bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mode of cell adhesion and migration facilitated by CD44-dependent microtentacles
Authors: Wolf Kayla J. , Shukla Poojan , Springer Kelsey , Lee Stacey , Coombes Jason D. , Choy Caleb J. , Kenny Samuel J. , Xu Ke , Kumar Sanjay 
Published: May 2020

Significance
We identify a mechanism used by tumor cells to adhere to and migrate through a nanoporous, three-dimensional extracellular matrix characteristic of brain tissue. In this mechanism, cells engage hyaluronic acid, a key component within brain matrix, by assembling “microtentacles” that can extend tens of micrometers from the cell body and adhere to the matrix via the CD44 receptor. We also elucidate a molecular mechanism through which these structures can support motility based on the interplay of actin, microtubules, IQGAP1, and CLIP170. Analogous structures have previously been observed in circulating tumor cells and hypothesized to facilitate endothelial attachment and extravasation. Our studies strongly support this concept and further indicate that microtentacles can facilitate adhesion and invasion into tissue.
The Greek connective gar
Authors: Casson Sarah 
Published: May 2020

Abstract
Traditional accounts of the Greek connective gar offer an inadequate causal definition,
while multiplying descriptive categories. Linguistic accounts have paid little attention to the role of
gar in different kinds of communication. This article proposes a relevance-theoretic procedural
explanation which provides a unifying cognitive explanation for gar’s communicative role.
Gar indicates that the premise it introduces is relevant in relation to a previously communicated
claim, which, when combined with implicit assumptions, it strengthens. This strengthening may work itself out
differently in diverse kinds of communication: typically, as confirmation in argumentation, and explanation in
narrative. Perceived differences in stylistic effects sometimes associated with gar are attributable
not to multiple functions, but to recognition of differing communicator goals in narrative and argumentation.
Relevance, style and multimodality
Authors: Sasamoto Ryoko , O'Hagan Minako 
Published: May 2020

Abstract
Brightly coloured textual inserts, which often occupy a sizable part of the TV screen, have become a key
feature in Japanese TV. This paper unpacks the contribution of such multimodal stimuli to inference, and the
consequences this has for the interpretation process. Using data derived from a mixed-methods approach (i.e.
eye-tracking and a multimodal content analysis), we evaluate the relationship between cognitive processing and
communicative stimuli. We demonstrate how typographical features (colours and fonts) are used as highlighting
stylistic devices by TV producers to manipulate the viewer comprehension process by guiding the audience to an
intended interpretation. The results suggest how editorial choices regarding typographical features to trigger certain
effects might be subsumed under the current view of style in relevance theory.
Towards a relevance-theoretic account of hate speech
Authors: Linde-Usiekniewicz Jadwiga 
Published: May 2020

Abstract
Hate speech has been studied as a social, psychological and legal phenomenon in various frameworks
offered by relevant disciplines, with most famous account being Judith Butler’s analysis of hate speech in
terms of Austinian speech act theory. This chapter explores the possibility of applying relevance-theoretic
analysis to hate speech. It argues that all kinds of hate speech, ranging from most direct to most covert, are
instances of ostensive behavior that requires being processed together with some mental representations,
corresponding to either intuitive or reflected beliefs about generalized inferiority of a group of people by
virtue of their race, ethnicity, faith/atheism, gender, sexual orientation, sexual identity, or etc. or, their
corresponding meta-representations, for greatest (tentatively optimal) relevance.
MiR-153-5p promotes sensibility of colorectal cancer cells to oxaliplatin via targeting Bcl-2-mediated autophagy pathway
Authors: He Yong , Zhang Ling , Tan Fei , Wang Li-Fang , Liu De-Hui , Wang Rong-Juan , Yin Xiong-Zhang 
Published: May 2020

Abstract
Oxaliplatin (L-OHP) is one of the effective chemotherapeutic drugs for colorectal cancer (CRC). Further investigation into the molecular mechanism of chemoresistance could improve outcomes for patients with colorectal cancer. Recently, microRNAs have been reported as a key in drug resistance of tumors. In this study, we aimed to investigate the effects of miR-153-5p in L-OHP-resistant CRC cells, and its underlying mechanism. Downregulation of miR-153-5p was observed in CRC cells, while upregulation of miR-153-5p enhances the chemosensitivity of CRC/L-OHP cells. The autophagy of CRC/L-OHP cells was markedly increased after exposure to L-OHP but abolished by the upregulation of miR-153-5p. Dual-luciferase reporter assays validated that Bcl-2 was a direct target of miR-153-5p. In conclusion, our data suggested that miR-153-5p was a mediator of cisplatin resistance in colorectal cancer by affecting Bcl-2-mediated autophagy, indicating a new therapeutic target for CRC treatment.
Evaluation of a multidisciplinary approach to reduce internal medicine readmissions using a readmission prediction index
Authors: McConachie Sean M , Raub Joshua N , Yost Raymond , Monday Lea , Agrawal Shivani , Tannous Pierre 
Published: May 2020

Abstract

Purpose
Readmission prediction indices are used to stratify patients by the risk of hospital readmission. We describe the integration of a 30-day hospital readmission prediction index into the electronic medical record (EMR) and its impact on pharmacist interventions during transitions of care (TOC).

Methods
A retrospective cohort study was conducted to compare 30-day readmission rates between adult internal medicine inpatients admitted by a multidisciplinary team providing TOC services (the TOC group) and those who received usual care (the control group). Interventions by a pharmacist serving on the TOC team were guided by an EMR-integrated readmission index, with patients at the highest risk for readmission receiving targeted pharmacist interventions. Inpatient encounters (n = 374) during the 5-month study period were retrospectively identified. Chi-square and Mann-Whitney U tests were performed to analyze differences in nominal and nonparametric continuous variables, respectively. Logistic regression was performed to identify variables associated with 30-day readmissions. The log-rank test was used to analyze hazard ratios for readmission outcomes in the 2 cohorts.

Results
Thirty-day readmission rates did not differ significantly in the TOC group and the control group (20.9% vs 18.3%, P = 0.52). However, patients who received additional direct pharmacist interventions, as guided by use of a hospital readmission index, had a lower 30-day readmission rate than patients who did not (11.4% vs 21.7%, P = 0.04). The readmission index score was significantly associated with the likelihood of 30-day readmission (odds ratio for readmission, 1.25; 95% confidence interval, 1.16-1.34; P &lt; 0.01). The difference in unadjusted log-rank scores at 30 days with and without pharmacist intervention was not significant (P = 0.05). A mean of 4.5 medication changes were identified per medication reconciliation performed by the TOC pharmacist.

Conclusion
A multidisciplinary TOC team approach did not reduce the 30-day readmission rate on an internal medicine service. However, patients who received additional direct pharmacist interventions guided by a readmission prediction index had a reduced readmission rate.
An early Oligocene stem Galbulae (jacamars and puffbirds) from southern France, and the position of the Paleogene family Sylphornithidae
Authors: Duhamel Anaïs , Balme Christine , Legal Stéphane , Riamon Ségolène , Louchart Antoine 
Published: May 2020

AbstractTogether, puffbirds (Bucconidae) and jacamars (Galbulidae) form the suborder Galbulae, sister group of all other Piciformes. Hitherto, the Galbulae had no ascertained pre-Pleistocene fossil record, and all previous alleged candidates have been refuted, except possibly the Sylphornithidae. Here we describe a wing of a tiny fossil bird from the early Oligocene of the Luberon region (southern France), which we assign to the Galbulae, as a new genus and species. Several characters, especially of the ulna and wing phalanx 1 of digit II, exclude the Passeriformes and Zygodactylidae, and indicate a representative of the Piciformes. Among Piciformes, absence of papillae remigales caudales and several characters of the wing phalanx 1 of digit II make it possible to assign the fossil to the Galbulae, and exclude all other clades. The fossil Sylphornithidae, with the carpometacarpus of Sylphornis being available, show some similarity with the Luberon fossil. The combination of features of the wing elements leads to the placement of the new fossil as stem Galbulae, and tentatively within the family Sylphornithidae. As such, it fills a gap and permits to better assign the whole enigmatic tiny sylphornithids, otherwise essentially known from leg bones. This yields the first firm pre-Pleistocene fossil record for the Galbulae. Today, both the Bucconidae and Galbulidae live exclusively in tropical America. The presence of stem Galbulae in the Oligocene of Europe, and probably the late Eocene, is a new example of a present-day Neotropical clade that had stem representatives in the Paleogene of Europe.
iBioProVis: interactive visualization and analysis of compound bioactivity space
Authors: Donmez Ataberk , Rifaioglu Ahmet Sureyya , Acar Aybar , Doğan Tunca , Cetin-Atalay Rengul , Atalay Volkan 
Published: May 2020

Abstract

Summary
iBioProVis is an interactive tool for visual analysis of the compound bioactivity space in the context of target proteins, drugs and drug candidate compounds. iBioProVis tool takes target protein identifiers and, optionally, compound SMILES as input, and uses the state-of-the-art non-linear dimensionality reduction method t-Distributed Stochastic Neighbor Embedding (t-SNE) to plot the distribution of compounds embedded in a 2D map, based on the similarity of structural properties of compounds and in the context of compounds’ cognate targets. Similar compounds, which are embedded to proximate points on the 2D map, may bind the same or similar target proteins. Thus, iBioProVis can be used to easily observe the structural distribution of one or two target proteins’ known ligands on the 2D compound space, and to infer new binders to the same protein, or to infer new potential target(s) for a compound of interest, based on this distribution. Principal component analysis (PCA) projection of the input compounds is also provided, Hence the user can interactively observe the same compound or a group of selected compounds which is projected by both PCA and embedded by t-SNE. iBioProVis also provides detailed information about drugs and drug candidate compounds through cross-references to widely used and well-known databases, in the form of linked table views. Two use-case studies were demonstrated, one being on angiotensin-converting enzyme 2 (ACE2) protein which is Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike protein receptor. ACE2 binding compounds and seven antiviral drugs were closely embedded in which two of them have been under clinical trial for Coronavirus disease 19 (COVID-19).

Availability and implementation
iBioProVis and its carefully filtered dataset are available at https://ibpv.kansil.org/ for public use.

Contact
vatalay@metu.edu.tr

Supplementary information
Supplementary data are available at Bioinformatics online.
SOMM4mC: a second-order Markov model for DNA N4-methylcytosine site prediction in six species
Authors: Yang Jiali , Lang Kun , Zhang Guangle , Fan Xiaodan , Chen Yuanyuan , Pian Cong 
Published: May 2020

Abstract

Motivation
DNA N4-methylcytosine (4mC) modification is an important epigenetic modification in prokaryotic DNA due to its role in regulating DNA replication and protecting the host DNA against degradation. An efficient algorithm to identify 4mC sites is needed for downstream analyses.

Results
In this study, we propose a new prediction method named SOMM4mC based on a second-order Markov model, which makes use of the transition probability between adjacent nucleotides to identify 4mC sites. The results show that the first-order and second-order Markov model are superior to the three existing algorithms in all six species (Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Escherichia coli, Geoalkalibacter subterruneus and Geobacter pickeringii) where benchmark datasets are available. However, the classification performance of SOMM4mC is more outstanding than that of first-order Markov model. Especially, for E.coli and C.elegans, the overall accuracy of SOMM4mC are 91.8% and 87.6%, which are 8.5% and 6.1% higher than those of the latest method 4mcPred-SVM, respectively. This shows that more discriminant sequence information is captured by SOMM4mC through the dependency between adjacent nucleotides.

Availability and implementation
The web server of SOMM4mC is freely accessible at www.insect-genome.com/SOMM4mC.

Contact
chenyuanyuan@njau.edu.cn or piancong@njau.edu.cn
Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)
Authors: Escobar Inelia , Ruiz-Ponce Eduardo , Rudall Paula J , Fay Michael F , Toro-Núñez Oscar , Villalobos-Barrantes Heidy M , Baeza Carlos M 
Published: May 2020

AbstractGilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.
High Burden of Bloodstream Infections Associated With Antimicrobial Resistance and Mortality in the Neonatal Intensive Care Unit in Pune, India
Authors: Johnson Julia , Robinson Matthew L , Rajput Uday C , Valvi Chhaya , Kinikar Aarti , Parikh Tushar B , Vaidya Umesh , Malwade Sudhir , Agarkhedkar Sharad , Randive Bharat , Kadam Abhay , Smith Rachel M , Westercamp Matthew , Mave Vidya , Gupta Amita , Milstone Aaron M , Manabe Yukari C 
Published: May 2020

Abstract

Background
Antimicrobial resistance (AMR) is a growing threat to newborns in low- and middle-income countries (LMIC).

Methods
We performed a prospective cohort study in 3 tertiary neonatal intensive care units (NICUs) in Pune, India, to describe the epidemiology of neonatal bloodstream infections (BSIs). All neonates admitted to the NICU were enrolled. The primary outcome was BSI, defined as positive blood culture. Early-onset BSI was defined as BSI on day of life (DOL) 0–2 and late-onset BSI on DOL 3 or later.

Results
From 1 May 2017 until 30 April 2018, 4073 neonates were enrolled. Among at-risk neonates, 55 (1.6%) developed early-onset BSI and 176 (5.5%) developed late-onset BSI. The majority of BSIs were caused by gram-negative bacteria (GNB; 58%); among GNB, 61 (45%) were resistant to carbapenems. Klebsiella spp. (n = 53, 23%) were the most common cause of BSI. Compared with neonates without BSI, all-cause mortality was higher among neonates with early-onset BSI (31% vs 10%, P &lt; .001) and late-onset BSI (24% vs 7%, P &lt; .001). Non–low-birth-weight neonates with late-onset BSI had the greatest excess in mortality (22% vs 3%, P &lt; .001).

Conclusions
In our cohort, neonatal BSIs were most commonly caused by GNB, with a high prevalence of AMR, and were associated with high mortality, even in term neonates. Effective interventions are urgently needed to reduce the burden of BSI and death due to AMR GNB in hospitalized neonates in LMIC.
The cruelest harvest: Virgilian agricultural pessimism in the poetry of the Brazilian colonial period
Authors: Vazquez Adriana 
Published: May 2020

AbstractClassical imagery and mythological narratives provided ready literary analogues for framing European expansion into the New World in the colonial and early modern periods. This article examines the manipulation of classical images of agricultural fecundity and Virgilian pessimism in select works of two Brazilian poets working in the neoclassical tradition during the colonial period, José Basílio da Gama (1740–95) and Inácio José de Alvarenga Peixoto (1744–93), by which both poets advance a critique of Iberian expansion into Latin America. I argue that both poets, writing in dialogue with one another, activate an especially Virgilian agricultural imagery that sets war in contradiction to agricultural production in a post-colonial critique of European imperialist expansion into Brazil. The poetry of these figures exhibits a remarkable reversal of sympathies that distinguishes South American treatment of ancient material from that of European receptions that aligned imperial Europe with the Roman empire and its traditional heroes, a comparison established in order to justify colonialist expansion into the New World.
PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax
Authors: Singh Ankita , Kaushik Rahul , Chaurasia Dheeraj Kumar , Singh Manpreet , Jayaram B 
Published: May 2020

Abstract
Despite Plasmodium vivax being the main offender in the majority of malarial infections, very little information is available about its adaptation and development in humans. Its capability for activating relapsing infections through its dormant liver stage and resistance to antimalarial drugs makes it as one of the major challenges in eradicating malaria. Noting the immediate necessity for the availability of a comprehensive and reliable structural and functional repository for P. vivax proteome, here we developed a web resource for the new reference genome, PvP01, furnishing information on sequence, structure, functions, active sites and metabolic pathways compiled and predicted using some of the state-of-the-art methods in respective fields. The PvP01 web resource comprises organized data on the soluble proteome consisting of 3664 proteins in blood and liver stages of malarial cycle. The current public resources represent only 163 proteins of soluble proteome of PvP01, with complete information about their molecular function, biological process and cellular components. Also, only 46 proteins of P. vivax have experimentally determined structures. In this milieu of extreme scarcity of structural and functional information, PvP01 web resource offers meticulously validated structures of 3664 soluble proteins. The sequence and structure-based functional characterization led to a quantum leap from 163 proteins available presently to whole soluble proteome offered through PvP01 web resource. We believe PvP01 web resource will serve the researchers in identifying novel protein drug targets and in accelerating the development of structure-based new drug candidates to combat malaria.
Database Availability: http://www.scfbio-iitd.res.in/PvP01
The Impact of Terrorism on Individual Well-Being: Evidence from the Boston Marathon Bombing
Authors: Clark Andrew E , Doyle Orla , Stancanelli Elena 
Published: May 2020

AbstractA growing literature has concluded that terrorism affects the economy, yet less is known about its impact on individual welfare. This article estimates the impact of the 2013 Boston marathon bombing on well-being, exploiting representative daily data from the American Time Use Survey and Well-Being Supplement. Using a combined regression discontinuity and differences-in-differences design, with the 2012 Boston marathon as a counterfactual, we find an immediate reduction in well-being of a third of a standard deviation. In particular, happiness declined sharply and negative emotions rose significantly. While the effects do not persist beyond one week, they may entail adverse health and economic consequences.
Safety and efficacy of transvenous mechanical lead extraction in patients with abandoned leads
Authors: Segreti Luca , Giannotti Santoro Mario , Di Cori Andrea , Fiorentini Federico , Zucchelli Giulio , Bernini Giulia , De Lucia Raffaele , Viani Stefano , Paperini Luca , Barletta Valentina , Soldati Ezio , Bongiorni Maria Grazia 
Published: May 2020

Abstract

Aims
Optimal management of redundant or malfunctioning leads is controversial. We aimed to assess safety and efficacy of mechanical transvenous lead extraction (TLE) in patients with abandoned leads.

Methods and results
Consecutive TLE procedures performed in our centre from January 2009 to December 2017 were considered. We evaluated the safety and efficacy of mechanical TLE in patients with abandoned (Group 1) compared to non-abandoned (Group 2) leads. We analysed 1210 consecutive patients that required transvenous removal of 2343 leads. Group 1 accounted for 250 patients (21%) with a total of 617 abandoned leads (26%). Group 2 comprised 960 patients (79%) with 1726 leads (74%). The total number of leads (3.0 vs. 2.0), dwelling time of the oldest lead (108.00 months vs. 60.00 months) and infectious indications for TLE were higher in Group 1. Clinical success was achieved in 1168 patients (96.5%) with a lower rate in Group 1 (90.4% vs. 98.1%; P &lt; 0.001). Major complications occurred in only 9 patients (0.7%), without significant differences among the two groups. The presence of one or more abandoned leads [odds ratio (OR) 3.47; 95% confidence interval (CI) 1.07–11.19; P = 0.037] and dwelling time of the oldest lead (OR 1.01 for a month; 95% CI 1.01–1.02; P &lt; 0.001) were associated with a higher risk of clinical failure.

Conclusion
Transvenous mechanical lead extraction is a safe procedure also in high-risk settings, as patients with abandoned leads. Success rate resulted a bit lower, especially in the presence of abandoned leads with long implantation time.