130 research outputs found
Scaling behavior of the overlap quark propagator in Landau gauge
The properties of the momentum space quark propagator in Landau gauge are
examined for the overlap quark action in quenched lattice QCD. Numerical
calculations are done on three lattices with different lattice spacings and
similar physical volumes to explore the approach of the quark propagator toward
the continuum limit. We have calculated the nonperturbative momentum-dependent
wave function renormalization function Z(p) and the nonperturbative mass
function M(p) for a variety of bare quark masses and perform an extrapolation
to the chiral limit. We find the behavior of Z(p) and M(p) are in reasonable
agreement between the two finer lattices in the chiral limit, however the data
suggest that an even finer lattice is desirable. The large momentum behavior is
examined to determine the quark condensate.Comment: 9 pages, 5 figures, Revtex 4. Streamlined presentation, additional
data. Final versio
A dynamical gluon mass solution in a coupled system of the Schwinger-Dyson equations
We study numerically the Schwinger-Dyson equations for the coupled system of
gluon and ghost propagators in the Landau gauge and in the case of pure gauge
QCD. We show that a dynamical mass for the gluon propagator arises as a
solution while the ghost propagator develops an enhanced behavior in the
infrared regime of QCD. Simple analytical expressions are proposed for the
propagators, and the mass dependency on the scale and its
perturbative scaling are studied. We discuss the implications of our results
for the infrared behavior of the coupling constant, which, according to fits
for the propagators infrared behavior, seems to indicate that as .Comment: 17 pages, 7 figures - Revised version to be consistent with erratum
to appear in JHE
Macrophage Ontogeny Underlies Differences in Tumor-Specific Education in Brain Malignancies.
Extensive transcriptional and ontogenetic diversity exists among normal tissue-resident macrophages, with unique transcriptional profiles endowing the cells with tissue-specific functions. However, it is unknown whether the origins of different macrophage populations affect their roles in malignancy. Given potential artifacts associated with irradiation-based lineage tracing, it remains unclear if bone-marrow-derived macrophages (BMDMs) are present in tumors of the brain, a tissue with no homeostatic involvement of BMDMs. Here, we employed multiple models of murine brain malignancy and genetic lineage tracing to demonstrate that BMDMs are abundant in primary and metastatic brain tumors. Our data indicate that distinct transcriptional networks in brain-resident microglia and recruited BMDMs are associated with tumor-mediated education yet are also influenced by chromatin landscapes established before tumor initiation. Furthermore, we demonstrate that microglia specifically repress Itga4 (CD49D), enabling its utility as a discriminatory marker between microglia and BMDMs in primary and metastatic disease in mouse and human
Analytic properties of the Landau gauge gluon and quark propagators
We explore the analytic structure of the gluon and quark propagators of
Landau gauge QCD from numerical solutions of the coupled system of renormalized
Dyson--Schwinger equations and from fits to lattice data. We find sizable
negative norm contributions in the transverse gluon propagator indicating the
absence of the transverse gluon from the physical spectrum. A simple analytic
structure for the gluon propagator is proposed. For the quark propagator we
find evidence for a mass-like singularity on the real timelike momentum axis,
with a mass of 350 to 500 MeV. Within the employed Green's functions approach
we identify a crucial term in the quark-gluon vertex that leads to a positive
definite Schwinger function for the quark propagator.Comment: 42 pages, 16 figures, revtex; version to be published in Phys Rev
The Infrared Behaviour of the Pure Yang-Mills Green Functions
We review the infrared properties of the pure Yang-Mills correlators and
discuss recent results concerning the two classes of low-momentum solutions for
them reported in literature; i.e. decoupling and scaling solutions. We will
mainly focuss on the Landau gauge and pay special attention to the results
inferred from the analysis of the Dyson-Schwinger equations of the theory and
from "{\it quenched}" lattice QCD. The results obtained from properly
interplaying both approaches are strongly emphasized.Comment: Final version to be published in FBS (54 pgs., 11 figs., 4 tabs
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Geographic variation in the sensitivity of recombinant antigen-based rapid tests for chronic trypanosoma cruzi infection
Chagas disease affects 8-11 million people throughout the Americas. Early detection is crucial for timely treatment and to prevent non-vectorial transmission. Recombinant antigen-based rapid tests had high sensitivity and specificity in laboratory evaluations, but no Peruvian specimens were included in previous studies. We evaluated Stat-Pak and Trypanosoma Detect rapid tests in specimens from Bolivia and Peru. Specimens positive by three conventional assays were confirmed positives; specimens negative by two or more assays were confirmed negatives. In Bolivian specimens, Stat-Pak and Trypanosoma Detect tests were 87.5% and 90.7% sensitive, respectively; both showed 100% specificity. Sensitivity in Peruvian specimens was much lower: 26.6-33.0% (Stat-Pak) and 54.3-55.2% (Trypanosoma Detect); both had specificities > 98%. Even in Bolivian specimens, these sensitivities are inadequate for stand-alone screening. The low sensitivity in Peru may be related to parasite strain differences. Chagas disease rapid tests should be field tested in each geographic site before widespread implementation for screening. Copyrigh
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.
Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy
Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types
Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers is lacking. Using computational approaches, we define genomic and proteomic features associated with MYC and the PMN across the 33 cancers of The Cancer Genome Atlas. Pan-cancer, 28% of all samples had at least one of the MYC paralogs amplified. In contrast, the MYC antagonists MGA and MNT were the most frequently mutated or deleted members, proposing a role as tumor suppressors. MYC alterations were mutually exclusive with PIK3CA, PTEN, APC, or BRAF alterations, suggesting that MYC is a distinct oncogenic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such as immune response and growth factor signaling; chromatin, translation, and DNA replication/repair were conserved pan-cancer. This analysis reveals insights into MYC biology and is a reference for biomarkers and therapeutics for cancers with alterations of MYC or the PMN. We present a computational study determining the frequency and extent of alterations of the MYC network across the 33 human cancers of TCGA. These data, together with MYC, positively correlated pathways as well as mutually exclusive cancer genes, will be a resource for understanding MYC-driven cancers and designing of therapeutics
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