bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis
Authors: Dubinkina Veronika B. , Ischenko Dmitry S. , Ulyantsev Vladimir I. , Tyakht Alexander V. , Alexeev Dmitry G. 
Published: January 2016

Abstract
Background
A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. “Shotgun” metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community. Recently, researchers started to analyze metagenomes using reference-free methods based on the analysis of oligonucleotides (k-mers) frequency spectrum previously applied to isolated genomes. However, little is known about their correlation with the existing approaches for metagenomic feature extraction, as well as the limits of applicability. Here we evaluated a metagenomic pairwise dissimilarity measure based on short k-mer spectrum using the example of human gut microbiota, a biomedically significant object of study.

Results
We developed a method for calculating pairwise dissimilarity (beta-diversity) of “shotgun” metagenomes based on short k-mer spectra (5≤k≤11). The method was validated on simulated metagenomes and further applied to a large collection of human gut metagenomes from the populations of the world (n=281). The k-mer spectrum-based measure was found to behave similarly to one based on mapping to a reference gene catalog, but different from one using a genome catalog. This difference turned out to be associated with a significant presence of viral reads in a number of metagenomes. Simulations showed limited impact of bacterial genetic variability as well as sequencing errors on k-mer spectra. Specific differences between the datasets from individual populations were identified.

Conclusions
Our approach allows rapid estimation of pairwise dissimilarity between metagenomes. Though we applied this technique to gut microbiota, it should be useful for arbitrary metagenomes, even metagenomes with novel microbiota. Dissimilarity measure based on k-mer spectrum provides a wider perspective in comparison with the ones based on the alignment against reference sequence sets. It helps not to miss possible outstanding features of metagenomic composition, particularly related to the presence of an unknown bacteria, virus or eukaryote, as well as to technical artifacts (sample contamination, reads of non-biological origin, etc.) at the early stages of bioinformatic analysis. Our method is complementary to reference-based approaches and can be easily integrated into metagenomic analysis pipelines.
IPLaminator: an ImageJ plugin for automated binning and quantification of retinal lamination
Authors: Li Shuai , Woodfin Michael , Long Seth S. , Fuerst Peter G. 
Published: January 2016

Abstract
Background
Information in the brain is often segregated into spatially organized layers that reflect the function of the embedded circuits. This is perhaps best exemplified in the layering, or lamination, of the retinal inner plexiform layer (IPL). The neurites of the retinal ganglion, amacrine and bipolar cell subtypes that form synapses in the IPL are precisely organized in highly refined strata within the IPL. Studies focused on developmental organization and cell morphology often use this layered stratification to characterize cells and identify the function of genes in development of the retina. A current limitation to such analysis is the lack of standardized tools to quantitatively analyze this complex structure. Most previous work on neuron stratification in the IPL is qualitative and descriptive.

Results
In this study we report the development of an intuitive platform to rapidly and reproducibly assay IPL lamination. The novel ImageJ based software plugin we developed: IPLaminator, rapidly analyzes neurite stratification patterns in the retina and other neural tissues. A range of user options allows researchers to bin IPL stratification based on fixed points, such as the neurites of cholinergic amacrine cells, or to define a number of bins into which the IPL will be divided. Options to analyze tissues such as cortex were also added. Statistical analysis of the output then allows a quantitative value to be assigned to differences in laminar patterning observed in different models, genotypes or across developmental time.

Conclusion
IPLaminator is an easy to use software application that will greatly speed and standardize quantification of neuron organization.
Hematopoietic stem cell transplantation for multiple sclerosis: is it a clinical reality?
Authors: Bakhuraysah Maha M. , Siatskas Christopher , Petratos Steven 
Published: January 2016

AbstractHematopoietic stem cell transplantation (HSCT) is a treatment paradigm that has long been utilized for cancers of the blood and bone marrow but has gained some traction as a treatment paradigm for multiple sclerosis (MS). Success in the treatment of patients with this approach has been reported primarily when strict inclusion criteria are imposed that have eventuated a more precise understanding of MS pathophysiology, thereby governing trial design. Moreover, enhancing the yield and purity of hematopoietic stem cells during isolation along with the utility of appropriate conditioning agents has provided a clearer foundation for clinical translation studies. To support this approach, preclinical data derived from animal models of MS, experimental autoimmune encephalomyelitis, have provided clear identification of multipotent stem cells that can reconstitute the immune system to override the autoimmune attack of the central nervous system. In this review, we will discuss the rationale of HSCT to treat MS by providing the benefits and complications of the clinically relevant protocols, the varying graft types, and conditioning regimens. However, we emphasize that future trials based on HSCT should be focused on specific therapeutic strategies to target and limit ongoing neurodegeneration and demyelination in progressive MS, in the hope that such treatment may serve a greater catchment of patient cohorts with potentially enhanced efficiency and lower toxicity. Despite these future ambitions, a proposed international multicenter, randomized clinical trial of HSCT should be governed by the best standard care of treatment, whereby MS patients are selected upon strict clinical course criteria and long-term follow-up studies of patients from international registries are imposed to advocate HSCT as a therapeutic option in the management of MS.
Central Nervous System–Toxic Lidocaine Concentrations Unmask L-Type Ca2+ Current–Mediated Action Potentials in Rat Thalamocortical Neurons: An In Vitro Mechanism of Action Study
Authors: Putrenko Igor , Ghavanini Amer A. , Meyer Schöniger Katrin S. , Schwarz Stephan K. W. 
Published: January 2016

BACKGROUND:
High systemic lidocaine concentrations exert well-known toxic effects on the central nervous system (CNS), including seizures, coma, and death. The underlying mechanisms are still largely obscure, and the actions of lidocaine on supraspinal neurons have received comparatively little study. We recently found that lidocaine at clinically neurotoxic concentrations increases excitability mediated by Na+-independent, high-threshold (HT) action potential spikes in rat thalamocortical neurons. Our goal in this study was to characterize these spikes and test the hypothesis that they are generated by HT Ca2+ currents, previously implicated in neurotoxicity. We also sought to identify and isolate the specific underlying subtype of Ca2+ current.

METHODS:
We investigated the actions of lidocaine in the CNS-toxic concentration range (100 μM–1 mM) on ventrobasal thalamocortical neurons in rat brain slices in vitro, using whole-cell patch-clamp recordings aided by differential interference contrast infrared videomicroscopy. Drugs were bath applied; action potentials were generated using current clamp protocols, and underlying currents were identified and isolated with ion channel blockers and electrolyte substitution.

RESULTS:
Lidocaine (100 μM–1 mM) abolished Na+-dependent tonic firing in all neurons tested (n = 46). However, in 39 of 46 (85%) neurons, lidocaine unmasked evoked HT action potentials with lower amplitudes and rates of de-/repolarization compared with control. These HT action potentials remained during the application of tetrodotoxin (600 nM), were blocked by Cd2+ (50 μM), and disappeared after superfusion with an extracellular solution deprived of Ca2+. These features implied that the unmasked potentials were generated by high-voltage–activated Ca2+ channels and not by Na+ channels. Application of the L-type Ca2+ channel blocker, nifedipine (5 μM), completely blocked the HT potentials, whereas the N-type Ca2+ channel blocker, ω-conotoxin GVIA (1 μM), had little effect.

CONCLUSIONS:
At clinically CNS-toxic concentrations, lidocaine unmasked in thalamocortical neurons evoked HT action potentials mediated by the L-type Ca2+ current while substantially suppressing Na+-dependent excitability. On the basis of the known role of an increase in intracellular Ca2+ in the pathogenesis of local anesthetic neurotoxicity, this novel action represents a plausible contributing candidate mechanism for lidocaine’s CNS toxicity in vivo.
Daily cycle in oxygen consumption by the sea anemone Nematostella vectensis Stephenson
Authors: Maas Amy E. , Jones Ian T. , Reitzel Adam M. , Tarrant Ann M. 
Published: January 2016

ABSTRACT
In bilaterian animals, the circadian clock is intimately involved in regulating energetic metabolism. Although cnidarians exhibit diel behavioral rhythms including cycles in locomotor activity, tentacle extension and spawning, daily cycles in cnidarian metabolism have not been described. To explore a possible circadian metabolic cycle, we maintained the anemone Nematostella vectensis in a 12 h light/dark cycle, a reversed light cycle, or in constant darkness. Oxygen consumption rates were measured at intervals using an optical oxygen meter. Respiration rates responded to entrainment with higher rates during light periods. During a second experiment with higher temporal resolution, respiration rates peaked late in the light period. The diel pattern could be detected after six days in constant darkness. Together, our results suggest that respiration rates in Nematostella exhibit a daily cycle that may be under circadian control and that the cycle in respiration rate is not driven by the previously described nocturnal increase in locomotor activity in this species.
Development of Novel Photocatalyst and Cocatalyst Materials for Water Splitting under Visible Light
Authors: Maeda Kazuhiko , Domen Kazunari 
Published: January 2016

Abstract
Overall water splitting using a semiconductor photocatalyst with sunlight has long been viewed as a potential means of large-scale H2 production from renewable resources. In general, the reaction can be accomplished when a photocatalyst is modified with a suitable cocatalyst that efficiently promotes water reduction. It is therefore essential to develop both photocatalysts and cocatalysts in harmony. Certain metal (oxy)nitrides are potential candidates as water-splitting photocatalysts because of their suitable band edge positions for water reduction/oxidation, small band gaps (&lt;3 eV), and stability under irradiation. However, efficient water splitting using visible-light-responsive oxynitrides has still remained a challenge. This account describes our recent developments over the last 10 years of new oxynitrides as well as cocatalysts for overall water splitting under visible light.
Enacting embodiment and Blue Muffins
Authors: Fraleigh Sondra 
Published: January 2016

Abstract
In this article, a dance of my imagining draws upon topics of embodiment, imperfection and lack of art, political art, implicatedness, boredom and being stupid. Questions of abstraction and records of thought hinge on discussions of disembodied movement, technology and performance. Key choreographic works include Blue Muffins; Bill T. Jones, GHOSTCATCHING; Troika Ranch, and Interactive Installations. Key sources include Susan Kozel’s Closer (2007); Antonio Damasio’s Self Comes to Mind (2012); and Francisco Varela’s, The Embodied Mind (1991). The article explains movement and stillness as bodily enactments that can be arrested and recorded in arts technologies. Such records become part of why we care to make art, and how we make it matter.
Shifting the self, intertwining the other: Exploring the potential of things in performance
Authors: Nuding Elise 
Published: January 2016

Abstract
This article draws on my experience of making and performing Shift, spin, warp, twine (2014) to explore the complex, messy relationship between people and things. Combining reflections on the practice with scholarship from a range of disciplines concerned with the study of material culture, it offers some thoughts on the potential of working with things in performance.
Towards a posthuman ethics: Moving with others in Karl Cronin’s Somatic Natural History Archive
Authors: Morris Michael J. 
Published: January 2016

Abstract
If the body is understood as a dynamic process of materialization, a becoming in relation to the world of which it is a part, then to engage with the movement behaviours of other forms of life is to orient the becoming of the body towards other ways of being in the world. Through its engagement with the movements and bodies of non-human plant and animal life, Karl Cronin’s Somatic Natural History Archive (SNHA) enacts a posthuman ethics, disrupting ‘the human’ with corporeal possibilities made available through the practice of embodiments derived from Cronin’s encounters with non-human others.
butoh 1.2.3…(wrecked beach)
Authors: Preece Bronwyn 
Published: January 2016

Abstract
A performer’s poems: written from the precarious and fragile, evocative alchemistic moments that butoh (re)presented for me…on this day, in and for that moment. Penned immediately following three consecutive day, outdoor events, these words capture my body-as-participant in Kokoro Dance’s 19th Annual Wreck Beach performances, Vancouver, Canada (July 2014). The poems chart the subtle fluidity and changing landscape – internally/externally – of each fresh performance. Performing in the waters of British Columbia’s west coast was particularly resonant following the Fukushima disaster (directly relating ‘our’ butoh back to its origins as a response to the horrors of Hiroshima and Nagasaki) – and these poems capture in their essence one woman’s quest to understand and relate to the built and the meltdown of ‘environment’ through a somatically, embodied ecological perspective.
Embedded and woven through these lines are references specific to choreographic elements of the piece, the location, the timing and/or local Indigenous Musqueam legends….from the Argentina vs. Germany World cup, to the sand dunes, to Xe-ls, the Creator… their imbrication enlivens the congruency of what was birthed on the beach, and the particulars are designed to conflate our understanding of the potency (and urgency) demanded of our/this place and time. My poetry is movement, simultaneously holding within its lexicon a tension between understanding, applicability, the local and the universal. My poetry is a butoh dance open to your interpretation. I offer it as a gift….
Participation and spectatorship in Tino Sehgal’s These Associations
Authors: Hildebrandt Antje 
Published: January 2016

Abstract
These Associations (2012) by British-German artist Tino Sehgal was commissioned as the thirteenth, and final, artwork of the Unilever Series. It took place in Tate Modern’s Turbine Hall between July and October 2012. As one of the people involved in the project and as a practice-based researcher, I am in a curious critical position: both deeply involved and immersed in the work, yet also striving to retain a degree of critical distance. From a methodological position I have the double privilege of ‘having been there’, not only as an observer, a spectator, a visitor, a viewer or an on-looker of the work but also as a participant in the work. In this article I take full advantage of the inside/outside perspective, proposing that it is possible to speak critically from within the art object.
Becoming plural: The distribution of the self in collaborative performance research
Authors: Colin Noyale 
Published: January 2016

Abstract
This article seeks to explore the shifting sense of identity experienced in collaborative choreographic practices. In this critical discussion I develop a concept of collaboration based upon my collaborative work in two specific practical enquiries. I reflect on how each practice accounts for a collaborative site of multiple selves; or better perhaps, I want to suggest that collaboration in dance research can on the one hand reveal the tension between self and other; and on the other hand it belongs to a process that tends towards the experience of a plurality of selves. The critique of the self as an individual entity is nothing new. Deleuze and Guattari’s rhizomatic view of subjectivity, for example, has permeated the discourse on collaboration in performance studies since the 1990s. However, the entanglement of digital and computational technologies with our human experience has further deepened the gap between the subject as a singular, unified individual and the sense of multiplicity expressed through computational-associated terms such as the networked or distributed self. If contemporary subjectivity is foremost relational, what might collaborative dance research illuminate in relation to distributed subjectivities? The essay considers the relationship between the plurality of self that I have experienced as a performer/choreographer engaged in (collaborative) practice as research and the specificity of process and product which has emerged out of these collaborations.
‘Our jolly marin wear’: The queer fashionability of the sailor uniform in interwar France and Britain
Authors: Stephenson Andrew 
Published: January 2016

Abstract
Examining autobiographies, letters, newspaper reports and photographs, this article argues that French sailor wear with its military exoticism and gender-blurring possibilities was adopted by fashionable metropolitan British and French groups in the interwar years as a recognizable signifier of an emerging gay and bisexual identity. The appropriation of the French military uniform by gay and bisexual men and by lesbians was tied, on the one hand, to their firsthand experience of travel to the Mediterranean coast, and to ideas about the Mediterranean ports as places of sexual liberalism and bohemianism that featured in contemporary ballet and the theatre. On the other hand, such promiscuous associations also drew upon popular mythologies about the sailor’s erotic appeal and his voracious sexual appetite that were circulating within contemporary French novels, the illustrated press, popular films and songs. As the appropriation of the naval uniform became visible in photographs documenting its growing fashionability in gay clubs, fancy dress balls and parties in Paris and London, sailor wear registered as queerly resonant to its wearers and admirers, leading to the French sailor becoming a recognizable and much-admired promiscuous gay icon.
Fashion brands and gay/lesbian-inclusive advertising in the USA
Authors: Chae Yoori , Kim Yumin , Johnson Kim K. P. 
Published: January 2016

Abstract
Within the United States general attitudes towards gays and lesbians (GL) are rapidly undergoing change. Several researchers have previously documented that heterosexual consumers respond negatively to advertisements featuring same-sex couples. At this critical juncture, it is important to reexamine consumer response to fashion advertisements featuring GL images. Using a small qualitative study (n = 10) and an experiment (n = 202) our research purpose was to determine whether consumer attitude towards advertisements, brand attitude, brand distinctiveness and/or brand attractiveness varied based on the level of inclusiveness of GL images (i.e. GL-inclusive vs. non-inclusive). Results from the qualitative project demonstrated most participants responded positively to the advertisements featuring GL images although two participants were worried about unidentified ‘negative’ influences on the sexual orientation of heterosexual viewers. The inclusiveness level of GL images did not negatively influence attitude towards the advertisements or brand attitude. Rather, GL-inclusive advertising resulted in higher ratings of brand distinctiveness and attractiveness as compared to the non-inclusive advertising. Implications and limitations of this study as well as suggestions for future research are discussed.
Dilapidated Dwelling
Authors: Keiller Patrick 
Published: January 2016

Where I live, there seem to be two kinds of space. There is new space, in which none of the buildings are more than about ten years old, and there is old space, in which most of the buildings are at least twenty years old, a lot of them over ninety years old, and all are more or less dilapidated.

Patrick Keiller begins his 1998 essay The Dilapidated Dwelling with a concise and simple description of the issues he raises in both the essay and the film to which it relates, The Dilapidated Dwelling, 2000. In both film and word Keiller’s description of the UK’s physical infrastructure at the turn of the millennium was both depressingly evident and in need of explanation. Continuing in the vein of his most famed films London, 1994, and Robinson in Space, 1997, The Dilapidated Dwelling is narrated by an invisible voice that probes the peculiarities of the economic, political and social conditions of late 20th century Britain through the prism of its infrastructure, urban blight and, in particular, its housing.
The narrator, a woman is recalled to Britain after two decades in the Arctic investigates ‘the predicament of the house’, discovering that the most recent advances in industrial manufacture have left the house building industry practically untouched. By contrast, changes to the global economy and the emergence of the digital age have conspired to create wealth that has seen the market price of the existing, dilapidated housing stock skyrocket. Revisiting the ideas of Constant, Buckminster Fuller and Archigram she discusses the anomalies of housing supply and demand that have allowed some to escape housing poverty and yet leave millions in ‘dilapidated dwellings’.
To coincide with the the launch of its three year project Housing – Critical Futures, Architecture, Media, Politics, Society, is republishing Keiller’s essay and re-showing his film. The essay is reprinted from Keiller’s recent book, The View From the Train, Vesro, 2013; and the film is shown as part of a one day series of film screenings and debates about the effects of housing on issues of public health, Housing, Health and Film. Screened at the Bluecoat Chambers Art Gallery, Liverpool, the film is accompanied by debates from architects, filmmakers and public health officials.