bluuebunny/crossref_metadata_2025 huggingface dataset:
Haemoglobin expression in in vivo murine preimplantation embryos suggests a role in oxygen-regulated gene expression
Authors: Lim M. , Brown H. M. , Kind K. L. , Breen J. , Anastasi M. R. , Ritter L. J. , Tregoweth E. K. , Dinh D. T. , Thompson J. G. , Dunning K. R.
Published: November 2018

Haemoglobin expression is not restricted to erythroid cells. We investigated the gene expression of the haemoglobin subunits haemoglobin, alpha adult chain 1 (Hba-a1) and haemoglobin, beta (Hbb), 2,3-bisphosphoglycerate mutase (Bpgm) and the oxygen-regulated genes BCL2/adenovirus E1B interacting protein 3 (Bnip3), solute carrier family 2 (facilitated glucose transporter), member 1 (Slc2a1) and N-myc downstream regulated gene 1 (Ndrg1) in the murine preimplantation embryo, comparing invivo to invitro gene expression. Relatively high levels of Hba-a1 and Hbb were expressed invivo from the 2-cell to blastocyst stage; in contrast, little or no expression occurred invitro. We hypothesised that the presence of haemoglobin invivo creates a low oxygen environment to induce oxygen-regulated gene expression, supported by high expression of Slc2a1 and Ndrg1 in invivo relative to invitro embryos. In addition, analysis of an invitro-derived human embryo gene expression public dataset revealed low expression of haemoglobin subunit alpha (HBA) and HBB, and high expression of BPGM. To explore whether there was a developmental stage-specific effect of haemoglobin, we added exogenous haemoglobin either up to the 4-cell stage or throughout development to the blastocyst stage, but observed no difference in blastocyst rate or the inner cell mass to trophectoderm cell ratio. We conclude that haemoglobin in the invivo preimplantation embryo raises an interesting premise of potential mechanisms for oxygen regulation, which may influence oxygen-regulated gene expression.
Realigning alignment
Authors: Bardagil-Mas Bernat , Lindenbergh Charlotte
Published: November 2018

We analyse case marking in the Jê language family (Brazilian Amazonia) with the new completeness alignment typology proposed byLindenbergh & Zwart (2017). In contrast with classical alignment typology, the completeness typology first determines whether all grammatical functions participate in a grammatical process (e.g. case marking) and only then determines how these grammatical functions are aligned, adding nine incomplete alignment types to the five types of classical alignment typology. Nine of the ten Jê languages are classified as split-ergative, while Panará is seen as fully ergative, making it a typologically odd language within the family. We show that applying the completeness typology to Jê languages more accurately describes the true variation in case marking patterns across the Jê language family.
Gender-mismatching pronouns in context
Authors: Piepers Joske , Redl Theresa
Published: November 2018

Gender-(mis)matching pronouns have been studied extensively in experiments. However, a phenomenon common to various languages has thus far been overlooked: the systemic use of non-feminine pronouns when referring to female individuals. The present study is the first to provide experimental insights into the interpretation of such a pronoun: Limburgian zien ‘his/its’ and Dutch zijn ‘his/its’ are grammatically ambiguous between masculine and neuter, but while Limburgian zien can refer to women, the Dutch equivalent zijn cannot. Employing an acceptability judgment task, we presented speakers of Limburgian (N = 51) with recordings of sentences in Limburgian featuring zien, and speakers of Dutch (N = 52) with Dutch translations of these sentences featuring zijn. All sentences featured a potential male or female antecedent embedded in a stereotypically male or female context. We found that ratings were higher for sentences in which the pronoun could refer back to the antecedent. For Limburgians, this extended to sentences mentioning female individuals. Context further modulated sentence appreciation. Possible mechanisms regarding the interpretation of zien as coreferential with a female individual will be discussed.
Empathy for the inanimate
Authors: Trompenaars Thijs
Published: November 2018

Narrative fiction may invite us to share the perspective of characters which are very much unlike ourselves. Inanimate objects featuring as protagonists or narrators are an extreme example of this. The way readers experience these characters was examined by means of a narrative immersion study. Participants (N = 200) judged narratives containing animate or inanimate characters in predominantly Agent or Experiencer roles. Narratives with inanimate characters were judged to be less emotionally engaging. This effect was influenced by the dominant thematic role associated with the character: inanimate Agents led to more defamiliarization compared to their animate counterparts than inanimate Experiencers. I argue for an integrated account of thematic roles and animacy in literary experience and linguistics in general.
Have-doubling constructions in historical and modern Dutch
Authors: Wall Joanna
Published: November 2018

Have-doubling constructions closely resemble periphrastic perfect tense constructions but have an additional, seemingly superfluous form of the verb have. Whilst these constructions are only found in a small number of modern Dutch dialects, they appear much more broadly in historical varieties of Dutch. In this article, I present new data from a corpus study of have-doubling constructions in Early Modern Dutch (ca. 1500-1700) which reveals both similarities and an important difference with the modern dialectal phenomenon. I argue that there are two structurally distinct types of have-doubling in this older period: one which contains a canonical adjective (i.e. with one internal argument) and one with a non-canonical adjective with a vP layer (Koeneman et al. 2011). I further show that this sheds new light on the observed link between doubling constructions and the rise of the periphrastic perfect tenses, with implications for the nature of this syntactic development.
A cross-linguistic study of new populist language
Authors: Lorenzetti Maria Ivana
Published: November 2018

This paper presents an analysis of the rhetorical strategies of some European and American politicians associated with the inherently ambiguous concept of populism. The theoretical framework adopted combines text linguistics and critical discourse analysis and has an interdisciplinary character. The data analysed demonstrate that populist rhetorical strategies do not differ markedly from those typically employed in political rhetoric. While each populist politician evokes a specific identity narrative to create common ground with the electorate, they all emphasise a profound dualism in society between “us and them” through metaphors, hyperboles, and personifications. This dichotomous view of society is sometimes exploited to send ambivalent messages of potential discrimination.
Understanding urban intervention as a translational activity
Authors: Ayhan Ayşe , Demirel Emine Bogenç
Published: November 2018

This article aims to examine Yeldeğirmeni, a historically multilingual and multicultural neighborhood in Istanbul, as a translation zone. The language landscape of Yeldeğirmeni, along with its social and cultural texture, has been transformed by both social and political changes in Turkey, and as a result of urban interventions by institutional and individual actors. We discuss the Yeldeğirmeni Revitalization Project and Mural Istanbul Festival as urban interventions that transform the social and cultural texture of the city in translation zones, owing to the significant role played by cultural mediators. Yeldeğirmeni is analyzed as a discourse in the context of cultural translation, and urban intervention is viewed as a medium of translation.
Forensic Afterlives
Authors: Crossland Zoë
Published: November 2018

The practices involved in forensic investigation center on a search for physical clues and traces that may be used to reconstruct past events. The forensic corpse is therefore involved in a materially grounded semiotics, which provides the basis for making claims about the past. Using the examples of forensic pattern matching (such as craniofacial mapping and fingerprints) and forensic entomology, I explore the different life worlds that emerge after a person’s death and how they are mobilized by forensic investigators. In this form of inquiry, claims to the real are articulated through the signs that different beings—whether human, insect, or microbe—perceive inhering in the corpse. Such forms of forensic investigation offer a productive site for thinking about the ontological status of fact and of the corpse in the context of posthumanism. Forensic signs stretch across our divided categories of the living and the dead, human and animal, nature and culture, providing alternate ways to conceptualize the relationships at play in such assemblages.
Undecontextualizable: Performativity and the Conditions of Possibility of Linguistic Symbolism
Authors: Fleming Luke
Published: November 2018

In this article I argue that the canceling out (or defeasing) of performative indexical functions is a condition of possibility on linguistic symbolism. I show this to be the case by looking at words and expressions—like curse words and name taboos—whose performative functions can be canceled out only with the greatest of metalinguistic labor. I show that these indefeasible or rigid performatives are the semiotic-functional converses of J. L. Austin’s explicit performatives (e.g., “promise,” “bequeath”) in terms of (i) the orders of regimentation between semantic-symbolic and pragmatic-indexical functions, (ii) the indexical anchoring of pragmatic effects within either denotationally mediated events-of-narration (En) or interactionally mediated events-of-signaling (Es), and (iii) the articulation of indexical function with speech participant roles. The article concludes with a reflection on how the architecture of the phonology-semantics interface (or duality of patterning) safeguards symbolism by impeding the processes of runaway semiotic naturalization that produce rigid performativity.
Linguistic Prerequisites to Cultural Analysis: Lars Levander’s Reocentric Vision of Vernacular Language and Swedish Peasant Life
Authors: Karlander David
Published: November 2018

This article takes interest in reocentric thinking, as well as in the ways such thinking is brought to bear on research on language and social life. Reocentric thinking, understood as referential theories that treat words as standing for things, is pervasive throughout the history of (Western) linguistic thought. Yet, its manifestations in descriptive linguistic research are scantly explored. Seeking to account for how a reocentric vision of language and social life is realized and concomitantly adapted in scholarly practice, the article analyses the research of Swedish linguist and folklorist Lars Levander (1883–1950). Levander spent most of his life documenting the vernacular languages and peasant life of Sweden’s Dalarna province. His assumptions about the relationship between words and things, as this article argues, significantly guided his research practice. Furthermore, they served to conceptualize, and concomitantly capture, certain configurations of time and vernacular authenticity. The article seeks, accordingly, to grasp the dialectic between Levander’s epistemic presuppositions and his scholarly production. More broadly, the article’s historical, epistemological mode of engagement exemplifies how early and potentially ingrained apprehensions of language, as well as their epistemic prerequisites and effects, can be understood and rectified.
Cycle doubling, merging, and renormalization in the tangent family
Authors: Chen Tao , Jiang Yunping , Keen Linda
Published: November 2018

In this paper we study the transition to chaos for the restriction to the real and imaginary axes of the tangent family

{

T
t

(
z
)
=
i
t
tan
⁡
z

}

0
>
t
≤
π

\{ T_t(z)=i t\tan z\}_{0> t\leq \pi }

. Because tangent maps have no critical points but have an essential singularity at infinity and two symmetric asymptotic values, there are new phenomena: as

t
t

increases we find single instances of “period quadrupling”, “period splitting”, and standard “period doubling”; there follows a general pattern of “period merging” where two attracting cycles of period

2
n

2^n

“merge” into one attracting cycle of period

2

n
+
1

2^{n+1}

, and “cycle doubling” where an attracting cycle of period

2

n
+
1

2^{n+1}

“becomes” two attracting cycles of the same period.

We use renormalization to prove the existence of these bifurcation parameters. The uniqueness of the cycle doubling and cycle merging parameters is quite subtle and requires a new approach. To prove the cycle doubling and merging parameters are, indeed, unique, we apply the concept of “holomorphic motions” to our context.

In addition, we prove that there is an “infinitely renormalizable” tangent map

T

t
∞

T_{t_\infty }

. It has no attracting or parabolic cycles. Instead, it has a strange attractor contained in the real and imaginary axes which is forward invariant and minimal under

T

t
∞

2

T^2_{t_\infty }

. The intersection of this strange attractor with the real line consists of two binary Cantor sets and the intersection with the imaginary line is totally disconnected, perfect, and unbounded.
A structural homology approach for computational protein design with flexible backbone
Authors: Simoncini David , Zhang Kam Y J , Schiex Thomas , Barbe Sophie
Published: November 2018

Motivation

Structure-based Computational Protein design (CPD) plays a critical role in advancing the field of protein engineering. Using an all-atom energy function, CPD tries to identify amino acid sequences that fold into a target structure and ultimately perform a desired function. Energy functions remain however imperfect and injecting relevant information from known structures in the design process should lead to improved designs.

Results

We introduce Shades, a data-driven CPD method that exploits local structural environments in known protein structures together with energy to guide sequence design, while sampling side-chain and backbone conformations to accommodate mutations. Shades (Structural Homology Algorithm for protein DESign), is based on customized libraries of non-contiguous in-contact amino acid residue motifs. We have tested Shades on a public benchmark of 40 proteins selected from different protein families. When excluding homologous proteins, Shades achieved a protein sequence recovery of 30% and a protein sequence similarity of 46% on average, compared with the PFAM protein family of the target protein. When homologous structures were added, the wild-type sequence recovery rate achieved 93%.

Availability and implementation

Shades source code is available at https://bitbucket.org/satsumaimo/shades as a patch for Rosetta 3.8 with a curated protein structure database and ITEM library creation software.

Supplementary information

Supplementary data are available at Bioinformatics online.
Intercalibration of survey methods using paired fishing operations and log-Gaussian Cox processes
Authors: Thygesen Uffe Høgsbro , Kristensen Kasper , Jansen Teunis , Beyer Jan E
Published: November 2018

We present a statistical method for intercalibration of fishery surveys methods, i.e. determining the difference in catchability and size selectivity of two methods, such as trawl gears or vessels, based on data from paired fishing operations. The model estimates the selectivity ratios in each length class by modelling the size distribution of the underlying population at each station and the size-structured clustering of fish at small temporal and spatial scales. The model allows for overdispersion and correlation between catch counts in neighbouring size classes. This is obtained by assuming Poisson-distributed catch numbers conditional on unobserved log-Gaussian variables, i.e. the catch is modelled using log-Gaussian Cox processes. We apply the method to catches of hake (Merluccius paradoxus and M. capensis) in 341 paired trawl hauls performed by two different vessels, viz. the RV Dr Fridtjof Nansen and the FV Blue Sea, operating off the coast of Namibia. The results demonstrate that it is feasible to estimate the selectivity ratio in each size class, and to test statistically the hypothesis that the selectivity is independent of size or species. For the specific case, we find that differences between size classes and species are statistically significant.
Progressive disseminated histoplasmosis in Latin America and the Caribbean in people receiving highly active antiretroviral therapy for HIV infection: A systematic review
Authors: Cano-Torres J Oggun , Olmedo-Reneaum Alejandro , Esquivel-Sánchez José M , Camiro-Zuñiga Antonio , Pérez-Carrisoza Arely , Madrigal-Iberri Carlos , Flores-Miranda Rommel , Ramírez-González Luis E , Belaunzarán-Zamudio Pablo F
Published: November 2018

Histoplasmosis is the most clinically significant mycosis in Latin America; still it has been neglected in people with human immunodeficiency virus (HIV). There is limited information about its contribution to morbidity and mortality in this population. We conducted a systematic review of scientific literature to provide an estimation of the frequency and mortality of histoplasmosis among people with HIV receiving highly active antiretroviral therapy (HAART) in Latin America, and factors associated with mortality. We searched articles in PubMed, Scopus, WHO Global health library, and Scielo using different combination of terms including “histoplasmosis” and HAART. We identified 949 articles, removed 662 duplicated; screened 287 abstracts; reviewed full text of 53 articles; and selected 15 articles that provided information on the number of patients studied, included patients receiving ART, and reported any measure of frequency estimate for qualitative synthesis. Studies were conducted in Argentina (n = 4), Brazil (n = 6), Colombia (n = 2), French Guyana and the Bahamas (=2), and Guatemala (n = 1). Heterogeneity of studies characteristics precluded any aggregated estimates. Histoplamosis was frequent in these cohort studies and mortality was high despite the use of HAART. Low CD4 counts, delayed HAART initiation and poor adherence were related to increased incidence, poor prognosis and increased mortality, respectively. Histoplasmosis may be an important contributor to mortality in people with HIV in Latin America. Diagnostic delays represent an important limitation for improving care of patients suspected to have histoplasmosis. Reducing histoplasmosis diagnostic delays and therapy initiation is needed to further decrease mortality.
Neuroendoscopic Aspiration of Blood Clots in the Cerebral Aqueduct and Third Ventricle During Posterior Fossa Surgery in the Prone Position
Authors: Feletti Alberto , Stanzani Riccardo , Alicandri-Ciufelli Matteo , Giliberto Giuliano , Martinoni Matteo , Pavesi Giacomo
Published: November 2018

BACKGROUND

During surgery in the posterior fossa in the prone position, blood can sometimes fill the surgical field, due both to the less efficient venous drainage compared to the sitting position and the horizontally positioned surgical field itself. In some cases, blood clots can wedge into the cerebral aqueduct and the third ventricle, and potentially cause acute hydrocephalus during the postoperative course.

OBJECTIVE

To illustrate a technique that can be used in these cases: the use of a flexible scope introduced through the opened roof of the fourth ventricle with a freehand technique allows the navigation of the fourth ventricle, the cerebral aqueduct, and the third ventricle in order to explore the cerebrospinal fluid pathways and eventually aspirate blood clots and surgical debris.

METHODS

We report on one patient affected by an ependymoma of the fourth ventricle, for whom we used a flexible neuroendoscope to explore and clear blood clots from the cerebral aqueduct and the third ventricle after the resection of the tumor in the prone position. Blood is aspirated with a syringe using the working channel of the scope as a sucker.

RESULTS

A large blood clot that was lying on the roof of the third ventricle was aspirated, setting the ventricle completely free. Other clots were aspirated from the right foramen of Monro and from the optic recess.

CONCLUSION

We describe this novel technique, which represents a safe and efficient way to clear the surgical field at the end of posterior fossa surgery in the prone position. The unusual endoscopic visual perspective and instrument maneuvers are easily handled with proper neuroendoscopic training.
Filtered finiteness of the image of the unstable Hurewicz homomorphism with applications to bordism of immersions
Authors: Zare Hadi
Published: November 2018

After recent work of Hill, Hopkins and Ravenel on the Kervaire invariant one problem [M. A. Hill, M. J. Hopkins and D. C. Ravenel, On the non-existence of elements of Kervaire invariant one, Ann. Math. (2), 184 (2016), 1–262], as well as Adams’ solution of the Hopf invariant one problem [J. F. Adams, On the non-existence of elements of Hopf invariant one, Ann. Math. (2), 72 (1960), 20–104], an immediate consequence of Curtis conjecture is that the set of spherical classes in H∗Q0S0 is finite. Similarly, Eccles conjecture, when specialized to X=Sn with n> 0, together with Adams’ Hopf invariant one theorem, implies that the set of spherical classes in H∗QSn is finite. We prove a filtered version of the above finiteness properties. We show that if X is an arbitrary CW-complex of finite type such that for some n, HiX≃0 for any i>n, then the image of the composition π∗ΩlΣl+2X→π∗QΣ2X→H∗QΣ2X is finite; the finiteness remains valid if we formally replace X with S−1. As an application, we provide a lower bound on the dimension of the sphere of origin on the potential classes of π∗QSn which are detected by homology. We derive a filtered finiteness property for the image of certain transfer maps ΣdimgBG+→QS0 in homology. As an application to bordism theory, we show that for any codimension k framed immersion f:M↬ℝn+k which extends to an embedding M→ℝd×ℝn+k, if n is very large with respect to d and k then the manifold M as well as its self-intersection manifolds are boundaries. Some results of this paper extend results of Hadi [Spherical classes in some finite loop spaces of spheres. Topol. Appl., 224 (2017), 1–18] and offer corrections to some minor computational mistakes, hence providing corrected upper bounds on the dimension of spherical classes H∗ΩlSn+l. All of our results are obtained at the prime p = 2.
Intrinsic pre-zygotic reproductive isolation of distantly related pea aphid host races
Authors: Fazalova Varvara , Nevado Bruno , McLean Ailsa , Godfray H. Charles J.
Published: November 2018

Human activities may weaken or destroy reproductive isolation between young taxa, leading to their fusion with consequences for population and community ecology. Pea aphid host races are adapted to different legume taxa, providing a degree of pre-mating isolation mediated by habitat choice. Yet, all races can feed and reproduce on the broad bean (
Vicia faba
), a major crop which represents a ‘universal host plant’, which can promote hybridization between races. Here, we ask if pea aphid host races have reproductive barriers which prevent or reduce gene flow when they co-occur on the universal host plant. We observed mating behaviour, female survival, number of eggs and egg fertilization rates for three types of crosses: among individuals of the same host race, between closely related host races and between distantly related host races. We did not find significant differences in mating behaviour and female survival among the three types of crosses. However, we observed a drastic reduction in the number of eggs laid, and in the number of fertilized eggs, in distant crosses. We conclude that widespread broad bean cultivation in agriculture may predispose closely related—but not distantly related—host races to hybridize, disrupting reproductive isolation between incipient species.
Microplastic leachates impair behavioural vigilance and predator avoidance in a temperate intertidal gastropod
Authors: Seuront Laurent
Published: November 2018

Microplastics are a ubiquitous source of contaminations in marine ecosystems, and have major implications for marine life. Much effort has been devoted to assessing the various effects of microplastics on marine life. No evidence exists, however, on the effects of microplastic leachates on chemically mediated predator–prey interactions and the ability of prey to detect and avoid its predator. This study shows that microplastic leachates have direct biological effects by disturbing the behavioural response of the intertidal gastropod
Littorina littorea
to the presence of
Carcinus maenas
chemical cues, hence increasing their vulnerability to predation. Leachates from virgin and beached pellets respectively impaired and inhibited
L. littorea
vigilance and antipredator behaviours. These results suggest that the biological effects from microplastic leachates may have major implications for marine ecosystems on taxa that rely on chemosensory cues to escape predation.
Differential response to heat stress among evolutionary lineages of an aquatic invertebrate species complex
Authors: Paraskevopoulou Sofia , Tiedemann Ralph , Weithoff Guntram
Published: November 2018

Under global warming scenarios, rising temperatures can constitute heat stress to which species may respond differentially. Within a described species, knowledge on cryptic diversity is of further relevance, as different lineages/cryptic species may respond differentially to environmental change. The
Brachionus calyciflorus
species complex (Rotifera), which was recently described using integrative taxonomy, is an essential component of aquatic ecosystems. Here, we tested the hypothesis that these (formerly cryptic) species differ in their heat tolerance. We assigned 47 clones with nuclear ITS1 (nuITS1) and mitochondrial COI (mtCOI) markers to evolutionary lineages, now named
B. calyciflorus
sensu stricto (s.s.) and
B. fernandoi
. We selected 15 representative clones and assessed their heat tolerance as a bi-dimensional phenotypic trait affected by both the intensity and duration of heat stress. We found two distinct groups, with
B. calyciflorus
s.s. clones having higher heat tolerance than the novel species
B. fernandoi
. This apparent temperature specialization among former cryptic species underscores the necessity of a sound species delimitation and assignment, when organismal responses to environmental changes are investigated.
More partners, more ranges: generalist legumes spread more easily around the globe
Authors: Harrison Tia L. , Simonsen Anna K. , Stinchcombe John R. , Frederickson Megan E.
Published: November 2018

How does mutualism affect range expansion? On the one hand, mutualists might thrive in new habitats thanks to the resources, stress tolerance or defence provided by their partners. On the other, specialized mutualists might fail to find compatible partners beyond their range margins, limiting further spread. A recent global analysis of legume ranges found that non-symbiotic legumes have been successfully introduced to more ranges than legumes that form symbioses with rhizobia, but there is still abundant unexplained variation in introduction success within symbiotic legumes. We test the hypothesis that generalist legumes have spread to more ranges than specialist legumes. We used published data and rhizobial 16S rRNA sequences from GenBank to quantify the number of rhizobia partners that associate with 159 legume species, spanning the legume phylogeny and the globe. We found that generalist legumes occur in more introduced ranges than specialist legumes, suggesting that among mutualists, specialization hinders range expansions.
Sex mosaics in the honeybee: how haplodiploidy makes possible the evolution of novel forms of reproduction in social Hymenoptera
Authors: Aamidor Sarah E. , Yagound Boris , Ronai Isobel , Oldroyd Benjamin P.
Published: November 2018

Hymenoptera are haplodiploid: females arise from fertilized, diploid eggs, while males arise from unfertilized, haploid eggs. The cytogenetic mechanisms underlying haplodiploidy enable remarkable phenomena including female cloning, male cloning and gynandromorphy (sex mosaics). We collected 11 newly emerged putative gynandromorph honeybees from a single colony, assessed the sex of various tissues morphologically and determined the genetic origin (maternal or paternal) of each tissue by genotyping. Ten bees were gynandromorphs with one to three distinct paternal origins. Remarkably, one bee carried no maternal alleles. This bee had female organs throughout, and arose from the fusion of two sperm nuclei. This is the first reported case in the Hymenoptera of sperm fusion resulting in a female, emphasizing the flexibility for social insect reproduction and potentially novel colony-level social structures.
Alan Cowey. 28 April 1935—19 December 2012
Authors: Passingham Dick
Published: November 2018

Alan Cowey's primary interest was in the way in which we interpret the visual world. This led him to study not only the early visual areas but also the inferotemporal and parietal cortex with which they are connected and the further projections into the eye field in the prefrontal cortex. His research interests were wide, covering colour vision, attention, visual neglect and the anatomical basis of the visual abilities that can be spared after a lesion in the primary visual cortex. Alan spent over 40 years at the University of Oxford, where he was involved in many initiatives and served on many committees, playing many important roles in the development of neuroscience as an interdisciplinary field of research.
Sir Bernard Crossland CBE. 20 October 1923—17 January 2011
Authors: Burdekin Michael
Published: November 2018

Bernard Crossland was one of the UK's most eminent engineers and an inspirational figure in his profession. He was a leading expert in materials and structural integrity, applied particularly to thick-walled pressure vessels and explosive welding. After an initial period with Rolls-Royce, his early academic career was at the University of Bristol where he developed his research into strength of thick cylinders under high pressure. He was appointed Professor of Mechanical Engineering and head of that department at Queen's University Belfast in 1959 at the age of 35, and he proceeded to transform both teaching and research in that department over the next 23 years. He continued his research into behaviour of thick-walled pressure vessels and also started research into explosive welding and forming in Belfast.

After his retirement from QUB he was appointed as an expert adviser or expert witness in a number of high-profile disaster inquiries, including the King's Cross Underground fire in 1987, the Bilsthorpe Colliery roof collapse in 1993 and the Ramsgate Ferry walkway collapse in 1994. He took a major part in professional affairs in engineering and was president of the Institution of Mechanical Engineers in 1986/87. He was knighted in 1990 for Services to Education and Industry in Northern Ireland and was presented with the Sustained Achievement Award of the Royal Academy of Engineering in 2010.
Enhanced locomotion, effective diffusion and trapping of undulatory micro-swimmers in heterogeneous environments
Authors: Kamal Arshad , Keaveny Eric E.
Published: November 2018

Swimming cells and microorganisms must often move through complex fluids that contain an immersed microstructure such as polymer molecules or filaments. In many important biological processes, such as mammalian reproduction and bacterial infection, the size of the immersed microstructure is comparable to that of the swimming cells. This leads to discrete swimmer–microstructure interactions that alter the swimmer’s path and speed. In this paper, we use a combination of detailed simulation and data-driven stochastic models to examine the motion of a planar undulatory swimmer in an environment of spherical obstacles tethered via linear springs to random points in the plane of locomotion. We find that, depending on environmental parameters, the interactions with the obstacles can enhance swimming speeds or prevent the swimmer from moving at all. We also show how the discrete interactions produce translational and angular velocity fluctuations that over time lead to diffusive behaviour primarily due to the coupling of swimming and rotational diffusion. Our results demonstrate that direct swimmer–microstructure interactions can produce changes in swimmer motion that may have important implications for the spreading of cell populations in or the trapping of harmful pathogens by complex fluids.
Survey stories in the history of British polar exploration: museums, objects and people
Authors: Connelly Charlotte , Warrior Claire
Published: November 2018

This essay considers the two institutions that, between them, contain the most significant collections relating to British polar exploration in the UK: the Scott Polar Research Institute and the National Maritime Museum. A discussion of the differences between the two institutions, from their foundations to the substance of their collections, is followed by an indication of their similarities—particularly relating to the interpretation of the objects of exploration in museums, including artefacts of science and surveying. Histories of exploration, particularly in the polar regions, have been dominated by stories of individual sacrifice and achievement. This is despite the origins of many of the expeditions being rooted in scientific goals. This paper considers the role of survey stories within narratives of exploration, and the challenges that curators face in presenting them to audiences who continue to be drawn in by stories of well-known figures such as Scott and Amundsen.
Hand-in-hand with the survey: surveying and the accumulation of knowledge capital at India House during the Napoleonic Wars
Authors: Ratcliff Jessica
Published: November 2018

In the early nineteenth century, the material culture of British science was being transformed by an increasingly centralized colonial information order. Surveys conducted during and immediately after the Napoleonic Wars were particularly important to the growth of the East India Company's new collections in London. In the wake of territorial gains, surveyors and their staff bought, plundered, collected and otherwise acquired a wide range of materials related to arts, sciences, history, natural history and literature. Focusing on survey collections formed in Ceylon, Mysore and Java between 1795 and 1820, this essay explores the place of the Company's culture of surveying and collecting within both Company science and wider shifts in the political economy of colonial collecting. Such shifts include changes in property claims, the growing clout of the Company's library and museum in London and, most importantly, the Napoleonic Wars. The wartime context enabled not only basic access to new materials but also cheap modes of collection and a motive to collect—or to value collections—driven by commercial and territorial competition.
2017 Wilkins–Bernal–Medawar Lecture: why philosophy of science matters to science
Authors: Massimi Michela
Published: November 2018

In an era where science is increasingly specialized, what is the value of interdisciplinary research? I argue that research across disciplinary boundaries plays a pivotal role in scientific inquiry, and it has a threefold value: it is
exploratory
; it is
unifying
; and it offers
critical engagement
. Philosophy of science is an interesting example of interdisciplinary research at the junction between the sciences and the humanities. What good can philosophy of science do for science? Despite anecdotal reports to the contrary, philosophy of science can in fact do important work for science. When it comes to critical engagement, I highlight what I call the
social function of philosophy of science
and I illustrate it with three examples taken from contemporary debates about evidence, progress and truth in science. A socially responsible philosophy of science—which is not afraid to speak up for evidence, progress and truth in science—best serves the needs of science in a tolerant, pluralist and democratic society.
Culturally transmitted song exchange between humpback whales (
Megaptera novaeangliae
) in the southeast Atlantic and southwest Indian Ocean basins
Authors: Rekdahl Melinda L. , Garland Ellen C. , Carvajal Gabriella A. , King Carissa D. , Collins Tim , Razafindrakoto Yvette , Rosenbaum Howard
Published: November 2018

In migratory marine species, investigating population connectivity and structure can be challenging given barriers to dispersal are less evident and multiple factors may influence individual movement patterns. Male humpback whales sing a song display that can provide insights into contemporary connectivity patterns, as there can be a cultural exchange of a single, population-wide shared song type with neighbouring populations in acoustic contact. Here, we investigated song exchange between populations located on the east and west coasts of Africa using 5 years of concurrent data (2001–2005). Songs were qualitatively and quantitatively transcribed by measuring acoustic features of all song units and then compared using both Dice’s similarity index and the Levenshtein distance similarity index (LSI) to quantitatively calculate song similarity. Song similarity varied among individuals and potentially between populations depending on the year (Dice: 36–100%, LSI: 21–100%), suggesting varying levels of population connectivity and/or interchange among years. The high degree of song sharing indicated in this study further supports genetic studies that demonstrate interchange between these two populations and reinforces the emerging picture of broad-scale connectivity in Southern Hemisphere populations. Further research incorporating additional populations and years would be invaluable for better understanding of fine-scale, song interchange patterns between Southern Hemisphere male humpback whales.
Copper/carbon nanotube composites: research trends and outlook
Authors: Sundaram Rajyashree M. , Sekiguchi Atsuko , Sekiya Mizuki , Yamada Takeo , Hata Kenji
Published: November 2018

We present research progress made in developing copper/carbon nanotube composites (Cu/CNT) to fulfil a growing demand for lighter copper substitutes with superior electrical, thermal and mechanical performances. Lighter alternatives to heavy copper electrical and data wiring are needed in automobiles and aircrafts to enhance fuel efficiencies. In electronics, better interconnects and thermal management components than copper with higher current- and heat-stabilities are required to enable device miniaturization with increased functionality. Our literature survey encouragingly indicates that Cu/CNT performances (electrical, thermal and mechanical) reported so far rival that of Cu, proving the material's viability as a Cu alternative. We identify two grand challenges to be solved for Cu/CNT to replace copper in real-life applications. The first grand challenge is to fabricate Cu/CNT with overall performances exceeding that of copper. To address this challenge, we propose research directions to fabricate Cu/CNT closer to ideal composites theoretically predicted to surpass Cu performances (i.e.
those containing uniformly distributed Cu and individually aligned CNTs with beneficial CNT–Cu interactions
). The second grand challenge is to industrialize and transfer Cu/CNT from lab bench to real-life use. Toward this, we identify and propose strategies to address market-dependent issues for niche/mainstream applications. The current best Cu/CNT performances already qualify for application in niche electronic device markets as high-end interconnects. However, mainstream Cu/CNT application as copper replacements in conventional electronics and in electrical/data wires are long-term goals, needing inexpensive mass-production by methods aligned with existing industrial practices. Mainstream electronics require cheap CNT template-making and electrodeposition procedures, while data/electrical cables require manufacture protocols based on co-electrodeposition or melt-processing. We note (with examples) that initiatives devoted to Cu/CNT manufacturing for both types of mainstream applications are underway. With sustained research on Cu/CNT and accelerating its real-life application, we expect the successful evolution of highly functional, efficient, and sustainable next-generation electrical and electronics systems.
Algorithm for a particle-based growth model for plant tissues
Authors: van Opheusden Joost H. J. , Molenaar Jaap
Published: November 2018

We have developed an algorithm for a particle-based model for the growth of plant tissues in three dimensions in which each cell is represented by a single particle, and connecting cell walls are represented as permanent bonds between particles. A sample of plant tissue is represented by a fixed network of bonded particles. If, and only if a cell divides, this network is updated locally. The update algorithm is implemented in a model where cell growth and division gives rise to forces between the cells, which are relaxed in steepest descent minimization. The same forces generate a pressure inside the cells, which moderates growth. The local nature of the algorithm makes it efficient computationally, so the model can deal with a large number of cells. We used the model to study the growth of plant tissues for a variety of model parameters, to show the viability of the algorithm.
Added value of autoregulation and multi-step kinetics of transcription initiation
Authors: Prajapat Mahendra Kumar , Ribeiro Andre S.
Published: November 2018

Bacterial gene expression regulation occurs mostly during transcription, which has two main rate-limiting steps: the close complex formation, when the RNA polymerase binds to an active promoter, and the subsequent open complex formation, after which it follows elongation. Tuning these steps' kinetics by the action of e.g. transcription factors, allows for a wide diversity of dynamics. For example, adding autoregulation generates single-gene circuits able to perform more complex tasks. Using stochastic models of transcription kinetics with empirically validated parameter values, we investigate how autoregulation and the multi-step transcription initiation kinetics of single-gene autoregulated circuits can be combined to fine-tune steady state mean and cell-to-cell variability in protein expression levels, as well as response times. Next, we investigate how they can be jointly tuned to control complex behaviours, namely, time counting, switching dynamics and memory storage. Overall, our finding suggests that, in bacteria, jointly regulating a single-gene circuit's topology and the transcription initiation multi-step dynamics allows enhancing complex task performance.
Attention and the motion after effect: New measurements with visual search reveal important individual differences in adaptability
Authors: Morgan Michael J. , Solomon Joshua A.
Published: November 2018

It is usually assumed that sensory adaptation is a universal property of human vision. However, in two experiments designed to measure adaptation without bias, we have discovered a minority of participants who were unusual in the extent of their adaptation to motion. One experiment was designed so that targets would be invisible without adaptation; the other, so that adaptation would interfere with target detection. In the first, participants adapted to a spatial array of moving Gabor patches. On each trial the adapting array was followed by a test array in which but all of the test patches except one were identical to their spatially corresponding adaptors; the target moved in the opposite direction to its adaptor. Participants were required to identify the location of the changed target with a mouse click. The ability to do so increased with the number of adapting trials. Neither search speed nor accuracy was affected by an attentionally-demanding conjunction task at the fixation point during adaptation, suggesting low-level (pre-attentive) sites in the visual pathway for the adaptation. However, a minority of participants found the task virtually impossible. In the second experiment the same participants were required to identify the one element in the test array that was slowly moving: reaction times in this case were elevated following adaptation. The putatively weak adapters from the first experiment found this task easier than the strong adapters.
The extracellular association of the bacterium “CandidatusDeianiraea vastatrix” with the ciliateParameciumsuggests an alternative scenario for the evolution ofRickettsiales
Authors: Castelli M. , Sabaneyeva E. , Lanzoni O. , Lebedeva N. , Floriano A.M. , Gaiarsa S. , Benken K. , Modeo L. , Bandi C. , Potekhin A. , Sassera D. , Petroni G.
Published: November 2018

Rickettsialesare a lineage of obligatorily intracellularAlphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novelRickettsialesbacterium associated withParamecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesize amino acids, compared to all investigatedRickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction ofRickettsialesbacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity inRickettsiales. According to our reconstruction, theRickettsialesancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity and genome reduction would have evolved later in parallel and independently in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria withinAlphaproteobacteria.
High-dimensional mapping of cognition to the brain using voxel-based morphometry and subcortical shape analysis
Authors: Zonneveld Hazel I , Roshchupkin Gennady V , Adams Hieab HH , Gutman Boris A , der Lugt Aad van , Niessen Wiro J , Vernooij Meike W , Ikram M Arfan
Published: November 2018

Background

It is increasingly recognized that the complex functions of human cognition are not accurately represented by arbitrarily-defined anatomical brain regions. Given the considerable functional specialization within such regions, more fine-grained studies of brain structure could capture such localized associations. However, such analyses/studies in a large community-dwelling population are lacking.

Methods

In 3,813 stroke-free and non-demented persons from the Rotterdam Study (mean age 69.1 (±8.8) years; 55.8% women) with cognitive assessments and brain MRI, we performed voxel-based morphometry and subcortical shape analysis on global cognition and separate tests that tapped into memory, information processing speed, fine motor speed, and executive function domains.

Results

We found that the different cognitive tests significantly associated with grey matter voxels in differential but also overlapping brain regions, primarily in the left hemisphere. Clusters of significantly associated voxels with global cognition were located within multiple anatomic regions: left amygdala, hippocampus, parietal lobule, superior temporal gyrus, insula and posterior temporal lobe. Subcortical shape analysis revealed associations primarily within the head and tail of the caudate nucleus, putamen, ventral part of the thalamus, and nucleus accumbens, more equally distributed among the left and right hemisphere. Within the caudate nucleus both positive (head) as well as negative (tail) associations were observed with global cognition.

Conclusions

In a large population-based sample, we mapped cognitive performance to (sub)cortical grey matter using a hypothesis-free approach with high-dimensional neuroimaging. Leveraging the power of our large sample size, we confirmed well-known associations as well as identified novel brain regions related to cognition.