bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strong and highly variable push of ocean waves on Southern Ocean sea ice
Authors: Stopa Justin E. , Sutherland Peter , Ardhuin Fabrice 
Published: May 2018

SignificanceSouthern Ocean sea ice plays a key role in regulating the uptake of carbon and heat by the global ocean. In this context, ocean waves have a strong influence, including ice break-up and pancake formation. These processes explain large differences in sea-ice properties between Arctic and Antarctic. Waves also decay in the ice, exerting a force in their propagation direction that compacts the ice. Here, we provide an extensive dataset on wave heights and its decay in sea ice, using satellite imagery. Wave decay can be much faster than previously reported but is highly variable. The resulting wave force on the ice can have a profound impact on both ice extent and thickness.
Trace, Revelation, and Interpretant in Archaeological Research: The Graffiti of Huaca Colorada, Peru
Authors: Swenson Edward 
Published: May 2018

AbstractRomantic notions that the advancement of archaeological knowledge depends on the thrill of unanticipated discoveries departs from the standard practice of interpreting data according to impartial research designs. However, the unexpected find commonly stymies the deductive testing of hypothesis, and the material traces (signs) upon which research relies often disrupt the course of archaeological investigations. The main objective of this article is to demonstrate that the distinct semiotic affordances of material remains can significantly affect archaeological interpretations. The undertheorized epistemological problems of revelation in archaeology are brought to bear through an examination of the spectral quality of graffiti etched onto the walls of the Moche ceremonial site of Huaca Colorada in northern Peru (CE 650–850). An interpretation of the graffiti in relationship to rituals of human sacrifice and architectural renovation demonstrates that the power of the monument was founded on its semiotic density; the complex layering of signs—that continually spawned new signs—created a place of limitless discovery and affect that profoundly shaped perceptions of the huaca for both Moche visitors and later archaeologists alike. Ultimately, the graffiti provide a rare data set that permits a consideration of the effects of signs as “intepretants” in the tradition of Peirce.
The Meaning Making of the Built Environment in the Fascist City: A Semiotic Approach
Authors: Nanni Antonio , Bellentani Federico 
Published: May 2018

AbstractThis article draws on interpretative semiotics to address how spatial designers endow the built environment with meaning. From a semiotic perspective, designing the built environment is an activity that extends beyond its physical reshaping. Designers use complex sociosemiotic strategies to funnel users’ interpretations, drawing upon their manifold resources. Analyzing these strategies is important to not naturalize the dominant meaning that is inscribed in the built environment. As a case study, we analyze spatial design in the city of Forlì, Italy, during the Fascist regime (1922–43). Through the case study, we delineate two complimentary design strategies: typification and environmental propaganda. Typification establishes and uses familiar types of buildings to channel individual interpretations; environmental propaganda spreads cultural artifacts and enacts political rituals about the built environment. Both of these strategies try to steer users’ interpretations of the built environment in everyday life. Finally, we provide a detailed analysis of a particular built form in Forlì—the headquarters of the Opera Nazionale Balilla—showing how these strategies were deployed for this particular building.
Rogue Pixels: Indexicality and Algorithmic Camouflage
Authors: Paulsen Kris 
Published: May 2018

AbstractThe resolution of publicly available satellite photography is limited to 50 cm a pixel. Every pixel in a satellite image is a single, solid color. The reasons for the resolution limit are tactical as well as protective: according to forensic architect Eyal Weizman, it maintains the privacy of individuals on the ground as well as makes the consequences of state violence harder to investigate. A uniformly colored pixel can be evidence of a drone attack or proof that it never happened. The indexical evidence ambivalently sustains both interpretations. If camouflage has been traditionally thought of as a blending into the contiguous environment, often geared toward a camera’s gaze, in this essay I look to the reorientation of camouflage away from the adjacent surroundings and toward the mediating structures of the interface and database. The objective of camouflage is now to merge into arrays of information and to slip below the threshold of detectability. This essay examines the work of artists and activists, such as Hito Steyerl, Zach Blas, and Adam Harvey, who strategize ways of becoming “rogue pixels” hiding in “the cracks of our standards of resolution,” resisting the means by which our bodies are indexed on virtual interfaces and algorithmically parsed as data.
Not Citizens of a Classical Mediterranean: Muslim Youth from Marseille Elude a Linguistic Gentrification by the French State
Authors: Evers Cécile 
Published: May 2018

AbstractA moral panic is afoot in contemporary France surrounding what place French-Muslim youth hold within the national identity. The French state, in particular, is actively engaged in regimenting what it means to be a young Muslim person from France. This article examines how, during Marseille’s year (2013) as the European Capital of Culture, the municipal government and the local branch of the Ministère de l’Éducation Nationale spearheaded several initiatives, a number of which focused on Arabic-language education, with the aim of transforming French-Muslim youth from Marseille’s housing projects into secular, upwardly mobile individuals. Ethnographic inquiry with the youth targeted by such “linguistic gentrification” programs reveals that the state’s reimagining of them in these terms remained largely at odds with how they themselves understood their identities. This article, as such, illustrates the analytical importance of attending to people’s uptake when evaluating the eventual scope of top-down discourses and projects, while also offering an example of how the label “Mediterranean” functions as a spatiotemporal shifter, deployed by different groups to activate alternative accounts of history, the present, and the future.
Design of robotic cells based on relative handling modules with use of SolidWorks system
Authors: Gaponenko E V , Anciferov S I 
Published: May 2018

Abstract
The article presents a diagramed engineering solution for a robotic cell with six degrees of freedom for machining of complex details, consisting of the base with a tool installation module and a detail machining module made as parallel structure mechanisms. The output links of the detail machining module and the tool installation module can move along X-Y-Z coordinate axes each. A 3D-model of the complex is designed in the SolidWorks system. It will be used further for carrying out engineering calculations and mathematical analysis and obtaining all required documentation.
Affairs of Humanity: Arguments for Humanitarian Intervention in England and Europe, 1698–1715
Authors: Arnold Catherine S 
Published: May 2018

Abstract
Why and how did a new type of intervention, intended to prevent rulers from punishing individuals for their religious beliefs and justified using natural law, emerge in England during the first decade of the eighteenth century? This article traces its origins to the War of the Spanish Succession, when Huguenot publicists and diplomats petitioned English politicians to negotiate freedom for Huguenot prisoners in France. In campaigning for prisoners’ freedom rather than for the restoration of Huguenot corporate rights in France, Huguenot publicists and diplomats had to justify intervention in universalising, non-confessional terms. Because those prisoners were not protected by treaty law, the laws of war, or the laws of France, they cited Protestant and humanist traditions of natural law and theories of natural sociability to justify negotiating their release. In so doing, they invited European readers, politicians and monarchs to sympathise with distant strangers—and even to take political action on their behalf—not only because they shared a common faith, but also because they belonged to human society and shared a common humanity. These arguments circulated both in print and among European diplomats, altering the conduct of international affairs. In England, this article shows, Huguenot campaigns influenced debates about intervention and English foreign policy-making. Thus, this article suggests a new narrative for the diffusion of humanitarian argument in eighteenth-century western European political culture.
Robotic Assisted MRI-Guided Interventional Interstitial MR-Guided Focused Ultrasound Ablation in a Swine Model
Authors: MacDonell Jacquelyn , Patel Niravkumar , Fischer Gregory , Burdette E Clif , Qian Jiang , Chumbalkar Vaibhav , Ghoshal Goutam , Heffter Tamas , Williams Emery , Gounis Matthew , King Robert , Thibodeau Juliette , Bogdanov Gene , Brooks Olivia W , Langan Erin , Hwang Roy , Pilitsis Julie G 
Published: May 2018

Abstract

BACKGROUND
Ablative lesions are current treatments for epilepsy and brain tumors. Interstitial magnetic resonance (MR) guided focused ultrasound (iMRgFUS) may be an alternate ablation technique which limits thermal tissue charring as compared to laser therapy (LITT) and can produce larger ablation patterns nearer the surface than transcranial MR guided focused ultrasound (tcMRgFUS).

OBJECTIVE
To describe our experience with interstitial focused ultrasound (iFUS) ablations in swine, using MR-guided robotically assisted (MRgRA) delivery.

METHODS
In an initial 3 animals, we optimized the workflow of the robot in the MR suite and made modifications to the robotic arm to allow range of motion. Then, 6 farm pigs (4 acute, 2 survival) underwent 7 iMRgFUS ablations using MRgRA. We altered dosing to explore differences between thermal dosing in brain as compared to other tissues. Imaging was compared to gross examination.

RESULTS
Our work culminated in adjustments to the MRgRA, iMRgFUS probes, and dosing, culminating in 2 survival surgeries; swine had ablations with no neurological sequelae at 2 wk postprocedure. Immediately following iMRgFUS therapy, diffusion-weighted imaging, and T1 weighted MR were accurate reflections of the ablation volume. T2 and fluid-attenuated inversion-recovery (FLAIR) images were accurate reflections of ablation volume 1-wk postprocedure.

CONCLUSION
We successfully performed MRgRA iFUS ablation in swine and found intraoperative and postoperative imaging to correlate with histological examination. These data are useful to validate our system and to guide imaging follow-up for thermal ablation lesions in brain tissue from our therapy, tcMRgFUS, and LITT.
Programmed Death Ligand 1 Is a Negative Prognostic Marker in Recurrent Isocitrate Dehydrogenase-Wildtype Glioblastoma
Authors: Pratt Drew , Dominah Gifty , Lobel Graham , Obungu Arnold , Lynes John , Sanchez Victoria , Adamstein Nicholas , Wang Xiang , Edwards Nancy A , Wu Tianxia , Maric Dragan , Giles Amber J , Gilbert Mark R , Quezado Martha , Nduom Edjah K 
Published: May 2018

Abstract

BACKGROUND
Checkpoint inhibition has demonstrated clinical efficacy in a variety of solid tumors. Reports of programmed death ligand 1 (PD-L1) expression in glioblastoma are highly variable (ranging from 6% to 88%) and its role as a prognostic marker has yielded conflicting results.

OBJECTIVE
To validate the prevalence and prognostic role of PD-L1 expression in a large cohort of diffuse gliomas according to the 2016 revised WHO classification.

METHODS
Using tissue microarrays, we compared 5 PD-L1 monoclonal antibodies (n = 56) and validated expression (n = 183) using quantitative immunohistochemistry (IHC) and RNA in situ hybridization (RISH). Expression data from The Cancer Genome Atlas (TCGA) and published studies were compared with clinical outcome. Multiplexed immunophenotyping was used to identify PD-L1+ cell populations in post-treatment glioblastoma.

RESULTS
Using a 5% cut-off, PD-L1 expression was significantly associated with a poor prognosis in both histologically defined (n = 125, log-rank P < .001) and recurrent isocitrate dehydrogenase (IDH)-wildtype glioblastoma (n = 60, log-rank P = .015). PD-L1 remained a significant negative prognosticator in Cox regression analysis (hazard ratio: 1.96, P = .021). Analysis of TCGA data confirmed decreased overall survival in recurrent non–glioma CpG island methylator phenotype (G-CIMP) glioblastoma (n = 12, log-rank P = .023), but not in glioblastoma as a group (n = 444, log-rank P = .135). PD-L1 RISH showed a significant correlation with IHC (P < .0001). PD-L1 was observed in the proliferating perivascular stem cell and immune niche of post-treatment glioblastoma.

CONCLUSION
A 5% PD-L1 expression cut-off identified a subset of glioblastoma that is associated with a worse clinical outcome. This association remained significant within the newly defined IDH-wildtype classification. These findings could have implications for patient stratification in future clinical trials of PD-1/PD-L1 blockade.
Preliminary exploration of a computerized cognitive battery and comparison with traditional testing in patients with high-grade glioma
Authors: Cerhan Jane H , Caine Chip , Anderson S Keith , Johnson Derek R , Lachance Daniel H , Yan Elizabeth , Brown Paul D 
Published: May 2018

Abstract

Background
Cognitive function is an important outcome measure in many brain tumor clinical trials, and investigators are interested in employing the most efficient methods of cognitive assessment for this purpose. Computerized testing can be appealing because of the perceived ease of use and electronic data generated. Traditional tests may have the advantage of accumulated validity evidence and comparability across historic trials.

Methods
We evaluated feasibility of a Cogstate battery in 39 patients with high-grade glioma, and compared it with a commonly used paper-and-pencil battery.

Results
Both batteries were well tolerated and rated equally likeable. Correlations between the batteries were low to low-moderate. More patients showed impairment at baseline and decline across trials on traditional tests.

Conclusions
Both batteries were well tolerated, but the most complicated tasks (from both batteries) could not be completed by all subjects. Preliminary validity evidence for the Cogstate tasks was mixed, but a larger sample is needed.
The gene regulatory network of mESC differentiation: a benchmark for reverse engineering methods
Authors: Meisig Johannes , Blüthgen Nils 
Published: May 2018

A large body of data have accumulated that characterize the gene regulatory network of stem cells. Yet, a comprehensive and integrative understanding of this complex network is lacking. Network reverse engineering methods that use transcriptome data to derive these networks may help to uncover the topology in an unbiased way. Many methods exist that use co-expression to reconstruct networks. However, it remains unclear how these methods perform in the context of stem cell differentiation, as most systematic assessments have been made for regulatory networks of unicellular organisms. Here, we report a systematic benchmark of different reverse engineering methods against functional data. We show that network pruning is critical for reconstruction performance. We also find that performance is similar for algorithms that use different co-expression measures, i.e. mutual information or correlation. In addition, different methods yield very different network topologies, highlighting the challenge of interpreting these resulting networks as a whole.
This article is part of the theme issue ‘Designer human tissue: coming to a lab near you’.
Integrating Hi-C and FISH data for modeling 3D organizations of chromosomes
Authors: Abbas Ahmed , He Xuan , Zhou Bin , Zhu Guangxiang , Ma Zishan , Gao Jun-Tao , Zhang Michael Q , Zeng Jianyang 
Published: May 2018

AbstractThe new advances in various experimental techniques that provide complementary in-formation about the spatial conformations of chromosomes have inspired researchers to develop computational methods to fully exploit the merits of individual data sources and combine them to improve the modeling of chromosome structure. In this paper, we propose GEM-FISH, a first method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model. Comprehensive tests on a set of chromosomes for which both Hi-C and FISH data were available have demonstrated that GEM-FISH can reconstruct the 3D models of chromosomes with more accurate spatial organizations of TADs and compartments than using only Hi-C data. In addition, GEM-FISH can accurately capture the spatial proximity of loop loci and the colocalization of loci from the same sub-compartments. Moreover, our reconstructed 3D models of chromosomes revealed novel patterns of spatial distributions of super-enhancers which can provide useful insights into understanding the functional roles of these super-enhancers in gene regulation. All these results demonstrated that, through integrating both Hi-C and FISH data into a unified framework, GEM-FISH can provide a better tool for modeling the 3D organizations of chromosomes than using the Hi-C data alone.
Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum
Authors: Armitage Andrew D. , Lysøe Eric , Nellist Charlotte F. , Lewis Laura A. , Cano Liliana M. , Harrison Richard J. , Brurberg May Bente 
Published: May 2018

AbstractThe oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, cultured from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of Clade 1A and 1C. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from Clade 1 and will facilitate effector informed breeding strategies in other crops.
Supragingival plaque microbiome ecology and functional potential in the context of health and disease
Authors: Espinoza Josh L , Harkins Derek M. , Torralba Manolito , Gomez Andres , Highlander Sarah K. , Jones Marcus B. , Leong Pamela , Saffery Richard , Bockmann Michelle , Kuelbs Claire , Inman Jason M. , Hughes Toby , Craig Jeffrey M. , Nelson Karen E. , Dupont Chris L. 
Published: May 2018

AbstractTo address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely-related previously-uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first completeGracilibacteriagenomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology and our results provide the information needed for next generation diagnostic tools and therapeutics for caries.
A comparison of auditory oddball responses in dorsolateral prefrontal cortex, basolateral amygdala and auditory cortex of macaque
Authors: Camalier Corrie R. , Scarim Kaylee C. , Mishkin Mortimer , Averbeck Bruno B. 
Published: May 2018

AbstractThe mismatch negativity (MMN) is an event-related potential component seen in response to unexpected “novel” stimuli, such as in an auditory oddball task. The MMN is of wide interest and application, but the neural responses that generate it are poorly understood. This is in part due to differences in design and focus between animal and human oddball paradigms. For example, one of the main explanatory models, the “predictive error hypothesis”, posits differences in timing and selectivity between signals carried in auditory and prefrontal cortex. However these predictions have not been fully tested because 1) noninvasive techniques used in humans lack the combined spatial and temporal precision necessary for these comparisons, and 2) single-neuron studies in animal models, which combine spatial and temporal precision, have not focused on higher order contributions to novelty signals. In addition, accounts of the MMN traditionally do not address contributions from subcortical areas known to be involved in novelty detection, such as the amygdala. To better constrain hypotheses and to address methodological gaps between human and animal studies, we recorded single neuron activity from the auditory cortex, dorsolateral prefrontal cortex, and basolateral amygdala of two macaque monkeys during an auditory oddball paradigm modeled after that used in humans. Consistent with predictions of the predictive error hypothesis, novelty signals in prefrontal cortex were generally later than in auditory cortex, and were abstracted from stimulus-specific effects seen in auditory cortex. However, we found signals in amygdala that were comparable in magnitude and timing to those in prefrontal cortex, and both prefrontal and amygdala signals were generally much weaker than those in auditory cortex. These observations place useful quantitative constraints on putative generators of the auditory oddball-based MMN, and additionally indicate that there are subcortical areas, such as the amygdala, that may be involved in novelty detection in an auditory oddball paradigm.