chapter first reviews the current state of the law of tort. It discusses the increase in tort claims due to our greater ability to cause more and greater harm and our reduced willingness to put up with the normal vicissitudes of life. It considers the law of individual responsibility. It suggests that tort law is becoming by the day a more complex set of rules than it ever was, where national law mixes with legal ideas emanating from foreign jurisdictions. Tort law rules are also becoming intermingled with those from other branches of English law. The second part of the chapter discusses the relationship between tort and contract.
16. The Rule in Rylands v. Fletcher
Authors: Deakin Simon , Adams Zoe
Published: September 2019

This chapter examines the rule in Rylands v. Fletcher, a rule which remains controversial to this day. The rule states that anyone who, in the course of a ‘non-natural’ use of his land ‘accumulates’ thereon for his own purposes anything likely to do mischief if it escapes, is answerable for all direct damage thereby caused. It discusses the requirements for liability, the various controlling mechanisms used to limit the scope of the rule; what and whose interests are protected by it; and the relationship between Rylands v. Fletcher and private nuisance. The chapter also explores the important questions that the rule in Rylands v. Fletcher raises about the nature, and future, of strict liability in the law of tort in general.
23. Defences
Authors: Deakin Simon , Adams Zoe
Published: September 2019

This chapter begins with a brief discussion of the role of defences in the law of torts. It then considers their application to torts which require proof of damage in order to be actionable, and in particular with the tort of negligence. The discussions cover contributory negligence; consent; exclusion and limitation of liability; illegality; necessity; inevitable accident; authorisation; and limitation of action. The chapter takes into account recent statutory developments including the effects of the Consumer Rights Act 2015 on the law governing exclusion and limitation of liability. It also examines the extensive Supreme Court case law reexamining the defence of illegality.
24. Damages
Authors: Deakin Simon , Adams Zoe
Published: September 2019

This chapter is the first of two chapters concerned with remedies. The focus of this chapter is monetary remedies; the financial consequences of a proven tort. It begins by discussing the notion of damage, and damages, before exploring different types of damages; the principle of full compensation; the interrelationship of tort and other compensation systems; pecuniary and non-pecuniary losses; death in relation to tort; and damage to property.
2. Copyright 1: history, rationale, and policy context
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter considers the evolution of modern copyright law against the background of its historical development in the UK and the international and European legal frameworks within which UK copyright law has been increasingly set since the nineteenth century. It examines the rationale and justifications for copyright and identifies the general policy context within which law and policy has developed in the UK and the EU. It also highlights the rapid development of new technologies which has brought copyright reform to the forefront in recent times, the difficulties which this new environment presents for the copyright framework, and how the framework has developed to such challenges.
3. Copyright 2: subject matter, first ownership, and term
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter first examines the subject matter in which copyright subsists and the criteria for copyright protection as set out in the Copyright, Designs, and Patents Act 1988 (CDPA 1988). This centres on the concept of the ‘protected work’ and makes use of a distinction between what are sometimes known as ‘author works’ (literary, dramatic, musical, artistic, and film works) and ‘media works’ (typographical arrangements, sound recordings, broadcasts, and adaptations). It then considers the identification of the first owner of copyright when it comes into existence. It discusses the concept of joint authorship and ownership of copyright works when created in the course of employment. The final section discusses the duration of copyright.
4. Copyright 3: economic rights and infringement
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter considers the ‘economic rights’ the copyright owner enjoys while copyright protection endures. These are the rights that the Copyright, Designs, and Patents Act 1988 (CDPA 1988) calls ‘acts restricted by copyright’, which may be exploited by transferring them to others or licensing others to use them for a price. The chapter discusses the rights flowing from ownership of copyright and the international framework that underpins them, noting the influence upon UK law of a number of EU Directives. It identifies the general principles pertaining to infringement of economic rights, before turning to the detailed rules on each economic right: to make copies, issue copies to the public; rent or lend commercially to the public; perform, show, or play in public; communication to the public; and make adaptations. It discusses authorisation of infringement (accessory liability) in relation to these economic rights, and finally considers secondary infringement of copyright.
15. Trade marks 3: relative ground for refusal and invalidation, infringement, and defences
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter discusses the relative grounds for refusal or invalidation of a registered trade mark, the circumstances in which a trade mark can be infringed, and defences to an action of infringement and their limits. As relative grounds and infringement overlap, these are considered together. Important additional legal issues on infringement—such as what constitutes infringing ‘use’ of a trade mark—are also considered. Key questions are the power conferred by a trade mark over the activities of others and the extent to which activities of others can prevent the registration of a trade mark. Again, the chapter reflects evolving legislation at an EU level (particularly the EU’s 2015 trade mark reform package), together with a rich body of case law.
6. Misrepresentation
Authors: Devenney James
Published: September 2019

The Concentrate Questions and Answers series offers the best preparation for tackling exam questions. Each book includes typical questions, answer plans and suggested answers, author commentary and other features. Misrepresentation is defined as a false statement of fact, made pre-contractually, which is intended to induce the representee to enter into a contract and which has that effect. If an actionable misrepresentation is found to exist a court will then need to consider the available remedies. This chapter considers the following issues relevant to answering any problem question on misrepresentation. Has there been a false statement of fact? Is there evidence of inducement? What type of misrepresentation has potentially been made? What remedies are potentially available? Has liability for misrepresentation been effectively excluded? Has there been a breach of contract?
7. Improper Pressure
Authors: Devenney James
Published: September 2019

The Concentrate Questions and Answers series offers the best preparation for tackling exam questions. Each book includes typical questions, answer plans and suggested answers, author commentary and other features. This chapter focuses on the doctrines of undue influence and duress. Between the parties to a con-tract there are broadly two ways that a contract can be avoided for undue influence: through affirmative proof of undue influence or through raising the presumption of undue influence which is not rebutted. As regards duress, there are two main forms: physical and economic. The more common type is economic duress, which focuses on the illegitimate pressure exerted by the dominant party.
12. Additional Remedies
Authors: Devenney James
Published: September 2019

The Concentrate Questions and Answers series offers the best preparation for tackling exam questions. Each book includes typical questions, answer plans and suggested answers, author commentary and other features. The standard common law remedy of damages will not always prove adequate for the victim of a breach of contract. Equity therefore developed a number of additional remedies, discretionary in nature, aimed at ensuring that a claimant was not unreasonably confined to an award of damages; in particular, specific performance and injunctions. The possibility of awarding restitutionary damages, in part to offset any unjust enrichment secured by a contract-breaker, is also considered.
Public Law
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

Public Law: Text, Cases, and Materials offers a fresh approach to the study of constitutional and administrative law. It provides clear and insightful commentary on the key institutions, legal principles, and conventions, and blends this with a carefully selected and diverse range of materials and case studies. Part I covers the fundamentals of the constitution. Part II examines the executive function including protecting rights, government and accountability Part III looks at the legislative function including primary and delegated legislation, European Union treaties, and legislative processes. Part IV considers judicial and dispute resolution functions in terms of the judiciary, tribunals, the ombuds human rights, and constitutional change; Part V examines the European Union, including th institutions of the European Union, joining and leaving the Union and European Law in the UK courts.
1. Introduction to Constitutional Fundamentals
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

This introduction examines the ideas of constitutions as a text of fundamental importance, setting out how a country should be governed, and as a system of government. Also explored is the question why the United Kingdom has not adopted a codified constitution and the consequences of this.
6. Multilevel Governing Within the United Kingdom
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

This chapter examines multilevel governing within the UK. It is organized around three levels of governing: national, regional, and local. For most of the twentieth century, Great Britain (England, Wales, and Scotland) formed a centralized political unit, with policymaking and law-making being led by the UK government and the UK Parliament. There was devolved government in Northern Ireland from 1922, but this was brought to an end by the UK government in 1972 amid mounting civil unrest and paramilitary violence. At the local level, there are more than 400 local authorities throughout the United Kingdom. These vary considerably in size, both in terms of their territorial area that they cover and their populations.
18. Administrative Justice: Tribunals and Ombuds
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

This chapter considers the main ways in which disputes between individuals and public bodies are resolved outside the court system in what is widely referred to as the landscape of ‘administrative justice’. The discussions cover initial decision-making; accessing the administrative justice ‘system’; and the two pillars of administrative justice—tribunals and ombuds.
19. Judicial Review
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

This chapter looks at judicial review. It considers its recent history, the constitutional foundations for judicial review, and some key issues relating to the practical use and effects of judicial review. It also surveys the grounds of judicial review, and examines what has happened when government and Parliament have attempted to oust judicial review.
23. European Union Law in the United Kingdom Courts
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

This chapter discusses the reception of Community (now EU law) in the UK courts, and in particular how UK courts reconciled the doctrine of supremacy with the doctrine of parliamentary sovereignty. The chapter will examine three ways in which the UK courts have attempted to reconcile these competing doctrines: by constructing national law in light of EU law; by disapplying conflicting national law; and by reasserting national sovereignty and threatening not to apply EU law automatically. Finally, the chapter will briefly re-visit the case of Miller in order to evaluate that case in light of earlier cases on the relationship between UK and EU law.