bluuebunny/crossref_metadata_2025 huggingface dataset:
24. Personal bankruptcy
Authors: Slorach J. Scott , Ellis Jason
Published: July 2020

The partner or sole trader may be made bankrupt if his liabilities exceed his assets or if he has insufficient liquid assets to pay his current liabilities, even if the value of his total assets exceeds the value of his total liabilities. The law of bankruptcy is mostly contained in the Enterprise Act (EA) 2002. This chapter discusses the bankruptcy procedure; the trustee in bankruptcy; effect of the bankruptcy order on the bankrupt personally; assets in the bankrupt’s estate; distribution of the bankrupt’s assets; duration of the bankruptcy and discharge of the bankrupt; fast track voluntary arrangement scheme; and individual voluntary arrangement.
27. Choice of business medium
Authors: Slorach J. Scott , Ellis Jason
Published: July 2020

This chapter makes a comparison between companies, on the one hand, and partnerships or sole traders, on the other, in order to explain the various factors which should be taken into account when choosing between the two business media. It considers factors such as risk of capital, expense, publicity, taxation, interest relief, capital gains, inheritance tax, pensions, and social security. Due to the range of variables, the desirability of limited liability means that incorporation may be the only viable option, although this can also be achieved by setting up a limited liability partnership. Where limited liability is not of great importance, the tax factors will be more significant, and these would have to be examined from a number of perspectives, including the size of anticipated profits, the particular financial circumstances of the promoters of the business, and any particular expectations they had about their stake in the business.
29. Sale of a business to a company
Authors: Slorach J. Scott , Ellis Jason
Published: July 2020

A sole trader or partnership may decide, for a variety of reasons, to incorporate the business. Incorporation will give rise to a number of tax and other problems. This chapter considers these problems and how they can be avoided, or at least mitigated. It shows that the tax rules are the most important consideration in this area, since if they are not appreciated, an unexpected tax bill can cause very serious cash flow problems. They include rules on income tax, capital gains tax, VAT, and stamp duty/stamp duty land tax.
3. An outline of a conveyancing transaction
Authors: Abbey Robert , Richards Mark
Published: July 2020

This chapter explains the process of conveyancing as a whole through an outline of a typical conveyancing transaction. It describes a transaction in outline; energy performance certificates; the Land Registry Portal; and the Law Society’s Conveyancing Quality Scheme; and the future of conveyancing.
4. Taking instructions and other initial matters
Authors: Abbey Robert , Richards Mark
Published: July 2020

This chapter discusses initial activities in the conveyancing process including advising joint buyers on co-ownership; advising buyers to have a survey of the property carried out before exchange of contracts; estate agents; capital gains tax; stamp duty land tax; client care and advice on costs; professional conduct; the Law Society’s National Conveyancing Protocol; and advising on finance.
10. Exchange of contracts
Authors: Abbey Robert , Richards Mark
Published: July 2020

Exchange of contracts is the most critical stage in the conveyancing process as it represents the point at which the parties become legally bound to proceed. This chapter examines pre-exchange matters; the process by which contracts are actually exchanged; and matters that should be attended to immediately after exchange has taken place. It also considers the risk and responsibility for buildings insurance, and the consequences of the buyer occupying the property before completion.
15. Delays and remedies
Authors: Abbey Robert , Richards Mark
Published: July 2020

This chapter considers what can be done if a conveyancing contract is delayed, disputed or denied. A practitioner must be able to advise a client when a transaction goes wrong and remedies are sought to correct that wrong. The discussions cover late completion; conditions when time is of the essence for a conveyancing contract; consequences of delay; notices to complete; and remedies.
Criminal Litigation 2020-2021
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

Criminal Litigation offers a guide to the areas of criminal litigation covered in the Legal Practice Course. Making use of realistic case studies backed up by online documentation, the text combines theory with practical considerations and encourages a focus on putting knowledge into a practical context. The volume covers all procedural and evidential issues that arise in criminal cases. The more complex areas of criminal litigation are examined using diagrams, flowcharts, and examples, while potential changes in the law are highlighted. This edition has been fully revised to reflect the most recent law and practice in all aspects of criminal litigation.
3. The Powers to Stop, Search and Arrest
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

The police have extensive statutory powers to stop and search and to arrest a person in connection with the investigation of a criminal offence under various statutes, including the Police and Criminal Evidence Act 1984 (PACE 1984), the Terrorism Act 2000, the Misuse of Drugs Act 1971, and the Serious Organised Crime and Police Act 2005. This chapter examines the powers of stop and search before arrest; powers of arrest under PACE 1984; powers to search a person and his property after arrest; the power to grant street bail; and the right to liberty under Article 5 European Convention on Human Rights (ECHR 1950).
14. Trial Before the Crown Court
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

This chapter considers the procedural and practical steps at a trial on indictment. It examines the rules dealing with the indictment; supporting counsel at trial; empanelling the jury; the presentation of the prosecution and defence cases; the judge’s summing-up; and the jury’s verdict.
17. Corroboration, the ‘Turnbull Guidelines’ and Opinion Evidence
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

This chapter considers the nature of corroborative evidence; the situations where corroborative evidence is required as a matter of law; the situations where a corroboration warning might be given as a matter of judicial discretion; and the application of the ‘Turnbull guidelines’ in cases where eye-witness identification is disputed. It also explains the rules relating to opinion evidence and to expert opinion evidence in particular.
18. Hearsay Evidence
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

Hearsay evidence in criminal cases most often arises in two situations: if a witness testifies about facts of which he has no personal knowledge because the facts were communicated to the witness by another person who is not in court; and where a witness’ written statement is put before the court because the witness is unable to attend court to give oral evidence. This chapter discusses the general rule of hearsay evidence; identifying hearsay evidence; statutory exceptions to the hearsay rule; hearsay evidence under the Criminal Justice Act (CJA) 2003; hearsay admissible under the preserved common law rules; procedure for admitting hearsay evidence; and hearsay evidence and the European Convention on Human Rights (ECHR) 1950.
23. Appeals
Authors: Hannibal Martin , Mountford Lisa
Published: July 2020

This chapter explains the practice and procedure involved in appealing against a decision of the magistrates’ court or the Crown Court. The discussions include the reopening of a case; appeal to the Crown Court; appeal by way of case stated; judicial review; appeal against sentence from the Crown Court; appeal to the Supreme Court; the Criminal Cases Review Commission; and whether the prosecution enjoys a right to appeal.
8. Corporation tax
Authors: Seymour Jennifer , Firth Clare , Crompton Lucy , Fox Helen , Seabridge Frances , Wigglesworth Susan , Smart Elizabeth
Published: July 2020

All companies incorporated in the UK which actively carry on business are liable to pay corporation tax (CT) on their taxable profits. This chapter considers the charge to CT with particular focus on calculating chargeable income profits and allowable deductions; the treatment of company capital gains and capital losses; trading loss relief; capital allowances; and close companies.
9. Value added tax
Authors: Seymour Jennifer , Firth Clare , Crompton Lucy , Fox Helen , Seabridge Frances , Wigglesworth Susan , Smart Elizabeth
Published: July 2020

Value added tax (VAT) is a tax charged on supplies of goods and services made by businesses that have (or should have) registered for VAT. This chapter discusses the circumstances in which VAT is charged; the rates of VAT; when VAT can be reclaimed; accounting for VAT; and doing VAT calculations.
16. Human rights
Authors: Seymour Jennifer , Firth Clare , Crompton Lucy , Fox Helen , Seabridge Frances , Wigglesworth Susan , Smart Elizabeth
Published: July 2020

This chapter provides an introduction to the European Convention on Human Rights and the Human Rights Act 1998, taking into account the origins of the Convention and the Human Rights Act 1998 and their incorporation into UK legislation; the general principles of European jurisprudence; the Articles and the Protocols themselves; and areas where potential breaches may occur.
3. The Draft Contract
Authors: Abbey Robert M. , Richards Mark B.
Published: July 2020

This chapter considers various issues relating to drafting a contract. These include preparatory steps by seller’s practitioner; formation of the contract; contents of the contract; sales of part; and special considerations.
4. Pre-Contract Searches and Enquiries, Town and Country Planning
Authors: Abbey Robert M. , Richards Mark B.
Published: July 2020

This chapter considers pre-contract searches, enquiries, and town and country planning. It explains the why, what, and when of pre-contract searches and enquiries; the National Land Information Service; effects of the Law Society Conveyancing Protocol; commercial property enquiries; planning and conveyancing; changes of use; enforcement notices and stop notices; and building regulations.
8. Pre-Completion Procedures and Completion
Authors: Abbey Robert M. , Richards Mark B.
Published: July 2020

This chapter begins with a discussion of pre-completion procedures, covering pre-completion when acting for the seller; pre-completion when acting for the buyer; pre-completion searches; and completion statements. It then focuses on completion, covering date, time, and place for completion; when the client is both selling and buying; and the mechanics of completion.
Leukocytospermia is not an informative predictor of positive semen culture in infertile men: results from a validation study of available guidelines
Authors: Ventimiglia Eugenio , Capogrosso Paolo , Boeri Luca , Cazzaniga Walter , Matloob Rayan , Pozzi Edoardo , Chierigo Francesco , Abbate Costantino , Viganò Paola , Montorsi Francesco , Salonia Andrea
Published: July 2020

STUDY QUESTION

Are the European Association of Urology (EAU) guidelines for performing semen culture accurate enough for detecting a positive semen culture in Caucasian-European infertile men?

SUMMARY ANSWER

The majority (80%) of asymptomatic infertile men with a positive sperm culture may miss a proper diagnostic assessment when relying on EAU guidelines; no single parameter can assist in medical decision-making.

WHAT IS KNOWN ALREADY

The EAU guidelines suggest performing semen culture in case of increased leukocytes in semen (>106 peroxidase positive white blood cells/ml, i.e. leukocytospermia).

STUDY DESIGN, SIZE, DURATION

A cross-sectional validation study including 523 infertile men was carried out during 2010–2018.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Infertile men who were asymptomatic for genital infections were enrolled at a single academic center, and a semen culture was obtained in every case. A concentration of >103 cfu/ml urinary tract pathogens in the ejaculate was considered indicative of significant bacteriospermia. Semen analysis values were assessed on the basis of 2010 World Health Organization reference criteria. EAU guidelines for semen culture were used to predict positive semen culture in our cohort and thus validated. Moreover, we tested the predictive performance and accuracy of several clinical parameters and compared them to EAU guidelines.

MAIN RESULTS AND THE ROLE OF CHANCE

A positive semen culture was found in 54 men (10%). The application of EAU guidelines would have missed 43 out of 54 (80%) positive semen cultures with 120/131 (92%) useless examinations. EAU guidelines specificity, sensitivity and discrimination were 74%, 20% and 47%, respectively. When trying to improve positive semen culture prediction, we were unable to find any informative baseline parameter except for serum neutrophil-to-lymphocyte ratio (odds ratio 1.70 (95% CI 1.04–2.77)), although without any improvement in terms of discrimination (P = 0.10).

LIMITATIONS, REASONS FOR CAUTION

The study was limited by the lack of a control group of fertile men its retrospective nature. Moreover, monoclonal antibodies were not used for leukocyte assessment.

WIDER IMPLICATIONS OF THE FINDINGS

Since it is not possible to identify infertile men at risk of semen infection, further studies are needed to tailor the execution of semen culture.

STUDY FUNDING/COMPETING INTEREST(S)

No funding was received for this study. There are no competing interests.
Trophic interactions and diel feeding rhythms of microzooplankton in a productive Swedish Fjord
Authors: Arias Anna , Saiz Enric , Tiselius Peter , Calbet Albert
Published: July 2020

Microzooplankton play a pivotal role in the energy transfer between lower and upper trophic levels in marine planktonic food webs. While laboratory data suggest that microzooplankton exhibit higher feeding rates during the daytime, evidence from the field is scarce and contradictory. In this study, we first characterized the nano- and microplanktonic communities of the Gullmar Fjord (Sweden) and its environmental conditions during July and August 2017. Then, we explored the grazing impact of microzooplankton on the phytoplankton community of this ecosystem and assessed their diel grazing activity using the dilution technique. Finally, we evaluated the impact of mesozooplankton at natural concentrations during the experiments. Microzooplankton removed 26% of the phytoplankton standing stock and 96% of the primary production daily, while mesozooplankton did not exert a significant impact on microplankton activity. We did not detect significant diel microzooplankton grazing rhythms during the first experimental period; however, during the second part of the study, after an upwelling event, grazing rates were significantly higher during the night. Therefore, the microzooplankton grazing rhythm in natural systems may vary according to the species composition and abundances of both microzooplankton and prey communities.
How to measure hospital antibiotic consumption: comparison of two methods from data surveillance in France
Authors: Stordeur Florence , Miliani Katiuska , Lacavé Ludivine , Rogues Anne-Marie , Dumartin Catherine , Alfandari Serge , Astagneau Pascal , L’Hériteau François ,   ATB-Raisin 2012 steering committee and the ENP 2012 steering committee, Bertrand X , Boussat S , Crémieux A-C , Dugravot L , Ingels A , Jarno P , Machut A , Péfau M , Rémy E , Schlemmer B , Touratier S , Vaux S , Bajolet O , Bernet C , Bervas C , Coignard B , Dégéfa M , Gautier C , Garreau N , Giard M , Jarno P , Hoff O , Lamy M , Léon L , Machut A , Migueres B , Péfau M , Simon L , Thiolet J-M , Vaux S , Verjat-Trannoy D
Published: July 2020

Background

Antibiotic use (ABU) surveillance in healthcare facilities (HCFs) is essential to guide stewardship. Two methods are recommended: antibiotic consumption (ABC), expressed as the number of DDD/1000 patient-days; and prevalence of antibiotic prescription (ABP) measured through point prevalence surveys. However, no evidence is provided about whether they lead to similar conclusions.

Objectives

To compare ABC and ABP regarding HCF ranking and their ability to identify outliers.

Methods

The comparison was made using 2012 national databases from the antibiotic surveillance network and prevalence study. HCF rankings according to each method were compared with Spearman’s correlation coefficient. Analyses included the ABU from entire HCFs as well as according to type, clinical ward and by antibiotic class and specific molecule.

Results

A total of 1076 HCFs were included. HCF rankings were strongly correlated in the whole cohort. The correlation was stronger for HCFs with a higher number of beds or with a low or moderate proportion of acute care beds. ABU correlation between ABC or ABP was globally moderate or weak in specific wards. Furthermore, the two methods did not identify the same outliers, whichever HCF characteristics were analysed. Correlation between HCF ranking varied according to the antibiotic class.

Conclusions

Both methods ranked HCFs similarly overall according to ABC or ABP; however, major differences were observed in ranking of clinical wards, antibiotic classes and detection of outliers. ABC and ABP are two markers of ABU that could be used as two complementary approaches to identify targets for improvement.
Comparative amino acid digestibility between broiler chickens and pigs fed different poultry by-products and meat and bone meal
Authors: Park Chan Sol , Naranjo Victor Daniel , Htoo John Kyaw , Adeola Olayiwola
Published: July 2020

The objective of this study was to compare the standardized ileal digestibility (SID) of amino acids (AA) in 3 poultry by-products including hydrolyzed feather meal (HFM), flash dried poultry protein (FDPP), and poultry meal (PM) and also a meat and bone meal (MBM) between broiler chickens and pigs. Experimental diets consisted of 4 diets containing each test ingredient as a sole source of nitrogen and a nitrogen-free diet. In experiment 1, 416 male broiler chickens with a mean initial body weight (BW) of 705 ± 100 g were allotted to 5 diets with 8 replicate cages per diet in a randomized complete block design with BW as a blocking factor at day 18 posthatching. After 5 d of feeding experimental diets, birds were euthanized by CO2 asphyxiation, and ileal digesta samples were collected from distal two-thirds of the ileum. In experiment 2, 10 barrows with a mean initial BW of 22.1 ± 1.59 kg were surgically fitted with T-cannulas at the distal ileum and allotted to a duplicate 5 × 4 incomplete Latin Square design with 5 diets and 4 periods. Each period lasted for 7 d including 5 d of adaptation and 2 d of ileal digesta collection. Data from experiments 1 and 2 were pooled together and analyzed as a 2 × 4 factorial arrangement with the effects of species (broiler chickens or pigs) and 4 experimental diets (HFM, FDPP, PM, or MBM). There were interactions (P < 0.05) between experimental diets and species in the SID of His, Lys, Thr, Trp, Val, and all dispensable AA except Tyr. In broiler chickens, the SID of Lys in FDPP (73.3%) was greater (P < 0.05) than in HFM (55.7%) but was lower (P < 0.05) than in MBM (86.5%), which was not different from PM (78.7%). In pigs, however, the SID of Lys in FDPP and PM (70.0 and 70.1%, respectively) were greater (P < 0.05) than in HFM (39.0%) but were lower (P < 0.05) than in MBM (79.2%). Broiler chickens fed FDPP and PM had lower (P < 0.05) SID of His, Thr, and Trp than those fed MBM; however, there was no difference in the SID of His, Thr, or Trp among pigs fed FDPP, PM, or MBM. The SID of Val in MBM was greater (P < 0.05) than in the other test ingredients for broiler chickens, but there was no difference in the SID of Val among test ingredients for pigs. Pigs had greater (P < 0.05) SID of Ile and Met than broiler chickens. In conclusion, the pattern of differences in the SID of His, Lys, Thr, Trp, and Val, but not the other indispensable AA, among poultry by-products and MBM were different between broiler chickens and pigs.
Genetic Color Polymorphism of the Whitelined Sphinx Moth larva (Lepidoptera: Sphingidae)
Authors: Francois C L , Davidowitz G
Published: July 2020

For a trait to be considered polymorphic, it must fulfill both genetic and ecological criteria. Genetically, a polymorphic trait must have multiple heritable variants, potentially from the same female, in high-enough frequency as to not be due to mutation. Ecologically, in a single wild population, these variants must co-occur, and be capable of interbreeding. Polymorphism is frequently considered in the context of either geographical cause or genetic consequence. However, the incorporation of both in a single study can facilitate our understanding of the role that polymorphism may play in speciation. Here, we ask if the two color morphs (green and yellow) exhibited by larvae of the whitelined sphinx moth, Hyles lineata (Fabricius), co-occur in wild populations, in what frequencies, and whether they are genetically determined. Upon confirmation from field surveys that the two color morphs do co-occur in wild populations, we determined heritability. We conducted a series of outcrosses, intercrosses and backcrosses using individuals that had exhibited yellow or green as laboratory-reared larvae. Ratios of yellow:green color distribution from each familial cross were then compared with ratios one would expect from a single gene, yellow-recessive model using a two-sided binomial exact test. The offspring from several crosses indicate that the yellow and green coloration is a genetic polymorphism, primarily controlled by one gene in a single-locus, two-allele Mendelian-inheritance pattern. Results further suggest that while one gene primarily controls color, there may be several modifier genes interacting with it.
Landscape-wide flight activity by wintering bats predictably follows pulses of warmth in the Midwestern United States
Authors: Arndt Robert J , Lima Steven L
Published: July 2020

During winter hibernation, bats may become active for a variety of reasons. Such winter activity occurs at or near hibernacula, but the degree to which this activity represents long-distance travel across a wider landscape largely is unstudied. We documented patterns in landscape-wide winter activity across a west-central Indiana study site, providing some new insights into winter flight activity. We deployed acoustic recording devices in areas without any known hibernacula, each night from December through March over three consecutive winters. Twilight temperatures (1 h post-sunset) ranged from −23°C to 21°C across three winters. We recorded 4,392 call files and attributed 89% to a phonic group based on characteristic frequencies. Flight activity was recorded at all stations and during all winter months. Nightly activity mainly was a function of the temperature on that night. We recorded low-phonic bats (most likely big brown bats, Eptesicus fuscus) down to −4°C, but most activity occurred when twilight temperatures were > 0°C. Mid-phonic bat activity (most likely eastern red bats, Lasiurus borealis) occurred when temperatures were > 0°C, with most activity occurring when temperatures were > 5°C. Wind speeds > 6 m/s tended to suppress activity. The duration of inactive periods during cold spells had no effect on activity during subsequent warm nights, indicating no increasing drive for activity following long periods of inactivity. Most activity occurred within a few hours of sunset, regardless of temperature. Little pre-sunset activity was recorded in low-phonic bats, but mid-phonic bats sometimes were active in the hour before sunset. Our results suggest widespread and potentially long-distance travel by bats across our study area during warm periods, but the impetus behind this activity remains unclear.
Highlights in Medical Entomology, 2019: Familiar Foes and New Frontiers
Authors: Smith Ryan C
Published: July 2020

The 2019 Entomological Society of America annual meeting was held in St. Louis, Missouri, just blocks away from the iconic Gateway Arch. Representing a ‘gateway to the West’, this inspired the theme of the Highlights in Medical Entomology to reflect on the accomplishments of the past year as we move into a ‘new frontier’ of vector biology research. Papers were selected broadly across arthropods that influence public health, focusing on topics ranging from West Nile virus transmission, ticks and tick-borne disease, to advances in genetics and ‘big data’ studies. This included current perspectives on West Nile virus ecology and epidemiology, which has now been endemic in the United States for 20 yr. Additional topics such as the advantages of citizen science and the importance of scientific communication were also discussed. Together, these papers demonstrate the achievements of the vector community while emphasizing the challenges that we collectively face to reduce the burden of vector-borne disease.
Terrorism and the Varieties of Civil Liberties
Authors: Rubin Michael A , Morgan Richard K
Published: July 2020

How do government protections, and violations, of its citizens’ civil liberties influence the country's exposure to terrorism? Existing research remains divided. We contribute clarity to these debates by examining the distinct effects of specific types of civil liberties: physical integrity (e.g., freedom from extra-judicial torture and killing), political liberties (e.g., freedom of expression and assembly), and private liberties (e.g., freedom of thought and religion and property rights). We distinguish these civil liberties dimensions from the role of institutions for political selection (e.g., elections) and horizontal accountability (e.g., checks and balances, executive constraints). We argue physical integrity rights decrease terrorism, by reducing grievances against and increasing trust in the state, while political liberties increase terrorism, by both incentivizing violence among those with extremist goals and protecting their ability to organize. Empirically, we measure a country's exposure to terrorism using the Global Terrorism Database. We isolate the effects of government actions on these civil liberties dimensions from each other, and from the effects of the state's political institutions, by leveraging the Varieties of Democracy data. Our sample covers 177 states from 1970 to 2018. We find evidence consistent with our hypotheses regarding the effects of the distinct component dimensions of civil liberties.
Strengthening Resiliency During Pacific Partnership Missions: Leadership Matters
Authors: King Heather C , Spritzer Natalie , Eadens Phonthip , Fisak Jean
Published: July 2020

The role of military leaders to promote resilience has never been more relevant. The following case highlights a Navy Nurse Corps Officer’s challenges with deployment stressors and building resilience during a ship-based Global Health Engagement. The case also highlights a follow-on project to enhance the resilience of deployed service members.
A Late Nineteenth-Century Rabbinic Critique of the Status of Women in Judaism
Authors: Schwartzmann Julia
Published: July 2020

This article aims to show that long before the famous debate over women’s suffrage (1918–25), women’s alienation from significant parts of Judaism was a fact that was obvious to those in the Orthodox community who were ready to admit it. To prove this, I discuss the late nineteenth-century essay Netiv Moshe: Maamar Mehkari 'al Mishpat haNashim baEmunah (A Scholarly Enquiry into the Case of Women in Religious Faith).1 This essay, written in Hungary by Mózes Salamon, the rabbi of a small provincial community, analyzes the gender problem in Judaism and reveals that the basic arguments of Jewish religious feminism had been expressed even before feminism as a movement came to terms with its objectives. This is the first scholarly analysis of this little known essay.
The impact of non-Gaussianity on the Epoch of Reionization parameter forecast using 21-cm power-spectrum measurements
Authors: Shaw Abinash Kumar , Bharadwaj Somnath , Mondal Rajesh
Published: July 2020

Measurements of the Epoch of Reionization (EoR) 21-cm signal hold the potential to constrain models of reionization. In this paper, we consider a reionization model with three astrophysical parameters namely (1) the minimum halo mass that can host ionizing sources, Mmin, (2) the number of ionizing photons escaping into the IGM per baryon within the halo, Nion, and (3) the mean free path of the ionizing photons within the IGM, Rmfp. We predict the accuracy with which these parameters can be measured from future observations of the 21-cm power spectrum (PS) using the upcoming SKA-Low. Unlike several earlier works, we account for the non-Gaussianity of the inherent EoR 21-cm signal. Considering cosmic variance only and assuming that foregrounds are completely removed, we find that non-Gaussianity increases the volume of the 1σ error ellipsoid of the parameters by a factor of 133 relative to the Gaussian predictions, the orientation is also different. The ratio of the volume of error ellipsoids is 1.65 and 2.67 for observation times of 1024 and 10 000 h, respectively, when all the $\boldsymbol {k}$ modes within the foreground wedge are excluded. With foreground wedge excluded and for 1024 h, the 1D marginalized errors are (ΔMmin/Mmin, ΔNion/Nion, ΔRmfp/Rmfp) = (6.54, 2.71, 7.75) × 10−2 that are, respectively, $2 {{\ \rm per\ cent}}$, $5 {{\ \rm per\ cent}}$, and $23 {{\ \rm per\ cent}}$ larger than the respective Gaussian predictions. The impact of non-Gaussianity increases for longer observations, and it is particularly important for Rmfp.
Improved photometric redshifts with colour-constrained galaxy templates for future wide-area surveys
Authors: Lee Bomee , Chary Ranga-Ram
Published: July 2020

Cosmology and galaxy evolution studies with LSST, Euclid, and Roman, will require accurate redshifts for the detected galaxies. In this study, we present improved photometric redshift estimates for galaxies using a template library that populates three-colour space and is constrained by HST/CANDELS photometry. For the training sample, we use a sample of galaxies having photometric redshifts that allows us to train on a large, unbiased galaxy sample having deep, unconfused photometry at optical-to-mid infrared wavelengths. Galaxies in the training sample are assigned to cubes in 3D colour space, V − H, I − J, and z − H. We then derive the best-fitting spectral energy distributions of the training sample at the fixed CANDELS median photometric redshifts to construct the new template library for each individual colour cube (i.e. colour-cube-based template library). We derive photometric redshifts (photo-z) of our target galaxies using our new colour-cube-based template library and with photometry in only a limited set of bands, as expected for the aforementioned surveys. As a result, our method yields σNMAD of 0.026 and an outlier fraction of 6 per cent using only photometry in the LSST and Euclid/Roman bands. This is an improvement of ∼10 per cent on σNMAD and a reduction in outlier fraction of ∼13 per cent compared to other techniques. In particular, we improve the photo-z precision by about 30 per cent at 2 < z < 3. We also assess photo-z improvements by including K or mid-infrared bands to the ugrizYJH photometry. Our colour-cube-based template library is a powerful tool to constrain photometric redshifts for future large surveys.
Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design
Authors: Rice Alan M , Castillo Morales Atahualpa , Ho Alexander T , Mordstein Christine , Mühlhausen Stefanie , Watson Samir , Cano Laura , Young Bethan , Kudla Grzegorz , Hurst Laurence D
Published: July 2020

Large-scale re-engineering of synonymous sites is a promising strategy to generate vaccines either through synthesis of attenuated viruses or via codon-optimized genes in DNA vaccines. Attenuation typically relies on deoptimization of codon pairs and maximization of CpG dinucleotide frequencies. So as to formulate evolutionarily informed attenuation strategies that aim to force nucleotide usage against the direction favored by selection, here, we examine available whole-genome sequences of SARS-CoV-2 to infer patterns of mutation and selection on synonymous sites. Analysis of mutational profiles indicates a strong mutation bias toward U. In turn, analysis of observed synonymous site composition implicates selection against U. Accounting for dinucleotide effects reinforces this conclusion, observed UU content being a quarter of that expected under neutrality. Possible mechanisms of selection against U mutations include selection for higher expression, for high mRNA stability or lower immunogenicity of viral genes. Consistent with gene-specific selection against CpG dinucleotides, we observe systematic differences of CpG content between SARS-CoV-2 genes. We propose an evolutionarily informed approach to attenuation that, unusually, seeks to increase usage of the already most common synonymous codons. Comparable analysis of H1N1 and Ebola finds that GC3 deviated from neutral equilibrium is not a universal feature, cautioning against generalization of results.
Leadership, academia, and the role of career coaching
Authors: Cheesebrough Kevin R , Bronzert Jessica , Frazier-De La Torre Elizabeth
Published: July 2020

In academia, the competencies necessary to be an effective leader, including focused training in leadership skills are often overlooked. Incorporating a coaching component in leadership training programs has shown to have a beneficial impact. The purpose of this commentary is to present the rationale, description, and process of the executive coaching component of the Society of Behavioral Medicine (SBM) Mid-Career Leadership Institute. Institute Fellows are provided with a list of executive career coaches that includes their biography and coaching philosophy. Fellows are asked to rank their preferences from 1 to 3. Usually, Fellows are paired with their first choice. Rigorous evaluations of the benefit of career coaching within a comprehensive leadership program, such as the SBM Leadership Institute has not been conducted However, our evaluations to date show that the coaching component is highly rated by the Fellows and over 90% report using their allotted three sessions. Career coaching, conducted as part of a comprehensive leadership program, has the potential to positively influence career trajectories. A more rigorous evaluation of the SBM coaching program is needed to assess the true benefits.
A Physiologically Based Pharmacokinetic Model for Naphthalene With Inhalation and Skin Routes of Exposure
Authors: Kapraun Dustin F , Schlosser Paul M , Nylander-French Leena A , Kim David , Yost Erin E , Druwe Ingrid L
Published: July 2020

Naphthalene, a volatile organic compound present in moth repellants and petroleum-based fuels, has been shown to induce toxicity in mice and rats during chronic inhalation exposures. Although simpler default methods exist for extrapolating toxicity points of departure from animals to humans, using a physiologically based pharmacokinetic (PBPK) model to perform such extrapolations is generally preferred. Confidence in PBPK models increases when they have been validated using both animal and human in vivo pharmacokinetic (PK) data. A published inhalation PBPK model for naphthalene was previously shown to predict rodent PK data well, so we sought to evaluate this model using human PK data. The most reliable human data available come from a controlled skin exposure study, but the inhalation PBPK model does not include a skin exposure route; therefore, we extended the model by incorporating compartments representing the stratum corneum and the viable epidermis and parameters that determine absorption and rate of transport through the skin. The human data revealed measurable blood concentrations of naphthalene present in the subjects prior to skin exposure, so we also introduced a continuous dose-rate parameter to account for these baseline blood concentration levels. We calibrated the three new parameters in the modified PBPK model using data from the controlled skin exposure study but did not modify values for any other parameters. Model predictions then fell within a factor of 2 of most (96%) of the human PK observations, demonstrating that this model can accurately predict internal doses of naphthalene and is thus a viable tool for use in human health risk assessment.
Invasion and Colonization Pattern of Fusarium fujikuroi in Rice
Authors: Chen Chieh-Yi , Chen Szu-Yu , Liu Chun-Wei , Wu Dong-Hong , Kuo Chien-Chih , Lin Chun-Chi , Chou Hau-Ping , Wang Yu-Yao , Tsai Yi-Chen , Lai Ming-Hsin , Chung Chia-Lin
Published: July 2020

Bakanae disease in rice can cause abnormal elongation of the stem and leaves, development of adventitious roots, a larger leaf angle, and even death. Little is known about the infection, colonization, and distribution of Fusarium fujikuroi in rice plants across different growth stages. In this study, microscopic observation and quantitative real-time PCR were combined to investigate the pathogenesis of bakanae, using artificially inoculated seedlings of a susceptible rice cultivar, Zerawchanica karatals (ZK), a resistant cultivar, Tainung 67 (TNG67), naturally infected adult field plants (cultivars Kaohsiung 139, Taikeng 2, and Tainan 11), and an F. fujikuroi isolate expressing green fluorescent protein. In rice seedlings, F. fujikuroi hyphae were found to directly penetrate the epidermis of basal stems and roots, then extend inter- and intracellularly to invade the vascular bundles. Occlusion of vascular bundles and radial hyphal expansion from vascular bundles to surrounding parenchyma were observed in adult plants. Analysis of consecutive 3-cm segments of the whole plant revealed that F. fujikuroi was largely confined to the embryo, basal stem, and basal roots in seedlings, and distributed unevenly in the lower aerial parts (including nodes and internodes) of adult plants. The elongation and development of adventitious roots did not necessarily correlate with the amount of F. fujikuroi in diseased plants. Treatment of rice seeds with gibberellic acid-3 (GA3) at 0.5 mg/liter resulted in significantly more elongation of ZK than TNG67 seedlings, suggesting that the susceptibility of ZK to bakanae is associated with its higher sensitivity to GA3.
Association of Aspirin and Other Nonsteroidal Anti-inflammatory Drugs With Vertebral Trabecular Bone: Data From Multiethnic Study of Atherosclerosis, a Population-Based Multicenter Cohort Study
Authors: Ahmad Khadije , Budoff Matthew J. , Delaney Joseph A. , Mao SongShou , Gao Yanlin , Nasir Khurram , Tracy Russell , Li Dong
Published: July 2020

Objective

The objective of this article was to study the association of aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) with bone mineral density (BMD).

Methods

Spine BMD was evaluated in a subset of 2028 participants from the Multiethnic Study of Atherosclerosis cohort who were NSAID users (including aspirin) and underwent both lumbar and thoracic imaging. Multiethnic Study of Atherosclerosis is a prospective cohort study that includes 4 ethnic groups (white, Asian, African American, and Hispanic). Trabecular BMD was evaluated by quantitative computed tomography based on cardiac computed tomography images, which were obtained during coronary calcium scans. The analyses were cross sectional using baseline examination data for exposure and outcomes.

Results

After adjustment for potential confounders including age, sex, race, and traditional cardiovascular risk factors, a small association between trabecular BMD and baseline use of COX-2–selective NSAID was observed. COX-2–selective NSAID use was associated with 7.4 mg/cm3(95% confidence interval [CI], 1.6–13.3;P= 0. 013) higher trabecular BMD in thoracic spine and 10.6 mg/cm3higher at lumbar spine (95% CI, 5.1–16.1;P< 0.001). Among regular aspirin users, there was no association between drug use and trabecular BMD. Considering all spine fractures together, the prevalence ratio of fractures among aspirin users was 1.0 (95% CI, 0.6–1.6) and 1.1 (95% CI, 0.5–2.3) among COX-2–selective NSAID users.

Conclusions

Regular use of aspirin has no significant association with trabecular BMD in either the thoracic or lumbar spine and no association with fracture prevalence. COX-2–selective NSAIDs may have modest positive association with BMD, but the mechanisms were not assessed and the observational study design makes residual confounding a possible alternate explanation. Potential pathological mechanisms warrant further longitudinal exploration.
Baseline Computed Tomography Radiomic and Genomic Assessment of Head and Neck Squamous Cell Carcinoma
Authors: Wang Colin Y. , Foy Joseph J. , Siewert Tanguy Y. , Haraf Daniel J. , Ginat Daniel T.
Published: July 2020

Purpose

To determine the relationship between computed tomography (CT) radiomic features and gene expression levels in head and neck squamous cell carcinoma (HNSCC).

Methods

This retrospective study included 66 patients with HNSCC primary lesions (36 oropharyngeal, 6 hypopharyngeal, 10 laryngeal, 14 oral cavity). Gene expression information for 6 targetable genes (fibroblast growth factor receptor [FGFR]1, epidermal growth factor receptor [EGFR], FGFR2, FGFR3, EPHA2, PIK3CA) was obtained via Agilent microarrays from samples collected between 1997 and 2010. Pretreatment contrast-enhanced soft tissue neck CT scans were reviewed, and 142 radiomics features were derived. R was used to calculate Pearson correlation coefficients were calculated between gene expression levels and each radiomic feature. P values were adjusted using the false discovery rate (FDR) method.

Results

There were significant correlations between FGFR1 and 5 gray level cooccurrence matrix (GLCM) features with FDR-adjusted P values less than 0.05: inertia (r = 0.366, FDR-adjusted P = 0.006), absolute value (r = 0.31, FDR-adjusted P = 0.024), contrast (r = 0.366, FDR-adjusted P = 0.006), difference average (r = 0.31, FDR-adjusted P = 0.024), and difference variance (r = 0.37, FDR-adjusted P = 0.005). There was 1 correlated feature for FGFR2 with an FDR-adjusted P value less than 0.05: fractal dimension box-coarse (r = 0.33, FDR-adjusted P = 0.018). There was 1 correlated feature for EPHA2 with an FDR-adjusted P value less than 0.05: GLCM entropy (r = −0.28, FDR-adjusted P = 0.049). Six of the 7 features that showed significant correlation belonged to the GLCM class of features.

Conclusions

The CT radiomic features demonstrate correlations with FGFR1 status in HNSCC and should be further investigated for their potential to predict FGFR1 status.
Multifractal signatures of perceptual processing on anatomical sleeves of the human body
Authors: Mangalam Madhur , Carver Nicole S. , Kelty-Stephen Damian G.
Published: July 2020

Research into haptic perception typically concentrates on mechanoreceptors and their supporting neuronal processes. This focus risks ignoring crucial aspects of active perception. For instance, bodily movements influence the information available to mechanoreceptors, entailing that movement facilitates haptic perception. Effortful manual wielding of an object prompts feedback loops at multiple spatio-temporal scales, rippling outwards from the wielding hand to the feet, maintaining an upright posture and interweaving to produce a nonlinear web of fluctuations throughout the body. Here, we investigated whether and how this bodywide nonlinearity engenders a flow of multifractal fluctuations that could support perception of object properties via dynamic touch. Blindfolded participants manually wielded weighted dowels and reported judgements of heaviness and length. Mechanical fluctuations on the anatomical sleeves (i.e. peripheries of the body), from hand to the upper body, as well as to the postural centre of pressure, showed evidence of multifractality arising from nonlinear temporal correlations across scales. The modelling of impulse–response functions obtained from vector autoregressive analysis revealed that distinct sets of pairwise exchanges of multifractal fluctuations entailed accuracy in heaviness and length judgements. These results suggest that the accuracy of perception via dynamic touch hinges on specific flowing patterns of multifractal fluctuations that people wear on their anatomical sleeves.
Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function
Authors: Li Ao , Laville Elisabeth , Tarquis Laurence , Lombard Vincent , Ropartz David , Terrapon Nicolas , Henrissat Bernard , Guieysse David , Esque Jeremy , Durand Julien , Morgavi Diego P. , Potocki-Veronese Gabrielle
Published: July 2020

Mannoside phosphorylases are involved in the intracellular metabolization of mannooligosaccharides, and are also useful enzymes for the in vitro synthesis of oligosaccharides. They are found in glycoside hydrolase family GH130. Here we report on an analysis of 6308 GH130 sequences, including 4714 from the human, bovine, porcine and murine microbiomes. Using sequence similarity networks, we divided the diversity of sequences into 15 mostly isofunctional meta-nodes; of these, 9 contained no experimentally characterized member. By examining the multiple sequence alignments in each meta-node, we predicted the determinants of the phosphorolytic mechanism and linkage specificity. We thus hypothesized that eight uncharacterized meta-nodes would be phosphorylases. These sequences are characterized by the absence of signal peptides and of the catalytic base. Those sequences with the conserved E/K, E/R and Y/R pairs of residues involved in substrate binding would target β-1,2-, β-1,3- and β-1,4-linked mannosyl residues, respectively. These predictions were tested by characterizing members of three of the uncharacterized meta-nodes from gut bacteria. We discovered the first known β-1,4-mannosyl-glucuronic acid phosphorylase, which targets a motif of the

Shigella

lipopolysaccharide O-antigen. This work uncovers a reliable strategy for the discovery of novel mannoside-phosphorylases, reveals possible interactions between gut bacteria, and identifies a biotechnological tool for the synthesis of antigenic oligosaccharides.
Characterisation of aTeladorsagia circumcinctaglutathione transferase
Authors: Umair Saleh , Bouchet Charlotte L.G. , Deng Qing , Palevich Nikola , Simpson Heather V.
Published: July 2020

A 615 bp full length cDNA encoding aTeladorsagia circumcinctaglutathione transferase (TcGST) was cloned, expressed inEscherichia coliand the recombinant protein purified and its kinetic properties determined. The predicted protein consisted of 205 amino acids and was present as a single band of about 24 kDa on SDS-PAGE. Multiple alignments of the protein sequence ofTcGST with homologues from other helminths showed that the highest identity of 53-68% with haem-binding nematode proteins designated as members of the nu class of GSTs. Substrate binding sites and conserved regions were identified and were generally conserved. The predicted 3-dimensional structures ofTcGST andHcGST revealed highly open binding cavities typical of this class of GST, considered to allow greater accessibility to diverse ligands compared with other classes of GST. At 25 °C, the optimum pH forTcGST activity was pH 7, the Vmaxwas 1535 ± 33 nmoles.min-1.mg-1protein and the apparent Kmfor the substrate 1-chloro-2,4-dinitrobenzene (CDNB) was 0.22 ± 0.01 mM (mean ± SD, n = 2). Antibodies in both serum and saliva from field-immune, but not nematode-naÏve, sheep, recognised recombinantTcGST in enzyme-linked immunosorbent assays. The recognition of the recombinant protein by antibodies generated by exposure of sheep to the native enzyme indicates similar antigenicity of the two proteins. These findings could aid in the design of novel drugs and vaccine antigens for economically important parasites of livestock.