bluuebunny/crossref_metadata_2025_split huggingface dataset:
Androgen receptor gene polymorphism and polycystic ovary syndrome
Authors: Lin Lawrence H. , Baracat Maria C.P. , Maciel Gustavo A.R. , Soares José M. , Baracat Edmund C. 
Published: November 2012

AbstractBackgroundPolycystic ovary syndrome (PCOS) is characterized by ovulatory dysfunction and hyperandrogenism. Its etiopathology is not well understood but genetic factors seem to have a role. Polymorphism of the androgen receptor (AR) gene has been associated with different androgen pattern diseases.ObjectiveTo review the association between AR gene polymorphism and PCOS.Search strategyA systematic review was performed via PUBMED, EMBASE, and LILACS (up to May 31, 2011).Selection criteriaStudies assessing the presence of the (CAG)n polymorphism of the AR gene in at least 2 comparison groups (PCOS and control). Studies that did not contain adequate information were excluded.Data collection and analysisStudy characteristics and results were analyzed. Meta‐analysis could not be performed because only 2 articles provided odds ratios.Main resultsTen studies met the inclusion criteria. Three studies reported a correlation between the polymorphism and PCOS; 2 studies linked the disorder to shorter repeats, whereas the other associated it with longer repeats.ConclusionPolymorphism of the AR gene seems to be a promising biomarker for PCOS because shorter repeats may be linked to the disorder. However, further studies are needed to understand the association fully.
Sex trafficking, physical and sexual violence, and HIV risk among young female sex workers in Andhra Pradesh, India
Authors: George Annie , Sabarwal Shagun 
Published: November 2012

AbstractObjectiveTo estimate the prevalence of sex trafficking as a mode of entry into sex work and to examine associations between sex trafficking and HIV vulnerability, recent violence experience, and symptoms of sexual ill health among young female sex workers (FSWs).MethodsA cross‐sectional survey of 1137 FSWS aged 18–25 years residing in Andhra Pradesh, India, was conducted.ResultsIn total, 574 (50.5%) FSWs entered sex work via trafficking. Trafficked FSWs had an increased risk of experiencing sexual violence (adjusted odds ratio [AOR] 2.09; 95% confidence interval [CI], 1.42–3.06) and physical/sexual violence (AOR 1.93; 95% CI, 1.24–3.01), and reporting more clients (AOR 2.25; 95% CI, 1.56–3.22) and more work days per week (AOR 1.48; 95% CI, 1.09–2.02). Symptoms of sexual ill health were not associated with mode of entry into sex work.ConclusionThere is a high prevalence of entry into sex work via trafficking among young FSWs. A history of sex trafficking is associated with greater risk of recent physical and sexual violence and of HIV. Public health interventions must focus attention on young FSWs.
Phase shifts of magneto-acoustic solitons in spin-1/2 fermionic quantum plasma during head-on collision
Authors: CHATTERJEE PRASANTA , ROYCHOUDHURY RAJKUMAR , GHORUI MALAY KUMAR 
Published: November 2012

AbstractThe head-on collision between two magneto-acoustic solitons in spin-1/2 fermionic quantum plasma is studied in the framework of the model proposed by Marklund et al. (Marklund, M., Eliasson, B. and Shukla, P. K. 2007 Phys. Rev. E. 76, 067401). The extended Poincare–Lighthill–Kuo method is used to obtain the phase shifts and the trajectories during the head-on collision of two solitons. The effect of the Zeeman energy for different speeds of the waves, the effect of the total mass density of the charged plasma particles for different strengths of magnetic field, the effect of the speed of the wave for different values of the Zeeman energy, and that of the ratio of the sound speed to Alfven speed for different values of Zeeman energ on the phase shift are studied. It is observed that the phase shifts are significantly affected in all the cases. The most interesting observation of this paper is that the phase shifts increase as well as decrease, and also they may be positive as well as negative depending upon the domain of the chosen parameters.
Dark energy and dark matter as due to zero point energy
Authors: LEHNERT BO 
Published: November 2012

AbstractAn attempt is made to explain dark energy and dark matter of the expanding universe in terms of the zero point vacuum energy. This analysis is mainly limited to later stages of an observable nearly flat universe. It is based on a revised formulation of the spectral distribution of the zero point energy, for an ensemble in a defined statistical equilibrium having finite total energy density. The steady and dynamic states are studied for a spherical cloud of zero point energy photons. The ‘antigravitational’ force due to its pressure gradient then represents dark energy, and its gravitational force due to the energy density represents dark matter. Four fundamental results come out of the theory. First, the lack of emitted radiation becomes reconcilable with the concepts of dark energy and dark matter. Second, the crucial coincidence problem of equal orders of magnitude of mass density and vacuum energy density cannot be explained by the cosmological constant, but is resolved by the present variable concepts, which originate from the same photon gas balance. Third, the present approach becomes reconcilable with cosmical dimensions and with the radius of the observable universe. Fourth, the deduced acceleration of the expansion agrees with the observed one. In addition, mass polarity of a generalized gravitation law for matter and antimatter is proposed as a source of dark flow.
Odd deposits and average practice. A critical history of the concept of structured deposition
Authors: Garrow Duncan 
Published: November 2012

AbstractThis paper presents a critical history of the concept of ‘structured deposition’. It examines the long-term development of this idea in archaeology, from its origins in the early 1980s through to the present day, looking at how it has been moulded and transformed. On the basis of this historical account, a number of problems are identified with the way that ‘structured deposition’ has generally been conceptualized and applied. It is suggested that the range of deposits described under a single banner as being ‘structured’ is unhelpfully broad, and that archaeologists have been too willing to view material culture patterning as intentionally produced – the result of symbolic or ritual action. It is also argued that the material signatures of ‘everyday’ practice have been undertheorized and all too often ignored. Ultimately, it is suggested that if we are ever to understand fully the archaeological signatures of past practice, it is vital to consider the ‘everyday’ as well as the ‘ritual’ processes which lie behind the patterns we uncover in the ground.
Curation as research. A case study in orphaned and underreported archaeological collections
Authors: Voss Barbara L. 
Published: November 2012

AbstractAs archaeologists grapple with the international curation crisis, new attention is being given to the problem of ‘orphaned’ archaeological collections and collections that are underanalysed and underreported. The common rationale for curating such collections is to restore research potential, but such efforts are met with frustration because of the difficulties of re-establishing provenance and quantitative control for artefacts long separated from their original archaeological context. Moreover, most archaeologists view curation as a process that manages, rather than investigates, archaeological collections. To the contrary, this article argues that accessioning, inventory, cataloguing, rehousing and conservation are not simply precursors to research, but rather meaningful generative encounters between scholars and objects. Examples from the curation of the Market Street Chinatown archaeological collection illustrate how the process of curation can generate innovative research undertakings. Because archaeological research on this collection cannot proceed in a typical way, the research developed through the curation process departs from archaeological conventions to bring new perspectives on the social history of the Overseas Chinese diaspora.
The uncreated man. A story of archaeology and imagination
Authors: Shepherd Nick 
Published: November 2012

AbstractWhat is the place of imagination in archaeology? This paper works with a set of materials from the deep archive of the South African archaeologist John Goodwin (1900–59) to explore the relationship between archaeology and imagination. The first half of the paper focuses on a short story written by Goodwin, describing the accidental creation and subsequent ‘uncreation’ of an indigenous person of the Cape (described in the story as a ‘Hottentot’) by the gods on Olympus. The second half of the paper describes two encounters in life between Goodwin and indigenous people of the Cape (the first with the so-called ‘Tweerivieren Bushmen’, exhibited in life at the Empire Exhibition of 1936; the second with the human remains from Oakhurst Cave). Encounters in life, in death and in imagination, the terms of these three episodes double and repeat one another in the different forms of writing to which they give rise (the imagined world of the short story, and the ‘bare description’ of Goodwin's archaeological texts). At the centre of each is the haunted figure of the ‘Bushman’/‘Hottentot’, a being whose status is figured as a kind of ‘death-in-life’. In my telling, forms of actual and epistemic violence are never far from these events. Looking, showing and telling are described as activities which range across a set of characteristic sites: the body, the archive and the grave. In so doing, they summon their counterparts, the categories of the unspeakable and the untellable.
Gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the Atlantic Ocean
Authors: Dixon Joanna L , Sargeant Stephanie , Nightingale Philip D , Colin Murrell J 
Published: November 2012

AbstractMethanol biogeochemistry and its importance as a carbon source in seawater is relatively unexplored. We report the first microbial methanol carbon assimilation rates (k) in productive coastal upwelling waters of up to 0.117±0.002 d−1 (∼10 nmol l−1d−1). On average, coastal upwelling waters were 11 times greater than open ocean northern temperate (NT) waters, eight times greater than gyre waters and four times greater than equatorial upwelling (EU) waters; suggesting that all upwelling waters upon reaching the surface (⩽20 m), contain a microbial population that uses a relatively high amount of carbon (0.3–10 nmol l−1d−1), derived from methanol, to support their growth. In open ocean Atlantic regions, microbial uptake of methanol into biomass was significantly lower, ranging between 0.04–0.68 nmol l−1d−1. Microbes in the Mauritanian coastal upwelling used up to 57% of the total methanol for assimilation of the carbon into cells, compared with an average of 12% in the EU, and 1% in NT and gyre waters. Several methylotrophic bacterial species were identified from open ocean Atlantic waters using PCR amplification of mxaF encoding methanol dehydrogenase, the key enzyme in bacterial methanol oxidation. These included Methylophaga sp., Burkholderiales sp., Methylococcaceae sp., Ancylobacter aquaticus, Paracoccus denitrificans, Methylophilus methylotrophus, Methylobacterium oryzae, Hyphomicrobium sp. and Methylosulfonomonas methylovora. Statistically significant correlations for upwelling waters between methanol uptake into cells and both chlorophyll a concentrations and methanol oxidation rates suggest that remotely sensed chlorophyll a images, in these productive areas, could be used to derive total methanol biological loss rates, a useful tool for atmospheric and marine climatically active gas modellers, and air–sea exchange scientists.
Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm
Authors: Probst Alexander J , Holman Hoi-Ying N , DeSantis Todd Z , Andersen Gary L , Birarda Giovanni , Bechtel Hans A , Piceno Yvette M , Sonnleitner Maria , Venkateswaran Kasthuri , Moissl-Eichinger Christine 
Published: November 2012

Abstract
Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth’s energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.
Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages
Authors: Flores Cesar O , Valverde Sergi , Weitz Joshua S 
Published: November 2012

Abstract
Bacteriophages are the most abundant biological life forms on Earth. However, relatively little is known regarding which bacteriophages infect and exploit which bacteria. A recent meta-analysis showed that empirically measured phage-bacteria infection networks are often significantly nested, on average, and not modular. A perfectly nested network is one in which phages can be ordered from specialist to generalist such that the host range of a given phage is a subset of the host range of the subsequent phage in the ordering. The same meta-analysis hypothesized that modularity, in which groups of phages specialize on distinct groups of hosts, should emerge at larger geographic and/or taxonomic scales. In this paper, we evaluate the largest known phage-bacteria interaction data set, representing the interaction of 215 phage types with 286 host types sampled from geographically separated sites in the Atlantic Ocean. We find that this interaction network is highly modular. In addition, some of the modules identified in this data set are nested or contain submodules, indicating the presence of multi-scale structure, as hypothesized in the earlier meta-analysis. We examine the role of geography in driving these patterns and find evidence that the host range of phages and the phage permissibility of bacteria is driven, in part, by geographic separation. We conclude by discussing approaches to disentangle the roles of ecology and evolution in driving complex patterns of interaction between phages and bacteria.
A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal
Authors: Kristiansen Rikke , Nguyen Hien Thi Thu , Saunders Aaron Marc , Nielsen Jeppe Lund , Wimmer Reinhard , Le Vang Quy , McIlroy Simon Jon , Petrovski Steve , Seviour Robert J , Calteau Alexandra , Nielsen Kåre Lehmann , Nielsen Per Halkjær 
Published: November 2012

Abstract
Members of the genus Tetrasphaera are considered to be putative polyphosphate accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) from wastewater. Although abundant in Danish full-scale wastewater EBPR plants, how similar their ecophysiology is to ‘Candidatus Accumulibacter phosphatis’ is unclear, although they may occupy different ecological niches in EBPR communities. The genomes of four Tetrasphaera isolates (T. australiensis, T. japonica, T. elongata and T. jenkinsii) were sequenced and annotated, and the data used to construct metabolic models. These models incorporate central aspects of carbon and phosphorus metabolism critical to understanding their behavior under the alternating anaerobic/aerobic conditions encountered in EBPR systems. Key features of these metabolic pathways were investigated in pure cultures, although poor growth limited their analyses to T. japonica and T. elongata. Based on the models, we propose that under anaerobic conditions the Tetrasphaera-related PAOs take up glucose and ferment this to succinate and other components. They also synthesize glycogen as a storage polymer, using energy generated from the degradation of stored polyphosphate and substrate fermentation. During the aerobic phase, the stored glycogen is catabolized to provide energy for growth and to replenish the intracellular polyphosphate reserves needed for subsequent anaerobic metabolism. They are also able to denitrify. This physiology is markedly different to that displayed by ‘Candidatus Accumulibacter phosphatis’, and reveals Tetrasphaera populations to be unusual and physiologically versatile PAOs carrying out denitrification, fermentation and polyphosphate accumulation.
Gut bacteria–host metabolic interplay during conventionalisation of the mouse germfree colon
Authors: El Aidy Sahar , Derrien Muriel , Merrifield Claire A , Levenez Florence , Doré Joël , Boekschoten Mark V , Dekker Jan , Holmes Elaine , Zoetendal Erwin G , van Baarlen Peter , Claus Sandrine P , Kleerebezem Michiel 
Published: November 2012

Abstract
The interplay between dietary nutrients, gut microbiota and mammalian host tissues of the gastrointestinal tract is recognised as highly relevant for host health. Combined transcriptome, metabonome and microbial profiling tools were employed to analyse the dynamic responses of germfree mouse colonic mucosa to colonisation by normal mouse microbiota (conventionalisation) at different time-points during 16 days. The colonising microbiota showed a shift from early (days 1 and 2) to later colonisers (days 8 and 16). The dynamic changes in the microbial community were rapidly reflected by the urine metabolic profiles (day 1) and at later stages (day 4 onward) by the colon mucosa transcriptome and metabolic profiles. Correlations of host transcriptomes, metabolite patterns and microbiota composition revealed associations between Bacilli and Proteobacteria, and differential expression of host genes involved in energy and anabolic metabolism. Differential gene expression correlated with scyllo- and myo-inositol, glutamine, glycine and alanine levels in colonic tissues during the time span of conventionalisation. Our combined time-resolved analyses may help to expand the understanding of host–microbe molecular interactions during the microbial establishment.
The Historiography of Missionary Linguistics
Authors: Zwartjes Otto 
Published: November 2012

SummaryThere is no need to repeat earlier complaints that the historiography of missionary linguistics was being neglected, since the situation has changed considerably sine the last decades of the past century. The first decade of the 21st century in particular has witnessed a veritable explosion of research activities. This article surveys the state of the art in the field of recent work in the historiographical subfield called ‘Missionary linguistics’, covering the period 2002–2012. It represents an update of Zimmermann (2004) and provides separate sections devoted to earlier studies of missionary linguistics, international conferences, published volumes, journals, reprints and editions of primary sources, exhibitions and other activities related to the subject. The reference list is divided in two sections, (1) primary sources, with some 140 entries, and (2) secondary sources, including more than 300 titles. It is hoped that this account will suggest several additional research topics and inspire scholars to make further advances in this fascinating field of research.
Intertextual unity in the Franciscan Friar Juan Baptista de Lagunas’s opus of 1574
Authors: Monzón Cristina 
Published: November 2012

Summary
The grammar, dictionary, and religious texts by Friar Juan Baptista de Lagunas (c.1530–1604) are three works that the author conceived as complementary and published within one cover (1574). Nevertheless, the content of each book is rather different in the theme developed and the influences that oriented its realization. The works of the French Franciscan monk Maturino Gilberti (c.1498–1585) had a great impact on all three texts; the Arte in particular. Lagunas’ dictionary, however, follows Ambrogio Calepino (c.1435–1511), while his doctrinal texts are guided by Catholic religious teachings. Furthermore, each of the three texts has its own pagination. Despite these details, the unity of the three texts as one single volume can be shown by the textual coherence achieved through the cross-references between them and by the printing decisions taken at the moment of production, both factors that strengthen the argument supporting the intertextual unity of Lagunas’ oeuvre.
Language Pedagogy and Political-Cognitive Autonomy in Mid-19th Century Geneva
Authors: Joseph John E. 
Published: November 2012

Summary
Charles-Louis Longchamp (1802–1874) was the dominant figure in Latin studies in Geneva in the 1850s and 1860s and had a formative influence on the Latin teachers of Ferdinand de Saussure (1857–1913). Longchamp’s work was in the grammaire générale tradition, which, on account of historical anomalies falling out from the Genevese Revolution of 1846 to 1848, was still being taught in Geneva up to the mid-1870s, despite having been put aside in France in the 1830s and 1840s. Longchamp succeeded briefly in getting his Latin grammars onto the school curriculum, replacing those imported from France, which Longchamp argued were making the Genevese mentally indistinguishable from the French, weakening their power to think for themselves and putting their political independence at risk. His own grammars offered “a sort of bulwark against invasion by the foreign mind, a guarantee against annexation”. Longchamp’s pedagogical approach had echoes in Saussure’s teaching of Germanic languages in Paris in the 1880s, and in the ‘stylistics’ of Saussure’s successor Charles Bally (1865–1947).
Determining the performance of the next generation of fusion experiments by a similarity transformation of the JET D–T experiments
Authors: Cordey J.G. , McDonald D.C. , Schippers W. 
Published: November 2012

Abstract
A similarity technique is described in which the temperature and density profiles and fusion performance of ITER and DEMO are determined from the D–T and D–D discharges completed on JET. The limitations and errors associated with this technique are also briefly described.