bluuebunny/crossref_metadata_2025 huggingface dataset:
Antiferro-ferromagnetic transition in ultrathin Ni(OH)2 layer grown on graphene surface and observation of interlayer exchange coupling in Ni(OH)2/graphene/Ni(OH)2 nanostructures
Authors: Bhattacharya Shatabda , Mathan Kumar E. , Thapa Ranjit , Saha Shyamal K.
Published: January 2017

The major limitation of using graphene as a potential spacer element in interlayer exchange coupling (IEC) might be due to destruction of ferromagnetism as a result of the charge transfer effect at the interface if a transition metal based ferromagnetic layer is grown on the graphene surface. To overcome this problem, we have used the antiferromagnetic Ni(OH)2 layer grown on the graphene surface to convert it ferromagnetic due to the charge transfer effect. By growing thin layers of Ni(OH)2 on both sides of the graphene surface, strong antiferromagnetic IEC with ultra-low coercivity (7 Oe) is observed. By lowering the nickel content, an ultrathin layer of Ni(OH)2 is grown on either side of graphene and shows complete ferromagnetism with a giant coercivity of 4154 Oe. Ab initio calculations have been done to substantiate this kind of charge transfer effect at the interface of Ni(OH)2 and graphene. Magnetotransport of the composite material is also investigated to understand the role of IEC in transport properties.
Role of aluminum in silver paste contact to boron-doped silicon emitters
Authors: Wu Wei , Roelofs Katherine E. , Subramoney Shekhar , Lloyd Kathryn , Zhang Lei
Published: January 2017

The addition of aluminum to silver metallization pastes has been found to lower the contact resistivity of a silver metallization on boron-doped silicon emitters for n-type Si solar cells. However, the addition of Al also induces more surface recombination and increases the Ag pattern′s line resistivity, both of which ultimately limit the cell efficiency. There is a need to develop a fundamental understanding of the role that Al plays in reducing the contact resistivity and to explore alternative additives. A fritless silver paste is used to allow direct analysis of the impact of Al on the Ag-Si interfacial microstructure and isolate the influence of Al on the electrical contact from the complicated Ag-Si interfacial glass layer. Electrical analysis shows that in a simplified system, Al decreases the contact resistivity by about three orders of magnitude. Detailed microstructural studies show that in the presence of Al, microscale metallic spikes of Al-Ag alloy and nanoscale metallic spikes of Ag-Si alloy penetrate the surface of the boron-doped Si emitters. These results demonstrate the role of Al in reducing the contact resistivity through the formation of micro- and nano-scale metallic spikes, allowing the direct contact to the emitters.
Temporal vegetation changes in a seasonally dry tropical forest enclave in an ecotonal region between savanna and semiarid zones of Brazil
Authors: Reis Geovany Heitor , Terra Marcela de Castro Nunes Santos , Tng David Yue Phin , Apgaua Deborah Mattos Guimaraes , Coelho Polyanne Aparecida , Manoel dos Santos Rubens , Nunes Yule Roberta Ferreira
Published: January 2017

Seasonally dry tropical forests (SDTFs) comprise a globally significant biome for biodiversity and conservation. Geographically, Brazilian SDTFs are primarily located within the country’s semiarid region (the Caatinga domain) in north-eastern Brazil. However, poorly studied and disjunct SDTF enclaves can occur within other regions, inside other Brazilian phytogeographical domains of vegetation such as savannas (i.e. the Cerrado domain) in central Brazil. These enclaves provide an opportunity to examine natural and non-anthropogenic edge effects on such vegetation. In 2007 and 2014, we studied a 120-ha SDTF enclave in the municipality of Januária in northern Minas Gerais, Brazil, to understand its (1) floristic composition and soil correlates, and (2) temporal variations in diversity, structure and dynamics. Three sets of 10 400-m2 plots were used to compare the vegetation at 0 m (edge), 100 m (middle) and 200 m (inner) into the forest. The edge plots were compositionally dissimilar from the interior plots because of soil fertility and soil textural gradients. Paradoxically also, the inner plots exhibited less stable vegetation-dynamic patterns than did both the middle and the edge plots, possibly owing to natural temporal fluctuations in vegetation dynamics. Overall, the SDTF enclave exhibited high diversity and structural complexity, likely because of its geographical setting within a matrix of savanna. These results highlight a conservation priority for further studies on such SDTF enclaves throughout their range.
Microstructure and enhanced atomic diffusion of friction stir welding aluminium/steel joints
Authors: Wei Yanni , Xiong Jiangtao , Li Jinglong , Zhang Fusheng , Liang Shuhua
Published: January 2017

Lap joints of friction stir welding between aluminium and stainless steel sheets were conducted using a welding tool with a cutting pin. The atomic diffusion of Fe–Al system during the severe plastic deformation was investigated. The interfacial microstructure and metallurgical reaction was analysed. The metallurgical reaction layers were identified as a compounds containing a phase of Al3Fe, partial solid solution of Fe and Al, and amorphous with a thickness of 0.9–3.3 μm which depending on the process parameters. The interdiffusion coefficient between Al and Fe atoms is about 4 orders of magnitude compared with that under thermal equilibrium state. The nanocrystalline and partial amorphous were formed near the interface which may caused by the enhanced atomic diffusion.
Negotiating the teaching of history in times of curriculum reform: the narrative accounts of four Australian primary teachers
Authors: Reitano Paul , Winter Satine
Published: January 2017

This research investigates the understandings of four teachers who teach history in primary and early childhood settings. Data were gathered from participants through semi‐structured interviews. The participants were experienced teachers who were in the process of curriculum change – from teachers of studies of society and environment to teachers of history, under the auspices of the Australian Curriculum: History. The focus of the study was on their understandings of content knowledge and the pedagogies involved in classroom teaching, using a pedagogical framework, which sought to identify and categorise the nature of their knowledge base in the implementation phase of the Australian Curriculum: History. The study used narrative inquiry to show how temporality, sociality, and place play out in the lives of these teachers of history. The findings from this study indicate the challenges and opportunities for teachers’ professional knowledge landscapes in times of curriculum reform. Whilst there are a small number of participants in this study, their stories provide insight into how teachers responded to the challenges and opportunities of teaching history and how these teachers have shaped the implementation of the history curriculum.
Centriole splitting caused by loss of the centrosomal linker protein C-NAP1 reduces centriolar satellite density and impedes centrosome amplification
Authors: Flanagan Anne-Marie , Stavenschi Elena , Basavaraju Shivakumar , Gaboriau David , Hoey David A. , Morrison Ciaran G.
Published: January 2017

Duplication of the centrosomes is a tightly regulated process. Abnormal centrosome numbers can impair cell division and cause changes in how cells migrate. Duplicated centrosomes are held together by a proteinaceous linker made up of rootletin filaments anchored to the centrioles by C-NAP1. This linker is removed in a NEK2A kinase-dependent manner as mitosis begins. To explore C-NAP1 activities in regulating centrosome activities, we used genome editing to ablate it. C-NAP1–null cells were viable and had an increased frequency of premature centriole separation, accompanied by reduced density of the centriolar satellites, with reexpression of C-NAP1 rescuing both phenotypes. We found that the primary cilium, a signaling structure that arises from the mother centriole docked to the cell membrane, was intact in the absence of C-NAP1, although components of the ciliary rootlet were aberrantly localized away from the base of the cilium. C-NAP1–deficient cells were capable of signaling through the cilium, as determined by gene expression analysis after fluid flow–induced shear stress and the relocalization of components of the Hedgehog pathway. Centrosome amplification induced by DNA damage or by PLK4 or CDK2 overexpression was markedly reduced in the absence of C-NAP1. We conclude that centriole splitting reduces the local density of key centriolar precursors to impede overduplication.
Automated mitotic spindle tracking suggests a link between spindle dynamics, spindle orientation, and anaphase onset in epithelial cells
Authors: Larson Matthew E. , Bement William M.
Published: January 2017

Proper spindle positioning at anaphase onset is essential for normal tissue organization and function. Here we develop automated spindle-tracking software and apply it to characterize mitotic spindle dynamics in the Xenopus laevis embryonic epithelium. We find that metaphase spindles first undergo a sustained rotation that brings them on-axis with their final orientation. This sustained rotation is followed by a set of striking stereotyped rotational oscillations that bring the spindle into near contact with the cortex and then move it rapidly away from the cortex. These oscillations begin to subside soon before anaphase onset. Metrics extracted from the automatically tracked spindles indicate that final spindle position is determined largely by cell morphology and that spindles consistently center themselves in the XY-plane before anaphase onset. Finally, analysis of the relationship between spindle oscillations and spindle position relative to the cortex reveals an association between cortical contact and anaphase onset. We conclude that metaphase spindles in epithelia engage in a stereotyped “dance,” that this dance culminates in proper spindle positioning and orientation, and that completion of the dance is linked to anaphase onset.
Munc13-4 functions as a Ca2+sensor for homotypic secretory granule fusion to generate endosomal exocytic vacuoles
Authors: Woo Sang Su , James Declan J. , Martin Thomas F. J.
Published: January 2017

Munc13-4 is a Ca2+-dependent SNARE (soluble N-ethylmaleimide–sensitive factor attachment protein receptor)- and phospholipid-binding protein that localizes to and primes secretory granules (SGs) for Ca2+-evoked secretion in various secretory cells. Studies in mast cell–like RBL-2H3 cells provide direct evidence that Munc13–4 with its two Ca2+-binding C2 domains functions as a Ca2+sensor for SG exocytosis. Unexpectedly, Ca2+stimulation also generated large (>2.4 μm in diameter) Munc13-4+/Rab7+/Rab11+endosomal vacuoles. Vacuole generation involved the homotypic fusion of Munc13-4+/Rab7+SGs, followed by a merge with Rab11+endosomes, and depended on Ca2+binding to Munc13-4. Munc13-4 promoted the Ca2+-stimulated fusion of VAMP8-containing liposomes with liposomes containing exocytic or endosomal Q-SNAREs and directly interacted with late endosomal SNARE complexes. Thus Munc13-4 is a tethering/priming factor and Ca2+sensor for both heterotypic SG-plasma membrane and homotypic SG-SG fusion. Total internal reflection fluorescence microscopy imaging revealed that vacuoles were exocytic and mediated secretion of β-hexosaminidase and cytokines accompanied by Munc13-4 diffusion onto the plasma membrane. The results provide new molecular insights into the mechanism of multigranular compound exocytosis commonly observed in various secretory cells.
Phospholipase Lpl1 links lipid droplet function with quality control protein degradation
Authors: Weisshaar Nina , Welsch Hendrik , Guerra-Moreno Angel , Hanna John
Published: January 2017

Protein misfolding is toxic to cells and is believed to underlie many human diseases, including many neurodegenerative diseases. Accordingly, cells have developed stress responses to deal with misfolded proteins. The transcription factor Rpn4 mediates one such response and is best known for regulating the abundance of the proteasome, the complex multisubunit protease that destroys proteins. Here we identify Lpl1 as an unexpected target of the Rpn4 response. Lpl1 is a phospholipase and a component of the lipid droplet. Lpl1 has dual functions: it is required for both efficient proteasome-mediated protein degradation and the dynamic regulation of lipid droplets. Lpl1 shows a synthetic genetic interaction with Hac1, the master regulator of a second proteotoxic stress response, the unfolded protein response (UPR). The UPR has long been known to regulate phospholipid metabolism, and Lpl1's relationship with Hac1 appears to reflect Hac1's role in stimulating phospholipid synthesis under stress. Thus two distinct proteotoxic stress responses control phospholipid metabolism. Furthermore, these results provide a direct link between the lipid droplet and proteasomal protein degradation and suggest that dynamic regulation of lipid droplets is a key aspect of some proteotoxic stress responses.
John of God
Authors: Rocha Cristina
Published: January 2017

This is the first ethnographic account of the global spiritual movement headed by John of God, a Brazilian faith healer. In just over a decade, John of God has become an international healer superstar—visited by thousands of the desperately ill, the wealthy, celebrities such as Oprah Winfrey, Ram Daas, Wayne Dyer, and Shirley MacLaine, and an increasing array of media. What sets John of God apart are his spectacular healing methods. He performs operations using kitchen knives, scissors, and scalpels without anesthetics or asepsis. He allegedly takes on “entities” (spirits) in a trance and does not remember the operations when he becomes conscious again. Most people claim they do not feel pain and do not develop infections. Drawing on a decade of multi-sited fieldwork in Brazil, the United States, the United Kingdom, Germany, Australia, and New Zealand, Cristina Rocha provides a rich and important case study of religious globalization which embodies themes that are central to the spread and practice of faith and healing in the twenty-first century. Rocha explores the ways in which religion is both globalized and localized in late modernity and the strategies of cultural translation involved, the establishment of transnational communities of belief, the transformation of poor rural areas into sites of globalization, the efficacy of healing across cultures, the increasing appeal of traditional medicine in the West, and the prominent place of healing (of the body, the spirit, and the planet) in late modernity.
Introduction
Authors: Hirota Hidetaka
Published: January 2017

The Introduction opens with the deportation of two Irish paupers from a Massachusetts almshouse to Ireland in 1855. The episode provides an entrée to the principal historical issues the book addresses: the practical impact of anti-Irish nativism, its influence on state immigration policies, how those policies laid the groundwork for later federal immigration law, and how state deportation policy unfolded in a transnational context. The Introduction emphasizes that the book focuses on the centrality of economic considerations in anti-Irish nativism. Nativists resented Irish immigrants’ inability to financially support themselves and the immigration policy they developed aimed to expel the indigent Irish dependent on public relief. This book fundamentally demonstrates how American immigration control emerged as a matter of class by tracing the institutionalization into regulatory immigration policy of an economic logic that considered paupers the antithesis of American citizens—a process driven by intense bias against people of Irish ancestry.
Style, sociolinguistic change, and political broadcasting
Authors: Lorenzo-Dus Nuria
Published: January 2017

This chapter explores the notion of sociolinguistic change in relation to a popular news show in Spain (Salvados). The selected episode concerns the Spanish government’s controversial handling of a tragic rail accident. The analysis covers both the interviewing style of the show’s anchor (Jordi Évole) and public uptake of his style across digital media. Évole’s style is found to rely on stances of moral evaluation, mock naïvety, and ordinariness. These represent a departure from traditional forms of interviewing in Spain; they contribute to, stimulate, mediate, and evaluate sociolinguistic change within Spanish contemporary broadcasting.
Style, change, and media
Authors: Androutsopoulos Jannis
Published: January 2017

Based on a critical reading of Chapters 2–10, this postscript discusses the present book’s contribution to the emerging framework of sociolinguistic change, which addresses a range of sociolinguistic processes beyond feature-based linguistic change. In a sociolinguistic change framework, media are theorized as spaces of sociolinguistic variation and change in their own right, and media language practices are examined in terms of their relations to non-mediatized language. These include the role of media representations in the enregisterment of speech forms, the uptake and recontextualization of media language fragments, and the circulation of linguistic innovations across modes of mediated communication and user networks. Research on sociolinguistic change offers new perspectives on the interaction between genre, style, and change, for example with regard to the impact of genre change on linguistic change, the role of highly visible media speakers, and the way media performance may reinforce enregisterment.
Gradability in Natural Language
Authors: Burnett Heather
Published: January 2017

This monograph presents a new theory of the relationship between vagueness, context sensitivity, gradability, and scale structure in natural language. The book argues that particular subclasses of adjectival predicates (relative adjectives (i.e. tall), total adjectives (i.e. dry), partial adjectives (i.e. wet), and non-scalar adjectives (i.e. hexagonal)) can be distinguished through looking how their criteria of application can vary depending on context; how they display the characteristic properties of vague language; and what the properties of their associated orders (a.k.a. scales) are. It has been known for a long time that there exist empirical connections between context sensitivity, vagueness, and scale structure in the adjectival domain; however, a formal system that expresses these connections has yet to be developed. By combining insights into the relationship between context sensitivity and gradability from the Delineation semantics framework with insights into the relationship between tolerance relations and the Sorites paradox from the Tolerant, Classical, Strict non-classical framework, the book proposes such a logical system (called DelTCS). Using this framework, it is shown that the association of particular classes of adjectives with their particular kinds of scales can be derived from their context sensitivity and vagueness properties. In the second part of the book, it gives a mereological extension of DelTCS to analyze vagueness and gradability outside the adjectival domain. It is shown that there exist correspondences between the major adjectival scale structure classes and certain well-known subclasses of determiner phrases, and the book shows how these correspondences can be captured within this system.
Estimation in Practice
Authors: Arndt Channing , Mahrt Kristi
Published: January 2017

This chapter furthers the discussion by outlining how each approach translates from theory to the practical estimation of poverty/wellbeing. It provides an overview of the specific steps involved in estimation and highlights the analyst’s role in customizing procedures to individual country contexts. The procedures in focus here are implemented via sets of Stata and GAMS code. The code whose default stream is associated with the utility-consistent CBN approach is referred to as the Poverty Line Estimation Analytical Software (PLEASe). The procedure for FOD analysis is called executing FOD (EFOD). The PLEASe and EFOD user guides contain more detailed descriptions of the technical aspects of implementation, such as data requirements and particulars of the code.
Estimating Utility-Consistent Poverty in Madagascar, 2001–10
Authors: Stifel David , Razafimanantena Tiaray , Rakotomanana Faly
Published: January 2017

This chapter describes how the standardized PLEASe computer code stream based on Arndt and Simler’s (2010) utility-consistent approach to measuring consumption poverty can be adapted in order to analyse poverty in Madagascar in 2001, 2005, and 2010. The chapter documents how the utility-consistent approach to intertemporal and spatial deflation differs from the approach undertaken by the national statistical office to produce the official poverty estimates and how the trends in these estimates differ substantially. Further, it illustrates the importance of addressing extreme values for calculating unit prices, and how to handle redistricting when conducting revealed preference tests of the utility consistency of not only regionally estimated poverty lines (i.e. do the consumption patterns in other spatial domains cost no less than the own-domain consumption patterns when both are evaluated at own-domain prices), but also of poverty lines over time.
Methods Matter
Authors: Beck Ulrik , Mussa Richard , Pauw Karl
Published: January 2017

This chapter decomposes differences between the ‘official’ poverty estimates of Malawi and a set of revised estimates by Pauw et al. (2016) with respect to five methodological differences: (i) the use of a revised set of unit conversion factors; (ii) the specification and use of regional poverty lines as opposed to a single national poverty line; (iii) the use of implicit survey-based prices rather than external price data; (iv) estimation of food separate poverty lines in the two surveys; and (v) permitting a change in the food/non-food composition of the consumption basket over. Our results suggest that the decline in national poverty varies between −3.4 and −8.4 percentage points, compared to the official estimate of −1.8 per cent.
Synthesis
Authors: Arndt Channing , Mahrt Kristi , Tarp Finn
Published: January 2017

This synthesis chapter seeks to draw general lessons from the case studies presented in the book. It does not include a review or summary of each chapter. Instead, we revert to themes that emerged from earlier in the book. Specifically, we argue that appropriately assessing living standards is challenging, and focus on the different nature of the challenges for consumption poverty line estimation and multidimensional poverty measurement. The six case studies uniformly indicate that the process of drawing appropriate absolute poverty lines is not straightforward and cannot be done mechanically. This is so principally due to five key factors: heterogeneity, volatility, vulnerability, data, and theory. The first three factors are usefully grouped together. In all of the case countries considered, poor people are heterogeneous, frequently live in environments with strikingly high levels of volatility, and are, almost by definition, vulnerable to shocks.
A digest of matrix models
Authors: Gurau Razvan
Published: January 2017

There are many excellent reviews on random matrices both in mathematics and in physics literature. This chapter presents only a very quick overview of some selected topics in random matrix theory: the 1/N expansion, the continuum limit, the double scaling limit and the Schwinger–Dyson equations. The results listed in this chapter for random matrices will be recovered one by one for random tensors in subsequent chapters.
The double scaling limit
Authors: Gurau Razvan
Published: January 2017

This chapter presents the double scaling limit of quartic tensor models. In the first part of this chapter it is shown show that the melonic family in the quartic melonic tensor model can be analytically resumed and that this resummation is encoded in a translation of the intermediate matrix fields to a nontrivial vacuum. The most striking consequence of this translation is that one can now show that the continuum limit of tensor models corresponds to a genuine phase transition (in the field theory sense) associated to a symmetry breaking. In the second part of this chapter the intermediate field representation is used to derive the double scaling limit of the quartic melonic model.
Conclusions
Authors: Gurau Razvan
Published: January 2017

This last chapter discusses some applications of tensor models as models of emergent random geometry. Tensor models generate weighted triangulations in any dimensions. The flexibility of tensor models comes from the freedom one has to choose the weight of the triangulation by choosing various vertex kernels and covariances. These choices encode the physical interpretation of a model and there exist several choices, leading to different physical interpretations. One such choice, leading to a natural interpretation of tensor models as generators of Euclidean dynamical triangulations, is discussed in detail.
Introduction
Authors: Kang S. Deborah
Published: January 2017

The introduction presents the book’s main argument that the INS on the US–Mexico border made and remade the nation’s immigration laws over the course of the twentieth century. This claim challenges popular and scholarly notions that the INS functioned primarily as a law enforcement agency, administering laws issued by Congress and the courts, and, instead, underscores the multiple ways in which the local branches of one federal agency defined American immigration law and policy. While the INS in the Southwest often created these measures in a highly haphazard and reactive fashion, they ultimately came to shape the capacities of the American state on the US-Mexico border. The introduction further discusses the implications of this argument for the study of the American administrative state, immigration law and policy history, and borderlands history. It closes with chapter summaries of the book.
Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken
Authors: Beauclercq Stéphane , Hennequet-Antier Christelle , Praud Christophe , Godet Estelle , Collin Anne , Tesseraud Sophie , Métayer-Coustard Sonia , Bourin Marie , Moroldo Marco , Martins Frédéric , Lagarrigue Sandrine , Le Bihan-Duval Elisabeth , Berri Cécile
Published: January 2017

The processing ability and sensory quality of chicken breast meat are highly related to its ultimate pH (pHu), which is mainly determined by the amount of glycogen in the muscle at death. To unravel the molecular mechanisms underlying glycogen and meat pHu variations and to identify predictive biomarkers of these traits, a transcriptome profiling analysis was performed using an Agilent custom chicken 8×60K microarray. The breast muscle gene expression patterns were studied in two chicken lines experimentally selected for high (pHu+) and low (pHu-) pHu values of the breast meat. Across the 1,436 differentially expressed (DE) genes found between the two lines, many were involved in biological processes related to muscle development and remodelling and carbohydrate and energy metabolism. The functional analysis showed an intensive use of carbohydrate metabolism to produce energy in the pHu- line, while alternative catabolic pathways were solicited in the muscle of the pHu+ broilers, compromising their muscle development and integrity. After a validation step on a population of 278 broilers using microfluidic RT-qPCR, 20 genes were identified by partial least squares regression as good predictors of the pHu, opening new perspectives of screening broilers likely to present meat quality defects.
Research on Mitochondrial DNA Mutations in Patients with SCA3/MJD
Authors: Liu Zhen , Zhou Jie , Yin Xiaomeng , Shi Shuying , Sun Weining , Jiang Hong , Shen Lu , Tang Beisha , Wang Junling
Published: January 2017

Spinocerebellar ataxia type 3 (SCA3) is a degenerative neurological disorders caused by trinucleotide repeat expansion within the ataxin-3 gene. It is characterized by multi-system involvement and diverse clinical phenotypes, which cannot be fully explained the length of the CAG repeats. One possible explanation for the phenotypic heterogeneity could be the presence of mitochondrial DNA mutations that modify disease severity. To explore the role of Mitochondrial DNA(mtDNA) variations in SCA3 pathogenesis, we analyzed polymorphisms of six mitochondrial genes,MT-LT1, MT-ND1, MT-CO2, MT-TK, MT-ATP8andMT-ATP6, in 102 unrelated SCA3/MJD patients and 100 healthy controls. The results showed that there were 24 variations of those mtDNA genes in the SCA3 patients and only 10 in the unrelated healthy controls. There was no difference of the relative mtDNA copy number variation between the SCA3 patients and healthy controls (93.20 vs. 89.66, P>0.05). In the group of SCA3 patients, the relative mtDNA copy number showed a negative correlation between the number of CAG repeats (r=−0.210, P < 0.05), but did not correlate with the age at diagnosis, the age of onset, disease duration, ICARS scores and SARA scores. Our research demonstrated that the frequency of mutated mtDNA in SCA3 patients was higher than that in the healthy group. The mtDNA relative copy number in SCA3 patients was not significantly different compared to the healthy group. Thus, the copy number might not be treated as a biomedical indicator when measuring the severity of illness in SCA3 patients.
Visual memories are stored along a compressed timeline
Authors: Singh Inder , Oliva Aude , Howard Marc W.
Published: January 2017

In continuous recognition the recency effect manifests as a decrease in accuracy and a sublinear increase in response time (RT) with the lag of a repeated stimulus. The recency effect could result from the gradual weakening of mnemonic traces. Alternatively, the recency effect could result from a search through a compressed timeline of recent experience. These two hypotheses make very different predictions about the shape of response time distributions. Using highly-memorable pictures to mitigate changes in accuracy enabled a detailed examination of the effect of recency on retrieval dynamics. The recency at which pictures were repeated ranged over two orders of magnitude across three experiments. Analysis of the RT distributions showed that the time at which memories became accessible changed with the recency of the probe, as predicted by a serial search model suggesting that visual memories can be accessed by sequentially scanning along a compressed representation of the past.
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
Authors: Yang Tao , Zhang Feipeng , Yardımcı Galip Gürkan , Song Fan , Hardison Ross C. , Noble William Stafford , Yue Feng , Li Qunhua
Published: January 2017

Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach.
Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA
Authors: Yuan Dejian , Lei Xiaoyun , Gui Yuanyuan , Wang Mingrui , Zhang Ye , Zhu Zuobin , Wang Dapeng , Yu Jun , Huang Shi
Published: January 2017

The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.
Predicting the structure and function of coalesced microbial communities
Authors: Sierocinski Pawel , Milferstedt Kim , Bayer Florian , Großkopf Tobias , Alston Mark , Bastkowski Sarah , Swarbreck David , Hobbs Phil J , Soyer Orkun S , Hamelin Jérôme , Buckling Angus
Published: January 2017

Microbial communities commonly coalesce in nature, but the consequences for resultant community structure and function is unclear. Consistent with recent theory, we demonstrate using methanogenic communities that the most productive communities in isolation dominated when communities were mixed. As a corollary of this dynamic, total methane production increased with the number of inoculated communities. The cohesion and dominance of single communities was explained by more “niche-packed” communities being both more efficient at exploiting resources and resistant to invasion, rather than a function of the average performance of component species. These results are likely to be relevant to the ecological dynamics of natural microbial communities, as well as demonstrating a simple method to predictably enhance microbial community function in biotechnology, health and agriculture.
Warburg-like metabolism coordinates FGF and Wnt signaling in the vertebrate embryo
Authors: Oginuma Masayuki , Moncuquet Philippe , Xiong Fengzhu , Karoly Edward , Chal Jérome , Guevorkian Karine , Pourquié Olivier
Published: January 2017

Mammalian embryos transiently exhibit aerobic glycolysis (Warburg effect), a metabolic adaptation also observed in cancer cells. The role of this particular type of metabolism during vertebrate organogenesis is currently unknown. Here, we provide evidence for spatio-temporal regulation of aerobic glycolysis in the posterior region of mouse and chicken embryos. We show that a posterior glycolytic gradient is established in response to graded transcription of glycolytic enzymes downstream of FGF signaling. We demonstrate that glycolysis controls posterior elongation of the embryonic axis by regulating cell motility in the presomitic mesoderm and by controlling specification of the paraxial mesoderm fate in the tail bud. Our results suggest that Warburg metabolism in the tail bud coordinates Wnt and FGF signaling to promote elongation of the embryonic axis.
Quality Assessment of High-throughput DNA Sequencing Data via Range analysis
Authors: Külekci M. Oğuzhan , Fotouhi Ali , Majidi Mina
Published: January 2017

In the recent literature there appeared a number of studies for the quality assessment of sequencing data. These efforts, to a great extent, focused on reporting the statistical parameters regarding to the distribution of the quality scores and/or the base-calls in a FASTQ file. We investigate another dimension for the quality assessment motivated with the fact that reads including long intervals having fewer errors improve the performances of the post-processing tools in the down-stream analysis. Thus, the quality assessment procedures proposed in this study aim to analyze the segments on the reads that are above a certain quality. We define an interval of a read to be of desired quality when there are at mostkquality scores less than or equal to a threshold valuev, for somevandkprovided by the user. We present the algorithm to detect those ranges and introduce new metrics computed from their lengths. These metrics include the mean values for thelongest, shortest, average, cubic average, and average variation coefficientof the fragment lengths that are appropriate according to thevandkinput parameters. We provide a new software tool QASDRA for quality assessment of sequencing data via range analysis. QASDRA, implemented in Python, and publicly available athttps://github.com/ali-cp/QASDRA.git, creates the quality assessment report of an input FASTQ file according to the user specifiedkandvparameters. It also has the capabilities to filter out the reads according to the metrics introduced.
Oscail, a program package for small-molecule single-crystal crystallography with crystal morphology prediction and molecular modelling
Authors: McArdle Patrick
Published: January 2017

Oscail is a program for small-molecule crystallography which includes crystal morphology prediction and an interface to molecular modelling. The Oscail graphical user interface can drive SHELX and Superflip for structure solution and SHELXL for structure refinement. The lattice analysis includes hydrogen bonding, halogen bonding and van der Waals contact stacking. Other facilities include interactive bar charts of space-group frequencies in the Cambridge Structural Database, powder diffraction pattern calculation and reduced cell cluster analysis of structures. The graphics output includes thermal ellipsoid plots and rendered OpenGL and Raster3D photorealism in stills and movies. The molecular modelling includes quantum calculations (MOPAC, extended Hückel and density functional theory) and TINKER molecular mechanics.
The seasonal climate niche predicts phenology and distribution of an ephemeral annual plant, Mollugo verticillata
Authors: Hereford Joe , Schmitt Johanna , Ackerly David D.
Published: January 2017

Many short‐lived species complete their life cycles during brief seasonal windows of favourable environmental conditions. Such species may persist in the face of climate warming by migration to track their seasonal climate niche in space and/or by phenological shifts to track favourable conditions in time within the year. To describe the seasonal climate niche of the short‐lived annual Mollugo verticillata in California, we used data from herbarium specimens and historic climate records to estimate environmental conditions at the location, month and year of each collection.

We used these data in a MaxEnt framework to construct a seasonal species distribution model (SDM) of the species’ climate niche within the total climate space available across all seasons and locations in California. The model provides fine‐scale spatial and temporal predictions of habitat suitability, predicting both where and when the species should be observed.

We compared the predictions of the model to those from a conventional SDM based on mean annual climate data. Both models showed that M. verticillata is limited to warm environments within California. However, the seasonal SDM also predicted phenology by mapping climate suitability across the state for each month of the year. Mollugo verticillata is limited to warm months, and its seasonal climate niche shifts in space across California in the course of the year.

We used the seasonal SDM to map the predicted future species distribution for each month of the year under three warming scenarios. The species is predicted to expand its range and occur earlier in the year in most locations; in the warmest locations, seasonal suitability is predicted to decline in the warmest months, which may result in bimodal phenology with a mid‐summer gap.

Synthesis. We developed a novel species distribution model using herbarium records and monthly weather data, which predicts not only where a short‐lived species should be found but also when during the year it is predicted to occur in those areas. This model can be used to predict how climate change will affect the species distribution in space as well as seasonal phenology across the landscape.
Some Lessons of the SDP for Labour's Present Predicament
Authors: Liddle Roger
Published: January 2017

Jeremy Corbyn's election and re‐election as Labour leader, together with the emergence of a new Conservative Prime Minister committed to Brexit, has led to renewed speculation about the possibility of a new party appealing to the ‘politically homeless’ in the centre and centre‐left of British politics. This article draws lessons from the SDP experience in the early 1980s. Are the structural conditions more favourable to the progressive centre‐left now than they were then? Is there the sociological, electoral and ideological space for a new party? Does first past the post remain an insuperable barrier to an electoral breakthrough? From whom and in what circumstances might the leadership for a new party come? For all the depth of Labour's current problems, a new party seems an unlikely immediate prospect. In 1981, the SDP made a major miscalculation about the irreversibility of Labour's decline. However, the process of fragmentation in British politics seems set to continue.
Wild Lactobacillus strains: Technological characterisation and design of Coalho cheese lactic culture
Authors: Bruno Laura Maria , Briggiler Marcó Mariángeles , Capra Maria Luján , Carvalho Juliane Döering Gasparin , Meinardi Carlos , Quiberoni Andrea
Published: January 2017

To design a specific lactic culture for the controlled manufacture of coalho cheese, 13 Lactobacillus rhamnosus, two Lactobacillus fermentum and one Lactobacillus plantarum strains isolated from artisanal coalho cheeses were identified and characterised. Two Lb. rhamnosus, one Lb. plantarum and one Lb. fermentum were selected and grouped in pairs designing four different culture formulations that demonstrated a good performance in cheesemaking experiments at pilot scale. Further studies to adjust the balance of strains used are necessary to attain adequate sensorial and technological attributes as expected for artisanal cheeses.
Functional analysis of the circadian clock gene timeless in Tribolium castaneum
Authors: Li Cheng‐Jun , Yun Xiao‐Pei , Yu Xiao‐Juan , Li Bin
Published: January 2017

Circadian rhythms are endogenous oscillations with a period of about 24 h driven by a circadian clock. So far, variable oscillators have been found in insects. To explore the circadian clock of Tribolium castaneum, we cloned the clock gene timeless (Tctimeless). Its open reading frame is 3240 bp in length and consists of 10 exons. Tctimeless is highly expressed in the late pupal stage. Tissue‐specific expression analysis in late adult stages revealed high expression of Tctimeless in the head, epidermis, fat body and accessory glands. Silencing of Tctimeless by RNA interference (RNAi) at the late larval stages caused a failure to initiate eclosion. Tctimeless knockdown in late pupal stages led to a gender‐independent decline in egg production and progeny survival. As a core clock gene, Tctimeless exhibited one expression peak in the middle of the circadian day. Knockdown of Tctimeless disrupted daily expression patterns of Tccycle, Tcclock, Tcperiod and itself, while Tctimeless and Tcperiod expression patterns over the circadian day were also perturbed when Tccycle or Tcclock is suppressed by RNAi. This study identified a complex transcriptional relationship among circadian clock genes in T. castaneum.
Making space for restoration: epistemological pluralism within mental health interventions in Kinshasa, Democratic Republic of Congo
Authors: Taylor Stephen
Published: January 2017

Global health policymakers have recently begun to focus their attention on high levels of untreated mental illness in low‐ and middle‐income countries. They have, in turn, initiated a series of interventions intended to reduce the global ‘treatment gap’ that has emerged between those requiring treatment and those able to access it. Yet critics have challenged the questionable epistemological assumptions embedded in these interventions and have decried the lack of attention given to the translation and implementation of such projects in resource‐limited contexts. In this paper, I focus on ongoing attempts to diminish the mental health treatment gap in Kinshasa, Democratic Republic of Congo to illuminate how dominant thinking about ameliorating the global treatment gap remains rooted in a reductive biomedical paradigm. Drawing on interviews conducted with 16 psychiatrists in the city, I show how a series of epistemological assumptions about treatment have affected the success of treatment delivery in two donor‐funded interventions. I then contrast the dominant biomedical approach with the perspectives of three younger voices in the city's psychiatric community. I reveal how an alternative epistemological framework, similar to that of the phenomenological tradition, informs their own successful treatment expansion efforts. This alternative perspective, I propose, challenges practitioners and geographers alike to cultivate new ways of approaching global mental health that acknowledge the value of patient experiences and make possible more responsive forms of treatment and care.