bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cost-effectiveness of endovascular thrombectomy in patients with acute stroke and M2 occlusion
Authors: Khunte Mihir , Wu Xiao , Payabvash Sam , Zhu Chengcheng , Matouk Charles , Schindler Joseph , Sanelli Pina , Gandhi Dheeraj , Malhotra Ajay 
Published: October 2020

BackgroundThe cost-effectiveness of endovascular thrombectomy (EVT) in patients with acute ischemic stroke due to M2 branch occlusion remains uncertain.ObjectiveTo evaluate the cost-effectiveness of EVT compared with medical management in patients with acute stroke presenting with M2 occlusion using a decision-analytic model.MethodsA decision-analytic study was performed with Markov modeling to estimate the lifetime quality-adjusted life years and associated costs of EVT-treated patients compared with no-EVT/medical management. The study was performed over a lifetime horizon with a societal perspective in the Unites States setting. Base case, one-way, two-way, and probabilistic sensitivity analyses were performed.ResultsEVT was the long-term cost-effective strategy in 93.37% of the iterations in the probabilistic sensitivity analysis, and resulted in difference in health benefit of 1.66 QALYs in the 65-year-old age groups, equivalent to 606 days in perfect health. Varying the outcomes after both strategies shows that EVT was more cost-effective when the probability of good outcome after EVT was only 4–6% higher relative to medical management in clinically likely scenarios. EVT remained cost-effective even when its cost exceeded US$200 000 (threshold was US$209 111). EVT was even more cost-effective for 55-year-olds than for 65-year-old patients.ConclusionOur study suggests that EVT is cost-effective for treatment of acute M2 branch occlusions. Faster and improved reperfusion techniques would increase the relative cost-effectiveness of EVT even further in these patients.
Susceptible-infected-spreading-based network embedding in static and temporal networks
Authors: Zhan Xiu-Xiu , Li Ziyu , Masuda Naoki , Holme Petter , Wang Huijuan 
Published: October 2020

AbstractLink prediction can be used to extract missing information, identify spurious interactions as well as forecast network evolution. Network embedding is a methodology to assign coordinates to nodes in a low-dimensional vector space. By embedding nodes into vectors, the link prediction problem can be converted into a similarity comparison task. Nodes with similar embedding vectors are more likely to be connected. Classic network embedding algorithms are random-walk-based. They sample trajectory paths via random walks and generate node pairs from the trajectory paths. The node pair set is further used as the input for a Skip-Gram model, a representative language model that embeds nodes (which are regarded as words) into vectors. In the present study, we propose to replace random walk processes by a spreading process, namely the susceptible-infected (SI) model, to sample paths. Specifically, we propose two susceptible-infected-spreading-based algorithms, i.e.,Susceptible-InfectedNetworkEmbedding (SINE) on static networks andTemporalSusceptible-InfectedNetworkEmbedding (TSINE) on temporal networks. The performance of our algorithms is evaluated by the missing link prediction task in comparison with state-of-the-art static and temporal network embedding algorithms. Results show thatSINEandTSINEoutperform the baselines across all six empirical datasets. We further find that the performance ofSINEis mostly better thanTSINE, suggesting that temporal information does not necessarily improve the embedding for missing link prediction. Moreover, we study the effect of the sampling size, quantified as the total length of the trajectory paths, on the performance of the embedding algorithms. The better performance ofSINEandTSINErequires a smaller sampling size in comparison with the baseline algorithms. Hence, SI-spreading-based embedding tends to be more applicable to large-scale networks.
Duas metáforas históricas sobre o problema do sentido da ação
Authors: Mora Ernesto 
Published: October 2020

O presente artigo descreve duas grandes tendências de abordagem do problema sociológico do sentido da ação. Elas podem ser melhor compreendidas fazendo uso de duas metáforas intuitivas. Trata a primeira da “mente como um computador”, e a segunda do “mundo como um texto”. Descrevem-se de modo geral os supostos filosóficos de cada tendência e os seus principais déficits ontológicos, epistemológicos e metodológicos. Em seguida, são apresentadas as suas convergências implícitas, ilustradas em três déficits teóricos: o dualismo, o atomismo e o holismo. O artigo ressalta a importância da pesquisa interdisciplinar, incluindo nela as chamadas ciências biossociais para a superação desses déficits.
Roberto Carlos como mediador cultural
Authors: Garson Marcelo 
Published: October 2020

Os anos 1960 experimentaram profundas modificações nas hierarquias de poder da música popular brasileira. Entre as causas para esse fenômeno, duas nos interessam em particular: a perda de centralidade do rádio, que cede terreno à televisão, além da construção de um nicho de música jovem, decorrente do fenômeno da Jovem Guarda. Este artigo tem por objetivo estudar a trajetória de Roberto Carlos nesse período, tomando-o como um mediador cultural, agente de trânsito e intersecção que conformou e adaptou os signos do rádio à televisão e, ao mesmo tempo, conseguiu se afirmar como ídolo das massas, mas também da juventude.
“Sou brasileiro, democrata e editor”
Authors: Czajka Rodrigo 
Published: October 2020

O artigo discute o problema da censura a livros durante a primeira fase do regime militar no Brasil e de que forma editores e empresários do ramo editorial criaram estratégias comerciais para a comercialização de obras classificadas como subversivas pelos órgãos de controle da ditadura. Para tanto, a Editora Civilização Brasileira assim como seu proprietário, Ênio Silveira, tornam-se aqui objetos centrais da análise para que possamos compreender as dinâmicas que se operaram no campo das esquerdas intelectualizadas, formado a partir da associação ambivalente entre engajamento e mercado.
In Vivo Magnetic Resonance Imaging‐Based Detection of Heterogeneous Endothelial Response in Thoracic and Abdominal Aorta to Short‐Term High‐Fat Diet Ascribed to Differences in Perivascular Adipose Tissue in Mice
Authors: Bar Anna , Kieronska‐Rudek Anna , Proniewski Bartosz , Suraj‐Prażmowska Joanna , Czamara Krzysztof , Marczyk Brygida , Matyjaszczyk‐Gwarda Karolina , Jasztal Agnieszka , Kuś Edyta , Majka Zuzanna , Kaczor Agnieszka , Kurpińska Anna , Walczak Maria , Pieterman Elsbet J. , Princen Hans M. G. , Chlopicki Stefan 
Published: October 2020

Background
Long‐term feeding with a high‐fat diet (HFD) induces endothelial dysfunction in mice, but early HFD‐induced effects on endothelium have not been well characterized.

Methods and Results

Using an magnetic resonance imaging‐based methodology that allows characterization of endothelial function in vivo, we demonstrated that short‐term (2 weeks) feeding with a HFD to
C57BL/6
mice or to
E3L.CETP
mice resulted in the impairment of acetylcholine‐induced response in the abdominal aorta (AA), whereas, in the thoracic aorta (TA), the acetylcholine‐induced response was largely preserved. Similarly, HFD resulted in arterial stiffness in the AA, but not in the TA. The difference in HFD‐induced response was ascribed to distinct characteristics of perivascular adipose tissue in the TA and AA, related to brown‐ and white‐like adipose tissue, respectively, as assessed by histology, immunohistochemistry, and Raman spectroscopy. In contrast, short‐term HFD‐induced endothelial dysfunction could not be linked to systemic insulin resistance, changes in plasma concentration of nitrite, or concentration of biomarkers of glycocalyx disruption (syndecan‐1 and endocan), endothelial inflammation (soluble form of vascular cell adhesion molecule 1, soluble form of intercellular adhesion molecule 1 and soluble form of E‐selectin), endothelial permeability (soluble form of fms‐like tyrosine kinase 1 and angiopoietin 2), and hemostasis (tissue plasminogen activator and plasminogen activator inhibitor 1).

Conclusions
Short‐term feeding with a HFD induces endothelial dysfunction in the AA but not in the TA, which could be ascribed to a differential response of perivascular adipose tissue to a HFD in the AA versus TA. Importantly, early endothelial dysfunction in the AA is not linked to elevation of classical systemic biomarkers of endothelial dysfunction.
Exploring North Atlantic and North Pacific Decadal Climate Prediction Using Self-Organizing Maps
Authors: Gu Qinxue , Gervais Melissa 
Published: October 2020

AbstractDecadal climate prediction can provide invaluable information for decisions made by government agencies and industry. Modes of internal variability of the ocean play an important role in determining the climate on decadal time scales. This study explores the possibility of using self-organizing maps (SOMs) to identify decadal climate variability, measure theoretical decadal predictability, and conduct decadal predictions of internal climate variability within a long control simulation. SOM is applied to an 11-yr running-mean winter sea surface temperature (SST) in the North Pacific and North Atlantic Oceans within the Community Earth System Model 1850 preindustrial simulation to identify patterns of internal variability in SSTs. Transition probability tables are calculated to identify preferred paths through the SOM with time. Results show both persistence and preferred evolutions of SST depending on the initial SST pattern. This method also provides a measure of the predictability of these SST patterns, with the North Atlantic being predictable at longer lead times than the North Pacific. In addition, decadal SST predictions using persistence, a first-order Markov chain, and lagged transition probabilities are conducted. The lagged transition probability predictions have a reemergence of prediction skill around lag 15 for both domains. Although the prediction skill is very low, it does imply that the SOM has the ability to predict some aspects of the internal variability of the system beyond 10 years.
Multi-Frequency Analysis of Simulated versus Observed Variability in Tropospheric Temperature
Authors: Pallotta Giuliana , Santer Benjamin D. 
Published: October 2020

AbstractStudies seeking to identify a human-caused global warming signal generally rely on climate model estimates of the “noise” of intrinsic natural variability. Assessing the reliability of these noise estimates is of critical importance. We evaluate here the statistical significance of differences between climate model and observational natural variability spectra for global-mean mid- to upper-tropospheric temperature (TMT). We use TMT information from satellites and large multimodel ensembles of forced and unforced simulations. Our main goal is to explore the sensitivity of model-versus-data spectral comparisons to a wide range of subjective decisions. These include the choice of satellite and climate model TMT datasets, the method for separating signal and noise, the frequency range considered, and the statistical model used to represent observed natural variability. Of particular interest is the amplitude of the interdecadal noise against which an anthropogenic tropospheric warming signal must be detected. We find that on time scales of 5–20 years, observed TMT variability is (on average) overestimated by the last two generations of climate models participating in the Coupled Model Intercomparison Project. This result is relatively insensitive to different plausible analyst choices, enhancing confidence in previous claims of detectable anthropogenic warming of the troposphere and indicating that these claims may be conservative. A further key finding is that two commonly used statistical models of short-term and long-term memory have deficiencies in their ability to capture the complex shape of observed TMT spectra.
Disintegration of the K1 Internal Tide in the South China Sea due to Parametric Subharmonic Instability
Authors: Liu Kun , Zhao Zhongxiang 
Published: October 2020

AbstractThe disintegration of the equatorward-propagating K1 internal tide in the South China Sea (SCS) by parametric subharmonic instability (PSI) at its critical latitude of 14.52°N is investigated numerically. The multiple-source generation and long-range propagation of K1 internal tides are successfully reproduced. Using equilibrium analysis, the internal wave field near the critical latitude is found to experience two quasi-steady states, between which the subharmonic waves develop constantly. The simulated subharmonic waves agree well with classic PSI theoretical prediction. The PSI-induced near-inertial waves are of half the K1 frequency and dominantly high modes, the vertical scales ranging from 50 to 180 m in the upper ocean. From an energy perspective, PSI mainly occurs in the critical latitudinal zone from 13° to 15°N. In this zone, the incident internal tide loses ~14% energy in the mature state of PSI. PSI triggers a mixing elevation of O(10−5–10−4) m2 s−1 in the upper ocean at the critical latitude, which is several times larger than the background value. The contribution of PSI to the internal tide energy loss and associated enhanced mixing may differ regionally and is closely dependent on the intensity and duration of background internal tide. The results elucidate the far-field dissipation mechanism by PSI in connecting interior mixing with remotely generated K1 internal tides in the Luzon Strait.
A Hybrid Differential-Ensemble Linear Forecast Model for 4D-Var
Authors: Payne T. J. 
Published: October 2020

AbstractA key component of the 4D-Var data assimilation method used widely for numerical weather prediction is the linear forecast model, which is approximately tangent linear to the forecast model. Traditionally this has been based on differentiating the forecast model, though recently some authors have experimented with an ensemble regression technique, the localized ensemble tangent linear model (LETLM). We propose a hybrid of the two, in which a simplified conventional tangent-linear model (e.g., just the dynamical core) is used together with an LETLM-like adjustment every time step to account for the remaining processes (in this example, the parameterized physics). This is much cheaper than the LETLM, and in tests using the Met Office’s linear model performs considerably better than either a pure LETLM (with a very large ensemble) or the existing linear model.
Overcoming T-cell exhaustion in LCH: PD-1 blockade and targeted MAPK inhibition are synergistic in a mouse model of LCH
Authors: Sengal Amel , Velazquez Jessica , Hahne Meryl , Burke Thomas M. , Abhyankar Harshal , Reyes Robert , Olea Walter , Scull Brooks , Eckstein Olive S. , Bigenwald Camille , Bollard Catherine M. , Yu Wendong , Merad Miriam , McClain Kenneth L. , Allen Carl E. , Chakraborty Rikhia 
Published: October 2020

AbstractLangerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia characterized by granulomatous lesions containing pathological CD207+ dendritic cells (DCs) with persistent MAPK pathway activation. Standard-of-care chemotherapies are inadequate for most patients with multisystem disease, and optimal strategies for relapsed and refractory disease are not defined. The mechanisms underlying development of inflammation in LCH lesions, the role of inflammation in pathogenesis, and the potential for immunotherapy are unknown. Analysis of the immune infiltrate in LCH lesions identified the most prominent immune cells as T lymphocytes. Both CD8+ and CD4+ T cells exhibited “exhausted” phenotypes with high expression of the immune checkpoint receptors. LCH DCs showed robust expression of ligands to checkpoint receptors. Intralesional CD8+ T cells showed blunted expression of Tc1/Tc2 cytokines and impaired effector function. In contrast, intralesional regulatory T cells demonstrated intact suppressive activity. Treatment of BRAFV600ECD11c LCH mice with anti-PD-1 or MAPK inhibitor reduced lesion size, but with distinct responses. Whereas MAPK inhibitor treatment resulted in reduction of the myeloid compartment, anti-PD-1 treatment was associated with reduction in the lymphoid compartment. Notably, combined treatment with MAPK inhibitor and anti-PD-1 significantly decreased both CD8+ T cells and myeloid LCH cells in a synergistic fashion. These results are consistent with a model that MAPK hyperactivation in myeloid LCH cells drives recruitment of functionally exhausted T cells within the LCH microenvironment, and they highlight combined MAPK and checkpoint inhibition as a potential therapeutic strategy.
Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks
Authors: Ceol Arnaud , Montanari Piero , Bartolini Ilaria , Ceri Stefano , Ciaccia Paolo , Patella Marco , Masseroli Marco 
Published: October 2020

Abstract
Background
Genome browsers are widely used for locating interesting genomic regions, but their interactive use is obviously limited to inspecting short genomic portions. An ideal interaction is to provide patterns of regions on the browser, and then extract other genomic regions over the whole genome where such patterns occur, ranked by similarity.

Results
We developed SimSearch, an optimized pattern-search method and an open source plugin for the Integrated Genome Browser (IGB), to find genomic region sets that are similar to a given region pattern. It provides efficient visual genome-wide analytics computation in large datasets; the plugin supports intuitive user interactions for selecting an interesting pattern on IGB tracks and visualizing the computed occurrences of similar patterns along the entire genome. SimSearch also includes functions for the annotation and enrichment of results, and is enhanced with a Quickload repository including numerous epigenomic feature datasets from ENCODE and Roadmap Epigenomics. The paper also includes some use cases to show multiple genome-wide analyses of biological interest, which can be easily performed by taking advantage of the presented approach.

Conclusions
The novel SimSearch method provides innovative support for effective genome-wide pattern search and visualization; its relevance and practical usefulness is demonstrated through a number of significant use cases of biological interest. The SimSearch IGB plugin, documentation, and code are freely available at https://deib-geco.github.io/simsearch-app/ and https://github.com/DEIB-GECO/simsearch-app/.
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study
Authors: Sinha Swati , Lynn Andrew M. , Desai Dhwani K. 
Published: October 2020

Abstract
Background
Homology based methods are one of the most important and widely used approaches for functional annotation of high-throughput microbial genome data. A major limitation of these methods is the absence of well-characterized sequences for certain functions. The non-homology methods based on the context and the interactions of a protein are very useful for identifying missing metabolic activities and functional annotation in the absence of significant sequence similarity. In the current work, we employ both homology and context-based methods, incrementally, to identify local holes and chokepoints, whose presence in the Mycobacterium tuberculosis genome is indicated based on its interaction with known proteins in a metabolic network context, but have not been annotated. We have developed two computational procedures using network theory to identify orphan enzymes (‘Hole finding protocol’) coupled with the identification of candidate proteins for the predicted orphan enzyme (‘Hole filling protocol’). We propose an integrated interaction score based on scores from the STRING database to identify candidate protein sequences for the orphan enzymes from M. tuberculosis, as a case study, which are most likely to perform the missing function.

Results
The application of an automated homology-based enzyme identification protocol, ModEnzA, on M. tuberculosis genome yielded 56 novel enzyme predictions. We further predicted 74 putative local holes, 6 choke points, and 3 high confidence local holes in the genome using ‘Hole finding protocol’. The ‘Hole-filling protocol’ was validated on the E. coli genome using artificial in-silico enzyme knockouts where our method showed 25% increased accuracy, compared to other methods, in assigning the correct sequence for the knocked-out enzyme amongst the top 10 ranks. The method was further validated on 8 additional genomes.

Conclusions
We have developed methods that can be generalized to augment homology-based annotation to identify missing enzyme coding genes and to predict a candidate protein for them. For pathogens such as M. tuberculosis, this work holds significance in terms of increasing the protein repertoire and thereby, the potential for identifying novel drug targets.
oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
Authors: Loeffler-Wirth Henry , Reikowski Jasmin , Hakobyan Siras , Wagner Jonas , Binder Hans 
Published: October 2020

Abstract
Background
oposSOM is a comprehensive, machine learning based open-source data analysis software combining functionalities such as diversity analyses, biomarker selection, function mining, and visualization.

Results
These functionalities are now available as interactive web-browser application for a broader user audience interested in extracting detailed information from high-throughput omics data sets pre-processed by oposSOM. It enables interactive browsing of single-gene and gene set profiles, of molecular ‘portrait landscapes’, of associated phenotype diversity, and signalling pathway activation patterns.

Conclusion
The oposSOM-Browser makes available interactive data browsing for five transcriptome data sets of cancer (melanomas, B-cell lymphomas, gliomas) and of peripheral blood (sepsis and healthy individuals) at www.izbi.uni-leipzig.de/opossom-browser.
Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)
Authors: Qu Zhe , Nong Wenyan , Yu Yifei , Baril Tobias , Yip Ho Yin , Hayward Alexander , Hui Jerome H. L. 
Published: October 2020

Abstract
Background
Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Additionally, the four-finger threadfin Eleutheronema tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is classified as endangered. However, no genomic resources are currently available for the threadfin family Polynemidae.

Results
We sequenced and assembled the first threadfin fish genome, the four-finger threadfin E. tetradactylum. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date. Just 9.07–10.91% of the genome sequence was found to consist of repetitive elements (standard RepeatMasker analysis vs custom analysis), making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, and we include analyses of developmental transcription factors, including the Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs.

Conclusions
The four-finger threadfin E. tetradactylum genome presented here represents the first available genome sequence for the ecologically, biologically, and commercially important clade of threadfin fish. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this valuable group of food fish.