bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing Ontology Alignment Through an Interactive Compact Genetic Algorithm
Authors: Xue Xingsi , Wu Xiaojing , Chen Junfeng 
Published: May 2021

Ontology provides a shared vocabulary of a domain by formally representing the meaning of its concepts, the properties they possess, and the relations among them, which is the state-of-the-art knowledge modeling technique. However, the ontologies in the same domain could differ in conceptual modeling and granularity level, which yields the ontology heterogeneity problem. To enable data and knowledge transfer, share, and reuse between two intelligent systems, it is important to bridge the semantic gap between the ontologies through the ontology matching technique. To optimize the ontology alignment’s quality, this article proposes an Interactive Compact Genetic Algorithm (ICGA)-based ontology matching technique, which consists of an automatic ontology matching process based on a Compact Genetic Algorithm (CGA) and a collaborative user validating process based on an argumentation framework. First, CGA is used to automatically match the ontologies, and when it gets stuck in the local optima, the collaborative validation based on the multi-relationship argumentation framework is activated to help CGA jump out of the local optima. In addition, we construct a discrete optimization model to define the ontology matching problem and propose a hybrid similarity measure to calculate two concepts’ similarity value. In the experiment, we test the performance of ICGA with the Ontology Alignment Evaluation Initiative’s interactive track, and the experimental results show that ICGA can effectively determine the ontology alignments with high quality.
Proteomic Screens for Suppressors of Anoikis Identify IL1RAP as a Promising Surface Target in Ewing Sarcoma
Authors: Zhang Hai-Feng , Hughes Christopher S. , Li Wei , He Jian-Zhong , Surdez Didier , El-Naggar Amal M. , Cheng Hongwei , Prudova Anna , Delaidelli Alberto , Negri Gian Luca , Li Xiaojun , Ørum-Madsen Maj Sofie , Lizardo Michael M. , Oo Htoo Zarni , Colborne Shane , Shyp Taras , Scopim-Ribeiro Renata , Hammond Colin A. , Dhez Anne-Chloe , Langman Sofya , Lim Jonathan K.M. , Kung Sonia H.Y. , Li Amy , Steino Anne , Daugaard Mads , Parker Seth J. , Geltink Ramon I. Klein , Orentas Rimas J. , Xu Li-Yan , Morin Gregg B. , Delattre Olivier , Dimitrov Dimiter S. , Sorensen Poul H. 
Published: May 2021

Abstract

Cancer cells must overcome anoikis (detachment-induced death) to successfully metastasize. Using proteomic screens, we found that distinct oncoproteins upregulate IL1 receptor accessory protein (IL1RAP) to suppress anoikis. IL1RAP is directly induced by oncogenic fusions of Ewing sarcoma, a highly metastatic childhood sarcoma. IL1RAP inactivation triggers anoikis and impedes metastatic dissemination of Ewing sarcoma cells. Mechanistically, IL1RAP binds the cell-surface system Xc− transporter to enhance exogenous cystine uptake, thereby replenishing cysteine and the glutathione antioxidant. Under cystine depletion, IL1RAP induces cystathionine gamma lyase (CTH) to activate the transsulfuration pathway for de novo cysteine synthesis. Therefore, IL1RAP maintains cyst(e)ine and glutathione pools, which are vital for redox homeostasis and anoikis resistance. IL1RAP is minimally expressed in pediatric and adult normal tissues, and human anti-IL1RAP antibodies induce potent antibody-dependent cellular cytotoxicity of Ewing sarcoma cells. Therefore, we define IL1RAP as a new cell-surface target in Ewing sarcoma, which is potentially exploitable for immunotherapy.

Significance:
Here, we identify cell-surface protein IL1RAP as a key driver of metastasis in Ewing sarcoma, a highly aggressive childhood sarcoma. Minimal expression in pediatric and adult normal tissues nominates IL1RAP as a promising target for immunotherapy.
See related commentary by Yoon and DeNicola, p. 2679 .
This article is highlighted in the In This Issue feature, p. 2659
Network alignment and similarity reveal atlas-based topological differences in structural connectomes
Authors: Frigo Matteo , Cruciani Emilio , Coudert David , Deriche Rachid , Natale Emanuele , Deslauriers-Gauthier Samuel 
Published: May 2021

Abstract
The interactions between different brain regions can be modeled as a graph, called connectome, whose nodes correspond to parcels from a predefined brain atlas. The edges of the graph encode the strength of the axonal connectivity between regions of the atlas that can be estimated via diffusion magnetic resonance imaging (MRI) tractography. Herein, we aim to provide a novel perspective on the problem of choosing a suitable atlas for structural connectivity studies by assessing how robustly an atlas captures the network topology across different subjects in a homogeneous cohort. We measure this robustness by assessing the alignability of the connectomes, namely the possibility to retrieve graph matchings that provide highly similar graphs. We introduce two novel concepts. First, the graph Jaccard index (GJI), a graph similarity measure based on the well-established Jaccard index between sets; the GJI exhibits natural mathematical properties that are not satisfied by previous approaches. Second, we devise WL-align, a new technique for aligning connectomes obtained by adapting the Weisfeiler-Leman (WL) graph-isomorphism test. We validated the GJI and WL-align on data from the Human Connectome Project database, inferring a strategy for choosing a suitable parcellation for structural connectivity studies. Code and data are publicly available.
The Trilingual Prayer Copied by Avraham Firkowicz: The First Hebrew, Judeo-Slavic, and Crimean Judeo-Turkic Trilingual Text
Authors: Grishchenko Alexander I. , Shapira Dan 
Published: May 2021

Abstract
This article presents a unique trilingual (Hebrew, Turkic, and Slavic) religious literary work from the personal archive of Avraham Firkowicz (National Library of Russia, St. Petersburg). The text, containing 129 lines (verses) in Hebrew characters, is written in Firkowicz’s own hand. Its author has not been reliably identified, but it is assumed that he could be a Karaite Jew from Łuck / Lutsk (Wolhynia, present-day Ukraine) with a good speaking-level knowledge of Slavic and Turkish (e.g., Joseph-Solomon Lutski or Mordechai Sultanski). The language of the Turkic version is a variety of Crimean Judeo-Turkic with many Turkish (Oğuz) features; the language of the Slavic version is based on standard Russian of the early 19th century with Church Slavonic, Ukrainian, and Polish elements.
Orthoptera Tettigoniidae as indicators of biodiversity hotspots in the Guinean Forests of Central and West Tropical Africa
Authors: MASSA BRUNO 
Published: May 2021

The present paper has two aims: 1) to present the results of the study of selected species of Orthoptera Tettigoniidae collected in the Guinean forests of West Africa and in the important hotspot of Dzanga-Ndoki National Park (Central African Republic); 2) to carry out a check-list of six subfamilies of Tettigoniidae (Pseudophyllinae, Conocephalinae, Hexacentrinae, Phaneropterinae, Mecopodinae and Hetrodinae) living in Central-West tropical Africa, in particular in two main tropical forests, in the subregion of upper Guinea, and in the subregion Nigeria-Cameroon plus the biodiversity hotspots of Central African Republic and Gabon. Many new records are reported and the following new species are described: Plangia astylata n. sp. from Central African Republic and Gabon, Plangia chopardi n. sp. from Côte d’Ivoire, and Catoptropteryx lineata n. sp. from Liberia. In addition the male of Plangia karschi Chopard, 1954 is described and some taxonomical notes on the recently described Arantia marginata Massa, 2021 are discussed. The new name Pseudorhynchus raggei is proposed for Pseudorhynchus robustus Ragge, 1969, junior primary homonym of Pseudorhynchus robustus Willemse, 1953. Then, the author lists all the Tettigoniidae of the above listed subfamilies presently known in central-west tropical Africa (Guinean forests). This wide tropical area holds important biodiversity hotspots that the author highlights through the study of katydids. Many groups of species tend to isolate and speciate probably more than other groups of insects. Overall, the total number amounts to 332 species, of which 242 live in Cameroon-Nigeria subregion plus Central African Republic and Gabon, 216 in the Upper Guinea subregion. The occurrence of endemic taxa is 35.9 and 40.3%, respectively; this resulted a very high percentage compared to that known for plants and animals in the area. Starting from the list of Tettigoniidae three remarkable biodiversity hotspots were examined, Dzanga-Ndoki National Park (Central African Republic), Mt. Tonkoui and Taï National Park (both in Côte d’Ivoire); overall they hold 134, 81 and 88 species, respectively. It seems that in tropical Africa there is a specific richness gradient with an East-West impoverishment, but also a possible increase of endemism occurrence. However, presently this richness suffers a high decline risk, due to deforestation and environmental degradation, in turn dependent on the inequality between human populations, wars and political instability in some tropical areas.
Subpolar Gyre – AMOC – Atmosphere Interactions on Multidecadal Timescales in a Version of the Kiel Climate Model
Authors: Sun Jing , Latif Mojib , Park Wonsun 
Published: May 2021

AbstractThere is a controversy about the nature of multidecadal climate variability in the North Atlantic (NA) region, concerning the roles of ocean circulation and atmosphere-ocean coupling. Here we describe NA multidecadal variability from a version of the Kiel Climate Model, in which both subpolar gyre (SPG)-Atlantic Meridional Overturning Circulation (AMOC) and atmosphere-ocean coupling are essential. The oceanic barotropic and meridional overturning streamfunctions, and sea level pressure are jointly analyzed to derive the leading mode of Atlantic sector variability. This mode accounting for 23.7 % of the total combined variance is oscillatory with an irregular periodicity of 25-50 years and an e-folding time of about a decade. SPG and AMOC mutually influence each other and together provide the delayed negative feedback necessary for maintaining the oscillation. An anomalously strong SPG, for example, drives higher surface salinity and density in the NA’s sinking region. In response, oceanic deep convection and AMOC intensify, which, with a time delay of about a decade, reduces SPG strength by enhancing upper-ocean heat content. The weaker gyre leads to lower surface salinity and density in the sinking region, which reduces deep convection and eventually AMOC strength. There is a positive ocean-atmosphere feedback between the sea surface temperature and low-level atmospheric circulation over the Southern Greenland area, with related wind stress changes reinforcing SPG changes, thereby maintaining the (damped) multidecadal oscillation against dissipation. Stochastic surface heat-flux forcing associated with the North Atlantic Oscillation drives the eigenmode.
The reduction of systematic temperature biases in soil moisture-limited regimes by stochastic root depth variations
Authors: Breil M. , Schädler G. 
Published: May 2021

AbstractIn soil moisture-limited evapotranspiration regimes, near-surface temperatures are strongly affected by the available soil water amount for evapotranspiration. Its spurious representation in climate models consequently results in an inaccurately simulated turbulent heat flux partitioning and associated temperature biases.Since the physical reasons for soil moisture induced temperature biases are different in every region and model, a new method is presented to reduce these biases systematically. To achieve this, a stochastic root depth variation is applied, whereby the root depths in each grid-box of the model domain are uniformly perturbed. Thus, the soil water supply for evapotranspiration is increased for 50 % of the grid-boxes in the model domain and reduced for the other 50 %. In energy-limited regimes, where soil moisture just slightly affects the near-surface temperatures, the turbulent heat flux partitioning is not affected. In moisture-limited regimes, the method has an asymmetric effect on evapotranspiration. In cases of overestimated supplies, the reduced root depths in 50 % of the model domain result in an overall evapotranspiration reduction. In cases of underestimated supplies, the opposite is the case. In cases of correctly simulated supplies, the evapotranspiration reduction in 50 % of the model domain and the evapotranspiration increase in the other 50 % balance each other on a climatological mean. In this way, the method affects the turbulent heat flux partitioning only if soil moisture is spuriously simulated in the model. The associated biases are then systematically reduced, independently of the underlying physical process, which caused the soil moisture deficiencies.
The shelf sources of estuarine inflow
Authors: Brasseale Elizabeth , MacCready Parker 
Published: May 2021

AbstractThe inflow to an estuary originates on the shelf. It flushes the estuary and can bring in nutrients, heat, salt, and hypoxic water, having consequences for estuarine ecosystems and fjordic glacial melt. However, the source of estuarine inflow has only been explored in simple models that do not resolve interactions between inflow and outflow outside of the estuarine channel. This study addressed the estuary inflow problem using variations on a three-dimensional primitive equation model of an idealized estuarine channel next to a sloping, unstratified shelf with mixing provided by a single frequency, 12-hour tide. Inflow was identified using particle tracking, momentum budgets, and Total Exchange Flow. Inflow sources were found in shelf water downstream of the estuary, river plume water, and shelf water upstream of the estuary. Downstream is defined here with respect to the direction of coastal trapped wave propagation, which is to the right for an observer looking seaward from the estuary mouth in the northern hemisphere. Downstream of the estuary and offshore of the plume, the dynamics were quasi-geostrophic, consistent with previous simple models. The effect of this inflowing current on the geometry of the river plume front was found to be small. Novel sources of inflow were identified which originated from within the plume and upstream of the estuary.
FOWD: A Free Ocean Wave Dataset for Data Mining and Machine Learning
Authors: Häfner Dion , Gemmrich Johannes , Jochum Markus 
Published: May 2021

AbstractThe occurrence of extreme (rogue) waves in the ocean is for the most part still shrouded in mystery, as the rare nature of these events makes them difficult to analyze with traditional methods. Modern data mining and machine learning methods provide a promising way out, but they typically rely on the availability of massive amounts of well-cleaned data.To facilitate the application of such data-hungry methods to surface ocean waves, we developed FOWD, a freely available wave dataset and processing framework. FOWD describes the conversion of raw observations into a catalogue that maps characteristic sea state parameters to observed wave quantities. Specifically, we employ a running window approach that respects the non-stationary nature of the oceans, and extensive quality control to reduce bias in the resulting dataset.We also supply a reference Python implementation of the FOWD processing toolkit, which we use to process the entire CDIP buoy data catalogue containing over 4 billion waves. In a first experiment, we find that, when the full elevation time series is available, surface elevation kurtosis and maximum wave height are the strongest univariate predictors for rogue wave activity. When just a spectrum is given, crest-trough correlation, spectral bandwidth, and mean period fill this role.
LncRNA XIST promotes liver cancer progression by acting as a molecular sponge of miR-200b-3p to regulate ZEB1/2 expression
Authors: Liu Lili , Jiang Hua , Pan Hongming , Zhu Xiuming 
Published: May 2021

Objective To evaluate the predictive value of long non-coding RNA (lncRNA) X-inactive specific transcript (XIST) for survival, and determine the involvement of miRNA(miR)-200b-3p and zinc finger E-box-binding homeobox (ZEB) 1/2 in the pro-tumor effect of lncRNA XIST in liver cancer. Methods We evaluated lncRNA XIST expression in liver cancer tissues and cell lines by quantitative reverse transcription polymerase chain reaction (RT-qPCR) and analyzed the correlation between its expression and overall survival of liver cancer patients by Kaplan–Meier analysis. Its effects on cell proliferation, migration, and invasion were analyzed by Cell-Counting Kit-8 and Transwell assays. The association between lncRNA XIST and miR-200b-3p, and the effects of lncRNA XIST on ZEB1/2 expression were explored using luciferase reporter assays, real-time PCR, and western blotting. Results The lncRNA XIST was significantly upregulated in liver cancer, and increased lncRNA XIST expression was associated with a poor prognosis. The lncRNA XIST promoted liver cancer cell proliferation, migration, and invasion in vitro, and acted as a molecular sponge for miR-200b-3p, and also regulated the expression of ZEB1/2 via miR-200b-3p. Conclusion The lncRNA XIST is an oncogenic lncRNA that promotes liver cancer metastasis, and its pro-metastatic phenotype can be partially attributed to the lncRNA XIST/miR-200b-3p/ZEB1/2 signaling axis.
Prophylactic intravenous gentamicin with sedation-free cystoscopic injection of BoNT-A: No demonstrable adverse extravesical neuromuscular effects in a pilot safety study of 220 idiopathic overactive bladder patients
Authors: Napier-Hemy Timothy P , Feyisetan Oladapo , Stewart Heather , Chamsin Alaa , Floyd Michael S , Samsudin Azizan , Omar Ahmad M 
Published: May 2021

Objectives: To determine whether administration of single dose prophylactic intravenous gentamicin prior to intravesical injection of botulinum toxin type A (BoNT-A) is associated with adverse extravesical neuromuscular effects in idiopathic overactive bladder syndrome. Patients and methods: A retrospective analysis of 220 consecutive idiopathic overactive bladder patients following sedation-free flexible cystoscopic injection of intravesical BoNT-A. All patients received a single dose of intravenous gentamicin (160 mg) followed by 100-200 IU of BoNT-A. They were followed up at intervals to determine whether they had experienced any adverse extravesical neuromuscular side effects. Results: None of our patients developed adverse extravesical neuromuscular side effects from intravesical botulinum injections with concomitant administration of intravenous gentamicin. Conclusion: Single dose intravenous gentamicin is safe to use as a prophylaxis for intravesical BoNT-A injections of 200 IU or below in idiopathic overactive bladder patients. Level of evidence: Not applicable.
The impact of COVID-19 pandemic on headache symptoms and drug withdrawal among patients with medication overuse headache: a cross-sectional study
Authors: Li Changling , Li Yanbo , Ma Mengmeng , Zhang Yang , Bao Jiajia , Ge Wenjing , Liu Yanqin , Peng Cheng , He Li 
Published: May 2021

Abstract
Background
Coronavirus disease 2019 (COVID-19) bring about a range of psychological distress and symptom deterioration to headache patients especially to some migraineurs. Compared to migraineurs or normal control, medication overuse headache (MOH) patients are more likely to experience a worse psychological distress and poorer outcome in non-COVID-19 time. However, in COVID-19 pandemic, whether MOH patients would have greater physical and mental symptom deterioration or worse relief of headache symptoms and medications overuse remained unclear. We aim to investigate the impact of COVID-19 on MOH patients to guide for a better management in this study.

Methods
We enrolled MOH patients who were diagnosed and treated at headache clinic of West China Hospital. Information of the pre-pandemic 3 months period and COVID-19 pandemic period was collected. Univariate and multivariate logistic regression were performed to identify independent factors associated with changes in headache symptoms and drug withdrawal.

Results
Seventy-eight MOH patients were enrolled into the study ultimately. In comparison to pre-pandemic period, fewer MOH patients reported decreased headache days, intensity and days with acute medications per month during the pandemic. Available access to regular prophylactic medications was significantly associated with a reduction of at least 50% in headache days and decrease in headache intensity per month with respective odds ratios of 39.19 (95% CI 3.75–409.15, P = 0.002) and 10.13 (95% CI 2.33–44.12, P = 0.002). Following abrupt withdrawal and high educational level were both significant factors in decreasing headache intensity. Male sex was significantly associated with decrease in days with acute medication per month during the pandemic (odds ratios 4.78, 95%CI 1.44–15.87, P = 0.011).

Conclusions
Our findings reflect that MOH patients experienced a worse relief of headache symptoms and drug withdrawal during the pandemic. Available access to regular prophylactic medications was the significant independent factor for improvement of headache symptoms. Male sex was significantly associated with decreased days with acute medications per month.
Functional connectivity of the visual cortex differentiates anxiety comorbidity from episodic migraineurs without aura
Authors: Wei Heng-Le , Li Jian , Guo Xi , Zhou Gang-Ping , Wang Jin-Jin , Chen Yu-Chen , Yu Yu-Sheng , Yin Xindao , Li Junrong , Zhang Hong 
Published: May 2021

Abstract
Background
Migraine is a common neurological disease that is often accompanied by psychiatric comorbidities. However, the relationship between abnormal brain function and psychiatric comorbidities in migraine patients remains largely unclear. Therefore, the present study sought to explore the correlations between the resting-state functional deficits and psychiatric comorbidities in migraine without aura (MwoA) patients.

Methods
Resting-state functional magnetic resonance images were obtained. In addition, the amplitude of low-frequency fluctuation (ALFF) and regional homogeneity (ReHo) values were obtained. Thereafter regional abnormalities in MwoA patients with and without anxiety (MwoA-A and MwoA-OA) were chosen as seeds to conduct functional connectivity (FC) analysis.

Results
Compared to the healthy controls (HCs), the MwoA-A and MwoA-OA patients had abnormal ALFF and ReHo values in the right lingual gyrus (LG). They also had abnormal FC of the right LG with the ipsilateral superior frontal gyrus (SFG) and middle cingulate cortex (MCC). Additionally, the MwoA-A patients showed higher ReHo values in the left posterior intraparietal sulcus (pIPS) and abnormal FC of the right LG with ipsilateral pIPS and primary visual cortex, compared to the MwoA-OA patients. Moreover, the MwoA-OA patients showed an increase in the FC with the right posterior cingulate cortex/precuneus (PCC/PCUN), left middle frontal gyrus (MFG) and left inferior temporal gyrus (ITG) relative to the HCs. Furthermore, the ALFF values of the right LG positively were correlated with anxiety scores in MwoA-A patients. The abnormal LG-related FCs with the PCC/PCUN, MFG and ITG were negatively associated with the frequency of headaches in MwoA-OA patients.

Conclusions
This study identified abnormal visual FC along with other core networks differentiating anxiety comorbidity from MwoA. This may therefore enhance the understanding of the neuropsychological basis of psychiatric comorbidities and provide novel insights that may help in the discovery of new marks or even treatment targets.