An investigation of the solar cycle response of odd-nitrogen in the thermosphere

This annual report covers the first year of funding for the study of the solar cycle variations of odd-nitrogen (N((sup 2)D), N((sup 4)S), NO) in the Earth's thermosphere. The study uses the extensive data base generated by the Atmosphere Explorer (AE) satellites, and the Solar Mesosphere Explorer Satellite. The AE data are being used, for the first time, to define the solar variability effect on the odd-nitrogen species through analysis of the emissions at 520 nano-m from N((sup 2)D) and the emission from O(+)((sup 2)P). Additional AE neutral and ion density data are used to help define and quantify the physical processes controlling the variations. The results from the airglow study will be used in the next two years of this study to explain the solar cycle changes in NO measured by the Solar Mesosphere Explorer

An analysis of Solar Mesospheric Explorer temperatures for the upper stratosphere and mesosphere

We proposed to analyze Solar Mesosphere Explorer (SME) limb profiles of Rayleigh scattered solar flux at wavelengths of 304, 313, and 443 nm to retrieve atmospheric temperature profiles over the 40-65 km altitude region. These temperatures can be combined with the previous analysis of SME 296 nm limb radiances to construct a monthly average climatology of atmospheric temperatures over the 40-90 km, upper stratosphere-mesosphere region, with approximately 4 km vertical resolution. We proposed to investigate the detailed nature of the global temperature structure of this poorly measured region, based on these 1982-1986 SME temperatures. The average vertical structure of temperatures between the stratopause and mesopause has never been determined globally with vertical resolution sufficient to retrieve even scale-height structures. Hence, the SME temperatures provided a unique opportunity to study the detailed thermal structure of the mesosphere, in advance of Upper Atmosphere Research Satellite (UARS) measurements and the Thermosphere Ionosphere Mesosphere Energy and Dynamics (TIMED) mission

Intraoperative localization of lymph node metastases with a replication-competent herpes simplex virus

ObjectivesLymph node status is the most important prognostic factor determining recurrence and survival in patients with mesothelioma and other thoracic malignancies. Accurate localization of lymph node metastases is therefore necessary to improve selection of resectable and curable patients for surgical intervention. This study investigates the potential to identify lymph node metastases intraoperatively by using herpes-guided cancer cell–specific expression of green fluorescent protein.MethodsAfter infection with NV1066, a herpes simplex virus carrying green fluorescent protein transgene, human mesothelioma cancer cell lines were assessed for cancer cell–specific infection, green fluorescent protein expression, viral replication, and cytotoxicity. Murine models of lymphatic metastasis were established by means of surgical implantation of cancer cells into the preauricular (drainage to cervical lymph nodes) and pleural (mediastinal and retroperitoneal lymph nodes) spaces of athymic mice. Fluorescent thoracoscopy, laparoscopy, and stereomicroscopy were used to localize lymph node metastases that were confirmed by means of immunohistochemistry.ResultsIn vitro NV1066 infected, replicated (5- to 17,000-fold), and expressed green fluorescent protein in all cancer cells, even when infected at a low ratio of one viral plaque-forming unit per 100 tumor cells. In vivo NV1066 injected into primary tumors was able to locate and infect lymph node metastases producing green fluorescent protein that was visualized by means of fluorescent imaging. Histology confirmed lymphatic metastases, and immunohistochemistry confirmed viral presence in regions that expressed green fluorescent protein.ConclusionsHerpes virus–guided cancer cell–specific production of green fluorescent protein can facilitate accurate localization of lymph node metastases. Fluorescent filters that detect green fluorescent protein can be incorporated into operative scopes to precisely localize and biopsy lymph node metastases

Predictive Value of Initial PET-SUVmax in Patients with Locally Advanced Esophageal and Gastroesophageal Junction Adenocarcinoma

Introduction:We have previously shown that in early clinical stage esophageal adenocarcinoma, a positron emission tomography standardized uptake values (PET SUVmax) of <4.5 is associated with earlier pathologic stage and predicts better survival. In this study, we analyze the impact of the pretreatment PET SUVmax in patients with locally advanced esophageal adenocarcinoma who undergo preoperative chemoradiotherapy.Methods:We performed a retrospective analysis, selecting patients with adenocarcinoma of the esophagus who had a pretreatment PET scan and who received chemoradiotherapy before esophagectomy. Data recorded included demographics, PET SUVmax, treatment details, pathologic details, and survival data. Comparison of categorical variables was done by χ2 analysis, continuous variables by t test, survival analysis by the Kaplan-Meier method, and comparisons of survival using the log-rank test.Results:Between January 1996 and September 2007, 189 patients were appropriate for this analysis. The initial PET SUVmax was <4.5 in 28 patients and ≥4.5 in 161 patients. The two groups were similar with regards to demographics and treatment details. Patients in the low SUV group were less likely to show evidence of treatment response after chemoradiotherapy, including a higher likelihood of residual nodal disease and a lower likelihood of a pathologic complete response and estimated treatment response. However, both groups had similar survival.Conclusions:Although the initial PET SUVmax does not predict survival in patients with locally advanced esophageal adenocarcinoma who receive preoperative chemoradiotherapy, patients with a high initial SUVmax respond better to preoperative therapy. These results can be used to better select esophageal cancer patients for combined modality treatment

Supplementary Prognostic Variables for Pleural Mesothelioma A Report from the IASLC Staging Committee

Introduction: The staging system for malignant pleural mesothelioma is controversial. To revise this system, the International Association for the Study of Lung Cancer Staging Committee developed an international database. This report analyzes prognostic variables in a surgical population, which are supplementary to previously published CORE variables (stage, histology, sex, age, and type of procedure). Methods: Supplementary prognostic variables were studied in three scenarios: (1) all data available, that is, patient pathologically staged and other CORE variables available (2) only clinical staging available along with CORE variables, and (3) only age, sex, histology, and laboratory parameters are known. Survival was analyzed by Kaplan– Meier, prognostic factors by log rank and stepwise Cox regression modeling after elimination of nonsignificant variables. p value less than 0.05 was significant. Results: A total of 2141 patients with best tumor, node, metastasis (TNM) stages (pathologic with/without clinical staging) had nonmissing age, sex, histology, and type of surgical procedure. Three prognostic models were defined. Scenario A (all parameters): best pathologic stage, histology, sex, age, type of surgery, adjuvant treatment, white blood cell count (WBC) (≥15.5 or not), and platelets (≥400 k or not) (n = 550). Scenario B (no surgical staging): clinical stage, histology, sex, age, type of surgery, adjuvant treatment, WBC, hemoglobin (<14.6 or not), and platelets (n = 627). Scenario C (limited data): histology, sex, age, WBC, hemoglobin, and platelets (n = 906). Conclusion: Refinement of these models could define not only the appropriate patient preoperatively for best outcomes after cytoreductive surgery but also stratify surgically treated patients after clinical and pathologic staging who do or do not receive adjuvant therapy

The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of <i>Synechococcus</i> inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

© 2015 Becraft, Wood, Rusch, Kühl, Jensen, Bryant, Roberts, Cohan and Ward. Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species (putative ecotypes), which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same putative ecotype formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the putative ecotypes are ecologically distinct, the members of each ecotype are ecologically homogeneous. Putative ecotypes responded differently to experimental perturbations of temperature and light, but the genetic variation within each putative ecotype was maintained as the relative abundances of putative ecotypes changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to putative ecotypes that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for putative ecotypes that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time

Induction chemoradiation and surgical resection for non–small cell lung carcinomas of the superior sulcus: Initial results of Southwest Oncology Group Trial 9416 (Intergroup Trial 0160)

AbstractObjective: The rate of complete resection (50%) and the 5-year survival (30%) for non–small cell lung carcinomas of the superior sulcus have not changed for 40 years. Recently, combined modality therapy has improved outcome in other subsets of locally advanced non–small cell lung carcinoma. This trial tested the feasibility of induction chemoradiation and surgical resection in non–small cell lung carcinoma of the superior sulcus with the ultimate aim of improving resectability and survival. Methods: Patients with mediastinoscopy-negative T3-4 N0-1 superior sulcus non–small cell lung carcinoma received 2 cycles of cisplatin and etoposide chemotherapy concurrent with 45 Gy of radiation. Patients with stable or responding disease underwent thoracotomy 3 to 5 weeks later. All patients received 2 more cycles of chemotherapy and were followed up by serial radiographs and scans. Survival was calculated by the Kaplan-Meier method and prognostic factors were assessed for significance by Cox regression analysis. Results: From April 1995 to September 1999, 111 eligible patients (77 men, 34 women) were entered in the study, including 80 (72.1%) with T3 and 31 with T4 tumors. Induction therapy was completed as planned in 102 (92%) patients. There were 3 treatment-related deaths (2.7%). Cytopenia was the main grade 3 to 4 toxicity. Of 95 patients eligible for surgery, 83 underwent thoracotomy, 2 (2.4%) died postoperatively, and 76 (92%) had a complete resection. Fifty-four (65%) thoracotomy specimens showed either a pathologic complete response or minimal microscopic disease. The 2-year survival was 55% for all eligible patients and 70% for patients who had a complete resection. To date, survival is not significantly influenced by patient sex, T status, or pathologic response. Conclusions: (1) This combined modality treatment is feasible in a multi-institutional setting; (2) the pathologic complete response rates were high; and (3) resectability and overall survival were improved compared with historical experience, especially for T4 tumors, which usually have a grim prognosis. (J Thorac Cardiovasc Surg 2001;121:472-83

Induction chemoradiation and surgical resection for non–small cell lung carcinomas of the superior sulcus: Initial results of Southwest Oncology Group Trial 9416 (Intergroup Trial 0160)

AbstractObjective: The rate of complete resection (50%) and the 5-year survival (30%) for non–small cell lung carcinomas of the superior sulcus have not changed for 40 years. Recently, combined modality therapy has improved outcome in other subsets of locally advanced non–small cell lung carcinoma. This trial tested the feasibility of induction chemoradiation and surgical resection in non–small cell lung carcinoma of the superior sulcus with the ultimate aim of improving resectability and survival. Methods: Patients with mediastinoscopy-negative T3-4 N0-1 superior sulcus non–small cell lung carcinoma received 2 cycles of cisplatin and etoposide chemotherapy concurrent with 45 Gy of radiation. Patients with stable or responding disease underwent thoracotomy 3 to 5 weeks later. All patients received 2 more cycles of chemotherapy and were followed up by serial radiographs and scans. Survival was calculated by the Kaplan-Meier method and prognostic factors were assessed for significance by Cox regression analysis. Results: From April 1995 to September 1999, 111 eligible patients (77 men, 34 women) were entered in the study, including 80 (72.1%) with T3 and 31 with T4 tumors. Induction therapy was completed as planned in 102 (92%) patients. There were 3 treatment-related deaths (2.7%). Cytopenia was the main grade 3 to 4 toxicity. Of 95 patients eligible for surgery, 83 underwent thoracotomy, 2 (2.4%) died postoperatively, and 76 (92%) had a complete resection. Fifty-four (65%) thoracotomy specimens showed either a pathologic complete response or minimal microscopic disease. The 2-year survival was 55% for all eligible patients and 70% for patients who had a complete resection. To date, survival is not significantly influenced by patient sex, T status, or pathologic response. Conclusions: (1) This combined modality treatment is feasible in a multi-institutional setting; (2) the pathologic complete response rates were high; and (3) resectability and overall survival were improved compared with historical experience, especially for T4 tumors, which usually have a grim prognosis. (J Thorac Cardiovasc Surg 2001;121:472-83

Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets

BACKGROUND: The scale and diversity of metagenomic sequencing projects challenge both our technical and conceptual approaches in gene and genome annotations. The recent Sorcerer II Global Ocean Sampling (GOS) expedition yielded millions of predicted protein sequences, which significantly altered the landscape of known protein space by more than doubling its size and adding thousands of new families (Yooseph et al., 2007 PLoS Biol 5, e16). Such datasets, not only by their sheer size, but also by many other features, defy conventional analysis and annotation methods. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we describe an approach for rapid analysis of the sequence diversity and the internal structure of such very large datasets by advanced clustering strategies using the newly modified CD-HIT algorithm. We performed a hierarchical clustering analysis on the 17.4 million Open Reading Frames (ORFs) identified from the GOS study and found over 33 thousand large predicted protein clusters comprising nearly 6 million sequences. Twenty percent of these clusters did not match known protein families by sequence similarity search and might represent novel protein families. Distributions of the large clusters were illustrated on organism composition, functional class, and sample locations. CONCLUSION/SIGNIFICANCE: Our clustering took about two orders of magnitude less computational effort than the similar protein family analysis of original GOS study. This approach will help to analyze other large metagenomic datasets in the future. A Web server with our clustering results and annotations of predicted protein clusters is available online at http://tools.camera.calit2.net/gos under the CAMERA project

Comprehensive Molecular and Clinicopathologic Analysis of 200 Pulmonary Invasive Mucinous Adenocarcinomas Identifies Distinct Characteristics of Molecular Subtypes

PURPOSE: Invasive mucinous adenocarcinoma (IMA) is a unique subtype of lung adenocarcinoma, characterized genomically by frequent KRAS mutations or specific gene fusions, most commonly involving NRG1. Comprehensive analysis of a large series of IMAs using broad DNA- and RNA-sequencing methods is still lacking, and it remains unclear whether molecular subtypes of IMA differ clinicopathologically. EXPERIMENTAL DESIGN: A total of 200 IMAs were analyzed by 410-gene DNA next-generation sequencing (MSK-IMPACT; n = 136) or hotspot 8-oncogene genotyping (n = 64). Driver-negative cases were further analyzed by 62-gene RNA sequencing (MSK-Fusion) and those lacking fusions were further tested by whole-exome sequencing and whole-transcriptome sequencing (WTS). RESULTS: Combined MSK-IMPACT and MSK-Fusion testing identified mutually exclusive driver alterations in 96% of IMAs, including KRAS mutations (76%), NRG1 fusions (7%), ERBB2 alterations (6%), and other less common events. In addition, WTS identified a novel NRG2 fusion (F11R-NRG2). Overall, targetable gene fusions were identified in 51% of KRAS wild-type IMAs, leading to durable responses to targeted therapy in some patients. Compared with KRAS-mutant IMAs, NRG1-rearranged tumors exhibited several more aggressive characteristics, including worse recurrence-free survival (P \u3c 0.0001). CONCLUSIONS: This is the largest molecular study of IMAs to date, where we demonstrate the presence of a major oncogenic driver in nearly all cases. This study is the first to document more aggressive characteristics of NRG1-rearranged IMAs, ERBB2 as the third most common alteration, and a novel NRG2 fusion in these tumors. Comprehensive molecular testing of KRAS wild-type IMAs that includes fusion testing is essential, given the high prevalence of alterations with established and investigational targeted therapies in this subset