Kinase inhibitor data set for systematic analysis of representative kinases across the human kinome

This study undertakes a systematic analysis of media discourse on migration in Sweden from 2012 to 2019. Using a novel data set consisting of mainstream newspapers, Twitter and forum data, the study answers two questions: What do Swedish media actually talk about when they talk about “migration”? And how do they talk about it? Using a combination of computational text analysis tools, I analyze a shift in the media discourse seen as one of the outcomes of the European refugee crisis in 2015 and try to understand the role of social media in this process. The results of the study indicate that messages on social media generally had negative tonality and suggest that some of the media frames can be attributed to a migration-hostile discourse. At the same time, the analysis of framing and sentiment dynamics provides little evidence for the discourse shift and any long-term effects of the European refugee crisis on the Swedish media discourse. Rather, one can hypothesize that the role of the crisis should be viewed in a broader political and historical context.

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Analysis of Kinase Inhibitors and Druggability of Kinase-Targets Using Machine Learning Techniques

Pattern Discovery Using Sequence Data Mining ◽

10.4018/978-1-61350-056-9.ch009 ◽

2012 ◽

pp. 155-165

Author(s):

S. Prasanthi ◽

S.Durga Bhavani ◽

T. Sobha Rani ◽

Raju S. Bapi

Keyword(s):

Machine Learning ◽

Decision Tree ◽

Kinase Inhibitors ◽

Kinase Inhibitor ◽

Classification Problem ◽

Machine Learning Techniques ◽

Learning Approaches ◽

Decision Tree Classifier ◽

Data Set ◽

Learning Techniques

Vast majority of successful drugs or inhibitors achieve their activity by binding to, and modifying the activity of a protein leading to the concept of druggability. A target protein is druggable if it has the potential to bind the drug-like molecules. Hence kinase inhibitors need to be studied to understand the specificity of a kinase inhibitor in choosing a particular kinase target. In this paper we focus on human kinase drug target sequences since kinases are known to be potential drug targets. Also we do a preliminary analysis of kinase inhibitors in order to study the problem in the protein-ligand space in future. The identification of druggable kinases is treated as a classification problem in which druggable kinases are taken as positive data set and non-druggable kinases are chosen as negative data set. The classification problem is addressed using machine learning techniques like support vector machine (SVM) and decision tree (DT) and using sequence-specific features. One of the challenges of this classification problem is due to the unbalanced data with only 48 druggable kinases available against 509 non-drugggable kinases present at Uniprot. The accuracy of the decision tree classifier obtained is 57.65 which is not satisfactory. A two-tier architecture of decision trees is carefully designed such that recognition on the non-druggable dataset also gets improved. Thus the overall model is shown to achieve a final performance accuracy of 88.37. To the best of our knowledge, kinase druggability prediction using machine learning approaches has not been reported in literature.

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Revolutions and the Military: Endgame Coups, Instability, and Prospects for Democracy

Armed Forces & Society ◽

10.1177/0095327x19881747 ◽

2019 ◽

Vol 47 (1) ◽

pp. 148-176 ◽

Cited By ~ 1

Author(s):

Kevin Koehler ◽

Holger Albrecht

Keyword(s):

Distinct Type ◽

Proportional Hazard ◽

Data Set ◽

Systematic Analysis ◽

Proportional Hazard Models ◽

Cox Proportional Hazard ◽

Original Medium ◽

Cox Proportional Hazard Models ◽

The Military ◽

Nondemocratic Regimes

This article presents a systematic analysis of military coups following popular mass uprisings in nondemocratic regimes, conceptualized as endgame coups. Drawing on our original, medium- n data set of revolutionary situations, we find that such endgame coups form a distinct type of military intervention in politics. Compared to regular coups, episodes of popular mass contestation prompt conservative interventions in politics of the military’s leadership aimed at preserving the regime’s authoritarian infrastructure. A systematic test of factors characterizing postcoup political trajectories is based on Cox proportional hazard models and provides empirical evidence in contrast to the widely held notion of “democratic coups.” Our findings reveal that endgame coups are conservative rollback coups, executed by military leaderships, that result in continued political instability and illiberal politics.

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Changes in commissioning home care: an English survey

Quality in Ageing and Older Adults ◽

10.1108/qaoa-10-2019-0055 ◽

2020 ◽

Vol 21 (1) ◽

pp. 3-14

Author(s):

Sue Davies ◽

Jane Hughes ◽

Karen Davies ◽

Elizabeth Dalgarno ◽

Rowan Elaine Jasper ◽

...

Keyword(s):

Home Care ◽

National Policy ◽

Free Text ◽

Local Authorities ◽

Data Set ◽

Systematic Analysis ◽

Content Type ◽

Care Workers ◽

Home Care Workers ◽

Combined Data

Purpose The purpose of this study is to examine changes in the nature, form and range of commissioning arrangements for home care. Design/methodology/approach Data from two discrete national surveys of English local authorities with social service responsibilities were used. In the first, undertaken in 2007, responses from 111 of the 151 local authorities (74%) were received; in the second, undertaken in 2017, responses from 109 local authorities (72%) were received. A combined data set of 79 complete cases, 52% of local authorities, was created. Percentage point differences across the two time periods were calculated and tested to identify significant changes and a systematic analysis of the free-text responses regarding intended changes to the commissioning process in each data set was undertaken. Findings Findings identified substantial changes in some aspects of the commissioning of home care in the 2007-2017 decade. Collaboration between stakeholders had increased, particularly regarding the identification of future needs. Improved conditions of service and remuneration for home care workers were evident within the commissioning process. Standardised charges for home care (regardless of time and day) had also become more widespread. Initiatives to prompt providers to deliver more personalised care were more evident. Originality/value This paper describes the evolution of commissioning arrangements for home care in localities in response to national policy initiatives. It provides guidance to commissioners in meeting the needs of current service users and emphasises the importance of collaboration with stakeholders, particularly providers, in securing future capacity.

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Revisiting the deformation transients before the 2011 Tohoku-Oki Megathrust Earthquake with GPS

10.5194/egusphere-egu2020-21477 ◽

2020 ◽

Author(s):

Anne Socquet ◽

Lou Marill ◽

David Marsan ◽

Baptiste Rousset ◽

Mathilde Radiguet ◽

...

Keyword(s):

Time Series ◽

Large Scale ◽

Gravity Anomalies ◽

Seismogenic Zone ◽

Double Difference ◽

Ocean Bottom ◽

Slow Slip ◽

Short Term ◽

Data Set ◽

Systematic Analysis

The precursory activity leading up to the Tohoku-Oki earthquake of 2011 has been suggested to feature both long- and short-term episodes of decoupling and suggests a particularly complex slow slip history. The analysis of the F3 solution of the Japanese GPS network suggested that an accelerated slip occurred in the deeper part of the seismogenic zone during the 10 years preceding the earthquake (Heki & Mitsui, EPSL 2013; Mavrommatis et al., GRL 2014; Yokota & Koketsu, Nat. Com. 2015). During the two months preceding the earthquake, no anomaly in the GPS position time series has been revealed so far, although several anomalous geophysical signals have been reported&#160;(an extended foreshock crisis near the future hypocenter (Kato et al., Science 2012), a synchronized increase of intermediate-depth background seismicity (Bouchon et al., Nat Geosc. 2016), a signal in ocean-bottom pressure gauges and on-land strainmeter time series (Ito et al., Tectonoph. 2013), and large scale gravity anomalies that suggest deep-seated slab deformation processes (Panet et al., Nat. Geosc. 2018&#160;; Wang & Burgmann, GRL 2019)).We present novel results based on an independent analysis of the Japanese GPS data set. We perform a full reprocessing of the raw data with a double-difference approach, a systematic analysis of the obtained time-series, including noise characterization and network filtering, and make a robust assessment of long- and short-term tectonic aseismic transients preceding the Tohoku-Oki earthquake. An accelerated slip on the lower part of the seismogenic zone over the last decade is confirmed, not only below the epicenter of Tohoku-Oki earthquake but also further south, offshore Boso peninsula, which is a worrying sign of an on-going slow decoupling east of Tokyo. At shorter time-scale, first results seem compatible with a slow slip close to the epicenter initiating ~&#160;2 months before the mainshock.

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Stress Drop Mapping in the Northern Chilean Subduction Zone

10.5194/egusphere-egu2020-5019 ◽

2020 ◽

Author(s):

Jonas Folesky ◽

Joern Kummerow ◽

Serge A. Shapiro

Keyword(s):

Subduction Zone ◽

Stress Drop ◽

Observation Interval ◽

Spectral Ratio ◽

Temporal Variations ◽

Data Set ◽

Systematic Analysis ◽

Megathrust Earthquakes ◽

Time Period ◽

Stress Drops

The Northern Chilean subduction zone has been monitored by the IPOC network for more than ten years. During this time period two very large earthquakes occurred, the 2007 MW7.7 &#160;Tocopilla earthquake and the 2014 MW8.1 Iquique earthquake. Over the entire subduction zone a vast amount of seismic activity has been recorded and a huge catalog was compiled including over 100000 events (Sippl et al. 2018). With this exceptional data base we attempt a systematic analysis of the stress drops of as many events from the catalog as possible. We apply different estimation techniques, namely the spectral ratio type, the spectral stacking approach, and the lower bound method. A goal of our research is a comparison and possibly a combination of the techniques to obtain reliable and well constrained results.The data set covers events at the interface, within the subducting plate, crustal events, and intermediate depth events. It therefore bears a great potential to better understand the stress drop distribution within a subduction zone. Also, the long observation interval allows to analyze temporal variations according to pre-, inter-, and post-seismic phases of megathrust earthquakes. &#160;&#160;We present preliminary results where a subset of 730 events with a magnitude range of ML2.7 - ML4.8 &#160;was used for analysis with the spectral ratio technique. For these events we show maps of spatial stress drop variation, and we analyze the time dependent stress drop variance.&#160;

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First-line avelumab + axitinib in patients with advanced hepatocellular carcinoma: Results from a phase 1b trial (VEGF Liver 100).

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.4072 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 4072-4072 ◽

Cited By ~ 18

Author(s):

Masatoshi Kudo ◽

Kenta Motomura ◽

Yoshiyuki Wada ◽

Yoshitaka Inaba ◽

Yasunari Sakamoto ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Kinase Inhibitor ◽

Objective Response ◽

Study Data ◽

Clinical Activity ◽

Advanced Hepatocellular Carcinoma ◽

Data Set ◽

Phase 1B ◽

Grade 3

4072 Background: Combining an immune checkpoint inhibitor with a targeted antiangiogenic agent may leverage complementary mechanisms of action for treatment of advanced/metastatic (a/m) hepatocellular carcinoma (HCC). Avelumab is a human anti–PD-L1 IgG1 antibody with clinical activity in various tumor types; axitinib is a tyrosine kinase inhibitor selective for VEGF receptors 1/2/3. VEGF Liver 100 (NCT03289533) is a phase 1b study evaluating safety and efficacy of avelumab + axitinib in treatment-naive patients (pts) with HCC; interim results are reported here. Methods: Eligible pts had confirmed a/m HCC, ≥1 measurable lesion, a fresh or archival tumor specimen, ECOG PS ≤1, and Child-Pugh class A. Pts received avelumab 10 mg/kg IV Q2W + axitinib 5 mg orally BID until progression, unacceptable toxicity, or withdrawal. Endpoints included safety and objective response (RECIST v1.1; modified [m] RECIST for HCC). Results: Interim assessment was performed after a minimum follow up of 6 months based on the released study data set (clinical cut-off date: Aug 1, 2018). As of the cut-off date, 22 pts (median age: 68.5 y) were treated with avelumab (median: 20.0 wk) and axitinib (median: 19.9 wk). The most common grade 3 treatment-related adverse events (TRAEs) (≥10% of patients) were hypertension (50.0%) and hand-foot syndrome (22.7%); no grade 4/5 TRAEs were reported. Immune-related AEs (irAEs) (≥10% of pts) were hypothyroidism (31.8%) and hyperthyroidism (13.6%). No grade ≥3 irAEs were reported; no pts discontinued treatment due to TRAEs or irAEs. Based on Waterfall plot calculations, tumor shrinkage was observed in 15 (68.2%) and 16 (72.7%) pts by RECIST and mRECIST, respectively. ORR was 13.6% (95% CI, 2.9%-34.9%) and 31.8% (95% CI, 13.9%-54.9%) by RECIST and mRECIST, respectively. OS data were immature at data cutoff. Conclusions: The preliminary safety of avelumab + axitinib in HCC is manageable and consistent with the known safety profiles of avelumab and axitinib when administered as monotherapies. This study demonstrates antitumor activity of the combination in HCC. Follow-up is ongoing. Clinical trial information: NCT03289533. [Table: see text]

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A Zero-Sum Game? Repression and Protest in China

Government and Opposition ◽

10.1017/gov.2017.24 ◽

2017 ◽

Vol 54 (2) ◽

pp. 309-335 ◽

Cited By ~ 8

Author(s):

Yao Li

Keyword(s):

Original Data ◽

Contentious Politics ◽

Authoritarian Regimes ◽

The State ◽

Data Set ◽

Systematic Analysis ◽

Quantitative Evidence ◽

Authoritarian State ◽

Zero Sum ◽

Evaluating the degree of domain specificity of terms in large terminologies

Online Information Review ◽

10.1108/oir-02-2015-0052 ◽

2015 ◽

Vol 39 (3) ◽

pp. 326-345 ◽

Cited By ~ 3

Author(s):

David Martín-Moncunill ◽

Miguel-Ángel Sicilia-Urban ◽

Elena García-Barriocanal ◽

Salvador Sánchez-Alonso

Keyword(s):

Controlled Vocabulary ◽

Domain Specificity ◽

Data Set ◽

Systematic Analysis ◽

Content Type ◽

Domain Experts ◽

Domain Specific ◽

Positive Effects ◽

Knowledge Organisation ◽

Depth Analysis

Purpose – Large terminologies usually contain a mix of terms that are either generic or domain specific, which makes the use of the terminology itself a difficult task that may limit the positive effects of these systems. The purpose of this paper is to systematically evaluate the degree of domain specificity of the AGROVOC controlled vocabulary terms as a representative of a large terminology in the agricultural domain and discuss the generic/specific boundaries across its hierarchy. Design/methodology/approach – A user-oriented study with domain-experts in conjunction with quantitative and systematic analysis. First an in-depth analysis of AGROVOC was carried out to make a proper selection of terms for the experiment. Then domain-experts were asked to classify the terms according to their domain specificity. An evaluation was conducted to analyse the domain-experts’ results. Finally, the resulting data set was automatically compared with the terms in SUMO, an upper ontology and MILO, a mid-level ontology; to analyse the coincidences. Findings – Results show the existence of a high number of generic terms. The motivation for several of the unclear cases is also depicted. The automatic evaluation showed that there is not a direct way to assess the specificity degree of a term by using SUMO and MILO ontologies, however, it provided additional validation of the results gathered from the domain-experts. Research limitations/implications – The “domain-analysis” concept has long been discussed and it could be addressed from different perspectives. A resume of these perspectives and an explanation of the approach followed in this experiment is included in the background section. Originality/value – The authors propose an approach to identify the domain specificity of terms in large domain-specific terminologies and a criterion to measure the overall domain specificity of a knowledge organisation system, based on domain-experts analysis. The authors also provide a first insight about using automated measures to determine the degree to which a given term can be considered domain specific. The resulting data set from the domain-experts’ evaluation can be reused as a gold standard for further research about these automatic measures.

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A systematic analysis of nuclear charge radii data

HNPS Proceedings ◽

10.12681/hnps.1817 ◽

2019 ◽

Vol 26 ◽

pp. 187

Author(s):

Patroklos-Miltiadis Mamaloukas ◽

Theo J. Mertzimekis

Keyword(s):

Experimental Data ◽

Laser Spectroscopy ◽

Empirical Formula ◽

Nuclear Charge ◽

Statistical Treatment ◽

Magic Numbers ◽

Data Set ◽

Systematic Analysis ◽

Fundamental Symmetries ◽

Charge Radii

Driven by the need to describe strong nuclear interactions between hadrons in a nucleus, we take a closer look at evaluated experimental data of nuclear charge radii acquired mainly with laser spectroscopy methods. Understanding the range at which the components of the nucleus interact with each other shall lead to even more accurate models of nuclear potentials, and even understanding limitations of fundamental symmetries. The present work takes advantage of the existing IAEA database by Angeli & Marinova, and an additional set of recently surveyed measurements, specifically between 2013–2018. Statistical treatment includes different polynomial fits for the entirety of the data set with the intention of confirming or improving the well-established empirical formula, R=roA1/3. Various trends of observed deviations from this formula are investigated in terms of structure effects spanning major shells and near magic numbers.

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