bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building a Common Language in Pluralist International Relations Theories
Authors: Telò Mario 
Published: April 2020

Abstract
This article aims to contribute to the gradual building of a common scientific language within the world International Relations (IR) epistemic community. The author shares the objective, indicated by many leading Chinese scholars, of a pluralist IR theory that goes beyond Western-centric mainstream theories to provide a European continental perspective. Such a perspective takes stock, on the one hand, of the legacy of Gramsci, Bobbio, and Habermas, and, on the other, of the theoretical implications of European unity as a sophisticated instance of regional cooperation. Since the dialogue must be at the highest possible theoretical level, the author selects as main partners two leading theories from the increasingly rich and internally various Chinese IR scholarship: the books recently published in English by Qin Yaqing and Yan Xuetong, who represent—not only in China, but at world level—two fundamental references in the international theoretical debate. They lead two innovative approaches: Qin’s relational theory and Yan’s theory of moral realism. The author discusses their main theses and concepts regarding IRT and global governance in a free, open, and dialectic way, notably, the balance between background cultures and multilateral convergence; and the differences between the crucial concepts of hegemony, domination, and leadership, as well as alternative perspectives on global governance within a multipolar world—a new post-hegemonic multilateralism? Or a bipolar global power structure competing for leadership?
Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases
Authors: Spoor Shawna , Wytko Connor , Soto Brian , Chen Ming , Almsaeed Abdullah , Condon Bradford , Herndon Nic , Hough Heidi , Jung Sook , Staton Meg , Wegrzyn Jill , Main Dorrie , Feltus F Alex , Ficklin Stephen P 
Published: April 2020

Abstract
Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a ‘plug-in’ for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.
High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population
Authors: Gounot Jean-Sébastien , Neuvéglise Cécile , Freel Kelle C , Devillers Hugo , Piškur Jure , Friedrich Anne , Schacherer Joseph 
Published: April 2020

AbstractGenome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype–phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to characterize at the population level the Brettanomyces bruxellensis yeast species, which is a major cause of wine spoilage and can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.
Functions of Gtf2i and Gtf2ird1 in the developing brain: transcription, DNA binding and long-term behavioral consequences
Authors: Kopp Nathan D , Nygaard Kayla R , Liu Yating , McCullough Katherine B , Maloney Susan E , Gabel Harrison W , Dougherty Joseph D 
Published: April 2020

Abstract
Gtf2ird1 and Gtf2i are two transcription factors (TFs) among the 28 genes deleted in Williams syndrome, and prior mouse models of each TF show behavioral phenotypes. Here we identify their genomic binding sites in the developing brain and test for additive effects of their mutation on transcription and behavior. GTF2IRD1 binding targets were enriched for transcriptional and chromatin regulators and mediators of ubiquitination. GTF2I targets were enriched for signal transduction proteins, including regulators of phosphorylation and WNT. Both TFs are highly enriched at promoters, strongly overlap CTCF binding and topological associating domain boundaries and moderately overlap each other, suggesting epistatic effects. Shared TF targets are enriched for reactive oxygen species-responsive genes, synaptic proteins and transcription regulators such as chromatin modifiers, including a significant number of highly constrained genes and known ASD genes. We next used single and double mutants to test whether mutating both TFs will modify transcriptional and behavioral phenotypes of single Gtf2ird1 mutants, though with the caveat that our Gtf2ird1 mutants, like others previously reported, do produce low levels of a truncated protein product. Despite little difference in DNA binding and transcriptome-wide expression, homozygous Gtf2ird1 mutation caused balance, marble burying and conditioned fear phenotypes. However, mutating Gtf2i in addition to Gtf2ird1 did not further modify transcriptomic or most behavioral phenotypes, suggesting Gtf2ird1 mutation alone was sufficient for the observed phenotypes.
Integrating the Quantitative Research on the Onset and Incidence of Violent Intrastate Conflicts
Authors: Trinn Christoph , Wencker Thomas 
Published: April 2020

Abstract
Quantitative research into the causes of violent intrastate conflicts has recently shifted away from classical country-year-level regression analyses. When taking steps in new directions, researchers should be mindful of the extent and quality, and indeed of the limitations, of the knowledge accumulated by the scholarly endeavors in the booming period between 2000 and 2015. This article traces trends and patterns regarding the use of explanatory variables and datasets in ninety-four individual studies. It synthesizes findings with regard to 107 explanatory concepts. Drawing on the sign test, the analysis identifies a set of consensus variables likely to determine the onset and incidence of violent intrastate conflict. These factors capture robust covariations and lend themselves as elements of a “standard model specification.” Turning to causal mechanisms, the article discusses why variables that turn out to be significant in statistical analyses should have any effect. This is completed by a substantial discussion of the remaining theoretical problems and of methodological prospects that promise paths for future research.
Mortality in Escherichia coli bloodstream infections: antibiotic resistance still does not make it
Authors: de Lastours V , Laouénan C , Royer G , Carbonnelle E , Lepeule R , Esposito-Farèse M , Clermont O , Duval X , Fantin B , Mentré F , Decousser J W , Denamur E , Lefort A 
Published: April 2020

AbstractBackgroundEscherichia coli bloodstream infections (BSIs) account for high mortality rates (5%–30%). Determinants of death are unclear, especially since the emergence of ESBL producers.ObjectivesTo determine the relative weight of host characteristics, bacterial virulence and antibiotic resistance in the outcome of patients suffering from E. coli BSI.MethodsAll consecutive patients suffering from E. coli BSI in seven teaching hospitals around Paris were prospectively included for 10 months. E. coli isolates were sequenced using Illumina NextSeq technology to determine the phylogroup, ST/ST complex (STc), virulence and antimicrobial resistance gene content. Risk factors associated with death at discharge or Day 28 were determined.ResultsOverall, 545 patients (mean ± SD age 68.5 ± 16.5 years; 52.5% male) were included. Mean Charlson comorbidity index (CCI) was 5.6 (± 3.1); 19.6% and 12.8% presented with sepsis and septic shock, respectively. Portals of entry were mainly urinary (51.9%), digestive (41.9%) and pulmonary (3.5%); 98/545 isolates (18%) were third-generation cephalosporin resistant (3GC-R), including 86 ESBL producers. In-hospital death (or at Day 28) was 52/545 (9.5%). Factors independently associated with death were a pulmonary portal of entry [adjusted OR (aOR) 6.54, 95% CI 2.23–19.2, P = 0.0006], the iha_17 virulence gene (aOR 4.41, 95% CI 1.23–15.74, P = 0.022), the STc88 (aOR 3.62, 95% CI 1.30–10.09, P = 0.014), healthcare-associated infections (aOR 1.98, 95% CI 1.04–3.76, P = 0.036) and high CCI (aOR 1.14, 95% CI 1.04–1.26, P = 0.006), but not ESBL/3GC-R.ConclusionsHost factors, portal of entry and bacterial characteristics remain major determinants associated with mortality in E. coli BSIs. Despite a high prevalence of ESBL producers, antibiotic resistance did not impact mortality. (ClinicalTrials.gov identifier: NCT02890901.)
A computerized decision support system (CDSS) for antibiotic prescription in primary care—Antibioclic: implementation, adoption and sustainable use in the era of extended antimicrobial resistance
Authors: Delory Tristan , Jeanmougin Pauline , Lariven Sylvie , Aubert Jean-Pierre , Peiffer-Smadja Nathan , Boëlle Pierre-Yves , Bouvet Elisabeth , Lescure François-Xavier , Le Bel Josselin 
Published: April 2020

Abstract

Objectives
To describe the implementation and use of a computerized decision support system (CDSS) for antibiotic prescription in primary care in France (Antibioclic). The CDSS targets 37 infectious diseases and has been freely available on a website since 2011.

Methods
Description and implementation of the architecture of a CDSS for antibiotic prescription in general practice. Analysis of the queries made between 2012 and 2018 on the CDSS by GPs. Analysis of two cross-sectional studies of users in 2014 and 2019.

Results
The number of queries increased from a median of 796/day [IQR, 578–989] in 2012 to 11 125/day [5592–12 505] in 2018. Unique users increased from 414/day [245–494] in 2012 to 5365/day [2891–5769] in 2018. Time taken to make a query was 2 min [1.9–2.1]. Among 3 542 347 queries in 2018, 78% were for adults. Six situations accounted for ≥50% of queries: cystitis; acute otitis media; acute sinusitis; community-acquired pneumonia; sore throat; and pyelonephritis. Queries concerned pathologies for which antibiotic prescription was necessary (64%), was conditional on additional clinical steps (34%) or was not recommended (2%). Most users (81%) were GPs, with median age of 38 years [31–52] and 58% were female. Among the 4016 GPs who responded to the surveys, the vast majority (96%) reported using the CDSS during the consultation, with 24% systematically using Antibioclic to initiate an antibiotic course and 93% having followed the CDSS recommendation for the latest prescription. Most GPs were comfortable using the CDSS in front of a patient.

Conclusions
Antibioclic has been adopted and is widely used in primary care in France. Its interoperability could allow its adaptation and implementation in other countries.
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events
Authors: Li Fang , Du Jingcheng , He Yongqun , Song Hsing-Yi , Madkour Mohcine , Rao Guozheng , Xiang Yang , Luo Yi , Chen Henry W , Liu Sijia , Wang Liwei , Liu Hongfang , Xu Hua , Tao Cui 
Published: April 2020

Abstract

Objective
The goal of this study is to develop a robust Time Event Ontology (TEO), which can formally represent and reason both structured and unstructured temporal information.

Materials and Methods
Using our previous Clinical Narrative Temporal Relation Ontology 1.0 and 2.0 as a starting point, we redesigned concept primitives (clinical events and temporal expressions) and enriched temporal relations. Specifically, 2 sets of temporal relations (Allen’s interval algebra and a novel suite of basic time relations) were used to specify qualitative temporal order relations, and a Temporal Relation Statement was designed to formalize quantitative temporal relations. Moreover, a variety of data properties were defined to represent diversified temporal expressions in clinical narratives.

Results
TEO has a rich set of classes and properties (object, data, and annotation). When evaluated with real electronic health record data from the Mayo Clinic, it could faithfully represent more than 95% of the temporal expressions. Its reasoning ability was further demonstrated on a sample drug adverse event report annotated with respect to TEO. The results showed that our Java-based TEO reasoner could answer a set of frequently asked time-related queries, demonstrating that TEO has a strong capability of reasoning complex temporal relations.

Conclusion
TEO can support flexible temporal relation representation and reasoning. Our next step will be to apply TEO to the natural language processing field to facilitate automated temporal information annotation, extraction, and timeline reasoning to better support time-based clinical decision-making.
Conditioned medium of the osteosarcoma cell line U2OS induces hBMSCs to exhibit characteristics of carcinoma-associated fibroblasts via activation of IL-6/STAT3 signalling
Authors: Lin Longshuai , Huang Kai , Guo Weihong , Zhou Chenghao , Wang Gangyang , Zhao Qinghua 
Published: April 2020

Abstract
As a research hotspot in recent years, bone mesenchymal stem cells (BMSCs) play an important role in the process of a variety of human diseases, including cancers. However, in osteosarcoma, the role of BMSCs and their communication with tumour cells are not clear. In this study, we validated the communication of osteosarcoma (OS) cells with BMSCs. The results showed that the conditioned medium of osteosarcoma cell line U2OS (U2OS-CM) induces the carcinoma-associated fibroblasts (CAFs)-like transformation of BMSCs and promotes the proliferation, migration and invasion of BMSCs. Mechanistically, treatment of human bone mesenchymal stem cells (hBMSCs) with U2OS-CM results in a significant increase in the IL-6 expression and phosphorylation of STAT3. Furthermore, blockade of the IL-6/STAT3 signalling in hBMSCs rescues the transformation of CAF phenotype induced by U2OS-CM. And, human IL-6 can directly increase the expression of the CAF marker genes in hMSCs. Meanwhile, IL-6/STAT3 signalling involves in promoting effects of U2OS-CM on the proliferation, migration and invasion of BMSCs. In summary, our results suggest that BMSCs communicate with OS cells through IL-6/STAT3 signalling and play an important role in the progress of osteosarcoma.
Comparative Analysis of Stylet Penetration Behaviors of Eriosoma lanigerum (Hemiptera: Aphididae) on Main Apple Cultivars in China
Authors: Hao Zhou , Lingjun Du , Fang-Hao Wan , Hongxu Zhou 
Published: April 2020

Abstract
The preference and behavioral mechanism of the feeding behavior of the woolly apple aphid, Eriosoma lanigerum (Hausmann), on Chinese apple cultivars was investigated using the electrical penetration graph (EPG) technique. Feeding of adult aphids was assessed for the four main cultivars of apple in China (Red Fuji, Ralls Genet, Starkrimson, and Jonagold) over an 8-h monitoring period, what that of fourth-instar nymphs was assessed for 8 h on Jonagold only. EPG waveforms representing the details of probing behaviors, parameters were measured for analysis. We found that at the nonphloem phase, the total duration of the nonpenetration (np) waveform and the total duration of the stylet pathway phase (the ‘C wave’) on Ralls Genet and Starkrimson were significantly longer than on Red Fuji. In addition, the phloem-feeding phase, the total duration of ‘release of saliva into the phloem’, (the E1 waveform) was significantly longer on Ralls Genet and Jonagold than on Red Fuji. The total duration of the ‘ingestion from sieve cells’ phase (the E2 waveform) on Red Fuji, meanwhile, was significantly longer than on Ralls Genet or Starkrimson. At the same time, when combined with EPG parameters, Red Fuji was found to have no obvious resistance to woolly apple aphid and to be a susceptible cultivar. This experiment also recorded the feeding waveform of fourth-instar aphid nymphs. Based on the phloem and nonphloem parameters recorded in this study, it was inferred that adult aphids are more likely than nymphs to feed on apple trees.
A phase III randomized controlled trial comparing surgery plus adjuvant chemotherapy with preoperative chemoradiotherapy followed by surgery plus adjuvant chemotherapy for locally recurrent rectal cancer: Japan Clinical Oncology Group study JCOG1801 (RC-SURVIVE study)
Authors: Kadota Tomohiro , Tsukada Yuichiro , Ito Masaaki , Katayama Hiroshi , Mizusawa Junki , Nakamura Naoki , Ito Yoshinori , Bando Hideaki , Ando Masahiko , Onaya Hiroaki , Fukuda Haruhiko , Kanemitsu Yukihide 
Published: April 2020

AbstractA randomized phase III trial was initiated in Japan in August 2019 to confirm the superiority of preoperative chemoradiotherapy followed by surgery plus adjuvant chemotherapy compared to the standard treatment, i.e. surgery plus adjuvant chemotherapy, for locally recurrent rectal cancer in local relapse-free survival. In all, 110 patients from 43 Japanese institutions will be recruited over a period of 6 years. Eligible patients would be registered and randomly assigned to each group with an allocation ratio of 1:1. The primary endpoint is local relapse-free survival. The secondary endpoints are overall survival, relapse-free survival, proportion of local relapse, proportion of distant relapse, proportion of patients with pathological R0 resection, response rate of preoperative chemoradiotherapy (preoperative chemoradiotherapy arm), pathological complete response rate (preoperative chemoradiotherapy arm), proportion of patients who completed the protocol treatment, incidence of adverse events (adverse reactions) and quality of life after surgery. This trial has been registered at the Japan Registry of Clinical Trial: jRCTs031190076 [https://jrct.niph.go.jp/latest-detail/jRCTs031190076] and ClinicalTrials.gov: NCT04288999 [https://clinicaltrials.gov/ct2/show/NCT04288999].
The Endoscopic Trans-Superior Articular Process Approach: A Novel Minimally Invasive Surgical Corridor to the Lateral Recess
Authors: Hasan Saqib , White-Dzuro Brie , Barber Jason K , Wagner Ralf , Hofstetter Christoph P 
Published: April 2020

Abstract

BACKGROUND
Transforaminal approaches to the lumbar spine are typically performed utilizing Kambin's triangle as approach corridor; however, degenerative changes can distort anatomy and expose the exiting nerve root to inadvertent injury.

OBJECTIVE
To describe the surgical technique of a novel full-endoscopic approach to access the lateral recess and report clinical outcomes.

METHODS
The trans-superior articular process (SAP) approach involves partial resection of the SAP, allowing access to the lateral recess both ventral and dorsal to the traversing nerve root. A retrospective review of 40 patients who had undergone a trans-SAP approach for decompression of lateral recess pathology was conducted. Outcomes were measured using visual analog scores (VAS) and Oswestry Disability Index (ODI) at 2 wk, 3 mo, and at last follow-up.

RESULTS
At a mean follow-up of 24 mo, patients experienced statistically significant improvement of the VAS for ipsilateral leg pain, VAS for back pain, and ODI when comparing preoperative values to all postoperative time points. The percentage of patients reaching a minimally clinically important difference for VAS leg pain and ODI was approximately 90% and 88%, respectively. The complication profile was favorable with no dural tears and no postoperative motor or sensory deficits. One patient required revision, with a total reoperation rate of 3%.

CONCLUSION
The trans-SAP approach is a novel approach that utilizes a safe surgical corridor via the SAP to access lateral recess pathology. Our initial clinical experience suggests that the trans-SAP approach allows for treatment of lateral recess and foraminal pathology with low complication rates.
Self-reported poor sleep on multiple dimensions is associated with higher total health care costs in older men
Authors: Schousboe John T , Kats Allyson M , Stone Katie L , Langsetmo Lisa , Vo Tien N , Blackwell Terri L , Buysse Daniel J , Ancoli-Israel Sonia , Ensrud Kristine E 
Published: April 2020

Abstract

Study Objectives
To estimate the association of self-reported poor sleep in multiple dimensions with health care costs in older men.

Methods
Participants were 1,413 men (mean [SD] age 76.5 [5.7] years) enrolled in both the Outcomes of Sleep Disorders in Older Men (MrOS Sleep) study and Medicare Fee-for-Service. Poor sleep was characterized at the baseline MrOS Sleep visit on five dimensions (satisfaction, daytime sleepiness, timing, latency, and duration). Health care costs and utilization were ascertained over 3 years of follow-up using Medicare Claims.

Results
Median (interquartile range [IQR]) annualized total health care costs (2018 US dollars) rose from $3,616 (IQR 1,523–7,875) for those with no impaired sleep dimensions to $4,416 (IQR 1,854–11,343) for men with two impaired sleep dimensions and $5,819 (IQR 1,936–15,569) for those with at least three impaired sleep dimensions. After multivariable adjustment, the ratio of total health care costs (CR) was significantly higher for men with two (1.24, 95% confidence interval [CI] 1.03– to 1.48) and men with at least three impaired sleep dimensions (1.78, 95% CI 1.42 to 2.23) vs. those with no impaired sleep dimensions. After excluding 101 men who died during the 3-year follow-up period, these associations were attenuated and not significant (CR 1.22, 95% CI 0.98 to 1.53 for men ≥3 impaired sleep dimensions vs. none).

Conclusions
Self-reported poor sleep on multiple dimensions is associated with higher subsequent total health care costs in older men, but this may be due to higher mortality and increased health care costs toward the end of life among those with poor sleep health.