bluuebunny/crossref_metadata_2025_split huggingface dataset:
The serum biomarker chemerin promotes tumorigenesis and metastasis in oral squamous cell carcinoma
Authors: Lu Zhiyuan , Liang Jianfeng , He Qianting , Wan Quan , Hou Jinsong , Lian Keqian , Wang Anxun 
Published: February 2019

Abstract
Chemerin, which is encoded by retinoic acid receptor responder 2 (RARRES2), has been found to be related to malignant tumours, but its role in the development of oral squamous cell carcinoma (OSCC) is largely unexplored. In the present study, a higher serum level of chemerin was evident in patients with OSCC than in healthy individuals, and this high level of chemerin significantly decreased after tumour resection. In addition, high chemerin levels were positively associated with advanced tumour stage and lymph node metastasis. The expression levels of chemerin and Chemerin Receptor 23 (ChemR23) were positively correlated with the migration and invasion of OSCC cell lines. Recombinant chemerin (R-chemerin) enhanced the in vitro migration, invasion and proliferation of OSCC cells in a concentration-dependent manner, and short hairpin RNAs (shRNAs) targeting RARRES2 decreased chemerin expression and inhibited OSCC cell metastasis and proliferation both in vitro and in vivo. Additionally, R-chemerin activated manganese superoxide dismutase (SOD2) and increased the amount of intracellular hydrogen peroxide (H2O2), leading to a significant decrease in E-cadherin expression and dramatic increase in the expression of phosphorylated ERK1/2 (p-ERK1/2), Slug, Vimentin and N-cadherin, but shRNAs targeting RARRES2 reversed these effects. Moreover, knockdown of ChemR23 with small interfering RNAs (siRNA) significantly inhibited chemerin-induced OSCC cell migration/invasion and SOD2 activity. Our results revealed that chemerin is a novel biomarker for OSCC. Chemerin/ChemR23 promotes tumorigenesis and metastasis in OSCC and may be a new therapeutic target for OSCC.
Investigating dynamical properties of evolved Galactic open clusters
Authors: Angelo M. S. , Santos J. F. C. , Corradi W. J. B. , Maia F. F. S. 
Published: February 2019

Context. The stellar content of Galactic open clusters is gradually depleted during their evolution as a result of internal relaxation and external interactions. The final residues of the long-term evolution of open clusters are called open cluster remnants. These are sparsely populated structures that can barely be distinguished from the field.Aims. We aimed to characterise and compare the dynamical states of a set of 16 objects catalogued as remnants or remnant candidates. We employed parameters that are intimately associated with the dynamical evolution: age, limiting radius, stellar mass, and velocity dispersion. The sample also includes 7 objects that are catalogued as dynamically evolved open clusters for comparison purposes.Methods. We used photometric data from the 2MASS catalogue, proper motions and parallaxes from theGaiaDR2 catalogue, and a decontamination algorithm that was applied to the three-dimensional astrometric space of proper motions and parallaxes (μα, μδ, ϖ) for stars in the objects’ areas. The luminosity and mass functions and total masses for most open cluster remnants are derived here for the first time. Our analysis used predictions ofN-body simulations to estimate the initial number of stars of the remnants from their dissolution timescales.Results. The investigated open cluster remnants present masses (M) and velocity dispersions (σv) within well-defined ranges:Mbetween ∼10−40 M⊙andσvbetween ∼1−7 km s−1. Some objects in the remnant sample have a limiting radiusRlim ≲ 2 pc, which means that they are more compact than the investigated open clusters; other remnants haveRlimbetween ∼2−7 pc, which is comparable to the open clusters. We suggest that cluster NGC 2180 (previously classified as an open cluster) is entering a remnant evolutionary stage. In general, our clusters show signals of depletion of low-mass stars. This confirms their dynamically evolved states.Conclusions. We conclude that the open cluster remnants we studied are in fact remnants of initially very populous open clusters (N0 ∼ 103−104stars). The outcome of the long-term evolution is to bring the final residues of the open clusters to dynamical states that are similar to each other, thus masking out the memory of the initial formation conditions of star clusters.
Gratification Phenomena in Infancy: A Report of Twenty-Nine Children
Authors: Koul Roshan , AlFutaisi Amna , Mani Renjith , Abdelrahim Rana , AlAdi Azza 
Published: February 2019

AbstractTwenty-nine children with gratification phenomena seen in last 10 years (January 2008 to December 2017) were analyzed retrospectively. A proper history, eyewitness account, and video recordings of the event helped in making the diagnosis. Twenty-seven out of 29 (93%) children with gratification phenomena were females. Four patterns of gratification phenomena were seen. Three of these patterns not described before are reported. A typical gratification phenomenon was seen in 16 of 29 (55%) children. At the time of referral, 24% of these children were labeled epileptic and were on antiepileptic medication. This benign condition has to be recognized and extensive investigations should be avoided.
Potential of exclosure on aboveground biomass carbon stock and ecological fitness of woody species in Jabi Tehnane district, northwestern Ethiopia
Authors: Asmare Melkamu Terefe , Gure Abdella 
Published: February 2019

ABSTRACT

Assessment of ecological fitness of woody species across land use is critical issues in degraded land restoration. However, little is known about AGBC stored capacity, important value and distribution index of woody species grows in exclosure and adjacent open lands. Therefore, this research is aimed to (i) analyse impact of exclosure on AGBC (ii) ecological fit species. A random sampling method was employed. Forty sample plots (50m*50m) were used. AGBC stocks (mean± SE) of woody species in adjacent open grazing and exclosure land use of GW site was 0.11±0.07 and 1.24±0.27Mg ha
-1
respectively. While in adjacent open grazing and exclosure land use of WG site, the value was 0.27±0.03 and 2.79±0.27Mgha
-1
respectively. In both site exclosure land uses, the proportion of rare, occasional and common woody species were better than their adjacent open grazing land. Cupressus lustanica from open grazing and Vernonia auriculifera from exclosure land use of WG as well as Croton macrostachyus from open grazing and Leucaena leucocephala from exclosure land use of GW site were recorded as top ecologically fit species. It is recommended to protect degraded lands via integrating ecologically adapted native species and fully used their diversity to achieve the potential benefits of land restoration.
The Belle II experiment: status and prospects
Authors: Martini Alberto 
Published: February 2019

Abstract
In this article the Belle II experiment will be described and its status and physics prospects will be presented. Belle II is situated in Japan, at the KEK laboratory and it is the upgraded version of the Belle experiment. It uses a new collider named SuperKEKB, a new generation of B-factory based on the innovative Nano-Beam scheme technique, which is expected to collect an integrated luminosity of 50 ab
−1. Using this amount of data, together with improved detector performances, it will be possible to provide important contributions about several flavour physics topics (i.e. UT angles, CKM matrix elements, FCNC processes, LFV studies, etc.) through high precision measurements. The main aim is to investigate new physics scenarios and validate highly suppressed SM predictions. The experiment is almost completely assembled; it already took the first data without the vertex detector installed while the data taking will start in February 2019.
Optimal selection of genetic variants for adjustment of population stratification in European association studies
Authors: Brinster Regina , Scherer Dominique , Lorenzo Bermejo Justo 
Published: February 2019

Abstract
Population stratification is usually corrected relying on principal component analysis (PCA) of genome-wide genotype data, even in populations considered genetically homogeneous, such as Europeans. The need to genotype only a small number of genetic variants that show large differences in allele frequency among subpopulations—so-called ancestry-informative markers (AIMs)—instead of the whole genome for stratification adjustment could represent an advantage for replication studies and candidate gene/pathway studies. Here we compare the correction performance of classical and robust principal components (PCs) with the use of AIMs selected according to four different methods: the informativeness for assignment measure ($IN$-AIMs), the combination of PCA and F-statistics, PCA-correlated measurement and the PCA weighted loadings for each genetic variant. We used real genotype data from the Population Reference Sample and The Cancer Genome Atlas to simulate European genetic association studies and to quantify type I error rate and statistical power in different case–control settings.
In studies with the same numbers of cases and controls per country and control-to-case ratios reflecting actual rates of disease prevalence, no adjustment for population stratification was required. The unnecessary inclusion of the country of origin, PCs or AIMs as covariates in the regression models translated into increasing type I error rates. In studies with cases and controls from separate countries, no investigated method was able to adequately correct for population stratification. The first classical and the first two robust PCs achieved the lowest (although inflated) type I error, followed at some distance by the first eight $IN$-AIMs.
Destin: toolkit for single-cell analysis of chromatin accessibility
Authors: Urrutia Eugene , Chen Li , Zhou Haibo , Jiang Yuchao 
Published: February 2019

Abstract

Summary
Single-cell assay of transposase-accessible chromatin followed by sequencing (scATAC-seq) is an emerging new technology for the study of gene regulation with single-cell resolution. The data from scATAC-seq are unique—sparse, binary and highly variable even within the same cell type. As such, neither methods developed for bulk ATAC-seq nor single-cell RNA-seq data are appropriate. Here, we present Destin, a bioinformatic and statistical framework for comprehensive scATAC-seq data analysis. Destin performs cell-type clustering via weighted principle component analysis, weighting accessible chromatin regions by existing genomic annotations and publicly available regulomic datasets. The weights and additional tuning parameters are determined via model-based likelihood. We evaluated the performance of Destin using downsampled bulk ATAC-seq data of purified samples and scATAC-seq data from seven diverse experiments. Compared to existing methods, Destin was shown to outperform across all datasets and platforms. For demonstration, we further applied Destin to 2088 adult mouse forebrain cells and identified cell-type-specific association of previously reported schizophrenia GWAS loci.

Availability and implementation
Destin toolkit is freely available as an R package at https://github.com/urrutiag/destin.

Supplementary information
Supplementary data are available at Bioinformatics online.
Functional geometry of protein interactomes
Authors: Malod-Dognin Noël , Pržulj Nataša 
Published: February 2019

AbstractMotivationProtein–protein interactions (PPIs) are usually modeled as networks. These networks have extensively been studied using graphlets, small induced subgraphs capturing the local wiring patterns around nodes in networks. They revealed that proteins involved in similar functions tend to be similarly wired. However, such simple models can only represent pairwise relationships and cannot fully capture the higher-order organization of protein interactomes, including protein complexes.ResultsTo model the multi-scale organization of these complex biological systems, we utilize simplicial complexes from computational geometry. The question is how to mine these new representations of protein interactomes to reveal additional biological information. To address this, we define simplets, a generalization of graphlets to simplicial complexes. By using simplets, we define a sensitive measure of similarity between simplicial complex representations that allows for clustering them according to their data types better than clustering them by using other state-of-the-art measures, e.g. spectral distance, or facet distribution distance. We model human and baker’s yeast protein interactomes as simplicial complexes that capture PPIs and protein complexes as simplices. On these models, we show that our newly introduced simplet-based methods cluster proteins by function better than the clustering methods that use the standard PPI networks, uncovering the new underlying functional organization of the cell. We demonstrate the existence of the functional geometry in the protein interactome data and the superiority of our simplet-based methods to effectively mine for new biological information hidden in the complexity of the higher-order organization of protein interactomes.Availability and implementationCodes and datasets are freely available at http://www0.cs.ucl.ac.uk/staff/natasa/Simplets/.Supplementary informationSupplementary data are available at Bioinformatics online.
The Invisible Flood: The Chemistry, Ecology, and Social Implications of Coastal Saltwater Intrusion
Authors: Tully Kate , Gedan Keryn , Epanchin-Niell Rebecca , Strong Aaron , Bernhardt Emily S , BenDor Todd , Mitchell Molly , Kominoski John , Jordan Thomas E , Neubauer Scott C , Weston Nathaniel B 
Published: February 2019

AbstractSaltwater intrusion is the leading edge of sea-level rise, preceding tidal inundation, but leaving its salty signature far inland. With climate change, saltwater is shifting landward into regions that previously have not experienced or adapted to salinity, leading to novel transitions in biogeochemistry, ecology, and human land uses. We explore these changes and their implications for climate adaptation in coastal ecosystems. Biogeochemical changes, including increases in ionic strength, sulfidation, and alkalinization, have cascading ecological consequences such as upland forest retreat, conversion of freshwater wetlands, nutrient mobilization, and declines in agricultural productivity. We explore the trade-offs among land management decisions in response to these changes and how public policy should shape socioecological transitions in the coastal zone. Understanding transitions resulting from saltwater intrusion—and how to manage them—is vital for promoting coastal resilience.
Structural Associations of Cortical Contrast and Thickness in First Episode Psychosis
Authors: Makowski Carolina , Lewis John D , Lepage Claude , Malla Ashok K , Joober Ridha , Lepage Martin , Evans Alan C 
Published: February 2019

AbstractThere is growing evidence that psychosis is characterized by brain network abnormalities. Analyzing morphological abnormalities with T1-weighted structural MRI may be limited in discovering the extent of deviations in cortical associations. We assess whether structural associations of either cortical white–gray contrast (WGC) or cortical thickness (CT) allow for a better understanding of brain structural relationships in first episode of psychosis (FEP) patients. Principal component and structural covariance analyses were applied to WGC and CT derived from T1-weighted MRI for 116 patients and 88 controls, to explore sets of brain regions that showed group differences, and associations with symptom severity and cognitive ability in patients. We focused on 2 principal components: one encompassed primary somatomotor regions, which showed trend-like group differences in WGC, and the second included heteromodal cortices. Patients’ component scores were related to general psychopathology for WGC, but not CT. Structural covariance analyses with WGC revealed group differences in pairwise correlations across widespread brain regions, mirroring areas derived from PCA. More group differences were uncovered with WGC compared with CT. WGC holds potential as a proxy measure of myelin from commonly acquired T1-weighted MRI and may be sensitive in detecting systems-level aberrations in early psychosis, and relationships with clinical/cognitive profiles.
Do International Rules and Norms Apply to Nonstate Actors?
Authors: Lemke Douglas 
Published: February 2019

AbstractThe nonstate actors of interest in this article are territorial contenders: political entities that control populated territory, function like sovereign states but are not recognized as sovereign states by other members of the international system. Sometimes they are de facto states, sometimes they are rebel groups, sometimes they are neither of these, instead existing in control of territory with neither conflict against the sovereign state within whose borders they exist nor claims to a state of their own. New data about territorial contenders permit me to evaluate arguments about changing rules and norms in the international system. I find support for claims about the consequences of changing rules about which actors are recognized as sovereign states but not for claims about a norm against conquest after World War II. In the discussion section, I consider implications of these findings for future research.
Recognizing and Overcoming Burnout in Breast Imaging
Authors: Mainiero Martha B , Parikh Jay R 
Published: February 2019

Abstract
Burnout is a psychological syndrome created by chronic job stress, and it is typified by emotional exhaustion, depersonalization, and feelings of decreased personal accomplishment. In physicians, burnout occurs at alarming rates, and it is on the rise. High burnout rates are ubiquitous in radiology across multiple subspecialties. We know of no study specifically examining burnout among breast imaging radiologists, but given the rates across multiple specialties in radiology, we must assume that a significant portion of breast imaging radiologists also experience burnout. As breast imaging increases in volume and complexity, we must find new ways of practicing that help achieve a healthy work environment.
Are Retaliatory Trade Measures Justified under the WTO Agreement on Safeguards?
Authors: Lee Yong-Shik 
Published: February 2019

Abstract
In March 2018, the USA adopted measures to increase tariffs on a range of imported steel and aluminum products, claiming that the measures are justified for its national security concerns. Several World Trade Organization Members, including the European Union, India, Russia, Turkey, and China, have argued that the US measures are in violation of WTO rules on safeguard measures and adopted retaliatory measures invoking Article 12.5 of the Agreement on Safeguards. The USA argues that its measures do not constitute safeguard measures under WTO rules, and, therefore, the retaliatory measures are not justified under the SA. This article reviews relevant cases and examines whether the US measures are safeguard measures under the SA and whether the retaliatory measures are also justified under the SA. The article also discusses the need for regulatory reform to address the issues with unilateral trade measures and retaliation.
Diagnostic-driven management of invasive fungal disease in hematology in the era of prophylaxis and resistance emergence: Dutch courage?
Authors: de Kort E A , Maertens J , Verweij P E , Rijnders B J A , Blijlevens N M A 
Published: February 2019

Abstract
Patients receiving intensive anti-leukemic treatment or recipients of allogeneic hematopoietic stem cell transplantation (HSCT) are prone to develop invasive fungal disease caused by both Aspergillus and non-Aspergillus moulds. Overall mortality following invasive mould disease (IMD) is high; adequate and timely antifungal treatment seems to ameliorate the outcome, yet early diagnosis in the haematological patient remains a challenge for most clinicians. Prophylaxis and the empiric addition of antifungal therapy to neutropaenic patients with fever persisting or recurring during broad-spectrum antibiotic treatment is therefore standard of care in many institutions. However, aside from the potential for overtreatment and important side effects, the emergence of resistance to medical triazoles in Aspergillus fumigatus poses a risk for inadequate initial treatment. Initial voriconazole therapy in patients with azole-resistant invasive aspergillosis was recently shown to be associated with a 23% increased mortality rate compared to the patients with azole-susceptible infection, despite changing to appropriate antifungal therapy once resistance was detected. Moreover, fever is not always present with IMD; therefore, cases may be missed when relying solely on this symptom for starting diagnostic procedures and antifungal treatment. At our institution, a diagnostic-driven treatment approach for IMD was implemented relying on clinical but also laboratory markers to start antifungal treatment. We describe the basis and clinical implementation of our diagnostic-driven approach in this review.
Investigating state transition luminosities of Galactic black hole transients in the outburst decay
Authors: Vahdat Motlagh A , Kalemci E , Maccarone T J 
Published: February 2019

Abstract
We have performed a comprehensive spectral and timing analyses of Galactic black hole transients (GBHTs) during outburst decay in order to obtain the distribution of state transition luminosities. Using the archival data of the Rossi X-ray Timing Explorer (RXTE), we have calculated the weighted mean for state transition luminosities of 11 BH sources in 19 different outbursts and for disc and power law luminosities separately. We also produced histograms of these luminosities in terms of Eddington luminosity fraction (ELF) and fitted them with a Gaussian. Our results show the tightest clustering in bolometric power law luminosity with a mean logarithmic ELF of −1.70 ± 0.21 during the index transition (as the photon index starts to decrease towards the hard state). We obtained mean logarithmic ELF of −1.80 ± 0.25 during the transition to the hard state (as the photon index reaches the lowest value) and −1.50 ± 0.32 for disc-blackbody luminosity (DBB) during the transition to the hard-intermediate state (HIMS). We discussed the reasons for clustering and possible explanations for sources that show a transition luminosity significantly below or above the general trends.
Repeated Phenotypic Evolution by Different Genetic Routes in Pseudomonas fluorescens SBW25
Authors: Gallie Jenna , Bertels Frederic , Remigi Philippe , Ferguson Gayle C , Nestmann Sylke , Rainey Paul B 
Published: February 2019

Abstract
Repeated evolution of functionally similar phenotypes is observed throughout the tree of life. The extent to which the underlying genetics are conserved remains an area of considerable interest. Previously, we reported the evolution of colony switching in two independent lineages of Pseudomonas fluorescens SBW25. The phenotypic and genotypic bases of colony switching in the first lineage (Line 1) have been described elsewhere. Here, we deconstruct the evolution of colony switching in the second lineage (Line 6). We show that, as for Line 1, Line 6 colony switching results from an increase in the expression of a colanic acid-like polymer (CAP). At the genetic level, nine mutations occur in Line 6. Only one of these—a nonsynonymous point mutation in the housekeeping sigma factor rpoD—is required for colony switching. In contrast, the genetic basis of colony switching in Line 1 is a mutation in the metabolic gene carB. A molecular model has recently been proposed whereby the carB mutation increases capsulation by redressing the intracellular balance of positive (ribosomes) and negative (RsmAE/CsrA) regulators of a positive feedback loop in capsule expression. We show that Line 6 colony switching is consistent with this model; the rpoD mutation generates an increase in ribosomal gene expression, and ultimately an increase in CAP expression.