bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatocellular Carcinoma with Portal Vein Tumor Involvement: Best Management Strategies
Authors: Liu Po-Hong , Huo Teh-Ia , Miksad Rebecca 
Published: July 2018

AbstractPortal vein tumor thrombosis (PVTT) commonly occurs in patients with hepatocellular carcinoma (HCC). Patients with PVTT usually have an aggressive disease course, decreased liver function reserve, limited treatment options, higher recurrence rates after treatment, and, therefore, worse overall survival. Among untreated HCC patients with PVTT, the median overall survival has been reported as low as 2 to 4 months. Historically, many aspects of PVTT have impacted the theoretical and practical safety and efficacy of treatment, for example, disordered blood flow and associated impairment of liver function, heat-sink effects of blood flow in the area of the PVTT, and risk of recurrence due to tumor location in the blood vessel. The current Barcelona Clinic Liver Cancer staging system categorizes HCC patients with PVTT as advanced stage, for which the standard of care is targeted therapy with sorafenib. However, sorafenib is associated with only marginal benefits among patients with PVTT. First-line lenvatinib, which was shown to be noninferior to sorafenib, excluded patients with main portal trunk invasion. Regorafenib and nivolumab, an immune-based therapy, were recently approved in the United States for second-line therapy after sorafenib. Preliminary results for cabozantinib suggest a benefit in the second-/third-line after sorafenib failure. In addition, rapid advances in many fields (surgery, interventional radiology, nuclear medicine, and immunotherapy) have increased the potential treatment options for the management of this complex disease entity. A large portion of the emerging evidence focuses on the broader category of advanced HCC of which PVTT is a subgroup. While many of these studies show promising results, the efficacy among PVTT patients requires validation in prospective studies. Real-world data may help fill the evidence gap for patients not eligible for clinical trials due to common hepatic function requirements. The variety of new treatment advances for the heterogeneous and complex disease entity of HCC with PVTT means that personalized, multidisciplinary management may be necessary to achieve optimal outcomes. In this narrative review, we summarize the evolving management strategies for patients with HCC and PVTT.
Potential Mechanisms Underlying the Role of Coffee in Liver Health
Authors: Alferink Louise , Kiefte-de Jong Jessica , Darwish Murad Sarwa 
Published: July 2018

AbstractCoffee, the most consumed hot beverage worldwide, is composed of many substances, of which polyphenols, caffeine, and diterpenoids are well studied. Evidence on potential effects of coffee on human health has been accumulating over the past decades. Specifically, coffee has been postulated to be hepatoprotective in several epidemiological and clinical studies. Several underlying molecular mechanisms as to why coffee influences liver health have been proposed. In this review, the authors summarized the evidence on potential mechanisms by which coffee affects liver steatosis, fibrosis, and hepatic carcinogenesis. The experimental models reviewed almost unanimously supported the theorem that coffee indeed may benefit the liver. Either whole coffee or its specific compounds appeared to decrease fatty acid synthesis (involved in steatogenesis), hepatic stellate activation (involved in fibrogenesis), and hepatic inflammation. Moreover, coffee was found to induce apoptosis and increased hepatic antioxidant capacity, which are involved in carcinogenesis.
Abdominal Wall Reconstruction: An Integrated Approach
Authors: Boukovalas Stefanos , Sisk Geoffrey , Selber Jesse 
Published: July 2018

AbstractAbdominal wall reconstruction has undergone substantial evolution over the last few decades. The optimal method of repair should be tailored to each patient's unique condition; however, a general approach that integrates four major factors can be applied as a conceptual framework to most clinical scenarios. Major factors to be considered include selection of mesh material, mesh inset position and technique, selective component separation, and management of soft tissue. These topics are inextricably intertwined in the sense that each can have specific implications, and in some cases, a determinative impact on the other decisions. When the relationship among these four factors is appreciated and applied to patient management, the reconstructive surgeon can achieve consistent outcomes that reflect skill, experience, and understanding.
Complicaciones vasculares durante la trombectomía mecánica en el ictus agudo, una experiencia multicéntrica en España
Authors: Meléndez Fernando , Tomasello Alejandro , Hernández David , Dinia Lavinia , Coscojuela Pilar , Ribó Marc 
Published: July 2018

Objetivo Determinar la frecuencia de las complicaciones observadas durante la trombectomía en el ictus isquémico agudo.
Materiales y Métodos Se revisó de forma retrospectiva las trombectomías realizadas en nuestra institución cuando los ictus isquémicos tuvieron una indicación de tratamiento endovascular. Se registraron los diferentes dispositivos utilizados en ese periodo de tiempo y si presentaron relación con el desarrollo de las complicaciones inmediatas mediante arteriografía.
Resultados De un total de 228 casos, se registraron complicaciones en el 16,6% de los casos. Se identificaron embolias (n = 31), hemorragias subaracnoideas (n = 2), hemorragia gangliobasal (n = 1), vasoespasmo (n = 1), disección (n = 1) y peusoaneurismas (n = 2). La embolia a nuevos territorios se presentó solo en 5 casos.
Discusión El tratamiento endovascular ha demostrado ser efectivo para la recanalización en oclusión de gran vaso. El uso de dispositivos presume un riesgo por la manipulación de los vasos.
Conclusión La embolia fue la complicación más frecuente. El tratamiento endovascular en el ictus genera un desenlace clínico favorable de los pacientes, al mismo tiempo, el bajo porcentaje de complicaciones que encontramos no suponen una afectación negativa en el desenlace final.
There is no haecceitic Euthyphro problem
Authors: Skiles Alexander 
Published: July 2018

AbstractJason Bowers and Meg Wallace (‘The Haecceitic Euthyphro Problem’, Analysis, 2018) have recently argued that those who hold that every individual instantiates a ‘haecceity’ (or ‘individual essence’) are caught up in a Euthyphro-style dilemma when confronted with familiar cases of fission and fusion. Key to Bowers and Wallace’s dilemma are certain assumptions about the nature of metaphysical explanation and the explanatory commitments of belief in haecceities. However, I argue that the dilemma only arises due to a failure to distinguish between providing a metaphysical explanation of why a fact holds vs. a metaphysical explanation of what it is for a fact to hold. In the process, I also shed light on the explanatory commitments of belief in haecceities.
zfRegeneration: a database for gene expression profiling during regeneration
Authors: Nieto-Arellano Rocío , Sánchez-Iranzo Héctor 
Published: July 2018

Abstract

Motivation
Zebrafish is a model organism with the ability to regenerate many different organs. Although RNA-Seq has been used extensively to study this process, there are no databases that allow easy access to data.

Results
Here we develop the first regeneration database that provides easy access to a large number of RNA-Seq datasets through custom-made plots of expression levels, differential expression analyses, correlations of genes and comparisons of the different datasets. zfRegeneration has a user-friendly web interface designed to enhance regeneration studies and to overcome the barriers between different research groups that study the regeneration of distinct organs. Using several case studies, we demonstrate that zfRegeneration provides a unique platform to analyse and understand gene expression during regeneration.

Availability and implementation
zfRegeneration is freely available at www.zfregeneration.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Quantifying the notions of canalizing and master genes in a gene regulatory network—a Boolean network modeling perspective
Authors: Kim Eunji , Ivanov Ivan , Dougherty Edward R 
Published: July 2018

Abstract

Motivation
Canalizing genes enforce broad corrective actions on cellular processes for the purpose of biological robustness maintaining a constant phenotype to remain unchanged in spite of genetic mutations or environmental perturbations. Despite their central role in biological systems, the observation/detection of canalizing genes is often impeded because the behavior of affected genes is highly varied relative to the inactive canalizer. Therefore, the activity of canalizing genes is difficult to predict to any significant degree by their subject genes under normal cell conditions.

Results
We investigate this question and present a quantitative framework that allows for the estimation of the power of canalizing genes in the context of Boolean Networks (BNs) with perturbation. This framework borrows tools from the Pattern Recognition theory and uses the coefficient of determination (CoD) to capture the capacity of the canalizing genes. The canalizing power (CP) of a gene is quantitatively characterized by two terms: regulation power (RP) and incapacitating power (IP). We base this assumption on the idea that canalizing power of a gene should be quantified by the extent of its regulation on the overall network and the extent of control that the gene takes over from other master genes when it is activated, which is equivalent to reduction of the control of other master genes upon its activation. Following this, the CP concept is illustrated with examples in which the goal is to provide preliminary evidence that CP can be used to characterize the ability of canalizing genes.

Availability and implementation
A library of functions written in MATLAB for computing CP is available at http://github.com/eunjikim-angie/CanalizingPower.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
Authors: Xia Li Charlie , Ai Dongmei , Lee Hojoon , Andor Noemi , Li Chao , Zhang Nancy R , Ji Hanlee P 
Published: July 2018

Abstract

Background
Simulating genome sequence data with variant features facilitates the development and benchmarking of structural variant analysis programs. However, there are only a few data simulators that provide structural variants in silico and even fewer that provide variants with different allelic fraction and haplotypes.

Findings
We developed SVEngine, an open-source tool to address this need. SVEngine simulates next-generation sequencing data with embedded structural variations. As input, SVEngine takes template haploid sequences (FASTA) and an external variant file, a variant distribution file, and/or a clonal phylogeny tree file (NEWICK) as input. Subsequently, it simulates and outputs sequence contigs (FASTAs), sequence reads (FASTQs), and/or post-alignment files (BAMs). All of the files contain the desired variants, along with BED files containing the ground truth. SVEngine's flexible design process enables one to specify size, position, and allelic fraction for deletions, insertions, duplications, inversions, and translocations. Finally, SVEngine simulates sequence data that replicate the characteristics of a sequencing library with mixed sizes of DNA insert molecules. To improve the compute speed, SVEngine is highly parallelized to reduce the simulation time.

Conclusions
We demonstrated the versatile features of SVEngine and its improved runtime comparisons with other available simulators. SVEngine's features include the simulation of locus-specific variant frequency designed to mimic the phylogeny of cancer clonal evolution. We validated SVEngine's accuracy by simulating genome-wide structural variants of NA12878 and a heterogeneous cancer genome. Our evaluation included checking various sequencing mapping features such as coverage change, read clipping, insert size shift, and neighboring hanging read pairs for representative variant types. Structural variant callers Lumpy and Manta and tumor heterogeneity estimator THetA2 were able to perform realistically on the simulated data. SVEngine is implemented as a standard Python package and is freely available for academic use .
Evolution, Diversification, and Biogeography of Grasshoppers (Orthoptera: Acrididae)
Authors: Song Hojun , Mariño-Pérez Ricardo , Woller Derek A , Cigliano Maria Marta 
Published: July 2018

AbstractThe grasshopper family Acrididae is one of the most diverse lineages within Orthoptera, including more than 6,700 valid species distributed worldwide. Grasshoppers are dominant herbivores, which have diversified into grassland, desert, semi-aquatic, alpine, and tropical forest habitats, and exhibit a wide array of morphological, ecological, and behavioral diversity. Nevertheless, the phylogeny of Acrididae as a whole has never been proposed. In this study, we present the first comprehensive phylogeny of Acrididae based on mitochondrial genomes and nuclear genes to test monophyly of the family and different subfamilies as well as to understand the evolutionary relationships among them. We recovered the monophyletic Acrididae and identified four major clades as well as several well-characterized subfamilies, but we also found that paraphyly is rampant across many subfamilies, highlighting the need for a taxonomic revision of the family. We found that Acrididae originated in the Paleocene of the Cenozoic period (59.3 million years ago) and, because the separation of South America and Africa predates the origin of the family, we hypothesize that the current cosmopolitan distribution of Acrididae was largely achieved by dispersal. We also inferred that the common ancestor of modern grasshoppers originated in South America, contrary to a popular belief that they originated in Africa, based on a biogeographical analysis. We estimate that there have been a number of colonization and recolonization events between the New World and the Old World throughout the diversification of Acrididae, and, thus, the current diversity in any given region is a reflection of this complex history.
Weak lensing by voids in weak lensing maps
Authors: Davies Christopher T , Cautun Marius , Li Baojiu 
Published: July 2018

ABSTRACT
Cosmic voids are an important probe of large-scale structure that can constrain cosmological parameters and test cosmological models. We present a new paradigm for void studies: void detection in weak lensing convergence maps. This approach identifies objects that relate directly to our theoretical understanding of voids as underdensities in the total matter field and presents several advantages compared to the customary method of finding voids in the galaxy distribution. We exemplify this approach by identifying voids using the weak lensing peaks as tracers of the large-scale structure. We find self-similarity in the void abundance across a range of peak signal-to-noise selection thresholds. The voids obtained via this approach give a tangential shear signal up to ∼40 times larger than voids identified in the galaxy distribution.
Smoking-Related Stigma: A Public Health Tool or a Damaging Force?
Authors: Lozano Paula , Thrasher James F , Forthofer Melinda , Hardin James , Shigematsu Luz Myriam Reynales , Arillo Santillán Edna , Fleischer Nancy L 
Published: July 2018

Abstract

Background
Tobacco control policies and other denormalization strategies may reduce tobacco use by stigmatizing smoking. This raises an important question: Does perceived smoking-related stigma contribute to a smoker’s decision to quit? The aim of this study was to evaluate if perceived smoking-related stigma was associated with smoking cessation outcomes among smokers in Mexico and Uruguay.

Methods
We analyzed prospective data from a panel of adult smokers who participated in the 2008–2012 administrations of the International Tobacco Control Policy Evaluation Surveys in Mexico and Uruguay. We defined two analytic samples of participants: the quit behavior sample (n = 3896 Mexico; n = 1525 Uruguay) and the relapse sample (n = 596 Mexico). Generalized estimating equations were used to evaluate if different aspects of perceived stigma (ie, discomfort, marginalization, and negative stereotype) at baseline were associated with smoking cessation outcomes at follow-up.

Results
We found that perceived smoking-related stigma was associated with a higher likelihood of making a quit attempt in Uruguay but with a lower likelihood of successful quitting in Mexico.

Conclusions
This study suggests that perceived smoking-related stigma may be associated with more quit attempts, but less successful quitting among smokers. It is possible that once stigma is internalized by smokers, it may function as a damaging force. Future studies should evaluate the influence of internalized stigma on smoking behavior.

Implications
Although perceived smoking-related stigma may prompt smokers to quit smoking, smoking stigma may also serve as a damaging force for some individuals, making quitting more difficult. This study found that perceived smoking-related stigma was associated with a higher likelihood of making a quit attempt in Uruguay but with a lower likelihood of successful quitting in Mexico.
Lucilius
Authors: Chahoud Anna 
Published: July 2018

Gaius Lucilius (fl. c. 130 bce–103/2 bce) was the inventor of Roman satire as we know it. Born of an equestrian family from Suessa Aurunca in Campania, he was an affluent landowner, the great uncle of Pompey the Great, and as such intended for a senatorial career, which he proudly turned down to undertake a career unprecedented for a Roman citizen: Lucilius was the first non-professional poet in Rome. He was a prominent figure in the Middle Republic, a personal friend of Laelius and Scipio Aemilianus, under whom he served in the Numantine War in 134/3 bce, and enjoyed such renown that he was awarded a public funeral, in Naples in 103/2 bce. He had an extensive Greek education and contacts with Greek intellectuals of his time; the skeptic philosopher Clitomachus, Head of the Academy (c. 127/6–110–109 bce), dedicated a work on problems of cognitive theory to him. Variety of themes, independence, and freedom of speech characterize his poetry, which he called sermones, “conversations,” apparently never using the term satura that his predecessor Ennius had given his experiments with miscellaneous verse. Personal poetry at Rome truly begins with Lucilius, whose pronounced subjectivity and unrestrained aggressiveness would become synonymous with satire itself for every subsequent writer in the genre, from Horace to Persius to Juvenal. Of Lucilius’s thirty books of verse satires––initially written in the iambo-trochaic meter of comic dialogue, before he settled on the hexameter––approximately thirteen hundred lines survive through the quotations of later writers from the late Republic through Late Antiquity.
Cdk5‐mediated phosphorylation regulates phosphatidylinositol 4‐phosphate 5‐kinase type I γ 90 activity and cell invasion
Authors: Li Liqing , Kołodziej Tomasz , Jafari Naser , Chen Jing , Zhu Haining , Rajfur Zenon , Huang Cai 
Published: July 2018

ABSTRACTPhosphatidylinositol 4‐phosphate 5‐kinase type I γ (PIPKIγ90) regulates cell migration, invasion, and metastasis. However, it is unknown how cellular signals regulate those processes. Here, we show that cyclin‐dependent kinase 5 (Cdk5), a protein kinase that regulates cell migration and invasion, phosphorylates PIPKIγ90 at S453, and that Cdk5‐mediated PIPKIγ90 phosphorylation is essential for cell invasion. Moreover, Cdk5‐mediated phosphorylation down‐regulates the activity of PIPKIγ90 and the secretion of fibronectin, an extracellular matrix protein that regulates cell migration and invasion. Furthermore, inhibition of PIPKIγ activity with the chemical inhibitor UNC3230 suppresses fibronectin secretion in a dose‐dependent manner, whereas depletion of Cdk5 enhances fibronectin secretion. With total internal reflection fluorescence microscopy, we found that secreted fibronectin appears as round dots, which colocalize with Tks5 and CD9 but not with Zyxin. These data suggest that Cdk5‐mediated PIPKIγ90 phosphorylation regulates cell invasion by controlling PIPKIγ90 activity and fibronectin secretion.—Li, L., Kotodziej, T., Jafari, N., Chen, J., Zhu, H., Rajfur, Z., Huang, C. Cdk5‐mediated phosphorylation regulates phosphatidylinositol 4‐phosphate 5‐kinase type I γ 90 activity and cell invasion. FASEB J. 33, 631–642 (2019). www.fasebj.org
RYBP modulates stability and function of Ring1B through targeting UBE3A
Authors: Li Meng , Zhang Shiqiang , Zhao Wen , Hou Congcong , Ma Xiaoli , Li Xuekun , Huang Bingren , Chen Hong , Chen Deng 
Published: July 2018

ABSTRACTRing1 and yin yang 1–binding protein (RYBP) are central components of noncanonical polycomb‐repressive complex 1 (nc‐PRC1), which represses target gene expression and is required for normal organismal development. However, the molecular function of RYBP in this complex is obscure. In this study, we showed that RYBP inhibits the polyubiquitination‐mediated proteasomal degradation of RingIB independently of its ubiquitin (Ub)‐protein isopeptide ligase (E3) ligase activity, leading to its stabilization and increased catalytic activity toward monoubiquitination of histone H2A at lysine 119. Mechanistic dissection further disclosed that RYBP directly binds to ubiquitin protein ligase E3A (UBE3A) to promote its ubiquitination and proteasomal degradation in an autoubiquitination‐independent manner. The resultant reduction of UBE3A protein level alleviates its effect on ubiquitination‐mediated degradation of Ring1B, therefore resulting in increased stability and enhanced transcriptional repressor activity on its target genes. Thus, our current findings lay a foundation for understanding how RYBP functions in nc‐PRC1 complexes, which is involved in development, stem cell maintenance, and carcinogenesis.—Li, M., Zhang, S., Zhao, W., Hou, C., Ma, X., Li, X., Huang, B., Chen, H., Chen, D. RYBP modulates stability and function of Ring1B through targeting UBE3A. FASEB J. 33, 683–695 (2019). www.fasebj.org
Integrative and conjugative elements and their hosts: composition, distribution, and organization
Authors: Cury Jean , Touchon Marie , Rocha Eduardo P. C. 
Published: July 2018

AbstractConjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species’ pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses show that ICEs are modular and that their gene repertoires can be grouped in function of their conjugation types, even if integrases were shown to be paraphyletic relative to the latter. We show that there are general trends in the functional organization of genes within ICEs and of ICEs within the bacterial chromosome paving the way for future functional and evolutionary analyses.