bluuebunny/crossref_metadata_2025 huggingface dataset:
phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
Authors: Bradley Patrick H , Pollard Katherine S
Published: September 2019

Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME 2 and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization.

Availability and implementation

phylogenize is available at https://phylogenize.org and https://bitbucket.org/pbradz/phylogenize.

Supplementary information

Supplementary data are available at Bioinformatics online.
L1EM: a tool for accurate locus specific LINE-1 RNA quantification
Authors: McKerrow Wilson , Fenyö David
Published: September 2019

Motivation

LINE-1 elements are retrotransposons that are capable of copying their sequence to new genomic loci. LINE-1 derepression is associated with a number of disease states, and has the potential to cause significant cellular damage. Because LINE-1 elements are repetitive, it is difficult to quantify LINE-1 RNA at specific loci and to separate transcripts with protein coding capability from other sources of LINE-1 RNA.

Results

We provide a tool, L1EM that uses the expectation maximization algorithm to quantify LINE-1 RNA at each genomic locus, separating transcripts that are capable of generating retrotransposition from those that are not. We show the accuracy of L1EM on simulated data and against long read sequencing from HEK cells.

Availability and implementation

L1EM is written in python. The source code along with the necessary annotations are available at https://github.com/FenyoLab/L1EM and distributed under GPLv3.

Supplementary information

Supplementary data are available at Bioinformatics online.
T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data
Authors: Bogaerts-Márquez María , Barrón Maite G , Fiston-Lavier Anna-Sophie , Vendrell-Mir Pol , Castanera Raúl , Casacuberta Josep M , González Josefa
Published: September 2019

Motivation

Transposable elements (TEs) constitute a significant proportion of the majority of genomes sequenced to date. TEs are responsible for a considerable fraction of the genetic variation within and among species. Accurate genotyping of TEs in genomes is therefore crucial for a complete identification of the genetic differences among individuals, populations and species.

Results

In this work, we present a new version of T-lex, a computational pipeline that accurately genotypes and estimates the population frequencies of reference TE insertions using short-read high-throughput sequencing data. In this new version, we have re-designed the T-lex algorithm to integrate the BWA-MEM short-read aligner, which is one of the most accurate short-read mappers and can be launched on longer short-reads (e.g. reads >150 bp). We have added new filtering steps to increase the accuracy of the genotyping, and new parameters that allow the user to control both the minimum and maximum number of reads, and the minimum number of strains to genotype a TE insertion. We also showed for the first time that T-lex3 provides accurate TE calls in a plant genome.

Availability and implementation

To test the accuracy of T-lex3, we called 1630 individual TE insertions in Drosophila melanogaster, 1600 individual TE insertions in humans, and 3067 individual TE insertions in the rice genome. We showed that this new version of T-lex is a broadly applicable and accurate tool for genotyping and estimating TE frequencies in organisms with different genome sizes and different TE contents. T-lex3 is available at Github: https://github.com/GonzalezLab/T-lex3.

Supplementary information

Supplementary data are available at Bioinformatics online.
CircaCompare: a method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms
Authors: Parsons Rex , Parsons Richard , Garner Nicholas , Oster Henrik , Rawashdeh Oliver
Published: September 2019

Motivation

A fundamental interest in chronobiology is to compare patterns between groups of rhythmic data. However, many existing methods are ill-equipped to derive statements concerning the statistical significance of differences between rhythms that may be visually apparent. This is attributed to both the form of data used (longitudinal versus cross-sectional) and the limitations of the statistical tests used to draw conclusions.

Results

To address this problem, we propose that a cosinusoidal curve with a particular parametrization be used to model and compare data of two sets of observations collected over a 24-h period. The novelty of our test is in the parametrization, which allows the explicit estimation of rhythmic parameters [mesor (the rhythm-adjusted mean level of a response variable around which a wave function oscillates), amplitude and phase], and simultaneously testing for statistical significance in all three parameters between two or more groups of datasets. A statistically significant difference between two groups, regarding each of these rhythmic parameters, is indicated by a P-value. The method is evaluated by applying the model to publicly available datasets, and is further exemplified by comparison to the currently recommended method, DODR. The results suggest that the method proposed may be highly sensitive to detect rhythmic differences between groups in phase, amplitude and mesor.

Availability and implementation

https://github.com/RWParsons/circacompare/
The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments
Authors: Bender Julian , Schmidt Carla
Published: September 2019

Motivation

A variety of search engines exists for the identification of peptide spectrum matches after cross-linking mass spectrometry experiments. The resulting diversity in output formats complicates data validation and visualization as well as exchange with collaborators, particularly from other research areas.

Results

Here, we present CroCo, a user-friendly standalone executable to convert cross-linking results to a comprehensive spreadsheet format. Using this format, CroCo can be employed to generate input files for a selection of the commonly utilized validation and visualization tools.

Availability and implementation

The source-code is freely available under a GNU general public license at https://github.com/cschmidtlab/croco. The standalone executable is available and documented at https://cschmidtlab.github.io/CroCo.

Supplementary information

Supplementary data are available at Bioinformatics online.
SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting
Authors: Yu Bin , Qiu Wenying , Chen Cheng , Ma Anjun , Jiang Jing , Zhou Hongyan , Ma Qin
Published: September 2019

Motivation

Mitochondria are an essential organelle in most eukaryotes. They not only play an important role in energy metabolism but also take part in many critical cytopathological processes. Abnormal mitochondria can trigger a series of human diseases, such as Parkinson's disease, multifactor disorder and Type-II diabetes. Protein submitochondrial localization enables the understanding of protein function in studying disease pathogenesis and drug design.

Results

We proposed a new method, SubMito-XGBoost, for protein submitochondrial localization prediction. Three steps are included: (i) the g-gap dipeptide composition (g-gap DC), pseudo-amino acid composition (PseAAC), auto-correlation function (ACF) and Bi-gram position-specific scoring matrix (Bi-gram PSSM) are employed to extract protein sequence features, (ii) Synthetic Minority Oversampling Technique (SMOTE) is used to balance samples, and the ReliefF algorithm is applied for feature selection and (iii) the obtained feature vectors are fed into XGBoost to predict protein submitochondrial locations. SubMito-XGBoost has obtained satisfactory prediction results by the leave-one-out-cross-validation (LOOCV) compared with existing methods. The prediction accuracies of the SubMito-XGBoost method on the two training datasets M317 and M983 were 97.7% and 98.9%, which are 2.8–12.5% and 3.8–9.9% higher than other methods, respectively. The prediction accuracy of the independent test set M495 was 94.8%, which is significantly better than the existing studies. The proposed method also achieves satisfactory predictive performance on plant and non-plant protein submitochondrial datasets. SubMito-XGBoost also plays an important role in new drug design for the treatment of related diseases.

Availability and implementation

The source codes and data are publicly available at https://github.com/QUST-AIBBDRC/SubMito-XGBoost/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features
Authors: Li Yuanyue , Kuhn Michael , Gavin Anne-Claude , Bork Peer
Published: September 2019

Motivation

Untargeted mass spectrometry (MS/MS) is a powerful method for detecting metabolites in biological samples. However, fast and accurate identification of the metabolites’ structures from MS/MS spectra is still a great challenge.

Results

We present a new analysis method, called SubFragment-Matching (SF-Matching) that is based on the hypothesis that molecules with similar structural features will exhibit similar fragmentation patterns. We combine information on fragmentation patterns of molecules with shared substructures and then use random forest models to predict whether a given structure can yield a certain fragmentation pattern. These models can then be used to score candidate molecules for a given mass spectrum. For rapid identification, we pre-compute such scores for common biological molecular structure databases. Using benchmarking datasets, we find that our method has similar performance to CSI: FingerID and those very high accuracies can be achieved by combining our method with CSI: FingerID. Rarefaction analysis of the training dataset shows that the performance of our method will increase as more experimental data become available.

Availability and implementation

SF-Matching is available from http://www.bork.embl.de/Docu/sf_matching.

Supplementary information

Supplementary data are available at Bioinformatics online.
Hexa-Longin domain scaffolds for inter-Rab signalling
Authors: Sanchez-Pulido Luis , Ponting Chris P
Published: September 2019

CPLANE is a protein complex required for assembly and maintenance of primary cilia. It contains several proteins, such as INTU, FUZ, WDPCP, JBTS17 and RSG1 (REM2- and RAB-like small GTPase 1), whose genes are mutated in ciliopathies. Using two contrasting evolutionary analyses, coevolution-based contact prediction and sequence conservation, we first identified the INTU/FUZ heterodimer as a novel member of homologous HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) complexes. Subsequently, we identified homologous Longin domains that are triplicated in each of these six proteins (MON1A, CCZ1, HPS1, HPS4, INTU and FUZ). HerMon complexes are known to be Rab effectors and Rab GEFs (Guanine nucleotide Exchange Factors) that regulate vesicular trafficking. Consequently, INTU/FUZ, their homologous complex, is likely to act as a GEF during activation of Rab GTPases involved in ciliogenesis.

Supplementary information

Supplementary data are available at Bioinformatics online.
Amino-terminal Pro-B-Type Natriuretic Peptide Among Patients Living With Both Human Immunodeficiency Virus and Heart Failure
Authors: Alvi Raza M , Zanni Markella V , Neilan Anne M , Hassan Malek Z O , Tariq Noor , Zhang Lili , Afshar Maryam , Banerji Dahlia , Mulligan Connor P , Rokicki Adam , Awadalla Magid , Januzzi James L , Neilan Tomas G
Published: September 2019

Background

Among persons living with human immunodeficiency virus (PHIV), incident heart failure (HF) rates are increased and outcomes are worse; however, the role of amino-terminal pro-B-type natriuretic peptide (NT-proBNP) concentrations among PHIV with HF has not been characterized.

Methods

Patients were derived from a registry of those hospitalized with HF at an academic center in a calender year. We compared the NT-proBNP concentrations and the changes in NT-proBNP levels between PHIV with HF and uninfected controls with HF.

Results

Among 2578 patients with HF, there were 434 PHIV; 90% were prescribed antiretroviral therapy and 62% were virally suppressed. As compared to controls, PHIV had higher admission (3822 [IQR, 2413–7784] pg/ml vs 5546 [IQR, 3257–8792] pg/ml, respectively; P < .001), higher discharge (1922 [IQR, 1045–4652] pg/ml vs 3372 [IQR, 1553–5452] pg/ml, respectively; P < .001), and lower admission-to-discharge changes in NT-proBNP levels (32 vs 48%, respectively; P = .007). Similar findings were noted after stratifying based on left ventricular ejection fraction (LVEF). In a multivariate analysis, cocaine use, a lower LVEF, a higher NYHA class, a higher viral load (VL), and a lower CD4 count were associated with higher NT-proBNP concentrations. In follow-up, among PHIV, a higher admission NT-proBNP concentration was associated with increased cardiovascular mortality (first tertile, 11.5; second tertile, 20; third tertile, 44%; P < .001). Among PHIV, each doubling of NT-proBNP was associated with a 19% increased risk of death. However, among patients living without HIV, each doubling was associated with a 27% increased risk; this difference was attenuated among PHIV with lower VLs and higher CD4 counts.

Conclusions

PHIV with HF had higher admission and discharge NT-proBNP levels, and less change in NT-proBNP concentrations. Among PHIV, VLs and CD4 counts were associated with NT-proBNP concentrations; in follow-up, higher NT-proBNP levels among PHIV were associated with cardiovascular mortality.
Relationship between serum phosphate levels and survival in chronic hemodialysis patients: interactions with age, malnutrition and inflammation
Authors: Ye Xiaoling , Kooman Jeroen P , van der Sande Frank M , Raimann Jochen G , Usvyat Len A , Wang Yuedong , Maddux Franklin W , Kotanko Peter
Published: September 2019

Background

Evidence indicates that the inverse relationships between phosphate levels and mortality maybe modified by age. Furthermore, malnutrition and inflammation could strengthen the risk associated with phosphate abnormalities. This study aimed to assess the associations between phosphate levels and mortality while accounting for the interactions with age and parameters associated with malnutrition and inflammation in hemodialysis (HD) patients.

Methods

Adult HD patients (n = 245 853) treated in Fresenius Medical Care North America clinics from January 2010 to October 2018 were enrolled. Baseline was defined as Months 4–6 on dialysis, with the subsequent 12 months as the follow-up period. Univariate and multivariate Cox proportional hazard models with spline terms were applied to study the nonlinear relationships between serum phosphate levels and mortality. The interactions of phosphate levels with albumin, creatinine, normalized protein catabolic rate (nPCR) and neutrophil–lymphocyte ratio (NLR) were assessed with smoothing spline analysis of variance Cox proportional hazard models.

Results

Older patients tended to have lower levels of serum phosphate, albumin, creatinine and nPCR. Additionally, both low (<4.0 mg/dL) and high (>5.5 mg/dL) phosphate levels were associated with higher risk of mortality across all age strata. The U-shaped relationships between phosphate levels and outcome persisted even for patients with low or high levels of serum albumin, creatinine, nPCR and NLR, respectively.

Conclusion

The consistent U-shaped relationships between serum phosphate and mortality across age strata and levels of inflammatory and nutritional status should prompt the search for underlying causes and potentially nutritional intervention in clinical practice.
2. Negligence I: Duty of Care
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 discusses negligence in terms of duty of care. In order to answer questions on this topic, students need to have the following: a general understanding of the tort of negligence; an understanding of the development of duty of care in negligence, in particular the key cases of Donoghue v Stevenson [1932] AC 562; Anns v Merton LBC [1978] AC 728; Caparo plc v Dickman [1990] 2 AC 605; an understanding of the development of duty of care in specialized aspects of negligence; and understanding of liability for omissions and of public authorities.
3. Negligence II: Breach of Duty
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 discusses negligence in terms of breach of duty. To answer questions on this topic, students need to understand the following: the concept of duty of care in negligence; the objective standard of care: the ‘reasonable person’ and factors relevant to the standard of care; variations of the objective standard: children, emergency situations, sporting events, and skilled persons ‘professing to have a special skill’; and res ipsa loquitur.
10. Defamation and Privacy
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. To answer questions on defamation, students need to understand the following: categories of defamation: libel and slander; what constitutes a defamatory statement: innuendo; defences to defamation: absolute privilege and qualified privilege; the Defamation Act 2013; and offer of amends, Defamation Act 1996 sections 2–4. To answer questions on privacy, students need to understand the following: the nature of privacy; the overlap between the torts of misuse of private information, and other causes of action; trespass; negligence; the Human Rights Act 1998; and the Protection from Harassment Act 1997.
19. Vicarious Liability and Non-Delegable Duties
Authors: Deakin Simon , Adams Zoe
Published: September 2019

Vicarious liability is liability imposed on an employer to a third party for the tort of his employee committed in the course of employment. Vicarious liability is another instance of stricter liability in the sense that the employer who is not at fault is made responsible for the employee’s default. It thereby gives the injured party compensation from the person who is better able to pay and spread the cost of the injury, namely the employer. Anyone who wishes to hold an employer vicariously liable must prove: that the wrongdoer was his employee, or that the relationship between them was ‘akin’ to employment; that he committed a tort; and that he committed it in the course of his employment. This chapter discusses each of this in turn. It also considers contribution between employer and employee; liability for the torts of independent contractors; the expanding categories of non-delegable duties; and the changing contours of employer’s liability.
21. Defamation and Injurious Falsehood
Authors: Deakin Simon , Adams Zoe
Published: September 2019

Defamation, a tort that protects a claimant’s reputation, has been the subject of much debate in recent years, culminating in the passing of the Defamation Act in 2013. A tort of historic origin, defamation raises novel challenges in an age of internet and digital communication technology, particularly given increasing concerns about freedom of expression, and the protection of privacy. Like many aspects of the law discussed in this book, moreover, defamation has not been left untouched by human rights developments. The chapter begins with an introduction to defamation, covering the meaning of ‘defamatory’ and libel and slander. It then discusses elements of liability, both in the common law, and under the Defamation Act 2013; defences; damages; mitigation of damage; and injurious falsehoods and passing off.
1. Intellectual property law: an introduction
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter provides an accessible introduction to intellectual property (IP) law. It provides and challenges some definitions of intellectual property law and IP itself. It discusses the development of IP law as a field of study in an increasingly global context and presents a realistic view of the law as it actually operates; the relationships between different levels of IP law—at national, European, European Union, and international levels; the various influences on the formation, justifications for, and development of IP law including between IP law and other legal fields; and the tensions that arise from different perspectives when the law seeks to protect IP.
8. Registered designs
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter discusses the law of registered designs. It explains the international treaty context for design law, and then considers the substantive law of registered designs in the UK and at an EU level, looking together at UK registered design protection and the Community registered design. Issues considered include: what designs may be validly registered, exclusions from protection, treatment of spare parts and component parts of complex products, challenging the validity of a registration, rights conferred by registration, and defences to infringement. The chapter also looks briefly at the interaction between registered design protection and other IP rights, in particular copyright.
9. Unregistered designs
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter discusses unregistered design protection which confers its own form of protection for a more limited period than is the case for other IP rights. The chapter examines the two main forms of unregistered design right: the UK unregistered design right established by Part III of the Copyright, Designs and Patents Act 1988; and the Community unregistered design right. While Community unregistered design right is closely connected to the scheme of registered design law discussed in Chapter 8, UK unregistered design right is a fully independent and distinct form of unregistered protection for designs which is unique to the UK and poses its own particular challenges. The chapter also considers in more detail the evolving and complex interaction of design protection and copyright including recent UK legislative developments.
12. The power of a patent
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter deals with who is entitled to be a patentee, the rights that a patentee enjoys (which are some of the strongest within intellectual property law), the circumstances in which infringement actions might be brought, the defences that are available, and some points on exploitation practices. A key thread is the construction and interpretation of the patent and the inextricable link between the power conferred by the patent and questions of novelty and obviousness. This chapter also looks at sufficiency, the circumstances in which a patent may be revoked, and the risk of a claim for revocation of the patent.
18. Control of information, reputation, and intellectual property
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter considers the extent to which individuals can and should be able to prevent others referring to them and their activities and, conversely, the extent to which individuals and companies should be able to commercialise and control a reputation that they have built up. The discussions cover the evolving right to personal privacy (through the tort of misuse of private information) and its base in human rights, particularly in respect of photographs; obtaining and dealing with trade marks in respect of well-known personalities; the relationship between passing off and endorsement and merchandising; and the extent to which individuals and businesses can and do control the use of their image through endorsement and sponsorship. The chapter also considers data protection, as well as the balancing of privacy and freedom of expression.
20. EU competition law and intellectual property
Authors: Brown Abbe , Kheria Smita , Cornwell Jane , Iljadica Marta
Published: September 2019

This chapter provides an overview of the tension between the application of competition law and the exercise of IPRs. Key issues are the circumstances in which competition law may be applied to moderate the exercise of IPRs in the relevant market; clauses in intellectual property (IP) licensing agreements between undertakings that might be permissible in terms of EU competition law and those which are not; the conditions under which a refusal to supply products protected by an IP right might constitute an abuse of a dominant position by the right holder; and when competition law can provide a defence to an infringement action.
1. Exam Skills for Success in Contract Law
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. Q&A Law of Contract provides guidance on answering questions on the law of contract. This chapter outlines how the book may be used to aid you in writing answers to contract essay and problem questions.
9. Illegality and Restraint of Trade
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. Illegality is one of the most confusing areas within the law of contract, particularly as regards the consequences of a finding of illegality. This chapter considers recent developments in this general area of law as well as contracts in restraint of trade.
14. Mixed Topic Questions
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 introduces students to examination questions which contain overlapping topics. Clearly, if students identify all the relevant areas then they will have established a firm base from which a good answer can be developed. The chapter aims to illustrate how different topics may be contained within one question; the suggested answers offer an explanation of how such questions may be approached in a written answer.
2. The Constitutional Rulebook
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

This chapter looks at the constitution of the United Kingdom to understand its function as a rulebook: for constitutional arrangements to work well, people need to know what the rules are and there also needs to be broad consensus that the rules are right. It explores the sources of the rules in the United Kingdom’s famously ‘unwritten’ constitution: these include Acts of Parliament, the common law, and constitutional conventions. It also considers the question: who makes the rulebook? To answer this, we must listen to a debate about the respective roles of politicians and judges (called ‘political constitutionalism’ and ‘common law’ or ‘legal’ constitutionalism).
17. The Judiciary
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

This chapter begins with discussions of the role of the judiciary in the UK, its relationships with other institutions, and qualifications for being a judge. It then considers the issue of judicial independence and how independence can be retained while ensuring that judges are accountable. There is a mini case study on the controversies surrounding media criticism of the judges following the decisions in the Miller case. The chapter also considers impartiality; the appointment of judges; the need to improve diversity of the judiciary; and the use of judges to chair public inquiries.
21. Institutions of the European Union
Authors: Le Sueur Andrew , Sunkin Maurice , Murkens Jo Eric Khushal
Published: September 2019

This chapter introduces the project of European integration and discusses the legal basis of the EU, which consists of treaties that authorize law-making. It will identify the principal executive institutions of the European Union and their functions. They will be classified under the headings of supranationalism and intergovernmentalism. The chapter will also examine the process of enacting legislation and the role of the European Parliament. Drawing on an understanding of similar institutions and processes in the UK, the discussion is particularly concerned with an assessment of the institutions in terms of public law values, such as legitimacy, accountability, and transparency.
3. Creation of Legal and Equitable Rights in Land
Authors: Bogusz Barbara , Sexton Roger
Published: September 2019

Titles in the Complete series combine extracts from a wide range of primary materials with clear explanatory text to provide readers with a complete introductory resource. This chapter discusses the changes made by the 1925 legislation. It covers legal estate and interests prior to 1925; s1 Law of Property Act 1925; legal estates and interests existing after 1925; and equitable interests after 1925. The creation of legal and equitable property rights is discussed; also the creation and transfer of legal property rights; the creation of equitable interests in land by express trust; the creation of equitable interests by contract to convey or create a legal estate or interest; treating an informal grant of rights in land as a contract, thus creating an equitable interest in land; grant of an estate or interest by someone with only an equitable interest; and grants of interests which can exist only in equity.
14. Termination of Leases
Authors: Bogusz Barbara , Sexton Roger
Published: September 2019

Titles in the Complete series combine extracts from a wide range of primary materials with clear explanatory text to provide readers with a complete introductory resource. This chapter discusses the ways in which leases may terminate (natural expiry, giving of notice, merger, surrender, frustration, repudiatory breach by the landlord accepted by the tenant, and forfeiture); forfeiture of leases; modes of forfeiture; forfeiture of a dwelling house; waiver of forfeiture; relief from forfeiture for breaches for non-payment of rent; relief from forfeiture for a breach of covenant other than rent; forfeiture by court proceedings under s146 LPA 1925; remediable or irremediable breaches; relief to sub-tenants; and the Leasehold Property (Repairs) Act 1938.
15. Adverse Possession and the Limitation Acts
Authors: Bogusz Barbara , Sexton Roger
Published: September 2019

Titles in the Complete series combine extracts from a wide range of primary materials with clear explanatory text to provide readers with a complete introductory resource. This chapter discusses the basic principles for adverse possession; adverse possession against land which is subject to a lease; and the complex rules applicable where adverse possession is taken against land which is registered title. It covers the rationale of adverse possession; possession giving a right to sue trespassers; the Limitation Act 1980; commencement of adverse possession; offence of squatting in a residential building; preventing the acquisition of title by adverse possession; and the effect of adverse possession.
18. Creation of Express and Implied Grant of Easements
Authors: Bogusz Barbara , Sexton Roger
Published: September 2019

Titles in the Complete series combine extracts from a wide range of primary materials with clear explanatory text to provide readers with a complete introductory resource. This chapter discusses the rules on the creation of an easement. Topics covered include express grant of easements (and profits); express reservation of easements (and profits); implied grant of easements (and profits), which includes ways of necessity, intended easements, the rule in Wheeldon v Burrows and s62 of the Law of Property Act 1925; implied reservation of easements covering necessity and intended easements; exclusion of the rules providing for implied grant and reservation; compulsory purchase and the rules for implied grant; and simultaneous sales or bequests.
19. Prescription for Easements (and Profits)
Authors: Bogusz Barbara , Sexton Roger
Published: September 2019

Titles in the Complete series combine extracts from a wide range of primary materials with clear explanatory text to provide readers with a complete introductory resource. This chapter discusses rules common to all three forms of prescription; user ‘as of right’ (without force, without secrecy and without permission), presumed acquiescence, user must be continuous, user must be by or on behalf of a fee simple against a fee simple, and user must be against a servient owner capable of granting an easement; prescription at common law; prescription by lost modern grant; prescription under the Prescription Act 1832; prescriptive easements and profits as legal interests; and extinguishment of easements.
21. Escaping from Restrictive Covenants
Authors: Bogusz Barbara , Sexton Roger
Published: September 2019

Titles in the Complete series combine extracts from a wide range of primary materials with clear explanatory text to provide readers with a complete introductory resource. This chapter discusses the various options available to developers whose plans are obstructed by restrictive covenants. It covers ignoring restrictive covenants; attempting to buy out the dominant owners; identifying who can enforce a restrictive covenant; obtaining a definitive list of dominant owners; modification or discharge of a covenant under s84(1) of the Law of Property Act 1925; grounds for discharge or modification of restrictive covenants (obsolete, obstructs some reasonable user of the land, practical benefit and public interest); and balancing interests of the parties.
1. The English Legal System
Authors: Gillespie Alisdair A. , Weare Siobhan
Published: September 2019

This chapter provides an introduction to the English Legal System. Specifically, it explains the meaning of the terms ‘English’, ‘legal’, and ‘system’. It first provides an overview of the constituent parts of the United Kingdom of Great Britain and Northern Ireland, namely England, Wales, Scotland, and Northern Ireland. It describes the types of law that exist and attempts to define what law is. It then discusses the English legal system, which is based on common law and is an adversarial system.
3. Domestic Sources of Law: Case Law
Authors: Gillespie Alisdair A. , Weare Siobhan
Published: September 2019

This chapter continues the discussion of sources of domestic law, focusing on material produced by the courts through cases. It covers the reporting of cases, the hierarchy of courts, legal principles, and the operation of precedent. The courts operate a system of precedent known as stare decisis (‘let the decision stand’). The type of precedent set depends on the court sitting, with the most complicated rules occurring in the Court of Appeal. As a general rule of thumb, the court setting the precedent will bind every court below it but the real question is under what circumstances that court is bound by itself.
5. Human Rights Act 1998
Authors: Gillespie Alisdair A. , Weare Siobhan
Published: September 2019

This chapter examines the Human Rights Act 1998 (HRA) and discusses some of the important issues that arise from its use. It also provides an overview of relevant articles in the European Convention on Human Rights (ECHR). The HRA 1998 is quite a short Act and its key parts are in a small number of sections. Perhaps the most important is that of s 6 which places an obligation on public authorities to act in a way compatible with the ECHR; s 7 which prescribes how it can be used to obtain a remedy in the courts. This chapter also links to the previous chapters in terms of discussing how the Act is interpreted.
6. The Structure of the Courts
Authors: Gillespie Alisdair A. , Weare Siobhan
Published: September 2019

This chapter discusses the organization of the modern court structure and what each court does. The courts in England and Wales (ie excluding the Supreme Court which is a UK court) are administered by a single agency, HM Courts and Tribunal Service. The courts of original jurisdiction (ie which hear trials of first instance) are ordinarily the magistrates’ court, county court, Crown Court, and High Court although they have now been joined by the Family Court. The Crown Court and High Court have both an original and appellate jurisdiction. The High Court is divided into three divisions (Queen’s Bench Division, Chancery Division, and Family Division) and when two or more judges sit together in the High Court it is known as a Divisional Court. The chapter also briefly describes the Judicial Committee of the Privy Council, Court of Protection, and Coroner’s Courts.
9. Judicial Independence
Authors: Gillespie Alisdair A. , Weare Siobhan
Published: September 2019

This chapter considers the fundamental constitutional principle of judges being independent. Securing the independence of the judiciary is difficult and involves not only separation from the legislature and executive, but also from each other and the media. This chapter explores how this separation is upheld and critically examines the practicalities associated with maintaining judicial independence, including judicial salaries, tenure, and promotions. Issues of judicial ethics and restrictions on practice are also discussed.
12. Pre-Trial Matters
Authors: Gillespie Alisdair A. , Weare Siobhan
Published: September 2019

This chapter on the criminal justice system focuses on preliminary issues, ie some of the issues that take place before trial begins. A prosecution begins at the earliest stage through a defendant being charged by the police but under the authority of the Crown Prosecution Service (CPS). The CPS must then review the decision to prosecute, which requires the CPS to have reference to two prosecution tests (evidential and public interest tests). The CPS has the ability to issue out of court disposals in appropriate cases as alternatives to prosecution. If a prosecution does take place it is necessary to identify in which court the proceedings will be heard. Crimes are divided into three categories: summary, indictable-only, and either-way. Criminal matters are heard in the magistrates’ court and the Crown Court and the categorization of offences has an impact on where the matter should be heard.
5. Member State liability in damages
Authors: Berry Elspeth , Homewood Matthew J. , Bogusz Barbara
Published: September 2019

Titles in the Complete series combine extracts from a wide range of primary materials with clear explanatory text to provide readers with a complete introductory resource. This chapter considers the circumstances in which Member State liability will arise. The discussions cover the establishment of the principle of State liability; the Francovich test governing the imposition of State liability; the development of the principle of State liability; the Factortame test governing the imposition of State liability; the relationship between State liability and direct effect/indirect effect; and the relationship between State liability and EU liability under Article 340 TFEU.
7. Remedies for breach of contract
Authors: Poole Jill , Devenney James , Shaw-Mellors Adam
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 focuses on damages, the aim of which is generally to protect the claimant’s contractual expectation and put the claimant into the position they would have been in had the contract been properly performed. The lost expectation may be measured in terms of the difference between what the claimant expected to get and what was actually received. There are limitations on the claimant’s ability to be fully compensated for losses as a result of breach, i.e. remoteness, mitigation, contributory negligence, and the ability to recover for non-pecuniary losses in contract. This chapter also examines agreed damages clauses and the operation of the penalty rule.
2. Sources of constitutional law and constitutional conventions
Authors: Faragher Colin
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 first discusses the five key sources of UK law: the common law in the form of judicial decisions and cases involving the interpretation of statutes, Acts of Parliament, EU law, the European Convention on Human Rights and Fundamental Freedoms, and the law and custom of Parliament. It then turns to the issue of constitutional conventions, covering the distinction between laws and conventions, whether constitutional conventions are binding, and examples of constitutional conventions.
10. Introduction to administrative law: the foundations and extent of judicial review
Authors: Faragher Colin
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 discusses the concept of judicial review. Judicial review allows a High Court judge to examine the lawfulness of decisions made by public bodies carrying out their public functions and enactments where there is no right of appeal or where all avenues of appeal have been exhausted. The defendant must be a public body, the subject matter of a claim must be a public law matter, and the claimant must have the right to claim. This chapter also looks at the basis procedure for judicial review.
2. Negligence: duty of care
Authors: Brennan Carol
Published: September 2019

This chapter discusses law on duty of care. Duty is the first element in the ‘negligence equation’ and the primary means of limiting liability in negligence. It begins with the fundamental ‘neighbour principle’ of Donoghue v Stevenson and charts its evolution throughout the twentieth century. The current ingredients of the test for determining duty of care in novel situations are: foreseeability; proximity; and fairness, justice, and reasonableness. This is the ‘three-stage’ test set out in Caparo v Dickman (1990), used in novel situations. Policy is a major influence on the development of duty in negligence.
15. Privacy
Authors: Brennan Carol
Published: September 2019

This chapter discusses the law on the protection of privacy. The passage of the Human Rights Act 1998, incorporating the ECHR into domestic law, enabled a new perspective on the question of protection of privacy, previously not covered by a specific tort. The art 8 right to respect for private and family life must be balanced with the equally powerful art 10 right to freedom of expression. Campbell v MGN (2004) provides a detailed consideration of this area of law by the House of Lords. The chapter covers the action for misuse of private information, the issue of photography, and that of remedies.
6. Law of torts
Authors: Marson James , Ferris Katy
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. Tort law is the focus of this chapter. It begins by distinguishing between contractual and tortious liability. It then discusses negligence, common defences to torts, and private nuisance. Negligence involves a breach of a duty to take care, owed in law by the defendant to the claimant, causing the claimant damage. Common defences to torts are illegality, consent, contributory negligence, and necessity. Private nuisance involves unlawful interference with another person’s enjoyment of their land/property which causes the claimant loss (and the loss/damage was reasonably foreseeable). When products cause injury/loss, rather than attempting to claim negligence, a claimant may seek protection through the Consumer Protection Act (CPA) 1987.
2. Statutory implied terms
Authors: Baskind Eric
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 examines the significance of the terms implied into sale of goods contracts under the Sale of Goods Act 1979 and the statutory rights that are implied in a contract between trader and consumer by virtue of the Consumer Rights Act 2015. It explains the seller’s right to sell the goods, the goods being free from encumbrances and the buyer enjoying quiet possession of them, sales by sample, and the description and quality of the goods as well as their fitness for purpose. Digital content is also discussed in relation to consumer transactions. The chapter also considers the terms implied into other kinds of contract by different statutes, including the terms implied by the Supply of Goods and Services Act 1982.
9. Opinion evidence
Authors: Spencer Maureen , Spencer John
Published: September 2019

This chapter, which focuses on opinion evidence in criminal and civil cases in the UK, explains the rule on the admissibility of opinion, including expert opinion, as well as notice and disclosure in criminal cases under the Criminal Procedure Rules 2014. The criteria for the admissibility of expert evidence, the responsibilities of expert witnesses, and the approach of the courts to new areas of expertise are examined in detail. It also considers the presentation of expert evidence, including the use of court-appointed experts, in civil cases under the Civil Procedure Rules, and, finally, examines the ultimate issue rule, which has been abolished by section 33(1) of the Civil Evidence Act 1972.
11. Privilege
Authors: Spencer Maureen , Spencer John
Published: September 2019

This chapter looks at the rules relating to legal professional privilege and, in outline, the doctrine of the privilege against self-incrimination. Under these provisions potentially relevant evidence may be excluded at trial. The role of legal professional privilege in protecting defendants in criminal trials is outlined and the absolutist stance of the courts discussed. The chapter outlines the various immunities which are embraced under the privilege against self-incrimination.