bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancing the conversational process by using a logical closure operator in phenotypes implications
Authors: Benito‐Picazo Fernando , Enciso Manuel , Rossi Carlos , Guevara Antonio
Published: February 2017

In this paper, we present a novel strategy to face the problem of dimensionality within datasets involved in conversational and feature selection systems. We base our work on a sound and complete logic along with an efficient attribute closure method to manage implications. All of them together allow us to reduce the overload of information we encounter when dealing with these kind of systems. An experiment carried out over a dataset containing real information comes to expose the benefits of our design. Copyright © 2017 John Wiley & Sons, Ltd.
Geometry calibration method for a cone‐beam CT system
Authors: Yang Hongkai , Kang Kejun , Xing Yuxiang
Published: February 2017

Purpose

The positioning accuracy of each component is important to ensure the image quality of cone‐beam CT. However, accurate positioning is not easy and requires experience and time. The option is to calibrate the geometric parameters and then plug them into a reconstruction algorithm which is the preferred solution in practice. In this case, the image quality is determined by the accuracy and precision of the calibration method. This work describes a method to independently calibrate an imaging system in each pose (projection angle) for a cone‐beam CT with a nonideal circular trajectory.

Methods

The calibration method uses a phantom with 12 beads on 2 planes that are observed on the radiographic images. This pose‐independent calibration method (PIC) can decorrelate the relationships among the geometric parameters so that the parameters can be estimated one‐by‐one. This simplifies the calibration process. Besides the pose‐independent calibration method, this paper also describes an extended calibration method with additional constraints on the system geometry. Both methods are validated with numerical simulations and then experimentally on a practical system with a scanning object loosely supported by rotating wheels. The object rotates during the CT data acquisition. The angular and pose information of the CT system are not accurately known a priori in this case.

Results

The numerical simulations and the experiments both provide satisfactory results. The relative error of the calibrated source‐to‐detector distance in the simulation is less than 0.1%. The errors in the calibrated roll, pitch, and yaw angles are less than 0.04°. A sensitivity study using various bead position uncertainties in random directions shows that the pose‐independent calibration method is robust to measurement errors. Tests were also done with a nonideal circular trajectory for further validation. Images reconstructed using the geometric parameters from both the pose‐independent and the extended calibration methods were free of artifacts and blur from misalignment. All these results demonstrate the effectiveness of these methods.

Conclusions

The PIC method can be used to independently calibrate the geometric parameters of a cone‐beam CT view‐by‐view. Thus, the PIC method can be implemented on commonly used systems such as circular, nonideal circular or C‐arm cone‐beam CTs. The PIC method can also be useful for some irregularly configured CT systems to fulfill special imaging requirements, for example, a CT system when the x ray source or the rotating platform cannot be easily located. The PIC method will reduce the costs of ensuring very precise mechanics and the labor in fine tuning CT systems.
The critical role of the ZNF217 oncogene in promoting breast cancer metastasis to the bone
Authors: Bellanger Aurélie , Donini Caterina F , Vendrell Julie A , Lavaud Jonathan , Machuca‐Gayet Irma , Ruel Maëva , Vollaire Julien , Grisard Evelyne , Győrffy Balázs , Bièche Ivan , Peyruchaud Olivier , Coll Jean‐Luc , Treilleux Isabelle , Maguer‐Satta Véronique , Josserand Véronique , Cohen Pascale A
Published: February 2017

Bone metastasis affects >70% of patients with advanced breast cancer. However, the molecular mechanisms underlying this process remain unclear. On the basis of analysis of clinical datasets, and in vitro and in vivo experiments, we report that the ZNF217 oncogene is a crucial mediator and indicator of bone metastasis. Patients with high ZNF217 mRNA expression levels in primary breast tumours had a higher risk of developing bone metastases. MDA‐MB‐231 breast cancer cells stably transfected with ZNF217 (MDA‐MB‐231‐ZNF217) showed the dysregulated expression of a set of genes with bone‐homing and metastasis characteristics, which overlapped with two previously described ‘osteolytic bone metastasis’ gene signatures, while also highlighting the bone morphogenetic protein (BMP) pathway. The latter was activated in MDA‐MB‐231‐ZNF217 cells, and its silencing by inhibitors (Noggin and LDN‐193189) was sufficient to rescue ZNF217‐dependent cell migration, invasion or chemotaxis towards the bone environment. Finally, by using non‐invasive multimodal in vivo imaging, we found that ZNF217 increases the metastatic growth rate in the bone and accelerates the development of severe osteolytic lesions. Altogether, the findings of this study highlight ZNF217 as an indicator of the emergence of breast cancer bone metastasis; future therapies targeting ZNF217 and/or the BMP signalling pathway may be beneficial by preventing the development of bone metastases. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Prenatal diagnosis of congenital cytomegalovirus infection in 115 cases: a 5 years' single center experience
Authors: Enders M. , Daiminger A. , Exler S. , Ertan K. , Enders G. , Bald R.
Published: February 2017

Objective

The objective of this study is to investigate the diagnostic value of invasive prenatal diagnosis (PD) of congenital cytomegalovirus (CMV) infection from amniotic fluid (AF) and fetal blood (FB).

Methods

A retrospective study was conducted on 115 pregnancies with CMV primary infection. A total of 111 AF and 106 FB samples were investigated for various virological and non‐virological markers. Detailed ultrasound examinations were performed at time of PD.

Results

Overall sensitivity of CMV PCR in FB (75.6%; 95%CI 60–87) and AF (72.7%; 95%CI 57–85) was comparable. In women with amniocentesis >8 weeks between seroconversion and PD, we did not observe significant differences between amniocentesis performed ≥17 + 0 (sensitivity 90.9%; 95%CI 71–99) and ≥20 + 0 gestational weeks (sensitivity 90.0%; 95%CI 68–99). Virological markers in FB were higher in symptomatic compared with asymptomatic fetuses (p < 0.05). No significant differences were observed for non‐virological markers. However, platelet counts <120 × 10e9/L and beta‐2 microglobulin values >14 mg/L were more frequently found in fetuses with severe ultrasound abnormalities compared with fetuses with no or mild abnormalities (p < 0.001).

Conclusion

Optimal timing of amniocentesis in women with primary infection in early gestation should be reevaluated in a prospective study. Analysis of FB markers may be beneficial in the individual management of pregnant women with confirmed congenital CMV infection. © 2017 John Wiley & Sons, Ltd.
Molecular dynamics simulation study of the “stay or leave” problem for two magnesium ions in gene transcription
Authors: Wu Shaogui
Published: February 2017

Two magnesium ions play important roles in nucleotide addition cycle (NAC) of gene transcription. However, at the end of each NAC, why does one ion stay in the active site while the other ion leaves with product pyrophosphate (PPi)? This problem still remains obscure. In this work, we studied the problem using all‐atom molecular dynamics simulation combined with steered molecular dynamics and umbrella sampling simulation methods. Our simulations reveal that although both ions are located in the active site after chemistry, their detailed positions are not symmetrical, leading to their different forces from surrounding groups. One ion makes weaker contacts with PPi than the whole protein. Hence, PPi release is less likely to take it away. The other one forms tighter contacts with PPi relative to the protein. The formed (Mg2+‐PPi)2− complex is found to break the contacts with surrounding protein residues one by one so as to dissociate from the active site. This effectively avoids the coexistence of two ions in the active site after PPi release and guarantees a reasonable Mg2+ ion number in the active site for the next NAC. The observations from this work can provide valuable information for comprehensively understanding the molecular mechanism of transcription. Proteins 2017; 85:1002–1007. © 2017 Wiley Periodicals, Inc.
Statistical issues in first‐in‐human studies on BIA 10‐2474: Neglected comparison of protocol against practice
Authors: Bird Sheila M. , Bailey Rosemary A. , Grieve Andrew P. , Senn Stephen
Published: February 2017

By setting the regulatory‐approved protocol for a suite of first‐in‐human studies on BIA 10‐2474 against the subsequent French investigations, we highlight 6 key design and statistical issues, which reinforce recommendations by a Royal Statistical Society Working Party, which were made in the aftermath of cytokine release storm in 6 healthy volunteers in the United Kingdom in 2006.

The 6 issues are dose determination, availability of pharmacokinetic results, dosing interval, stopping rules, appraisal by safety committee, and clear algorithm required if combining approvals for single and multiple ascending dose studies.
Potency of Human Cardiosphere-Derived Cells from Patients with Ischemic Heart Disease Is Associated with Robust Vascular Supportive Ability
Authors: Harvey Emma , Zhang Huajun , Sepúlveda Pilar , Garcia Sara P. , Sweeney Dominic , Choudry Fizzah A. , Castellano Delia , Thomas George N. , Kattach Hassan , Petersen Romina , Blake Derek J. , Taggart David P. , Frontini Mattia , Watt Suzanne M. , Martin-Rendon Enca
Published: February 2017

Cardiosphere-derived cell (CDC) infusion into damaged myocardium has shown some reparative effect; this could be improved by better selection of patients and cell subtype. CDCs isolated from patients with ischemic heart disease are able to support vessel formation in vitro but this ability varies between patients. The primary aim of our study was to investigate whether the vascular supportive function of CDCs impacts on their therapeutic potential, with the goal of improving patient stratification. A subgroup of patients produced CDCs which did not efficiently support vessel formation (poor supporter CDCs), had reduced levels of proliferation and increased senescence, despite them being isolated in the same manner and having a similar immunophenotype to CDCs able to support vessel formation. In a rodent model of myocardial infarction, poor supporter CDCs had a limited reparative effect when compared to CDCs which had efficiently supported vessel formation in vitro. This work suggests that not all patients provide cells which are suitable for cell therapy. Assessing the vascular supportive function of cells could be used to stratify which patients will truly benefit from cell therapy and those who would be better suited to an allogeneic transplant or regenerative preconditioning of their cells in a precision medicine fashion. This could reduce costs, culture times and improve clinical outcomes and patient prognosis.
Authenticated encryption: how reordering can impact performance
Authors: Alomair Basel
Published: February 2017

In this work, we look at authenticated encryption schemes from a new perspective. As opposed to focusing solely on the “security” implications of the different methods for constructing authenticated encryption schemes, we investigate the effect of the method used to construct an authenticated encryption scheme on the “performance” of the construction. We show that, as opposed to the current National Institute of Standards and Technology standard, by performing the authentication operation before the encryption operation, the computational efficiency of the construction can be increased, without affecting the security of the overall construction. In fact, we show that the proposed construction is even more secure than standard authentication based on universal hashing in the sense that the hashing key is resilient to key recovery attacks. Copyright © 2017 John Wiley & Sons, Ltd.
Concise Review: An (Im)Penetrable Shield: How the Tumor Microenvironment Protects Cancer Stem Cells
Authors: Relation Theresa , Dominici Massimo , Horwitz Edwin M.
Published: February 2017

Cancer stem cells (CSCs) are defined by their unlimited self-renewal ability and their capacity to initiate and maintain malignancy, traits that are not found in most cells that comprise the tumor. Although current cancer treatments successfully reduce tumor burden, the tumor will likely recur unless CSCs are effectively eradicated. This challenge is made greater by the protective impact of the tumor microenvironment (TME), consisting of infiltrating immune cells, endothelial cells, extracellular matrix, and signaling molecules. The TME acts as a therapeutic barrier through immunosuppressive, and thereby tumor-promoting, actions. These factors, outside of the cancer cell lineage, work in concert to shelter CSCs from both the body's intrinsic anticancer immunity and pharmaceutical interventions to maintain cancer growth. Emerging therapies aimed at the TME offer a promising new tool in breaking through this shield to target the CSCs, yet definitive treatments remain unrealized. In this review, we summarize the mechanisms by which CSCs are protected by the TME and current efforts to overcome these barriers.
Temporal-Spatial Establishment of Initial Niche for the Primary Spermatogonial Stem Cell Formation Is Determined by an ARID4B Regulatory Network
Authors: Wu Ray-Chang , Zeng Yang , Chen Yu-Fang , Lanz Rainer B. , Wu Mei-Yi
Published: February 2017

During neonatal testis development, centrally located gonocytes migrate to basement membrane of the seminiferous cords, where physical contact with a niche established by Sertoli cells is essential for transition of gonocytes into spermatogonial stem cells (SSCs). To provide structural support and signaling stimuli for the gonocyte-to-SSC transition that occurs at a specific location during a finite phase, temporal-spatial establishment of the niche is critical. To date, the factors that guide Sertoli cells to establish the initial stem cell niche remain largely unknown. Using the Sertoli cell-specific Arid4b knockout (Arid4bSCKO) mice, we demonstrated that ablation of AT-rich interaction domain 4B (ARID4B) resulted in abnormal detachment of Sertoli cells from the basement membrane of seminiferous cords during the gonocyte-to-SSC transition phase, suggesting failure to establish a niche for the SSC formation. Without support by a niche environment, gonocytes showed disarranged cell distribution in the Arid4bSCKO testes and underwent apoptosis. The commitment of gonocytes to differentiate into the spermatogonial lineage was broken and the capability of SSCs to self-renew and differentiate was also impaired. Gene expression profiling revealed the molecular mechanisms responsible for the phenotypic changes in the Arid4bSCKO testes, by identifying genes important for stem cell niche function as downstream effectors of ARID4B, including genes that encode gap junction protein alpha-1, KIT ligand, anti-Müllerian hormone, Glial cell-line derived neurotrophic factor, inhibin alpha, inhibin beta, and cytochrome P450 family 26 subfamily b polypeptide 1. Our results identified ARID4B as a master regulator of a signaling network that governs the establishment of a niche during the critical gonocyte-to-SSC transition phase to control the fate of gonocytes and SSCs.
Toxicological evaluation of the topoisomerase inhibitor, etoposide, in the model animal Caenorhabditis elegans and 3T3‐L1 normal murine cells
Authors: Lee So Young , Kim Joo Yeon , Jung Yu‐Jin , Kang Kyungsu
Published: February 2017

Etoposide, a topoisomerase II inhibitor, has been widely used as a clinical anticancer drug to treat diverse cancer patients. Since not only rapidly dividing cancer cells but also the cells of normal human tissues and every living organism in environmental ecosystems have topoisomerases, it is crucial to study the toxicity of etoposide in other organisms in addition to cancer cells. In this study, we evaluated the toxicity of etoposide in both a soil nematode, Caenorhabditis elegans, and 3T3‐L1 normal murine cells. Etoposide significantly retarded the growth, egg laying, and hatching in C. elegans. Etoposide also affected the reproductive gonad tissue, decreased the number of germ cells and induced abnormally enlarged nuclei in C. elegans. In addition, etoposide inhibited 3T3‐L1 cell proliferation, with IC50 values of 37.8 ± 7.3 and 9.8 ± 1.8 μM after 24 and 48 hours of treatment, respectively, via the induction of cell cycle arrest at the G2/M phase and apoptotic cell death. Etoposide also induced nuclear enlargement in 3T3‐L1 normal murine cells. The reproductive toxicity and abnormal nuclear morphological changes seemed to correlate with the adverse effects of etoposide. We suggest that these experimental platforms, i.e., the toxicological evaluation of both nematodes and 3T3‐L1 cells, may be useful to study the mechanisms underlying the side effects of chemicals, including topoisomerase inhibitors.
Experiences of Pre‐Implantation Genetic Diagnosis (PGD) in Sweden: a Three‐Year Follow‐Up of Men and Women
Authors: Järvholm Stina , Thurin‐Kjellberg Ann , Broberg Malin
Published: February 2017

Men and women with a hereditary genetic disease are faced with different options when they wish to become parents. One is pre‐implantation genetic diagnosis (PGD) which is a combination of in vitro fertilization (IVF) and genetic analysis of the embryo before implantation. The present study focused on men and women's psychological experiences of PGD three years after applying for PGD. Nineteen women and seventeen men (i.e. seventeen couples and two women) participated. The interviews were analysed by thematic method. It is better to have tried was identified as a master theme, under which came three underlying sub‐themes, which had the following headings: Practical experience of PGD, Psychological experience of PGD and Goals of PGD. The results show that men and women three years after PGD are still psychologically affected by their experience. The men and women raised concerns that their relationship had been affected, both positively and negatively, and feelings of anxiety and depression still remained. Healthcare services should recognize the heterogeneous nature of the group being studied and therefore the need for counselling can arise at different times and in relation to different areas, regardless of the outcome of the PGD.
« What is the best theory of generation? »: argumentation et débats d'étudiants en médecine à la société royale de médecine d'édimbourg au dix-huitième siècle
Authors: Vasset Sophie
Published: February 2017

Cet article propose d'aborder différemment la longue querelle de la génération, qui divise les ovistes, les spennistes et les partisans de l'épigénèse tout au long des 17° et l8° en Europe. Plutôt que d'en définir les acteurs à partir des publiants, à savoir les médecins ou naturalistes français, anglais et européens qui contredisent les théories ovistes ou spennistes de leurs pairs, je chercherai à poser quelques questions en marge de cette querelle: que reste-t-il d'une querelle une fois qu'elle semble terminée? Comment une querelle est-elle perçue par les contemporains qui auraient un accès fragmentaire à la querelle? Quel est le rôle des querelles scientifiques dans l'éducation des médecins? Je traiterai ces questions en analysant quatre dissertations rédigées par les étudiants en médecine de la Royal Medical Society d'Édimbourg au l8e siècle.
Evidence against vs. in favour of a null hypothesis
Authors: Leppink Jimmie , O’Sullivan Patricia , Winston Kal
Published: February 2017

None
Erasmus and More: A Friendship Revisited
Authors: Baker-Smith Dominic
Published: February 2017

Writing in 1532, the elderly Erasmus reflected on the hazards of marriage and parenthood: friendship, he concluded, is the prime source of comfort in human life, praecipuum humanae vitae solatium, ‘but even there trust is rare and inconstancy is common’. Given the span of acquaintance covered by the eleven volumes of correspondence collected by P. S. Allen in his Erasmi epistolae, Erasmus had plenty of opportunity to test this rather pessimistic view. Indeed, one suspects that it derived as much from his own touchiness as from the unreliability of his friends. Few of his friendships have received so much attention as that which he established with Thomas More, a relationship which lasted some thirty-six years, from Erasmus’ first visit to England in 1499 down to More's execution on 6th July 1535, and indeed until Erasmus’ own more domestic death in Basel almost exactly a year later. From an early date this was seen as a model friendship, something to be celebrated in the Republic of Letters. As we shall see, its religious implications were to prove more complex; but for much of the twentieth century More and Erasmus were conveniently paired as representatives of Christian humanism, a perception reinforced by More's canonization in 1935.
‘Without any Letter’: Some History Outside the Library
Authors: Brückmann Patricia C.
Published: February 2017

In her recent study of the Bayeux tapestry, Suzanne Lewis argues persuasively that we cannot use only the simple Latin tags on this long embroidery (it is not a tapestry) to come to know its story. The more we attend to the exceptionally detailed images, the more we see ambiguity and complexity. Why does Harold have two hands on reliquaries for oath-taking? Why does he look in one direction while a ship leaves in the other? Why does the Fable of the Fox and the Crow appear three times?
The King's Laceman and the Bishop's Friend: Bryant Barrett (c. 1715–1790), Merchant and Squire
Authors: Murphy Martin
Published: February 2017

A career in business was one of the few outlets open to Catholics in eighteenth century London, yet among such businessmen only Thomas Mawhood, the Smithfield woollen draper, and the publisher J. P. Coghlan have been studied in any depth. Bryant Barrett, who will be the subject of this article, is in a different category. His contacts with the wider world of Georgian society allowed him to cross boundaries of class and religion, and although he made his considerable fortune by supplying high society with its luxury fashion accessories, his private life was marked by unostentatious piety and a practical Christian ethos inspired in part by his mentor Richard Challoner. Though his two marriages brought him within the fold of the Catholic gentry, and his wealth earned him the status of a country squire, he remained true to his origins.
The Two Lives of Thomas Metcalfe
Authors: Korsten Frans , Blom Jos , Blom Frans
Published: February 2017

In his 1990 article ‘Holzhauser and England: Three Episodes' T. A. Birrell tells the story of John Dryden's intervention with the Secretary of State, Sir William Trumbull, on behalf of a Catholic publisher who had got into trouble with the authorities for publishing and disseminating ‘several popish and seditious books’. The publisher's name was Thomas Metcalfe, his main crime was the publication of Constitutiones clericorum saecularium in commune viventium, and Dryden asks Trumbull to be lenient since Metcalfe is ‘a young man and this is his first offence’. Moreover Dryden predicts, that ‘upon asking pardon’ Metcalfe will promise to offend no more.
Prelates at War: Cardinal Bourne, Bishop Ward and the St. Edmund's College Cadet Corps Dispute
Authors: Foster Stewart
Published: February 2017

Ernest Oldmeadow, in the second volume of his biography—some have said hagiography—of Cardinal Bourne, begins the chapter in which he deals with the First World War with the following statement:

When the ‘Great’ War broke out, Cardinal Bourne was in a better position than that of some other religious leaders. Many of them, before calling their followers to fight with might and main against the enemy, had to recant or explain away their pacifist pasts. Some of them had pronounced all war unjustifiable, and had obstructed the training of their fatherland's manhood, even for defence. Not so Francis Bourne.
The Recusancy of Hamlet
Authors: Milward Peter
Published: February 2017

As Jane Austen would say, it is a truth universally acknowledged, even among Shakespeare scholars, that Shakespeare is the great enigma in English literature. To some extent this truth was partially covered up during the long period of Shakespeare scholarship when any discussion of Shakespeare's religion was considered taboo. But in the past couple of decades this taboo has been lifted to the extent that the theme proposed for the biennial Shakespeare Conference at Stratford in the year 2000 was ‘Shakespeare and Religions’. On the other hand, so far from resolving the Shakespearian enigma, the recent weakening of the taboo has only served to bring it more prominently into the foreground of scholarly attention and discussion. And of all the plays that may be said to centre on this enigma, it hardly needs to be said that Hamlet is not only one among many but the one play that may be called uniquely so—as being the most problematic of all Shakespeare's so-called ‘problem plays’.
The Making of a Convert: John Henry Newman's Oriel and Littlemore Experience
Authors: Nockles Peter
Published: February 2017

‘The flood is round thee, but thy towers as yet

Are safe, and clear as by a summer’s sea

…

Lo! On the top of each aerial spire

What seems a star by day, so high and bright

It quivers from afar in golden light.

But ‘tis a form of earth, though touched with fire

Celestial, raised in other days, to tell

How, when they tired of prayer, Apostles fell’.

John Henry Newman's poem ‘On Oxford’ published within a section called ‘Champions of the Truth’ in the verse collection, Lyra Apostolica, which he edited in 1836, encapsulates Newman's vision of Oxford and its colleges. Oxford was portrayed in the poem as an embattled but triumphant ‘city on a hill’ (in spite of its valley location surrounded by hills); a bulwark against contemporary forces, religious, and political, which for Newman, seemed to threaten it in the 1830s. The poem reminds us that the Oxford Movement, the great movement of religious revival within the Church of England commonly dated from 1833, the movement which Newman famously led and inspired, was rooted in Newman's keen and abiding sense of place (genius loci, as he put it), of memory, tradition, ethos, and association.
Religion, Politics, and the Parish in Tudor England and Wales: A View from the Marches of Wales, 1534–1553
Authors: Olson Katharine K.
Published: February 2017

Historians of early modern England benefit from a rich and varied array of contemporary accounts by individuals that shed light on the local, regional, and wider impact of religious and other policies of successive monarchs. These include the narrative of Robert Parkyn, a Yorkshire priest, of the years 1532–54, Rose Hickman's recollections of Protestant life during the reign of Mary Tudor, to the chronicle of Henry Machyn in 1550–1563, to name but a few. More broadly, too, the history of the book and its import in illuminating various aspects of medieval and early modern popular culture, devotion, piety, reading practices and other related topics has been widely recognised. They have been successfully mined in recent years by various scholars of medieval and early modern England, Ireland, and beyond, from Eamon Duffy to Salvador Ryan and Raymond Gillespie.
The Stuart Relics in the Stonyhurst Collections
Authors: Graffius Jan
Published: February 2017

The Stuart artefacts described in this article have not previously been examined as an entity, and many are relatively unfamiliar to scholars. This paper will consider this unique collection of relics and discuss their significance within the personal as well as national and international contexts of their origins. That significance rests largely in their royal provenance, which was valued by the custodians at the English Jesuit College of St Omers, the predecessor of Stonyhurst College, founded to educate English Catholic boys in 1593. The Stuart cause, from Mary Queen of Scots to Charles Edward Stuart represented the best hope of English Catholics for a formal restoration of the faith. Relics, such as Mary Queen of Scots’ Thorn, were powerful symbols of tenacity and hope, providing an unbroken thread from the Passion of Christ to the martyred Queen, the more valued as the College gained its own seventeenth-century martyrs. Artefacts which arrived at Stonyhurst College after 1794 were valued for their romantic association with the failed Stuart cause. The creation of the Stuart Parlour in 1911and the adoption of the Borrodale tartan as part of the girls’ uniform in the 1990s demonstrate the significance these objects possess well into the twentieth century.
‘The Condition and State of a Scholar’: Disputation in William Alabaster's Conversion Narrative
Authors: Rodda Joshua
Published: February 2017

This article examines the role of disputation in the conversion narrative of the clergyman and poet William Alabaster, written after he converted to Catholicism in the 1590s. Disputation, a mode of debate that had developed in the universities, is a preoccupation of the narrative, and is here used to place the work within the immediate history of religious disputation, and in the wider struggle over scholarship that accompanied post-Reformation religious controversy. The article asks why formal disputation was so important to religious writers and polemicists, drawing on Alabaster's perception of reason and its relationship to faith. It is asserted that the convert's eagerness for scholarly disputation arose from a fusion of religious with intellectual assurance: certainty in faith, and in the academic process. A comparison with examples taken from a long catalogue of works describing public, cross-confessional disputation is then used to enhance our understanding of Alabaster's influences; the building-blocks of his newfound religious identity. Taking Alabaster as its model, the article directs attention not only to the hitherto undervalued phenomenon of public or ‘professional’ religious disputation in post-Reformation England, but also to the role played by reason and scholarship in the thought and faith of Catholic—and Protestant—divines.
The Lady is a Catholic: Lady Lovell's Reply to Sir Edward Hoby
Authors: Hunt Arnold
Published: February 2017

The first decade of James I's reign saw a wave of high-profile clerical conversions to the Church of Rome. Among the best-known cases are those of James Wadsworth, who travelled to Spain with Sir Charles Cornwallis's embassy in 1605, where, as William Bedell's biographer Alexander Clogie disgustedly recalled, he was ‘cheated out of his religion by the Jesuits and turned apostate’; Theophilus Higgons, a member of Christ Church, Oxford, who converted in 1607; his friend and Oxford contemporary Humphrey Leech, who followed him in 1609 and later joined the Society of Jesus; and Benjamin Carier, a royal chaplain and prebendary of Canterbury, who converted in 1613. As the work of Michael Questier has taught us, religious conversion was by no means an uncommon phenomenon in early modern England. Yet these cases had the potential to inflict serious damage on the Jacobean church, not only because they threatened to neutralise the propaganda advantages to be gained from Roman Catholic converts to the Church of England such as Marc’ Antonio de Dominis, but also because they drew unwelcome attention to doctrinal divisions within the Church of England over such issues as anti-popery and the theology of grace.
Recusancy and the Rising Generation
Authors: Underwood Lucy
Published: February 2017

This article examines the involvement of young people in recusancy in Elizabethan England. It explores how two issues – the meaning of recusancy and the appeal of religion (specifically Catholicism) to youth – can illuminate each other. After looking at some of the evidence for the role of recusancy in juvenile experiences of Catholicism, the article focuses on three contrasting cases which illustrate young people's engagement with recusancy and Catholicism, and how it was interpreted by adult authorities, Catholic and Protestant: a case of recusant proselytising by the young men of a gentry household, as reported to the Privy Council; the alleged visions of fourteen-year-old Elizabeth Orton in Flintshire in 1581; and the autobiographical testimony of Robert Colton, a recusant youth imprisoned in London's Bridewell in 1595–6. It is argued that including recusancy will help us to better understand the complexity of youthful engagement with religion in early modern England, and also to appreciate the implications of recusancy.
The Library of Bryant Barrett, Laceman and Country Squire
Authors: Korsten Frans , Blom Jos , Blom Frans
Published: February 2017

Bryant Barrett (c.1715–1790) was a Catholic tradesman who managed to become affluent enough to be able to collect a library of nearly 2,000 volumes. His library catalogues are still extant and the aim of the present article is to analyse these in order to get an insight into the intellectual world of an eighteenth-century RC self-made man. There are a number of catalogues of institutional RC libraries and the occasional catalogue of an RC clergyman, but as far as we know the Barrett catalogues are a unique register of the books possessed by an ‘ordinary’ RC layman. The traditional picture of eighteenth-century English Catholic life is that of a dwindling community with a rather provincial and conservative outlook on life. Heroic martyrdom was a feature of the past: ordinary life entailed guarding against modern enlightenment views and – towards the end of the century – internal discussions about the concessions necessary to achieve Catholic emancipation. Barrett's library modifies this picture in a number of ways: it reveals an eminently practical man who was also an intellectual, someone interested in the past, loyal to his faith, knowledgeable about the latest developments in industry and science, intrigued by perspectives opening up through exploration and travel, fascinated with new developments and ideas. Barrett was a both a devout Roman Catholic and a well-read man of the world.
Mirage: an O(n) time analytical solution to 3D camera pose estimation with multi-camera support
Authors: Dinc Semih , Fahimi Farbod , Aygun Ramazan
Published: February 2017

Mirage is a camera pose estimation method that analytically solves pose parameters in linear time for multi-camera systems. It utilizes a reference camera pose to calculate the pose by minimizing the 2D projection error between reference and actual pixel coordinates. Previously, Mirage has been successfully applied to trajectory tracking (visual servoing) problem. In this study, a comprehensive evaluation of Mirage is performed by particularly focusing on the area of camera pose estimation. Experiments have been performed using simulated and real data on noisy and noise-free environments. The results are compared with the state-of-the-art techniques. Mirage outperforms other methods by generating fast and accurate results in all tested environments.
Rethinking the Cognitive Mechanisms Underlying Pantomime of Tool Use: Evidence from Alzheimer’s Disease and Semantic Dementia
Authors: Lesourd Mathieu , Baumard Josselin , Jarry Christophe , Etcharry-Bouyx Frédérique , Belliard Serge , Moreaud Olivier , Croisile Bernard , Chauviré Valérie , Granjon Marine , Le Gall Didier , Osiurak François
Published: February 2017

Objectives: Pantomiming the use of familiar tools is a central test in the assessment of apraxia. However, surprisingly, the nature of the underlying cognitive mechanisms remains an unresolved issue. The aim of this study is to shed a new light on this issue by exploring the role of functional, mechanical, and manipulation knowledge in patients with Alzheimer’s disease and semantic dementia and apraxia of tool use. Methods: We performed multiple regression analyses with the global performance and the nature of errors (i.e., production and conception) made during a pantomime of tool use task in patients and control participants as dependent variables and tasks investigating functional, mechanical, and manipulation knowledge as predictors. Results: We found that mechanical problem solving, assessing mechanical knowledge, was a good predictor of the global performance of pantomime of tool use. We also found that occurrence of conception errors was robustly predicted by the task assessing functional knowledge whereas that of production errors was not explained by only one predictor. Conclusions: Our results suggest that both functional and mechanical knowledge are important to pantomime the use of tools. To our knowledge, this is the first demonstration that mechanical knowledge plays a role in pantomime of tool use. Although impairment in pantomime of tool use tasks (i.e., apraxia) is widely explained by the disruption of manipulation knowledge, we propose that pantomime of tool use is a complex problem-solving task. (JINS, 2017, 23, 128–138)
Cognitive Control, Learning, and Clinical Motor Ratings Are Most Highly Associated with Basal Ganglia Brain Volumes in the Premanifest Huntington’s Disease Phenotype
Authors: Misiura Maria B. , Lourens Spencer , Calhoun Vince D. , Long Jeffrey , Bockholt Jeremy , Johnson Hans , Zhang Ying , Paulsen Jane S. , Turner Jessica A. , Liu Jingyu , Kara Betul , Fall Elizabeth ,   for the PREDICT-HD Investigators & Working Group
Published: February 2017

Objectives:Huntington’s disease (HD) is a debilitating genetic disorder characterized by motor, cognitive and psychiatric abnormalities associated with neuropathological decline. HD pathology is the result of an extended chain of CAG (cytosine, adenine, guanine) trinucleotide repetitions in theHTTgene. Clinical diagnosis of HD requires the presence of an otherwise unexplained extrapyramidal movement disorder in a participant at risk for HD. Over the past 15 years, evidence has shown that cognitive, psychiatric, and subtle motor dysfunction is evident decades before traditional motor diagnosis. This study examines the relationships among subcortical brain volumes and measures of emerging disease phenotype in prodromal HD, before clinical diagnosis.Methods:The dataset includes 34 cognitive, motor, psychiatric, and functional variables and five subcortical brain volumes from 984 prodromal HD individuals enrolled in the PREDICT HD study. Using cluster analyses, seven distinct clusters encompassing cognitive, motor, psychiatric, and functional domains were identified. Individual cluster scores were then regressed against the subcortical brain volumetric measurements.Results:Accounting for site and genetic burden (the interaction of age and CAG repeat length) smaller caudate and putamen volumes were related to clusters reflecting motor symptom severity, cognitive control, and verbal learning.Conclusions:Variable reduction of the HD phenotype using cluster analysis revealed biologically related domains of HD and are suitable for future research with this population. Our cognitive control cluster scores show sensitivity to changes in basal ganglia both within and outside the striatum that may not be captured by examining only motor scores. (JINS, 2017,23, 159–170)
Critical Motor Involvement in Prediction of Human and Non-biological Motion Trajectories
Authors: de Wit Matthieu M. , Buxbaum Laurel J.
Published: February 2017

Objectives: Adaptive interaction with the environment requires the ability to predict both human and non-biological motion trajectories. Prior accounts of the neurocognitive basis for prediction of these two motion classes may generally be divided into those that posit that non-biological motion trajectories are predicted using the same motor planning and/or simulation mechanisms used for human actions, and those that posit distinct mechanisms for each. Using brain lesion patients and healthy controls, this study examined critical neural substrates and behavioral correlates of human and non-biological motion prediction. Methods: Twenty-seven left hemisphere stroke patients and 13 neurologically intact controls performed a visual occlusion task requiring prediction of pantomimed tool use, real tool use, and non-biological motion videos. Patients were also assessed with measures of motor strength and speed, praxis, and action recognition. Results: Prediction impairment for both human and non-biological motion was associated with limb apraxia and, weakly, with the severity of motor production deficits, but not with action recognition ability. Furthermore, impairment for human and non-biological motion prediction was equivalently associated with lesions in the left inferior parietal cortex, left dorsal frontal cortex, and the left insula. Conclusions: These data suggest that motor planning mechanisms associated with specific loci in the sensorimotor network are critical for prediction of spatiotemporal trajectory information characteristic of both human and non-biological motions. (JINS, 2017, 23, 171–184)
EDITORIAL
Authors: DIERGARTEN FELIX
Published: February 2017

Quo vadis, eighteenth-century music analysis? This is the question I wish to pose in 2017, a year marking some notable anniversaries. It has been ten years since the appearance of Robert Gjerdingen's Music in the Galant Style (New York: Oxford University Press, 2007), a book that opened up a wide range of new perspectives on eighteenth-century music and simultaneously shook Anglo-American music analysis at a time when it was on the look-out for post-Schenkerian alternatives. Likewise, 2017 is the tenth anniversary of Giorgio Sanguinetti's presentation on Neapolitan partimenti at the European Music Analysis Conference in Freiburg, where he addressed an audience that was similarly looking for answers in a post-Riemannian vacuum (but already familiar with diverse approaches to schemata, or Satzmodelle). Thirdly, and on a personal note, 2017 also marks a decade since the publication of an article by Ludwig Holtmeier (‘Heinichen, Rameau, and the Italian Thoroughbass Tradition: Concepts of Tonality and Chord in the Rule of the Octave’, Journal of Music Theory 51/1 (2007), 5–49) that guided me through Fedele Fenaroli's partimenti by using the ‘rule of the octave’, a first encounter that profoundly and irreversibly affected the way I perform, hear, teach, conceptualize and contextualize eighteenth-century music. Finally, it should be said that all this happened fifteen years after Thomas Christensen described partimenti and ‘The Règle de l'Octave in Theory and Practice’ (Acta Musicologica 64 (1992), 91–117) in a forward-looking article that celebrates its twenty-fifth birthday in 2017.
Suicidal ideation and behaviour among community and health care seeking populations in five low- and middle-income countries: a cross-sectional study
Authors: Jordans M. , Rathod S. , Fekadu A. , Medhin G. , Kigozi F. , Kohrt B. , Luitel N. , Petersen I. , Shidhaye R. , Ssebunnya J. , Patel V. , Lund C.
Published: February 2017

Aims

Suicidal behaviour is an under-reported and hidden cause of death in most low- and middle-income countries (LMIC) due to lack of national systematic reporting for cause-specific mortality, high levels of stigma and religious or cultural sanctions. The lack of information on non-fatal suicidal behaviour (ideation, plans and attempts) in LMIC is a major barrier to design and implementation of prevention strategies. This study aims to determine the prevalence of non-fatal suicidal behaviour within community- and health facility-based populations in LMIC.

Methods

Twelve-month prevalence of suicidal ideation, plans and attempts were established through community samples (n = 6689) and primary care attendees (n = 6470) from districts in Ethiopia, Uganda, South Africa, India and Nepal using the Composite International Diagnostic Interview suicidality module. Participants were also screened for depression and alcohol use disorder.

Results

We found that one out of ten persons (10.3%) presenting at primary care facilities reported suicidal ideation within the past year, and 1 out of 45 (2.2%) reported attempting suicide in the same period. The range of suicidal ideation was 3.5–11.1% in community samples and 5.0–14.8% in health facility samples. A higher proportion of facility attendees reported suicidal ideation than community residents (10.3 and 8.1%, respectively). Adults in the South African facilities were most likely to endorse suicidal ideation (14.8%), planning (9.5%) and attempts (7.4%). Risk profiles associated with suicidal behaviour (i.e. being female, younger age, current mental disorders and lower educational and economic status) were highly consistent across countries.

Conclusion

The high prevalence of suicidal ideation in primary care points towards important opportunities to implement suicide risk reduction initiatives. Evidence-supported strategies including screening and treatment of depression in primary care can be implemented through the World Health Organization's mental health Global Action Programme suicide prevention and depression treatment guidelines. Suicidal ideation and behaviours in the community sample will require detection strategies to identify at risks persons not presenting to health facilities.
The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies
Authors: Li Zenggang , Ivanov Andrei A. , Su Rina , Gonzalez-Pecchi Valentina , Qi Qi , Liu Songlin , Webber Philip , McMillan Elizabeth , Rusnak Lauren , Pham Cau , Chen Xiaoqian , Mo Xiulei , Revennaugh Brian , Zhou Wei , Marcus Adam , Harati Sahar , Chen Xiang , Johns Margaret A. , White Michael A. , Moreno Carlos S. , Cooper Lee A. D. , Du Yuhong , Khuri Fadlo R. , Fu Haian
Published: February 2017

As genomics advances reveal the cancer gene landscape, a daunting task is to understand how these genes contribute to dysregulated oncogenic pathways. Integration of cancer genes into networks offers opportunities to reveal protein–protein interactions (PPIs) with functional and therapeutic significance. Here, we report the generation of a cancer-focused PPI network, termed OncoPPi, and identification of >260 cancer-associated PPIs not in other large-scale interactomes. PPI hubs reveal new regulatory mechanisms for cancer genes like MYC, STK11, RASSF1 and CDK4. As example, the NSD3 (WHSC1L1)–MYC interaction suggests a new mechanism for NSD3/BRD4 chromatin complex regulation of MYC-driven tumours. Association of undruggable tumour suppressors with drug targets informs therapeutic options. Based on OncoPPi-derived STK11-CDK4 connectivity, we observe enhanced sensitivity of STK11-silenced lung cancer cells to the FDA-approved CDK4 inhibitor palbociclib. OncoPPi is a focused PPI resource that links cancer genes into a signalling network for discovery of PPI targets and network-implicated tumour vulnerabilities for therapeutic interrogation.