bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of immunoglobulin heavy chain, immunoglobulin light chain, and T‐cell receptor clonality testing in the diagnosis of feline lymphoid neoplasia
Authors: Rout Emily D. , Burnett Robert C. , Yoshimoto Janna A. , Avery Paul R. , Avery Anne C. 
Published: September 2019

AbstractBackgroundDifferentiation between neoplastic and reactive lymphocytic proliferations can be challenging in cats. PCR for antigen receptor rearrangements (PARR) testing is a useful diagnostic tool to assess clonality of a lymphoid population. Previous feline PARR studies evaluated clonality of complete immunoglobulin heavy chain V‐D‐J (IGH‐VDJ) and T‐cell receptor gamma (TRG) gene rearrangements.ObjectivesWe aimed to evaluate the sensitivity and specificity of feline PARR primers targeting complete IGH‐VDJ and TRG rearrangements, as well as incomplete IGH‐DJ, kappa deleting element (Kde), and immunoglobulin lambda light chain (IGL) gene rearrangements in defined feline neoplasms and nonneoplastic controls.MethodsFluorescently labeled PCR primers were designed to amplify complete IGH‐VDJ, incomplete IGH‐DJ, Kde, IGL, and TRG gene rearrangements in two multiplexed PCR reactions, and PCR products were analyzed by fragment analysis. Fresh tissue samples from 12 flow cytometrically confirmed B‐cell lymphomas, 26 cytologically confirmed gastric and renal lymphomas of presumed B‐cell origin, 30 flow cytometrically confirmed T‐cell leukemias, and 11 negative control cats were tested.ResultsUsing four immunoglobulin primer sets (IGH‐VDJ, IGH‐DJ, Kde, and IGL), clonal immunoglobulin rearrangements were detected in 87% (33/38) of the presumed B‐cell neoplasms. The IGH‐VDJ reaction alone only detected clonality in 50% (19/38) of these cases. TRG rearrangements were clonal in 97% (29/30) of the T‐cell leukemia cases. All negative control samples had polyclonal immunoglobulin and TRG rearrangements.ConclusionsThe PARR assay developed in this study is useful for assessing clonality in feline lymphoid neoplasms. Clonality assessment of incomplete IGH‐DJ, Kde, and IGL rearrangements helped identify clonal B‐cell neoplasms not detected with complete IGH‐VDJ PARR alone.
Comparative Study of the Gasification of Coal and Its Macerals and Prediction of the Synergistic Effects Under Typical Entrained-Bed Pulverized Coal Gasification Conditions
Authors: Jiang Peng , Guo Dengting , Luo Xiang , Xu Mengxia , Wu Tao 
Published: September 2019

Abstract
This research is focused on the gasification performance of coal and its corresponding macerals as well as on the interactions among macerals under typical gasification conditions by Aspen Plus modeling. The synergistic coefficient was employed to show the degree of interactions, while the performance indicators including specific oxygen consumption (SOC), specific coal consumption (SCC), cold gas efficiency (CGE), and effective syngas (CO + H2) content were used to evaluate the gasification process. Sensitivity analyses showed that the parent coal and its macerals exhibited different gasification behaviors at the same operating conditions, such as the SOC and SCC decreased in the order of inertinite > vitrinite > liptinite, whereas CGE changed in the order of liptinite > vitrinite > inertinite. The synergistic coefficients of SOC and SCC for the simulated coals were in the range of 0.94–0.97, whereas the synergistic coefficient of CGE was 1.05–1.13. Moreover, it was found that synergistic coefficients of gasification indicators correlated well with maceral contents. In addition, the increase in temperature was found to promote the synergistic coefficients slightly, whilst at an oxygen to coal mass ratio of 0.8 and a steam to coal mass ratio of 0.8, the highest synergistic coefficient was obtained.
Molecular Dynamic Study of a Pyrolysis Process of a Coal Particle in Different Environments
Authors: Li Hanqing , Xu Bonan , Jin Hanhui , Luo Kun , Fan Jianren 
Published: September 2019

Abstract
The pyrolysis processes of a coal particle containing 19,638 atoms in different atmospheres are studied with a reactive force field molecular dynamics (ReaxFF MD) method. The detailed chemical reactions with the corresponding occurrence frequencies are obtained. The generation paths of the main products are disclosed, including CO, H2, H2O, and CH4. The nonuniform effect of temperature on the pyrolysis production is analyzed, among which the productions of CH4 and CO nonmonotonically vary with temperature, while the H2 production increases linearly with temperature. The kinds of atmospheres can significantly influence the coal pyrolysis. Hydrogen atmosphere can apparently improve the CH4 production, which results from the enhancement of the C–H bond generation.
Quantum skyrmionics
Authors: Ochoa Hector , Tserkovnyak Yaroslav 
Published: September 2019

Skyrmions are topological solitons that emerge in many physical contexts. In magnetism, they appear as textures of the spin-density field stabilized by different competing interactions and characterized by a topological charge that counts the number of times the order parameter wraps the sphere. They behave as classical objects when the spin texture varies slowly on the scale of the microscopic lattice of the magnet. However, the fast development of experimental tools to create and stabilize skyrmions in thin magnetic films has led to a rich variety of textures, sometimes of atomistic sizes. In this paper, we discuss, in a pedagogical manner, how to introduce quantum interference in the translational dynamics of skyrmion textures, starting from the micromagnetic equations of motion for a classical soliton. We study how the nontrivial topology of the spin texture manifests in the semiclassical regime, when the microscopic lattice potential is treated quantum-mechanically, but the external driving forces are taken as smooth classical perturbations. We highlight close relations to the fields of noncommutative quantum mechanics, Chern–Simons theories, and the quantum Hall effect.
The electrical current characteristics of thermally annealed Co/anodic oxide layer/n-GaAs sandwich structures
Authors: Yıldırım N. , Turut A. , Biber M. , Saglam M. , Guzeldir B. 
Published: September 2019

The Co/anodic oxide layer/n-GaAs MOS structures have been fabricated by us. The MOS structures have shown an excellent rectifying behavior before and after thermal annealing of 500[Formula: see text]C for 2 min. It has been stated in the literature that the thermal annealing at a relatively low-temperature can improve the quality and performance of the anodic MOS structure. The current–voltage (I–V) measurements of the annealed MOS structure have been attempted in the measurement temperature range 60–320 K with the steps of 20 K. The I–V plot at 300 K has given the diode parameter values as barrier height [Formula: see text] = 0.96 eV and ideality factor n = 1.22, diode series resistance R[Formula: see text] = 124 [Formula: see text] for the annealed sample, and [Formula: see text] = 0.87 eV and n = 2.11, R[Formula: see text] = 204 [Formula: see text] for the nonannealed structure. A mean tunneling potential barrier value of 0.59 eV for the anodic oxide layer at the Co/n-GaAs interface has been calculated from the current–voltage–temperature curves. Furthermore, [Formula: see text](T) versus (2kT)[Formula: see text] curve has followed a double Gaussian distribution (GD) of the barrier heights. It has been stated that the double GD may be originated from the presence of the surface patches and phases arisen at the anodic oxide layer/n-GaAs interface.
Unsupervised Approaches for Textual Semantic Annotation, A Survey
Authors: Liao Xiaofeng , Zhao Zhiming 
Published: September 2019

Semantic annotation is a crucial part of achieving the vision of the Semantic Web and has long been a research topic among various communities. The most challenging problem in reaching the Semantic Web’s real potential is the gap between a large amount of unlabeled existing/new data and the limited annotation capability available. To resolve this problem, numerous works have been carried out to increase the degree of automation of semantic annotation from manual to semi-automatic to fully automatic. The richness of these works has been well-investigated by numerous surveys focusing on different aspects of the problem. However, a comprehensive survey targeting unsupervised approaches for semantic annotation is still missing and is urgently needed. To better understand the state-of-the-art of semantic annotation in the textual domain adopting unsupervised approaches, this article investigates existing literature and presents a survey to answer three research questions: (1) To what extent can semantic annotation be performed in a fully automatic manner by using an unsupervised way? (2) What kind of unsupervised approaches for semantic annotation already exist in literature? (3) What characteristics and relationships do these approaches have?
In contrast to existing surveys, this article helps the reader get an insight into the state-of-art of semantic annotation using unsupervised approaches. While examining the literature, this article also addresses the inconsistency in the terminology used in the literature to describe the various semantic annotation tools’ degree of automation and provides more consistent terminology. Based on this, a uniform summary of the degree of automation of the many semantic annotation tools that were previously investigated can now be presented.
Runtime Monitoring and Resolution of Probabilistic Obstacles to System Goals
Authors: Cailliau Antoine , Lamsweerde Axel Van 
Published: September 2019

Software systems are deployed in environments that keep changing over time. They should therefore adapt to changing conditions to meet their requirements. The satisfaction rate of these requirements depends on the rate at which adverse conditions prevent their satisfaction. Obstacle analysis is a goal-oriented form of risk analysis for requirements engineering (RE), whereby obstacles to system goals are identified, assessed, and resolved through countermeasures. The selection of effective countermeasures relies on environment assumptions and on the assessed likelihood and criticality of the corresponding obstacles. Those various factors estimated at RE time may, however, evolve at system runtime.
To meet the system’s goals under changing conditions, this article proposes to defer obstacle resolution to system runtime. Techniques are presented for monitoring obstacle satisfaction rates; deciding when adaptation should be triggered; and adapting the system on-the-fly to countermeasures that are more effective. The approach relies on a model where goals and obstacles are refined and specified in a probabilistic linear temporal logic. The techniques allow for monitoring the satisfaction rate of probabilistic leaf obstacles; determining the severity of obstacle consequences on goal satisfaction rates computed from the monitored obstacle satisfaction rates; and shifting to countermeasures that better meet the required goal satisfaction rates. Our approach is evaluated on fragments of an ambulance dispatching system.
Heparanase Accelerates Obesity-Associated Breast Cancer Progression
Authors: Hermano Esther , Goldberg Rachel , Rubinstein Ariel M. , Sonnenblick Amir , Maly Bella , Nahmias Daniela , Li Jin-Ping , Bakker Marinka A.H. , van der Vlag Johan , Vlodavsky Israel , Peretz Tamar , Elkin Michael 
Published: September 2019

Abstract

Obese women have higher risk of bearing breast tumors that are highly aggressive and resistant to therapies. Tumor-promoting effects of obesity occur locally via adipose inflammation and related alterations to the extracellular matrix (ECM) as well as systemically via circulating metabolic mediators (e.g., free fatty acids, FFA) associated with excess adiposity and implicated in toll-like receptor-mediated activation of macrophages—key cellular players in obesity-related cancer progression. Although the contribution of macrophages to proneoplastic effects of obesity is well documented, the role of ECM components and their enzymatic degradation is less appreciated. We show that heparanase, the sole mammalian endoglucuronidase that cleaves heparan sulfate in ECM, is preferentially expressed in clinical/experimental obesity-associated breast tumors. Heparanase deficiency abolished obesity-accelerated tumor progression in vivo. Heparanase orchestrated a complex molecular program that occurred concurrently in adipose and tumor tissue and sustained the cancer-promoting action of obesity. Heparanase was required for adipose tissue macrophages to produce inflammatory mediators responsible for local induction of aromatase, a rate-limiting enzyme in estrogen biosynthesis. Estrogen upregulated heparanase in hormone-responsive breast tumors. In subsequent stages, elevated levels of heparanase induced acquisition of procancerous phenotype by tumor-associated macrophages, resulting in activation of tumor-promoting signaling and acceleration of breast tumor growth under obese conditions. As techniques to screen for heparanase expression in tumors become available, these findings provide rational and a mechanistic basis for designing antiheparanase approaches to uncouple obesity and breast cancer in a rapidly growing population of obese patients.

Significance:
This study reveals the role of heparanase in promoting obesity-associated breast cancer and provides a mechanistically informed approach to uncouple obesity and breast cancer in a rapidly growing population of obese patients.
Recent Developments and Therapeutic Strategies against Hepatocellular Carcinoma
Authors: Yarchoan Mark , Agarwal Parul , Villanueva Augusto , Rao Shuyun , Dawson Laura A. , Karasic Thomas , Llovet Josep M. , Finn Richard S. , Groopman John D. , El-Serag Hashem B. , Monga Satdarshan P. , Wang Xin Wei , Karin Michael , Schwartz Robert E. , Tanabe Kenneth K. , Roberts Lewis R. , Gunaratne Preethi H. , Tsung Allan , Brown Kimberly A. , Lawrence Theodore S. , Salem Riad , Singal Amit G. , Kim Amy K. , Rabiee Atoosa , Resar Linda , Meyer Jeffrey , Hoshida Yujin , He Aiwu Ruth , Ghoshal Kalpana , Ryan Patrick B. , Jaffee Elizabeth M. , Guha Chandan , Mishra Lopa , Coleman C. Norman , Ahmed Mansoor M. 
Published: September 2019

Abstract
Hepatocellular carcinoma (HCC) has emerged as a major cause of cancer deaths globally. The landscape of systemic therapy has recently changed, with six additional systemic agents either approved or awaiting approval for advanced stage HCC. While these agents have the potential to improve outcomes, a survival increase of 2–5 months remains poor and falls short of what has been achieved in many other solid tumor types. The roles of genomics, underlying cirrhosis, and optimal use of treatment strategies that include radiation, liver transplantation, and surgery remain unanswered. Here, we discuss new treatment opportunities, controversies, and future directions in managing HCC.
Serine-Phosphorylated STAT3 Promotes Tumorigenesis via Modulation of RNA Polymerase Transcriptional Activity
Authors: Balic Jesse J. , Garama Daniel J. , Saad Mohamed I. , Yu Liang , West Alison C. , West Alice J. , Livis Thaleia , Bhathal Prithi S. , Gough Daniel J. , Jenkins Brendan J. 
Published: September 2019

AbstractDeregulated activation of the latent oncogenic transcription factor STAT3 in many human epithelial malignancies, including gastric cancer, has invariably been associated with its canonical tyrosine phosphorylation and enhanced transcriptional activity. By contrast, serine phosphorylation (pS) of STAT3 can augment its nuclear transcriptional activity and promote essential mitochondrial functions, yet the role of pS–STAT3 among epithelial cancers is ill-defined. Here, we reveal that genetic ablation of pS–STAT3 in the gp130F/F spontaneous gastric cancer mouse model and human gastric cancer cell line xenografts abrogated tumor growth that coincided with reduced proliferative potential of the tumor epithelium. Microarray gene expression profiling demonstrated that the suppressed gastric tumorigenesis in pS–STAT3-deficient gp130F/F mice associated with reduced transcriptional activity of STAT3-regulated gene networks implicated in cell proliferation and migration, inflammation, and angiogenesis, but not mitochondrial function or metabolism. Notably, the protumorigenic activity of pS–STAT3 aligned with its capacity to primarily augment RNA polymerase II–mediated transcriptional elongation, but not initiation, of STAT3 target genes. Furthermore, by using a combinatorial in vitro and in vivo proteomics approach based on the rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) assay, we identified RuvB-like AAA ATPase 1 (RUVBL1/Pontin) and enhancer of rudimentary homolog (ERH) as interacting partners of pS–STAT3 that are pivotal for its transcriptional activity on STAT3 target genes. Collectively, these findings uncover a hitherto unknown transcriptional role and obligate requirement for pS–STAT3 in gastric cancer that could be extrapolated to other STAT3-driven cancers.Significance:These findings reveal a new transcriptional role and mandatory requirement for constitutive STAT3 serine phosphorylation in gastric cancer.
Quantification and Localization of Protein–RNA Interactions in Patient-Derived Archival Tumor Tissue
Authors: Blanchard Emmeline L. , Argyropoulou Danae , Zurla Chiara , Bhosle Sushma M. , Vanover Daryll , Santangelo Philip J. 
Published: September 2019

Abstract

Abnormal post-transcriptional regulation induced by alterations of mRNA–protein interactions is critical during tumorigenesis and cancer progression and is a hallmark of cancer cells. A more thorough understanding is needed to develop treatments and foresee outcomes. Cellular and mouse tumor models are insufficient for vigorous investigation as they lack consistency and translatability to humans. Moreover, to date, studies in human tumor tissue are predominately limited to expression analysis of proteins and mRNA, which do not necessarily provide information about the frequency of mRNA–protein interactions. Here, we demonstrate novel optimization of a method that is based on FISH and proximity ligation techniques to quantify mRNA interactions with RNA-binding proteins relevant for tumorigenesis and cancer progression in archival patient-derived tumor tissue. This method was validated for multiple mRNA-protein pairs in several cellular models and in multiple types of archival human tumor samples. Furthermore, this approach allowed high-throughput analysis of mRNA–protein interactions across a wide range of tumor types and stages through tumor microarrays. This method is quantitative, specific, and sensitive for detecting interactions and their localization at both the individual cell and whole-tissue scales with single interaction sensitivity. This work presents an important tool in investigating post-transcriptional regulation in cancer on a high-throughput scale, with great potential for translatability into any applications where mRNA–protein interactions are of interest.

Significance:
This work presents an approach to sensitively, specifically, and quantitatively detect and localize native mRNA and protein interactions for analysis of abnormal post-transcriptional regulation in patient-derived archival tumor samples.
A Biophysical Model Uncovers the Size Distribution of Migrating Cell Clusters across Cancer Types
Authors: Bocci Federico , Kumar Jolly Mohit , Onuchic José Nelson 
Published: September 2019

Abstract

Migration from the primary tumor is a crucial step in the metastatic cascade. Cells with various degrees of adhesion and motility migrate and are launched into the bloodstream as single circulating tumor cells (CTC) or multicellular CTC clusters. The frequency and size distributions of these clusters have been recently measured, but the underlying mechanisms enabling these different modes of migration remain poorly understood. We present a biophysical model that couples the phenotypic plasticity enabled by the epithelial–mesenchymal transition (EMT) and cell migration to explain the modes of individual and collective cancer cell migration. This reduced physical model captures how cells undergo a transition from individual migration to collective cell migration and robustly recapitulates CTC cluster fractions and size distributions observed experimentally across several cancer types, thus suggesting the existence of common features in the mechanisms underlying cancer cell migration. Furthermore, we identify mechanisms that can maximize the fraction of CTC clusters in circulation. First, mechanisms that prevent a complete EMT and instead increase the population of hybrid epithelial/mesenchymal (E/M) cells are required to recapitulate CTC size distributions with large clusters of 5 to 10 cells. Second, multiple intermediate E/M states give rise to larger and heterogeneous clusters formed by cells with different epithelial–mesenchymal traits. Overall, this biophysical model provides a platform to continue to bridge the gap between the molecular and biophysical regulation of cancer cell migration and highlights that a complete EMT might not be required for metastasis.

Significance:
A biophysical model of cancer cell invasion integrates phenotypic heterogeneity and cell migration to interpret experimental observations of circulating tumor cell clusters and provides new predictions.
Antibody Responses to Fusobacterium nucleatum Proteins in Prediagnostic Blood Samples are not Associated with Risk of Developing Colorectal Cancer
Authors: Butt Julia , Jenab Mazda , Pawlita Michael , Overvad Kim , Tjonneland Anne , Olsen Anja , Boutron-Ruault Marie-Christine , Carbonnel Franck , Mancini Francesca Romana , Kaaks Rudolf , Kühn Tilman , Boeing Heiner , Trichopoulou Antonia , Karakatsani Anna , Palli Domenico , Pala Valeria Maria , Tumino Rosario , Sacerdote Carlotta , Panico Salvatore , Bueno-de-Mesquita Bas , van Gils Carla H. , Vermeulen Roel C.H. , Weiderpass Elisabete , Quirós José Ramón , Duell Eric Jeffrey , Sánchez Maria-Jose , Dorronsoro Miren , Huerta José María , Ardanaz Eva , Van Guelpen Bethany , Harlid Sophia , Perez-Cornago Aurora , Gunter Marc J. , Murphy Neil , Freisling Heinz , Aune Dagfinn , Waterboer Tim , Hughes David J. 
Published: September 2019

Abstract

Background:
There is a lack of prospective data on the potential association of Fusobacterium nucleatum (F. nucleatum) and colorectal cancer risk. In this study, we assessed whether antibody responses to F. nucleatum are associated with colorectal cancer risk in prediagnostic serum samples in the European Prospective Investigation into Nutrition and Cancer (EPIC) cohort.

Methods:
We applied a multiplex serology assay to simultaneously measure antibody responses to 11 F. nucleatum antigens in prediagnostic serum samples from 485 colorectal cancer cases and 485 matched controls. Conditional logistic regression models were used to estimate odds ratios (ORs) and 95% confidence intervals (CI).

Results:
We observed neither a statistically significant colorectal cancer risk association for antibodies to individual F. nucleatum proteins nor for combined positivity to any of the 11 proteins (OR, 0.81; 95% CI, 0.62–1.06).

Conclusions:
Antibody responses to F. nucleatum proteins in prediagnostic serum samples from a subset of colorectal cancer cases and matched controls within the EPIC study were not associated with colorectal cancer risk.

Impact:
Our findings in prospectively ascertained serum samples contradict the existing literature on the association of F. nucleatum with colorectal cancer risk. Future prospective studies, specifically detecting F. nucleatum in stool or tissue biopsies, are needed to complement our findings.