bluuebunny/crossref_metadata_2025 huggingface dataset:
Software for tracking aquatic environment geographic information systems for further integration with advanced search capabilities
Authors: Volkov D A , Gorodov A A , Goncharov A E , Shepeta N A , Bashmur K A
Published: July 2020

A close inspection of existing software for relatively accessible underwater imaging and data-gathering systems reveals its inadequacy for conducting search operations and subsequent map making. In order to broaden the application of existing recreational and low-cost echo sounders and side scan sonar (SSS), the authors of this paper propose a program, which is part of a specialized software and hardware complex under implementation. Being the initial stage of the project, the proposed program is capable of visualizing routes on a graph and displaying the resulting trajectory using a GNSS receiver, further synchronizing it with hydrographic data from a sonar device.
Breast Reconstruction in the Social Media Age
Authors: Nguyen Jonathan , Thompson Peter , Losken Albert
Published: July 2020

Background

The internet and social media are sources of information regarding breast reconstruction, which can educate and influence patients.

Objectives

This study aimed to evaluate internet and social media usage by breast reconstruction patients and its impact on patients.

Methods

Eighty-six breast reconstruction patients over a 7-month period answered an anonymous survey, which queried demographics, reconstruction type, internet usage, social media usage, expectations, and impact on decisions. Fisher’s exact test was performed to evaluate the use of social media.

Results

Overall, 95% of patients used the internet for breast reconstruction information. The information was found to be easy to understand by 70% of patients, helpful by 76%, and trustworthy by 60%. The information influenced decisions regarding procedure by 23% of patients, regarding surgeon by 23%, and regarding hospital by 22%. Social media was used by 71% of the patients; 62% of patients found it easy to understand, 57% found it helpful, and 48% found it trustworthy. The information influenced decisions regarding procedure by 16% of patients, regarding surgeon by 11%, and regarding hospital by 10%. Twenty-six percent of women expected their final breast reconstruction to look better than their premastectomy breasts, 55% as good or similar, and 12% reported appearance to be unimportant. Women found social media information to be less helpful than internet information. There was no significant association between expectations and social media vs no social media usage.

Conclusions

Patients who undergo breast reconstruction use the internet and social media as sources of information. Although the information is generally trusted, it does not seem to heavily influence patient decision-making. Providers remain patients’ main source of information, and need to direct patients to high-quality and accessible resources.
Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response
Authors: Hu Fei-Fei , Liu Chun-Jie , Liu Lan-Lan , Zhang Qiong , Guo An-Yuan
Published: July 2020

Immune checkpoint genes (ICGs) play critical roles in circumventing self-reactivity and represent a novel target to develop treatments for cancers. However, a comprehensive analysis for the expression profile of ICGs at a pan-cancer level and their correlation with patient response to immune checkpoint blockade (ICB) based therapy is still lacking. In this study, we defined three expression patterns of ICGs using a comprehensive survey of RNA-seq data of tumor and immune cells from the functional annotation of the mammalian genome (FANTOM5) project. The correlation between the expression patterns of ICGs and patients survival and response to ICB therapy was investigated. The expression patterns of ICGs were robust across cancers, and upregulation of ICGs was positively correlated with high lymphocyte infiltration and good prognosis. Furthermore, we built a model (ICGe) to predict the response of patients to ICB therapy using five features of ICG expression. A validation scenario of six independent datasets containing data of 261 patients with CTLA-4 and PD-1 blockade immunotherapies demonstrated that ICGe achieved area under the curves of 0.64–0.82 and showed a robust performance and outperformed other mRNA-based predictors. In conclusion, this work revealed expression patterns of ICGs and underlying correlations between ICGs and response to ICB, which helps to understand the mechanisms of ICGs in ICB signal pathways and other anticancer treatments.
The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge
Authors: Pham Vu V H , Li Xiaomei , Truong Buu , Nguyen Thin , Liu Lin , Li Jiuyong , Le Thuc D
Published: July 2020

Motivation

Predicting cell locations is important since with the understanding of cell locations, we may estimate the function of cells and their integration with the spatial environment. Thus, the DREAM challenge on single-cell transcriptomics required participants to predict the locations of single cells in the Drosophila embryo using single-cell transcriptomic data.

Results

We have developed over 50 pipelines by combining different ways of preprocessing the RNA-seq data, selecting the genes, predicting the cell locations and validating predicted cell locations, resulting in the winning methods which were ranked second in sub-challenge 1, first in sub-challenge 2 and third in sub-challenge 3. In this paper, we present an R package, SCTCwhatateam, which includes all the methods we developed and the Shiny web application to facilitate the research on single-cell spatial reconstruction. All the data and the example use cases are available in the Supplementary data.
Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae
Authors: Wang Dan , Lai Fei-Liao , Gao Feng
Published: July 2020

DNA replication is a fundamental process in all organisms; this event initiates at sites termed origins of replication. The characteristics of eukaryotic replication origins are best understood in Saccharomyces cerevisiae. For this species, origin prediction algorithms or web servers have been developed based on the sequence features of autonomously replicating sequences (ARSs). However, their performances are far from satisfactory. By utilizing the Z-curve methodology, we present a novel pipeline, Ori-Finder 3, for the computational prediction of replication origins in S. cerevisiae at the genome-wide level based solely on DNA sequences. The ARS exhibiting both an AT-rich stretch and ARS consensus sequence element can be predicted at the single-nucleotide level. For the identified ARSs in the S. cerevisiae reference genome, 83 and 60% of the top 100 and top 300 predictions matched the known ARS records, respectively. Based on Ori-Finder 3, we subsequently built a database of the predicted ARSs identified in more than a hundred S. cerevisiae genomes. Consequently, we developed a user-friendly web server including the ARS prediction pipeline and the predicted ARSs database, which can be freely accessed at http://tubic.tju.edu.cn/Ori-Finder3.
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity
Authors: Pan Xiaoyong , Zuallaert Jasper , Wang Xi , Shen Hong-Bin , Campos Elda Posada , Marushchak Denys O , De Neve Wesley
Published: July 2020

Motivation

Genetically engineering food crops involves introducing proteins from other species into crop plant species or modifying already existing proteins with gene editing techniques. In addition, newly synthesized proteins can be used as therapeutic protein drugs against diseases. For both research and safety regulation purposes, being able to assess the potential toxicity of newly introduced/synthesized proteins is of high importance.

Results

In this study, we present ToxDL, a deep learning-based approach for in silico prediction of protein toxicity from sequence alone. ToxDL consists of (i) a module encompassing a convolutional neural network that has been designed to handle variable-length input sequences, (ii) a domain2vec module for generating protein domain embeddings and (iii) an output module that classifies proteins as toxic or non-toxic, using the outputs of the two aforementioned modules. Independent test results obtained for animal proteins and cross-species transferability results obtained for bacteria proteins indicate that ToxDL outperforms traditional homology-based approaches and state-of-the-art machine-learning techniques. Furthermore, through visualizations based on saliency maps, we are able to verify that the proposed network learns known toxic motifs. Moreover, the saliency maps allow for directed in silico modification of a sequence, thus making it possible to alter its predicted protein toxicity.

Availability and implementation

ToxDL is freely available at http://www.csbio.sjtu.edu.cn/bioinf/ToxDL/. The source code can be found at https://github.com/xypan1232/ToxDL.

Supplementary information

Supplementary data are available at Bioinformatics online.
Geographical differences in competitive hierarchy in a native–invasive system
Authors: Pujol-Buxó Eudald , Kaliontzopoulou Antigoni , Unanue-Goikoetxea Gerezti , Ambrós Bàrbara , Llorente Gustavo A
Published: July 2020

Biological invasions can create novel competitive interactions and force ecological shifts in both native and invasive species. Anuran tadpoles are able to modify their behaviour, morphology, growth and development to cope with competitive pressure. This plasticity is a good target for natural selection and can drive rapid evolutionary changes in response to novel interactions. Here, we explore changes in plastic responses and fitness of competing invasive and native tadpoles by exposing tadpoles from different locations with contrasting evolutionary histories to the same set of varied competitive conditions. Eggs were collected from one site near the first introduction of the invasive frog (~110 years of coexistence) and from a second site that was invaded recently. We hypothesized less favourable outcomes for the invasive species in long-coexisting populations, where the native competitor might have developed adaptive responses. Most results support the hypothesis. Where the invasion was older, invasive tadpoles exposed to native competitors grew less, developed more slowly and displayed morphologies linked to competitive stress, whereas the developmental stability and canalization of native tadpoles increased. On the whole, the asymmetric competitive relationship thus appeared to approach symmetry after ~35 generations, highlighting a noteworthy example of rapid adaptation after an invasion.
Potentially functional variants in nucleotide excision repair pathway genes predict platinum treatment response of Chinese ovarian cancer patients
Authors: Li Haoran , Dai Hongji , Shi Tingyan , Cheng Xi , Sun Menghong , Chen Kexin , Wang Mengyun , Wei Qingyi
Published: July 2020

Acquired platinum resistance impedes successful treatment of epithelial ovarian cancer (EOC), and this resistance may be associated with inherited DNA damage–repair response. In the present study, we performed a two-phase analysis to assess associations between 8191 single-nucleotide polymorphisms within 127 genes of nucleotide excision repair pathway from a genome-wide association study dataset and platinum treatment response in 803 Han Chinese EOC patients. As a result, we identified that platinum-based chemotherapeutic response was associated with two potentially functional variants MNAT1 rs2284704 T>C [TC + CC versus TT, adjusted odds ratio (OR) = 0.89, 95% confidence interval (CI) = 0.83–0.95 and P = 0.0005] and HUS1B rs61748571 A>G (AG + GG versus AA, OR = 1.10, 95% CI = 1.03–1.18 and P = 0.005). Compared with the prediction model for clinical factors only, models incorporating HUS1B rs61748571 [area under the curve (AUC) 0.652 versus 0.672, P = 0.026] and the number of unfavorable genotypes (AUC 0.652 versus 0.668, P = 0.040) demonstrated a significant increase in the AUC. Further expression quantitative trait loci analysis suggested that MNAT1 rs2284704 T>C significantly influenced mRNA expression levels of MNAT1 (P = 0.003). These results indicated that MNAT1 rs2284704 T>C and HUS1B rs61748571 A>G may serve as potential biomarkers for predicting platinum treatment response of Chinese EOC patients, once validated by further functional studies.
Response System for and Epidemiological Features of COVID-19 in Gyeongsangnam-do Province in South Korea
Authors: Wi Yu Mi , Lim Su Jin , Kim Si-Ho , Lim Seungjin , Lee Su Jin , Ryu Byung-Han , Hong Sun In , Cho Oh-Hyun , Moon Kyunglan , Hong Kyung-Wook , Kim Sunjoo , Bae In-Gyu
Published: July 2020

Background

The South Korean government has been combating the coronavirus disease 2019 (COVID-19) outbreak using public information and extensive viral screening. We describe the application of the Korean response system in Gyeongsangnam-do province and outline the epidemiological features of COVID-19 in the cohort.

Methods

A Rapid Response Team tracked the patients’ activities and identified close contacts. A Patient Management Team made decisions regarding the severity of illness, hospital allocation depending on severity, and time of discharge. A national medical center with 155 beds and 4 university-affiliated hospitals with 48 negative-pressure isolation rooms were dedicated for patients with COVID-19.

Results

As of 15 April, 17 400 residents were tested, of whom 111 were confirmed positive cases. Of the 111 patients, 78 were cured and discharged, 2 recovered after mechanical ventilation, and none died. One healthcare worker at the national center tested positive for SARS-CoV-2. All 412 staff members at the center were tested, but there were no additional infections. Cough (30.0%) was the most common initial symptom, whereas anosmia and ageusia were the first symptoms in 14.7% and 15.7% of the patients, respectively. Overall, 25 patients (22.5%) reported having no symptoms at admission and 7 (6.3%) remained asymptomatic at discharge.

Conclusions

A response system that enabled the early detection of COVID-19 cases, including asymptomatic and presymptomatic cases, and timely quarantine of these patients and their contacts, along with efficient allocation of medical resources, was the key to curbing the COVID-19 outbreak in Gyeongsangnam-do Province.
Measuring disturbance at swift breeding colonies due to the visual aspects of a drone: a quasi-experiment study
Authors: Mesquita Geison P , Rodríguez-Teijeiro José D , Wich Serge A , Mulero-Pázmány Margarita
Published: July 2020

There is a growing body of research indicating that drones can disturb animals. However, it is usually unclear whether the disturbance is due to visual or auditory cues. Here, we examined the effect of drone flights on the behavior of great dusky swifts Cypseloides senex and white-collared swifts Streptoprocne zonaris in 2 breeding sites where drone noise was obscured by environmental noise from waterfalls and any disturbance must be largely visual. We performed 12 experimental flights with a multirotor drone at different vertical, horizontal, and diagonal distances from the colonies. From all flights, 17% caused <1% of birds to temporarily abandon the breeding site, 50% caused half to abandon, and 33% caused more than half to abandon. We found that the diagonal distance explained 98.9% of the variability of the disturbance percentage and while at distances >50 m the disturbance percentage does not exceed 20%, at <40 m the disturbance percentage increase to > 60%. We recommend that flights with a multirotor drone during the breeding period should be conducted at a distance of >50 m and that recreational flights should be discouraged or conducted at larger distances (e.g. 100 m) in nesting birds areas such as waterfalls, canyons, and caves.
SPDB: a specialized database and web-based analysis platform for swine pathogens
Authors: Wang Xiaoru , Liu Zongbao , Li Xiaoying , Li Danwei , Cai Jiayu , Yan He
Published: July 2020

The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research.

Database URL: http://spdatabase.com:2080/
Evaluating the diagnostic and prognostic value of biomarkers for heart disease and major adverse cardiac events in patients with muscular dystrophy
Authors: Nikhanj Anish , Miskew Nichols Bailey , Wang Kaiming , Siddiqi Zaeem A , Oudit Gavin Y
Published: July 2020

Aims

Heart disease is recognized as the leading cause of morbidity and mortality in patients with muscular dystrophy (MD). Our study demonstrates the clinical utility of cardiac biomarkers to improve the diagnosis of cardiomyopathy and prognostication of major adverse cardiac events (MACE) in these vulnerable patients.

Methods and results

We prospectively followed 117 patients [median age, 42 [interquartile range (IQR), 26–50) years; 49 (41.9%) women] at the Neuromuscular Multidisciplinary clinic diagnosed with a dystrophinopathy, limb-girdle MD, type 1 myotonic dystrophy, or facioscapulohumeral MD. We determined that B-type natriuretic peptide (BNP) and high-sensitive troponin I (hsTnI) were effective diagnostic markers of cardiomyopathy [area under the curve (AUC), 0.64; P = 0.017; and AUC, 0.69; P = 0.001, respectively]. Patient risk stratification for MACE was based on cut-off values of BNP and hsTnI defined a priori as 30.5000 pg/mL and 7.6050 ng/L, respectively. Over a median follow-up period of 2.09 (IQR, 1.17–2.81) years there were 36 confirmed MACE. Multivariate regression analyses showed that patients with BNP and hsTnI levels above the respective cut-off values had a 3.70-fold (P = 0.001) and 3.24-fold (P = 0.002) greater risk of MACE, respectively, compared with patients with biomarker levels below. Furthermore, patients with biomarker levels above both cut-off values had a 4.08-fold (P = 0.001) greater risk of MACE. Inflammatory biomarkers did not show clinical utility for heart disease in these patients.

Conclusion

Our study demonstrates important diagnostic and prognostic value of BNP and hsTnI as part of a comprehensive cardiac assessment to augment the management and treatment of heart disease in patients with MD.
Comparison between conventional and piezocision-assisted orthodontics in relieving anterior crowding: a systematic review and meta-analysis
Authors: Afzal Erum , Fida Mubassar , Malik Durre Shahwar , Irfan Sarah , Gul Meisha
Published: July 2020

Background

Prolonged duration of orthodontic treatment is of great concern and poses risks to the teeth and surrounding tissues. Orthodontic tooth movement can be accelerated by introducing regional insult. Evidence suggests piezocision to be minimally invasive and clinically effective.

Objective

The aim of the present study was to compare the effectiveness of conventional and piezocision-assisted orthodontics in relieving anterior crowding.

Search methods

Electronic and manual searches were conducted in databases including PubMed, Dental and Oral Science, CINAHL, and Cochrane Central Register of Controlled Trials until April 2019.

Selection criteria

Randomized and non-randomized controlled trials were included.

Data collection and analysis

Data were extracted independently by two authors from the studies that fulfilled inclusion criteria. The primary outcome assessed was time required for the alleviation of crowding. The secondary outcomes evaluated were pain, root resorption, and periodontal health. The risk of bias in the clinical trials was evaluated according to the Cochrane Collaboration’s tool. Studies having homogenous data were included in the meta-analysis using the RevMan software.

Results

Initial search yielded 3018 studies with eight articles meeting the inclusion criteria, six were randomized controlled trials and two were non-randomized controlled trials. Significant differences were found in alignment time between conventional and piezocision-assisted orthodontic treatment. However, gingival health, pain experienced by the patient, and root resorption showed non-significant differences. The forest plot of meta-analysis depicted significant mean difference of −46.44; 95 per cent confidence interval (CI) −87.95, −4.93; P ≤ 0.03 in the alignment time. Difference in pain levels was found to be non-significant (P = 0.78).

Limitations

There is a shortage of high-quality randomized controlled trials with a limited sample size and lack of standardization of piezocision protocol.

Conclusions and implications

According to the existing evidence, piezocision is effective in reducing tooth alignment time and alleviating crowding when compared to conventional therapy. Pain levels showed insignificant differences revealed in meta-analysis. Weak evidence suggests that there are no negative effects on periodontal health and root resorption after performing piezocision.

Registration

PROSPERO (CRD42019134398).
Post-procedural radial artery occlusion and patency detection using duplex ultrasound vs. the reverse Barbeau test
Authors: Jirous Stepan , Bernat Ivo , Slezak David , Miklik Roman , Rokyta Richard
Published: July 2020

The transradial approach is recommended as a first choice in coronary catheterizations and interventions, for among other reasons, the reduction in the number of local complications. A head-to-head comparison of the reverse Barbeau test (RBT) and duplex ultrasonography (DUSG) for the detection of post-procedural radial artery patency and occlusion has not yet been evaluated. In 500 patients from our same-day discharge program (age 65 ± 9.4 years, 148 women), radial artery patency and occlusion, compression time, haematomas, and other local complications were evaluated. Radial artery patency was confirmed in 495 patients (99.0%), and complete radial artery occlusion (RAO) was detected in 2 (0.4%) patients using both methods. In 3 patients (0.6%), the RBT was negative, while incomplete RAO was detected by DUSG. Superficial haematomas (˃ 5 but ≤10 cm) were found in 27 (5.4%) patients. There were no other local complications. Detection of radial artery patency and occlusion using the RBT and DUSG was comparable. The incidence of RAO in our study was extremely low. Thanks to its simplicity, the RBT has the potential to be used as the first method of detection of radial occlusion after coronary catheterizations.
Judicial diplomacy: dealing with defectors and conspirators after the French Wars of Religion (1598–1610)
Authors: Micallef Fabrice
Published: July 2020

This article examines the cooperation that took place between Henri IV’s monarchy and neighbouring powers to monitor and deal with the defectors and conspirators who fled France following the Wars of Religion. In the political and legal culture of the time, intergovernmental cooperation in judicial matters was seen as an obligation between friendly princes. Powers allied to France, such as England, Lorraine, Venice, Tuscany or the Papacy, shared an interest in this form of cooperation, and this generated a vast European network of information-sharing dealing with fugitives from France, a network that mobilized diplomatic channels, but also relied upon the initiative of non-governmental actors. Friendly powers also agreed to extradite opponents to Henri IV under variable arrangements. Alongside diplomats, governors, officers and local magistrates played an important role in these practices. This cooperation, however, was also enveloped in ambiguities, misunderstandings and tensions.
1. Introduction
Authors: Sime Stuart
Published: July 2020

The civil courts perform the important function of resolving disputes that cannot be resolved by agreement between the parties. This introductory chapter briefly sets out the book’s focus, namely the mechanics of how legal and equitable rights are asserted, determined, and enforced through the civil courts. It then discusses the legal profession, lawyers’ duties, initial instructions, confidentiality and conflict of interest, pre-action correspondence, and the main stages in court proceedings.
6. Issuing and Serving
Authors: Sime Stuart
Published: July 2020

Civil proceedings commence with the issuance of a claim form. Issuing a claim involves the court sealing the claim form with its official seal. This chapter discusses issuing and serving proceedings. It covers the claim form; jurisdictional endorsements; particulars of claim; specialist claims; issuing a claim form; service of the claim form; deemed date of service of the claim form; service of documents other than a claim form; deemed date of service (non-claim form documents); certificate of service; irregular service; and filing of documents at court.
15. Track Allocation and Case Management
Authors: Sime Stuart
Published: July 2020

Judicial case management of civil litigation is one of the central planks of the Civil Procedure Rules 1998 (CPR). In exercising their powers to manage cases, the courts will be seeking to secure the overriding objective of the CPR of ensuring that cases are dealt with justly and at proportionate cost. This chapter discusses procedural judges; docketing; provisional track allocation; filing directions questionnaires; track allocation rules; notice of allocation; allocation directions; ADR and stays to allow for settlement; transfer to appropriate court; trial in the Royal Courts of Justice; changing tracks; and subsequent case management.
19. Parties and Joinder
Authors: Sime Stuart
Published: July 2020

This chapter first looks at the rules relating to different classes of party and then considers the rules governing multi-party litigation. Topics discussed include description of parties; particular classes of party; vexatious litigants; joinder; representative proceedings; representation of unascertained persons; intervention; consolidation; stakeholder claims; assignment; and group litigation.
44. Search Orders
Authors: Sime Stuart
Published: July 2020

This chapter discusses the rules for search orders. A search order is a bundle of interim orders which require the respondent to admit another party to premises for the purpose of preserving evidence which might otherwise be destroyed or concealed by the respondent. Search orders are principally, but not exclusively, used in intellectual property claims against defendants who are likely to destroy incriminating evidence rather than disclose it voluntarily under standard disclosure.
45. Norwich Pharmacal and Related Disclosure Orders
Authors: Sime Stuart
Published: July 2020

This chapter considers a number of other special forms of disclosure orders, the best known of which is the Norwich Pharmacal order. Norwich Pharmacal orders are primarily used for finding the identity of an unknown potential defendant. They can only be sought against a person who facilitated and got ‘mixed up’ in the wrongdoing. Norwich Pharmacal orders therefore cannot be made against ‘mere witnesses’. Pre-action disclosure orders bring forward the time when disclosure of documents takes place to the period before a claim is issued. Disclosure against non-parties enables the court to order a witness to produce documents in advance of the trial, thus avoiding adjournments when documents are produced at the last minute at trial.
46. Costs
Authors: Sime Stuart
Published: July 2020

This chapter focuses on legal costs. It discusses the two main principles for deciding which party should pay the costs of an application or of the whole proceedings; the rule that costs follow the event; range of possible costs orders; interim costs orders; indemnity principle; basis of quantification; proportionality; summary and detailed assessments; fast track fixed costs; fixed and scale costs; costs and track allocation; publicly funded litigants; pro bono costs orders; costs against non-parties; and wasted costs orders.
47. Qualified One-Way Costs Shifting
Authors: Sime Stuart
Published: July 2020

Qualified one-way costs shifting (QOCS) provides costs protection to claimants in personal injuries claims. If the claimant wins, the defendant should be ordered to pay the claimant’s costs in the usual way. However, if the claimant loses, under QOCS while the claimant remains liable to pay its own lawyers’ costs, and may be ordered to pay the successful defendant’s costs, the claimant will be protected against actually having to pay those costs to the defendant. This chapter discusses cases where QOCS applies; the effects of QOCS; and loss of QOCS protection.
2. Partnership management and finance
Authors: Slorach J. Scott , Ellis Jason
Published: July 2020

This chapter first discusses the legal relationship between the partners under section 24 of the Partnership Act 1890. It then explains the duty of good faith; the partnership’s finances; the distinction between a partner and a lender; division of profits and sharing of losses between partners; payment of interest; and partnership property.
3. Liability of partners to outsiders
Authors: Slorach J. Scott , Ellis Jason
Published: July 2020

Partners will incur debts and other obligations in the course of carrying on the partnership’s business. This chapter examines the nature of the partners’ liabilities in these circumstances and the extent to which an individual partner can bind the partnership as a whole. It then considers whether it is possible for individuals who are not partners at the time the debt or obligation was incurred to be liable for that debt or obligation.
18. The corporation tax system
Authors: Slorach J. Scott , Ellis Jason
Published: July 2020

This chapter deals with the corporation tax system, which determines the tax liability of companies. It discusses the calculation of profits; tax assessment; relief for trade losses; and taxation of close companies.
21. Capital allowances
Authors: Slorach J. Scott , Ellis Jason
Published: July 2020

This chapter discusses the capital allowances system. Most businesses will need to acquire fixed assets for their operations, nearly all of which will depreciate in value over time due to wear and tear. While this depreciation may not be deducted from the business’s trading profits, certain limited types of fixed asset entitle a business to claim relief in the form of a capital allowance, which can be deducted when calculating taxable profits. The purpose of this allowance is to give tax relief for the depreciation in value of specific assets bought and owned for business use, by allowing the owner to write off their cost against the taxable income of the business. The amount to be written off is calculated using a fixed formula. Relief is only available if the capital expenditure has been incurred in respect of the items of expenditure prescribed by the Capital Allowances Act 2001.
25. Company insolvency proceedings
Authors: Slorach J. Scott , Ellis Jason
Published: July 2020

This chapter deals with the procedures available when a company is insolvent or facing financial difficulties. It also considers the ways in which insolvent partnerships can be subject to the same procedures as companies. The law relating to these matters is principally contained in the Insolvency Act 1986 together with the Insolvency Rules 1986, as amended by the Insolvency Act 2000 and the Enterprise Act 2002. The insolvency legislation provides four procedures for companies in financial difficulties: administration, voluntary arrangement, receivership, and liquidation.
19. Landlord and Tenant Act 1954, Part II
Authors: Abbey Robert , Richards Mark
Published: July 2020

This chapter considers the provisions of the Landlord and Tenant Act 1954, Part II, which provides security of tenure for the majority of business tenants by giving them a statutory right to renew their lease or tenancy. It explains the need for ‘tenancy’; need for ‘occupation’; need for ‘the purposes of a business’; key methods of termination under the Act; section 40 notices; interim rent applications; landlord’s statutory grounds of opposition; tenant’s right to compensation; and the terms of the new tenancy.
1. Introduction
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

This introductory chapter briefly sets out the volume’s purpose, which is to explain the legal, procedural and evidential rules governing how cases are dealt with by the criminal justice system. It then explains the philosophy of the text and its unique features; introduces the key personnel and organisations within the criminal justice system; introduces the Criminal Procedure Rules; explains the classification of offences according to their trial venue; summarizes the jurisdiction of the criminal courts; stresses the importance of the pervasive issue of human rights; and highlights professional conduct considerations in the context of criminal litigation.
5. The Right to Silence at the Police Station
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

This chapter explains the substantive law governing a defendant’s silence at the police station under ss. 34, 36, and 37 Criminal Justice and Public Order Act (CJPOA) 1994. It covers the risks associated with s. 34 CJPOA 1994; drawing inferences from a failure to account under ss. 36 and 37 CJPOA 1994; and the practical aspects associated with remaining silent.
8. The Decision to Prosecute and the Prosecution’s Duties of Disclosure of Evidence
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

This chapter first explains the role of the Crown Prosecution Service (CPS) and the factors that are taken into account when deciding to charge a suspect or to divert him from prosecution. It then examines the important obligations which are placed upon the CPS both at common law and under statute to serve pre-trial disclosure of evidence upon the defendant and their importance to the right to a fair trial. Defence disclosure obligations are also considered.
16. Witness Evidence
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

This chapter explains the law, procedure, and the practical issues associated with witness evidence. It considers the circumstances in which a witness can refresh his memory from an earlier written statement; the test to decide a witness’ competence to give evidence; the compellability of a witness; the assistance available to ‘vulnerable’ or ‘intimidated’ witnesses to give evidence under a special measures direction; a witness taking the oath or affirming; the rules associated with examination-in-chief; and the rules associated with cross-examination including admission of non-defendant bad character and re-examination.
1. Ethics, professional conduct, and regulation
Authors: Seymour Jennifer , Firth Clare , Crompton Lucy , Fox Helen , Seabridge Frances , Wigglesworth Susan , Smart Elizabeth
Published: July 2020

This chapter begins with a description of how the legal services market has undergone recent change, with the Solicitors Regulation Authority’s (SRA) Principles and Codes of Conduct within the Standards and Regulations replacing the previous outcomes-focused regulation code (OFR Code). It considers what being a member of the profession and a good solicitor means, the Principles, relevant paragraphs of the Codes of Conduct, the Transparency Rules, and the SRA’s Enforcement Strategy currently in force and how this has widened legal services provision and introduced further flexibility into how solicitors and firms justify their compliance with the regulation. It then looks at the practical application of the principles and paragraphs which are most relevant to readers at this stage of their legal career as a student (covering practical examples relevant to each core legal practice area) and trainee.
3. Money laundering
Authors: Seymour Jennifer , Firth Clare , Crompton Lucy , Fox Helen , Seabridge Frances , Wigglesworth Susan , Smart Elizabeth
Published: July 2020

A concerted effort is being made within the EU to crack down on money laundering. This is reflected by both the European Money Laundering Directives, which have led to changes in the UK legislation, in particular the Money Laundering, Terrorist Financing and Transfer of Funds (Information on the Payer) Regulations (MLR). Solicitors are usually unwittingly involved in a money laundering scheme. They can avoid this by being conversant with the requirements of the money laundering legislation and fully complying with it. This chapter explains the process of money laundering; the primary legislation and offences; and the relevance of the legislation to solicitors.
5. Income tax
Authors: Seymour Jennifer , Firth Clare , Crompton Lucy , Fox Helen , Seabridge Frances , Wigglesworth Susan , Smart Elizabeth
Published: July 2020

Income tax is an essential part of a lawyer’s knowledge and professional training. Whilst it is not necessary to have knowledge to the extent that a specialist tax lawyer would have, it is necessary to have knowledge and understanding sufficient to recognise its implications as they arise and affect the client and ourselves. This chapter discusses sources of income tax law; collection and payment of income tax; rates of income tax and allowances; calculation of income tax; sources of taxable income; and charitable giving. This chapter covers the changes introduced by the March 2020 Budget.
7. Inheritance tax
Authors: Seymour Jennifer , Firth Clare , Crompton Lucy , Fox Helen , Seabridge Frances , Wigglesworth Susan , Smart Elizabeth
Published: July 2020

This chapter deals with inheritance tax (IHT). It explains the charge to IHT; potentially exempt transfers (PETs); the transfer of value on death; the occasions to tax; the charge to tax and a lifetime chargeable transfer (LCT); the charge to tax and a LCT where the transferor dies within seven years of the LCT; the charge to tax and a PET; the charge to tax and death; gifts subject to a reservation; liability, burden, and payment of tax; and tax planning.
10. Leaseholds and Commonhold
Authors: Abbey Robert M. , Richards Mark B.
Published: July 2020

This chapter begins by considering leases, dealing with leases when acting for a lessee or lender, liability on covenants in leases, and lease variations. It then discusses new leases, existing leases, statutes and leases, and the Commonhold and Leasehold Reform Act 2002.
Estimation Without Representation: Early Severe Acute Respiratory Syndrome Coronavirus 2 Seroprevalence Studies and the Path Forward
Authors: Shook-Sa Bonnie E , Boyce Ross M , Aiello Allison E
Published: July 2020

The recent development and regulatory approval of a variety of serological assays indicating the presence of antibodies against severe acute respiratory syndrome coronavirus 2 has led to rapid and widespread implementation of seroprevalence studies. Accurate estimates of seroprevalence are needed to model transmission dynamics and estimate mortality rates. Furthermore, seroprevalence levels in a population help guide policy surrounding reopening efforts. The literature to date has focused heavily on issues surrounding the quality of seroprevalence tests and less on the sampling methods that ultimately drive the representativeness of resulting estimates. Seroprevalence studies based on convenience samples are being reported widely and extrapolated to larger populations for the estimation of total coronavirus disease 2019 (COVID-19) infections, comparisons of prevalence across geographic regions, and estimation of mortality rates. In this viewpoint, we discuss the pitfalls that can arise with the use of convenience samples and offer guidance for moving towards more representative and timely population estimates of COVID-19 seroprevalence.
Applying a Selection Experiment to Test for Fitness Costs of Bt Resistance in Western Corn Rootworm (Coleoptera: Chrysomelidae) and the Effect of Density on Fitness Costs
Authors: St. Clair Coy R , Clifton Eric H , Dunbar Mike W , Masloski Kenneth E , Paolino Aubrey R , Shrestha Ram B , Gassmann Aaron J
Published: July 2020

Western corn rootworm, Diabrotica virgifera virgifera LeConte, is a serious pest of corn and is often managed with transgenic corn producing insecticidal toxins from the bacterium Bacillus thuringiensis (Bt). This pest has developed field-evolved resistance to all commercially available Bt traits, beginning with Cry3Bb1 in 2009. Fitness costs may accompany Bt resistance, where individuals with alleles for Bt resistance have reduced fitness on non-Bt corn compared to Bt-susceptible individuals. In conjunction with non-Bt refuges, fitness costs can delay the evolution of Bt resistance. Importantly, ecological factors may affect the presence and magnitude of fitness costs. For western corn rootworm, available data suggest that fitness costs of Bt resistance may be present in some cases. Using two Cry3Bb1-resistant western corn rootworm strains (Hopkinton and Cresco), a fitness-cost experiment was performed by rearing rootworm in the absence of Bt for six generations to test for fitness costs of Cry3Bb1 resistance and the effect of larval rearing density on fitness costs. Fitness costs were detected for both strains; however, strains were still resistant to Cry3Bb1 corn at the end of the experiment. Cresco experienced a greater loss of resistance at low versus high density, but no effect of density was detected in Hopkinton. Our study shows that fitness costs can accompany Bt resistance in western corn rootworm and may be more pronounced under low larval density. Even though fitness costs were present, it appears that rootworm populations may remain resistant to Cry3Bb1 corn for years after resistance has evolved.
Position optimisation for a roadway under small coal mines in same coal seam: a case study
Authors: Tai Yang , Lu Guozhi , Xia Hongchun , Zhang Wenyang , Liu Hongjie , Zhang Yanqun
Published: July 2020

According to the failure law of the 1070 main roadway, this paper proposes a reasonable position for large section roadways under small coal mines and a design for seven roadway positions. RS2 software was used to establish a numerical model to select a reasonable position for the roadway. The influences of roadway positions on roof separation amount, roof subsidence, lateral displacement on the ribs, vertical stress on ribs and roadway failure areas were revealed. On the basis of influence laws, reasonable positions for the roadway could be determined. In this study, a center distance of 5 m was deemed a reasonable position. Finally, an industrial test was conducted at the original roadway. The experimental results indicate that the deformation of the roadway could be well controlled and the roadway position is reasonable.
Acute Exercise Induced Compartment Syndrome in an 22-Year-Old Active-Duty Man and Review of the Literature
Authors: Guenther Timothy M , Sherazee Elan A , Curtis Bryan C , Riojas Ramon A
Published: July 2020

Acute exercise induced compartment syndrome is a rare clinical diagnosis with serious long-term ramifications if not diagnosed in a timely fashion. We present a case of acute exercise induced compartment syndrome of the right lower extremity in a 22-year-old active-duty man that occurred during a physical fitness assessment. He was treated with a two incision four compartment fasciotomy, however required debridement of muscle from the anterior compartment on subsequent washouts of the wound that led to significant foot drop postoperatively. We reviewed the literature for published cases of acute exercise induced compartment syndrome and provide some information from the 47 patients identified in our review. This case highlights a unique pathology for which military providers should have a strong index of suspicion. It additionally stresses the importance of adequate hydration and musculoskeletal conditioning in the setting of military fitness assessments.
Evaluating Candida albicans biofilm formation in silkworms
Authors: Matsumoto Yasuhiko , Kurakado, Sanae , Sugita Takashi
Published: July 2020

Candida albicans is a pathogenic fungus that causes deep mycosis in immunocompromised patients and forms a biofilm on catheter surfaces. Here we showed that C. albicans infection of silkworms led to biofilm formation on the surface of polyurethane fibers, a catheter substrate material, while inside the silkworm body. Silkworms inserted with polyurethane fibers survived for at least 48 hours. When silkworms inserted with polyurethane fibers were subsequently infected with C. albicans, biofilm formed on the surface of the polyurethane fiber within 24 hours in the silkworm body. These results suggest that silkworms can be used to evaluate C. albicans biofilm formation.
The Magellanic Edges Survey I: Description and first results
Authors: Cullinane L R , Mackey A D , Da Costa G S , Koposov S E , Belokurov V , Erkal D , Koch A , Kunder A , Nataf D M
Published: July 2020

We present an overview of, and first science results from, the Magellanic Edges Survey (MagES), an ongoing spectroscopic survey mapping the kinematics of red clump and red giant branch stars in the highly substructured periphery of the Magellanic Clouds. In conjunction with Gaia astrometry, MagES yields a sample of ~7000 stars with individual 3D velocities that probes larger galactocentric radii than most previous studies. We outline our target selection, observation strategy, data reduction, and analysis procedures, and present results for two fields in the northern outskirts (>10° on-sky from the centre) of the Large Magellanic Cloud (LMC). One field, located in the vicinity of an arm-like overdensity, displays apparent signatures of perturbation away from an equilibrium disc model. This includes a large radial velocity dispersion in the LMC disc plane, and an asymmetric line-of-sight velocity distribution indicative of motions vertically out of the disc plane for some stars. The second field reveals 3D kinematics consistent with an equilibrium disc, and yields Vcirc = 87.7 ± 8.0 km s−1 at a radial distance of ~10.5 kpc from the LMC centre. This leads to an enclosed mass estimate for the LMC at this radius of (1.8 ± 0.3) × 1010 M⊙.
The 2020 April–June super-outburst of OJ 287 and its long-term multiwavelength light curve with Swift: binary supermassive black hole and jet activity
Authors: Komossa S , Grupe D , Parker M L , Valtonen M J , Gómez J L , Gopakumar A , Dey L
Published: July 2020

We report detection of a very bright X-ray–UV–optical outburst of OJ 287 in 2020 April–June, the second brightest since the beginning of our Swift multiyear monitoring in late 2015. It is shown that the outburst is predominantly powered by jet emission. Optical–UV–X-rays are closely correlated, and the low-energy part of the XMM–Newton spectrum displays an exceptionally soft emission component consistent with a synchrotron origin. A much harder X-ray power-law component (Γx = 2.4, still relatively steep when compared to expectations from inverse Compton models) is detected out to 70 keV by NuSTAR. We find evidence for reprocessing around the Fe region, consistent with an absorption line. If confirmed, it implies matter in outflow at ∼0.1c. The multiyear Swift light curve shows multiple episodes of flaring or dipping with a total amplitude of variability of a factor of 10 in X-rays, and 15 in the optical–UV. The 2020 outburst observations are consistent with an after-flare predicted by the binary black hole model of OJ 287, where the disc impact of the secondary black hole triggers time-delayed accretion and jet activity of the primary black hole.