Next-Generation Sequencing (NGS) Methods Show Superior or Equivalent Performance to Non-NGS Methods on , , and Proficiency Testing Samples.

Context.—: There has been a rapid expansion of next-generation sequencing (NGS)-based assays for the detection of somatic variants in solid tumors. However, limited data are available regarding the comparative performance of NGS and non-NGS assays using standardized samples across a large number of laboratories.

Trends in High-Grade Cervical Cancer Precursors in the Human Papillomavirus Vaccine Era.

Introduction: The 2006 introduction of human papillomavirus vaccine targeted against genotypes 6, 11, 16, and 18 should result in decreased cervical dysplasia in vaccinated women. However, new cervical cancer guidelines to increase screening intervals complicate interpretation of trends. The hypothesis is that cervical dysplasia would decrease only in young vaccine-eligible women, and not older women.

Proximal tibial extra-axial chordoma masquerading as renal cell carcinoma metastasis.

Chordomas are rare, locally aggressive notochordal tumors, which most frequently occur in the neuraxis. We describe the case of a 74-year-old male with a history of renal cell carcinoma, who presented with a slowly enlarging mass in his left leg. While the clinical history and imaging suggested metastatic renal cell carcinoma, immunohistochemical staining with brachyury ultimately made the diagnosis of extra-axial chordoma.

Transfusion reactions in pediatric compared with adult patients: a look at rate, reaction type, and associated products.

Background: The majority of reports on transfusion reactions address adult patients. Less is known about the types, incidence, and other clinical details of transfusion reactions in pediatric populations. Furthermore, to our knowledge, there have been no previous reports directly comparing these aspects between adults and pediatric patient populations to assess if there are differences.

The impact of tumor size in breast needle biopsy material on final pathologic size and tumor stage: a detailed analysis of 222 consecutive cases.

Tumor size is a significant prognostic indicator for invasive mammary carcinoma. By current standards, this is routinely reported during pathologic evaluation of the definitive excision, but no recommendations exist for reporting tumor size in needle biopsy material. The purpose of this study is to evaluate the relationship between tumor size on breast needle biopsy specimens and that on subsequent definitive excision specimens and to evaluate the impact of the former, if any, in determining the final pathologic tumor stage.

Lipid rafts and caveolin-1 coordinate interleukin-1beta (IL-1beta)-dependent activation of NFkappaB by controlling endocytosis of Nox2 and IL-1beta receptor 1 from the plasma membrane.

Recent evidence suggests that signaling by the proinflammatory cytokine interleukin-1beta (IL-1beta) is dependent on reactive oxygen species derived from NADPH oxidase. Redox signaling in response to IL-1beta is known to require endocytosis of its cognate receptor (IL-1R1) following ligand binding and the formation of redox-active signaling endosomes that contain Nox2 (also called redoxosomes). The consequent generation of reactive oxygen species by redoxosomes is responsible for the downstream recruitment of IL-1R1 effectors (IRAK, TRAF6, and IkappaB kinase kinases) and ultimately for activation of the transcription factor NFkappaB.

Endosomal Nox2 facilitates redox-dependent induction of NF-kappaB by TNF-alpha.

Growing evidence suggests that NADPH oxidase (Nox)-derived reactive oxygen species (ROS) play important roles in regulating cytokine signaling. We have explored how TNF-alpha induction of Nox-dependent ROS influences NF-kappaB activation. Cellular stimulation by TNF-alpha induced NADPH-dependent superoxide production in the endosomal compartment, and this ROS was required for IKK-mediated activation of NF-kappaB.

Signaling components of redox active endosomes: the redoxosomes.

Subcellular compartmentalization of reactive oxygen species (ROS) plays a critical role in transmitting cell signals in response to environmental stimuli. In this regard, signals at the plasma membrane have been shown to trigger NADPH oxidase-dependent ROS production within the endosomal compartment and this step can be required for redox-dependent signal transduction. Unique features of redox-active signaling endosomes can include NADPH oxidase complex components (Nox1, Noxo1, Noxa1, Nox2, p47phox, p67phox, and/or Rac1), ROS processing enzymes (SOD1 and/or peroxiredoxins), chloride channels capable of mediating superoxide transport and/or membrane gradients required for Nox activity, and novel redox-dependent sensors that control Nox activity.

JunD protects the liver from ischemia/reperfusion injury by dampening AP-1 transcriptional activation.

The AP-1 transcription factor modulates a wide range of cellular processes, including cellular proliferation, programmed cell death, and survival. JunD is a major component of the AP-1 complex following liver ischemia/reperfusion (I/R) injury; however, its precise function in this setting remains unclear. We investigated the functional significance of JunD in regulating AP-1 transcription following partial lobar I/R injury to the liver, as well as the downstream consequences for hepatocellular remodeling.

Comparative EST analyses in plant systems.

Expressed sequence tag (EST) data are a major contributor to the known plant sequence space. Organization of the data into non-redundant clusters representing tentative unique genes provides snapshots of the gene repertoires of a species. This chapter reviews availability of sequences and sequence analysis results and describes several resources and tools that should facilitate broad-based utilization of EST data for gene structure annotation, gene discovery, and comparative genomics.

Identification of X-linked genes required for migration and programmed cell death of Drosophila melanogaster germ cells.

Drosophila germ cells form at the posterior pole of the embryo and migrate to the somatic gonad. Approximately 50% of the germ cells that form reach their target. The errant cells within the embryo undergo developmentally regulated cell death.