tbuckley/cabot-search huggingface dataset:
Voluntary submission of biological specimens from cancer clinical trials: An update of the Eastern Cooperative Oncology Group experience
Authors: J. Jenab-Wolcott, P. J. Catalano, B. Fillingham, M. Ferriere, P. J. O'Dwyer, B. J. Giantonio
Journal: Journal of Clinical Oncology (2009)

6597 Background: Recent advances in cancer therapy underscore the need to acquire biological specimens from participants in well-conducted clinical trials. The Eastern Cooperative Oncology Group (ECOG) has previously reported a high rate of assent to the banking of biological specimens from participants in ECOG led trials. Methods: Since November 2000, ECOG trials include the Intergroup Specimen Banking Committee (ISBC) consent form governing biological specimen use. Data collected at patient registration regarding assent to specimen submission for correlative projects and/or banking are maintained in a data-base at the ECOG Coordinating Center. These data include participant responses to all questions contained in the consent from, and can be associated with study specific information and demographic data. Results: From November 2000 to August 2008, 30,695 participants were accrued from both academic centers and community based practices to ECOG led trials that included a voluntary request for biological specimens for correlative research, banking, or both. Overall, of the 30,496 participants presented with a request for specimen banking, 88.0% agreed to do so. Variance in assent rates for banking was noted by disease type. Permission to bank specimens was provided by 93.8% of leukemia patients (pts), 93.5% of breast cancer pts, and 91% of gastrointestinal cancer pts, whereas 75.7% of thoracic cancer pts, 75.0% multiple myeloma pts, and 63% of pts on prevention trials agreed. Data from 12,605 participants presented with a protocol-specified correlative project consent form are currently being analyzed. Interactions based on disease type, age, gender, type of institution and phase of study will be evaluated for biological specimen acquisition for banking and correlative use. Conclusions: Overall, a high rate of assent is demonstrated for biological specimen acquisition for banking purposes from participants in ECOG led clinical trials. Differences in assent rates for banking are suggested based on disease types. Further study to better define associations for suboptimal participation and reasons for refusal are planned. No significant financial relationships to disclose.
CDC Grand Rounds: Prevention and Control of Skin Cancer
Authors: Meg Watson, Cheryll C. Thomas, Greta M. Massetti, Sharon McKenna, Jeffrey E. Gershenwald, Susan Laird, John Iskander, Boris Lushniak
Journal: MMWR Morbidity and Mortality Weekly Report (2015)

Skin cancer is the most common cancer in the United States, and most cases are preventable. Persons with certain genetic risk factors, including having a lighter natural skin color; blue or green eyes; red or blonde hair; dysplastic nevi or a large number of common moles; and skin that burns, freckles, or reddens easily or becomes painful after time in the sun, have increased risk for skin cancer. Persons with a family or personal history of skin cancer, especially melanoma, are also at increased risk. Although these genetic factors contribute to individual risk, most skin cancers are also strongly associated with ultraviolet (UV) radiation exposure. Most UV exposure comes from the sun, although some persons use UV-emitting indoor tanning devices (e.g., beds, booths, and lamps).
EpCAM expression in lymph node and bone metastases of prostate carcinoma: A pilot study.
Authors: Hilde Hoving, Karen Campos, Igle De Jong
Journal: Journal of Clinical Oncology (2014)

165 Background: Correct staging of prostate carcinoma has huge treatment implications since metastasized prostate carcinoma cannot be treated curatively. Nowadays, skeletal scintigraphy is the mainstay for the assessment for bone metastases despite its poor sensitivity. Lymph node metastases can be diagnosed accurately with Computed Tomography. However, the gold standard is a pelvic lymph node dissection. A non-invasive diagnostic modality, that can assess both lymph node and bone metastases simultaneously, is preferred. In this retrospective pilot study expression of epithelial cell adhesion molecule (EpCAM) was investigated in lymph node metastases, normal lymph nodes, and bone metastases of prostate carcinoma. Furthermore, EpCAM expression was correlated to clinicopathological parameters. Methods: Lymph node metastases (n = 22) and matched normal lymph nodes (n = 22) were available in 17 patients who underwent a pelvic lymph node dissection because of suspicion of nodal involvement on CT. Bone metastases (n = 24) were available in 24 patients who underwent surgery to confirm the disease or to treat skeletal related events. Immunohistochemistry was performed to determine EpCAM expression. Two researchers, blinded to clinical data, scored the immunoreactivity according to Allred. Sensitivity and specificity of EpCAM immunoreactivity in lymph node and bone metastases was calculated. Fisher’s Exact Test was used to correlate EpCAM expression to the clinicopathological parameters Gleason score, prior radiotherapy and prior hormonal treatment. Results: Sensitivity and specificity of EpCAM expression was 100% in lymph nodes. In bone metastases sensitivity was 92%. No correlation between EpCAM expression and clinicopathological parameters was found. Conclusions: Molecular imaging of EpCAM is promising for prostate carcinoma staging, due to the high sensitivity and specificity in lymph node metastases and the high sensitivity in bone metastases. Even in poorly differentiated metastases and after hormonal treatment and radiotherapy, EpCAM was expressed.
Surgery of hydatid disease of the lungs complicated with perforation into pleural cavity
Authors: Georgiy Pakhomov, Rustem Hayaliev, Kobiljon Pardaev, Jahongir Biybalaev
Journal: European Respiratory Journal (2014)

Hydatid disease (HD) is a severe human parasitic disease that affects almost all organs and tissues, including the lungs.

Purpose of the study is to develop and improve the methods of surgical treatment of HD of the lungs complicated with perforation into pleural cavity.

Materials and methods . The paper analyzes the results of surgical treatment of 61 patients with HD of the lungs complicated with perforation into pleural cavity for the period of 2000 to 2012. Men were 45 (73.8%), women were 16 (26.2%) and 26 (42.62%) patients were young people and were at the working age - 20-40 years old. Patients with an established diagnosis of HD of the lungs complicated with perforation into pleural cavity with no signs of sepsis were subjected to surgical treatment with a short preoperative preparation. The criteria for readiness for elective surgery were: absence of pathogen microflora in repeated crops of the flora from the pleural cavity through the drainage tube in 45 (40.5%), of which radiographic reduction of the residual cavity of the cyst in 43 (38.7%) patients, improvement of general condition of all patients. Organ sparing surgery in 53 (87%) patients outnumbered the resections in 8 (13%) patients. Effectiveness of operations in a certain extent depended on the infection of the pleural cavity.

Conclusions . Thus, HD of the lungs complicated with perforation into pleural cavity is a severe combined pulmonary pleural disease and occurs with severe bronchopulmonary and general symptomatology. The number and the volume of resections increase with the extension of the length of time after perforation which is associated with the development of irreversible organic changes in the lung tissue.
Pattern of presentation and treatment of early primary breast cancer in the elderly
Authors: H. K. Parker, L. Winterbottom, K. Hassell, I. O. Ellis, D. A. Morgan, K. L. Cheung
Journal: Journal of Clinical Oncology (2007)

11030 Background: There is a high prevalence of breast cancer in the elderly population; however the majority of data available is obtained from younger patients. This study aimed to identify the patterns of presentation and treatment subsequently received by elderly women with early breast cancer. Methods: Patients included were &gt;70 years and had operable primary breast cancer (&lt;5 cm) managed in a dedicated clinic. Personal characteristics, patterns of presentation, pathological features of diagnostic needle core biopsies and treatments both recommended and received were reviewed in 265 consecutive female patients diagnosed over a 30-month period (between January 2004 and June 2006). Results: The mean age was 78.5 (range: 70–100 years). Majority (83%) presented with symptomatic cancer with the remaining ones detected through mammographic screening. These cancers were predominantly oestrogen receptor positive (histochemical (H) score &gt;10) (84%) with high H scores (83% had H scores &gt;200). Most of them were grade 2 (63%), followed by grade 1 and 3. Treatment undertaken was often in compliance with the clinicians’ advice if specifically recommended; however, when choice was given, there was a tendency to accept non-operative intervention. Documented reasons include surgical refusal, feeling un-fit for surgery and personal commitments disallowing post-operative recovery time. In addition, patients who received primary hormone therapy were on average 7 years older and suffered significantly more co-morbidity than those who had surgery. Conclusions: The elderly breast cancer population often receive different treatments possibly due to biological characteristics and personal reasons distinct from their younger counterpart. Further work is ongoing to link these findings to long-term clinical outcome. [Table: see text] No significant financial relationships to disclose.
Propagation of &lt;italic&gt;Herpesvirus saimiri&lt;/italic&gt; in Human Cells
Authors: D. V. Ablashi, G. R. Armstrong, U. Heine, R. A. Manaker
Journal: JNCI Journal of the National Cancer Institute (1971)

Herpesvirus saimiri (HVS) was found to replicate in human cell cultures. Cytopathic effects in WI-38 cells were produced by HVS when cells were pretreated with diethylaminoethyl-dextran. The presence of complement-fixation (CF) antigen in HVS-infected cells could be used as a determinant of the viral infection. The relative yields of CF antigen parallel the relative yield of infectious virus.
Vasoactive substances induce cytoskeletal changes in cultured rat glomerular epithelial cells.
Authors: R Sharma, H B Lovell, T B Wiegmann, V J Savin
Journal: Journal of the American Society of Nephrology (1992)

Angiotensin II (ANG II), atrial natriuretic peptide III (ANP), and sodium nitroprusside (SNP) alter capillary hydraulic conductivity in isolated glomeruli. These agents also affect cyclic nucleotide levels of glomerular epithelial cells (GEC). ANG II increases cAMP, whereas ANP and SNP increase cGMP. The effects of these vasoactive substances on GEC cytoskeleton were tested by incubating cells from primary cultures or an established cell line with each agent. Changes in the cytoskeleton were assessed by staining for F-actin with Bodipy phallacidin and for tubulin with NBD-colcemid. Control cells exhibited short bundles of F-actin or stress fibers near the base of the cells. These were frequently arranged in parallel and occasionally appeared to radiate from the center of the cell. Microtubules were arranged in a fine network throughout the cell with increased density adjacent to the nucleus and within the nucleolus. Incubation of GEC with 10(-7) M ANG II, cholera toxin, or 8Br-cAMP for 2 at 37 degrees C resulted in rearrangement of F-actin into distinct stellate patterns with a decrease in the relative intensity of the peripheral staining, all concurrent with a fivefold increase in intracellular cAMP. The incubation of GEC with 10(-6) M ANP or 10(-7) M SNP for 2 h at 37 degrees C resulted in apparent disassembly of stress fibers, sparse and more diffuse fluorescence, and some increase of fluorescence at the periphery of the cells, all concurrent with a 10-fold increase in intracellular cGMP. Cytochalasin D incubation led to complete disassembly of actin filaments.(ABSTRACT TRUNCATED AT 250 WORDS)
Long-term responses to thalidomide and rituximab in Waldenstrom's macroglobulinemia
Authors: J. D. Soumerai, A. R. Branagan, C. J. Patterson, Z. R. Hunter, S. P. Treon
Journal: Journal of Clinical Oncology (2007)

8017 Background: Rituximab is active in Waldenstrom's macroglobulinemia (WM), producing response rates of 40–50%. Lower response rates are observed among patients with the FcγRIIIA-158 FF polymorphism; high B 2 M (≥3.0 mg/dL), and high serum IgM levels (≥6,000 mg/dL). Thalidomide enhances rituximab-mediated ADCC of lymphoplasmacytic cells and produces response rates of 25% in WM. As such, we conducted this phase II study using thalidomide and rituximab in patients naïve to either agent. Methods: Intended therapy was: Weeks 1–52: Thalidomide (200 mg po qHS for 2 wks, then 400 mg po qHS) Weeks 2–5, 13- 16: Rituximab (375 mg/m 2 /wk) Twenty-five patients were enrolled, 20 of whom were previously untreated, with a baseline median age of 62 (range 44–86 yrs), BM involvement of 40 (range 5–80%), serum IgM of 3,670 (range 924–8,610 mg/dL), B 2 M of 2.6 (range 1.4–8.3 mg/L), Hct of 34.1 (range 23.6–42.6%). Results: Grade ≥2 toxicities to thalidomide included neuroparesthesias (n=11); somnolence (n=3); confusion (n=3); rash (n=2); tremors (n=2); bradycardia (n=2) and palpitations (n=1). Among patients experiencing neuroparesthesias, 10 demonstrated resolution to grade 1 (n=3) or complete resolution (n=7) at a median of 6.7 (range 0.4- 22.5 months). Dose reduction of thalidomide occurred in all patients and led to discontinuation in 11 patients. Twenty-three patients were evaluable. Responses among evaluable patients: CR (n=1); PR (n=15); MR (n=2); SD (n=1) for an overall and a major response rate of 78% and 70%, respectively. Median serum IgM decreased from 3,670 (924–8,610 mg/dL) to 1,590 (36–5,230 mg/dL) (p&lt;0.001), while median hematocrit rose from 33.0 (23.6–42.6%) to 37.6 (29.3–44.3%) (p=0.004) at best response. With a median follow-up of 42+ months, the median TTP for all evaluable patients on study was 35 months, and 38+ months for responders. Overall response was associated with median cumulative thalidomide dose: CR/PR/MR (29,275 mg) vs. SD/NR (7,400 mg); p=0.004. Overall responses were unaffected by FcγRIIIA-158 polymorphism status (81% vs. 71% for VV/FV vs. FF); serum IgM (78% vs. 80% for &lt;6,000 vs. ≥6,000 mg/dL); and B 2 M levels (71% vs. 89% for &lt;3 vs. ≥3 g/dL); p=NS. Conclusions: Thalidomide in combination with rituximab is highly active and produces long- term responses in patients with WM. No significant financial relationships to disclose.
Uveal Melanomas with SF3B1 Mutations
Authors: Serdar Yavuzyigitoglu, Anna E. Koopmans, Robert M. Verdijk, Jolanda Vaarwater, Bert Eussen, Alice van Bodegom, Dion Paridaens, Emine Kiliç, Annelies de Klein
Journal: Ophthalmology (2016)
Evaluation of age at diagnosis in breast cancer as a prognostic factor for disease-free survival.
Authors: C. Arce-Salinas, Lara-Medina Fernando, Alvarado-Miranda Alberto, Castaneda-Soto Noel
Journal: Journal of Clinical Oncology (2010)

e11105 Background: Women diagnosed with breast cancer, who are younger than 35 years-old, and older than 65 years-old seem to have a poorer prognosis. Younger women with breast cancer are more likely to have affected lymph nodes, to be negative for estrogen receptors, and to have larger and anaplastic tumors. On the contrary, women older than 65 years-old, usually are considered as a fragile patients, with co-morbidities (obesity, renal failure and diabetes), and could not receive chemotherapy at full doses. Methods: To investigate whether age at diagnosis is an independent negative prognostic factor in primary breast cancer. Design: Retrospective cohort study based on a population-based database of patients diagnosed with breast cancer in the period from January 1998 to December 1999. Results: Patients were staged I, II or III and were treated with at least four cycles of doxorubicin-based neoadjuvant or adjuvant chemotherapy. We defined younger patients, those aged less than 35 years-old, middle age those having between 35 to 64 years-old and older women those aged more than 64 years. The median follow-up time was 91 months interpercentile interval was 46 to 102 months. The distribution of the groups according stage, tumor grade, presence of lymphatic permeation and treatment were not different. We estimated disease free-survival with the Kaplan-Meier method and compared with the log-rank test. At 91 months, the median disease-free survival for age group was 68, 93 and 91 months respectively (p = 0.047). In the multivariate Cox analysis, besides stage, age at diagnosis but no treatment was an independent prognostic factor for disease free survival p = 0.001. There were not differences in overall survival among the groups. Conclusions: Age and stage at diagnosis are independent prognostic factor for disease free-survival. Younger women have poor prognosis in comparison with middle age and older women when treated with doxorubicin-based chemotherapy No significant financial relationships to disclose.
Proposed Staging System for Patients With HPV-Related Oropharyngeal Cancer Based on Nasopharyngeal Cancer N Categories
Authors: Kristina R. Dahlstrom, Adam S. Garden, William N. William, Ming Yann Lim, Erich M. Sturgis
Journal: Journal of Clinical Oncology (2016)

Patients with human papillomavirus (HPV)-related oropharyngeal cancer (OPC) generally present with more advanced disease but have better survival than patients with HPV-unrelated OPC. The current American Joint Commission on Cancer (AJCC)/Union for International Cancer Control (UICC) TNM staging system for OPC was developed for HPV-unrelated OPC. A new staging system is needed to adequately predict outcomes of patients with HPV-related OPC.Patients with newly diagnosed HPV-positive OPC (by p16 immunohistochemistry or in situ hybridization) treated at our institution from January 2003 through December 2012 were included. By using recursive partitioning analysis (RPA), we developed new stage groupings with both traditional OPC regional lymph node (N) categories and nasopharyngeal carcinoma (NPC) N categories. Survival was estimated by the Kaplan-Meier method, and the relationship between stage and survival was examined by using Cox proportional hazards regression analysis.A total of 661 patients with HPV-positive OPC met the inclusion criteria. With the traditional TNM staging system, there was no difference in survival between stages (P = .141). RPA with NPC N categories resulted in more balanced stage groups and better separation between groups for 5-year survival than RPA with traditional OPC N categories. With the stage groupings that were based in part on NPC N categories, the risk of death increased with increasing stage (P for trend < .001), and patients with stage III disease had five times the risk of death versus patients with stage IA disease.New stage groupings that are based on primary tumor (T) categories and NPC N categories better separate patients with HPV-positive OPC with respect to survival than does the current AJCC/UICC TNM staging system. Although confirmation of our findings in other patient populations is needed, we propose consideration of NPC N categories as an alternative to the traditional OPC N categories in the new AJCC/UICC TNM staging system that is currently being developed.
Engaging Stakeholders in Surgical Research
Authors: Anne P. Ehlers, Giana H. Davidson, Bonnie J. Bizzell, Mary K. Guiden, Elliott Skopin, David R. Flum, Danielle C. Lavallee
Journal: JAMA Surgery (2016)

tion rate of (7 of 7 vs 31 of 35; P = .81).Asking for a preferred contact time (76% vs 85%; P = .32)and mailing reminder letters (78% vs 89%; P = .31)resulted in nonsignificant improvements in retention rates.Discussion | The participation of a multidisciplinary stakeholder team provided unique perspectives that helped improve recruitment and retention rates in the RCT.Implementation of stakeholder recommendations on how to explain the purpose of the trial to eligible participants in the urgent emergency care setting significantly improved enrollment.The implementation of stakeholder recommendations for maximizing patient follow-up also significantly improved retention rates.We believe that our success in achieving these goals stems in part from involving stakeholders throughout the entirety of the project, building strong ongoing relationships, fostering open communication, and appreciating all opinions.This study demonstrates the potential value and effect of involving patients, families, and other health care stakeholders in the design and performance of surgical trials.
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
Authors: Anna Vlasova, Salvador Capella-Gutiérrez, Martha Rendón-Anaya, Miguel Hernández-Oñate, André E. Minoche, Ionas Erb, Francisco Câmara, Pablo Prieto-Barja, André Corvelo, Walter Sanseverino, Gastón Westergaard, Juliane C. Dohm, Georgios J. Pappas, Soledad Saburido-Alvarez, Darek Kedra, Irene Gonzalez, Luca Cozzuto, Jessica Gómez-Garrido, María A. Aguilar-Morón, Nuria Andreu, O. Mario Aguilar, Jordi Garcia-Mas, Maik Zehnsdorf, Martín P. Vázquez, Alfonso Delgado-Salinas, Luis Delaye, Ernesto Lowy, Alejandro Mentaberry, Rosana P. Vianello-Brondani, José Luís García, Tyler Alioto, Federico Sánchez, Heinz Himmelbauer, Marta Santalla, Cedric Notredame, Toni Gabaldón, Alfredo Herrera-Estrella, Roderic Guigó
Journal: Genome biology (2016)

Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes.
Exclusions to use of bevacizumab in elderly veterans with advanced non-small cell lung cancer (NSCLC)
Authors: T. Merza, L. M. Howard, M. Junagadhwalla, A. Gajra
Journal: Journal of Clinical Oncology (2007)

18046 Background: Bevacizumab (BEV) is a monoclonal antibody against VEGF approved for treatment of advanced NSCLC in the 1 st line setting. BEV is being evaluated in other settings in NSCLC (2 nd line, adjuvant). BEV is associated with a distinct toxicity profile including hemorrhage, delayed wound healing, viscus perforation, hypertension (HTN), and thrombosis which limits its use. At the VA medical center, we noticed poor accrual to trials with BEV. We retrospectively studied all patients diagnosed with NSCLC in the past 3 years to identify the factors that would exclude patients from participating in clinical trials with BEV. Methods: Patients were identified from our tumor registry and clinical data was reviewed. We used the exclusion criteria as per ECOG 4599 and an open industry sponsored trial (erlotinib ± BEV for 2 nd line NSCLC) as listed in the table below. Results: A total of 106 male veterans with stage 4 NSCLC were identified with a median age of 72 years. Patients with squamous predominant histology (n=26) were excluded. Of the remaining 80 patients evaluated for use of BEV, 72 patients (90%) met 1 or more exclusion criteria. The following table displays the breakdown of exclusion criteria both non-specific and specific to BEV. Conclusions: Elderly veterans with NSCLC have multiple co-morbidities precluding use of cytotoxic chemotherapy. Use of BEV is further limited in this population. There is a need for agents with a favorable toxicity profile in the treatment of NSCLC. Clinical trials specific to the needs of this group of patients with poor PS and multiple co-morbidities are needed to improve participation and to offer newer therapies to the elderly veteran with lung cancer. [Table: see text] No significant financial relationships to disclose.