tbuckley/cabot-search huggingface dataset:
Indispensability of Horizontally Transferred Genes and Its Impact on Bacterial Genome Streamlining
Authors: Ildikó Karcagi, Gábor Draskovits, Kinga Umenhoffer, Gergely Fekete, Károly Kovács, Orsolya Méhi, Gabriella Balikó, Balázs Szappanos, Zsuzsanna Györfy, Tamás Fehér, Balázs Bogos, Frederick R. Blattner, Csaba Pál, György Pósfai, Balázs Papp
Journal: Molecular Biology and Evolution (2016)

Why are certain bacterial genomes so small and compact? The adaptive genome streamlining hypothesis posits that selection acts to reduce genome size because of the metabolic burden of replicating DNA. To reveal the impact of genome streamlining on cellular traits, we reduced the Escherichia coli genome by up to 20% by deleting regions which have been repeatedly subjects of horizontal transfer in nature. Unexpectedly, horizontally transferred genes not only confer utilization of specific nutrients and elevate tolerance to stresses, but also allow efficient usage of resources to build new cells, and hence influence fitness in routine and stressful environments alike. Genome reduction affected fitness not only by gene loss, but also by induction of a general stress response. Finally, we failed to find evidence that the advantage of smaller genomes would be due to a reduced metabolic burden of replicating DNA or a link with smaller cell size. We conclude that as the potential energetic benefit gained by deletion of short genomic segments is vanishingly small compared with the deleterious side effects of these deletions, selection for reduced DNA synthesis costs is unlikely to shape the evolution of small genomes.
A Solid-Phase Radioimmunoassay for Epstein-Barr Virus-Associated Membrane Antigen Prepared From 895-8 Cell Culture Supernatants 2
Authors: Gottfried Dölken, George Klein
Journal: JNCI Journal of the National Cancer Institute (1977)

Epstein-Barr virus (EBV)-associated membrane antigen (MA) was concentrated from B95-8 cell culture media by precipitation with polyethylene glycol followed by chromatography on Bio-Gel A-50m. In a RAJI cell-binding assay, MA-positive material could only be found in the void volume of the column. After ultracentrifugation all antigenic activity appeared in the pellet, which suggested that MA was present in aggregates, presumably fragments of cellular membranes and/or virus envelopes. The MA-containing preparation was photopolymerized in polyacrylamide gel. The homogenized gel was used in a solid-phase radioimmunoassay with 125I-labeled lgG from an anti-MA positive reference serum and an anti-MA negative control serum. The specificity of the reaction was confirmed in blocking tests with anti-EBV positive and negative sera. A good correlation was found between the results obtained in the radioimmunoassay and the results obtained in direct immunofluorescence tests for the detection of MA. The existence of at least two subspecificities of the MA complex could be confirmed by this radioimmunoassay.
The relevance of performing a bone marrow aspirate and biopsy in breast cancer patients with suspected bone marrow metastasis
Authors: P. Sobrevilla-Calvo, M. Jaramillo-Restrepo, S. Rivas-Vera, A. Avilés-Salas, A. Acosta-Barreda, E. Cervera-Ceballos, J. Labardini-Méndez
Journal: Journal of Clinical Oncology (2006)

18605 Background: Patients with breast cancer often presents hematological abnormalities during the disease evolution, frequently it is difficult to define if these are due to bone marrow infiltartion or are due to drug toxicity or a new hematological disorder. To determine the proportion of patients with bone marrow metastasis we reviewed the bone marrow aspirates and biopsies of patients with histological proven breast cancer and an abnormal peripheral blood count referred to the Hematology Department. Methods: We reviewed the medical records of 88 patients referred to our Department from april 1998 to april 2005 with breast cancer and with bone marrow smears and biopsies. The BM smears were interpreted blindly by one of us. The BM biopsies were reviewed independently by a hematopatologist. A statistician analysed the data and estimated frequencies and rates, survival analysis was estimated by means of the Kaplan-Meier method. Results: Median age 47.7 years (range 28–80), clinical stage at diagnosis was: II, 19 (21.1%); IIIA, 19 (21.1%); IIIB, 16 (17.8%); IV, 34 (40%). The hematological abnormality that triggered the referral was: Thrombocytopenia, 61 (67.8%); anemia, 53 (58.9%); leucopenia, 47 (53.4%); thrombocytopenia and anemia, 39 (43.3%). The median time from the initial diagnosis to the BM biopsy was 12.8 months (range 1 to 176.7). Regarding the BM aspirates interpretatrion: 17 were not evaluable, 53 were negative for infiltration, 17 were positive for carcinoma and 1 with plasma cell infiltration (this patients had concurrent Breast cancer and myeloma). BM biopsies: 19 were not evaluable, 48 were negative, 20 positive and 1 with myeloma. The sensitivity of the BM aspirates was 75% (12/16) and the specificity 95% (41/43). The median survival of the patients with BM metastais was 109 months, and 104 of the patients without BM metastasis (p = 0.9767) Conclusions: Most of the patients with hematological abnormalities do not have BM infiltration, bone marrow biopsies have more sensitivity than aspirates. The presence of BM metastasis does not necessarily predicts a short survival period. No significant financial relationships to disclose.
Response to treatment with denosumab in patients with giant cell tumor of bone (GCTB): FDG PET results from two phase 2 trials.
Authors: Keith M. Skubitz, David Morgan Thomas, Sant P. Chawla, Arthur P. Staddon, Jacob Engellau, Amy Feng, Bruce A. Bach
Journal: Journal of Clinical Oncology (2014)

10505 Background: GCTB is a primary osteolytic tumor characterized by local invasiveness and limited non-surgical treatment options. Osteoclast-like giant cells expressing surface RANK, and stromal cells expressing RANK ligand (RANKL), are features of GCTB. Denosumab, a monoclonal antibody against RANKL, is approved in the US for treatment of GCTB that is unresectable or where surgery would be associated with severe morbidity. Here, we report sequential FDG-PET as a sensitive early indicator of GCTB response to denosumab from 2 phase 2 trials. Methods: Adult or skeletally mature patients with GCTB (N=360) received subcutaneous (SC) denosumab 120 mg on days 1, 8, and 15, and every 4 weeks thereafter. In some centers, combination FDG-PET and CT images were obtained sequentially as part of routine care. All evaluable scans were reviewed by central independent treatment-blinded reviewers. Results: Paired pre- and post-treatment FDG PET scans from 26 patients (144 scans) showed marked reductions in FDG-PET avidity and reductions in standardized uptake values (SUV) early in response to denosumab at the first post-treatment scan (median [Q1, Q3] 68.5 [50, 84] days from first dose). All paired samples showed a best EORTC response of >25% reduction in SUV uptake following initiation of denosumab treatment. Sequential PET imaging studies revealed a sustained and progressive SUVmax reduction in GCTB lesions with continued denosumab treatment. Conclusions: This study represents the largest GCTB FDG-PET imaging data set from an interventional clinical trial reported to date. It shows that FDG-PET is a sensitive early indicator of tumor response to denosumab, preceding both cytoreduction (RECIST) and new bone formation/calcification (HU density), and that this response is sustained in denosumab-treated GCTB. Clinical trial information: NCT00396279, NCT00680992. Tumor site (N patients) Baseline SUVmax, median (range) Best on-study SUVmax, median (range) EORTC standard uptake, mean Best SUVmax response (mean % change from baseline) Appendecular skeleton (11) 10.0 (6.4-21.6) 4.0 (1.3-10.4) 2.1 -66 Axial skeleton (11) 9.2 (2.9-16.1) 2.7 (1.1-5.1) 1.7 -64 Lung (5) 6.5 (3.6-11.0) 1.8 (1.1-5.0) 1.4 -64 All lesions (26) 9.8 (2.9-21.6) 2.7 (1.1-10.4) 1.8 -64
Lessons From Ebola Outbreak Point to Reforms
Authors: M. J. Friedrich
Journal: JAMA (2016)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Impact of an outpatient interdisciplinary team (IDT) consultation on symptom clusters in advanced cancer patients seen at a supportive care outpatient clinic (OSC) in a tertiary cancer center
Authors: S. Yennurajalingam, D. L. Urbauer, R. Chacko, D. Hui, Y. A. Amin, A. C. Evans, C. Orihuela, K. L. Casper, V. Poulter, B. Coldman, E. Bruera
Journal: Journal of Clinical Oncology (2009)

e20542 Background: Advanced cancer patients develop severe physical and psychosocial symptom clusters. There is limited data on the impact of an outpatient interdisciplinary team (IDT) consultation lead by palliative care specialists on symptom clusters. Cluster composition and consistence, response rate and predictors of response are unknown. Methods: 914 consecutive patients with advanced cancer presenting in the OSC from Jan 2003 to Oct 2008 with a complete Edmonton symptom assessment scale at the initial and follow-up visit (median 14 days, range 1–4 wks), and CAGE status (alcohol screening) were reviewed. Wilcoxon ranked sign test was used to determine whether symptoms changed over time. Principal components factor analysis with varimax rotation was used to determine clusters of symptoms at baseline and at follow-up. The number of factors calculated was determined based upon the number of eigen values that were greater than one. Results: Median age was 59 yrs, female were 46%. The most common primary cancer was Lung (19%). Baseline and follow-up visit scores (mean, SD) were: fatigue 5.7 (2.1) and 5.2 (2.2, p&lt;0.0001), pain 4.9 (2.6) and 4.1 (2.6 p&lt;0.0001), nausea 1.8 (2.4) and 1.7 (2.3, p=0.1), depression 2.6 (2.5) and 2.2(2.4,p&lt;0.0001), anxiety 2.9 (2.7) and 2.4 (2.4, p&lt;0.0001), drowsiness 3.2 (2.8) and 3.2 (2.6, p=0.7), dyspnea 2.6 (2.7) and 2.4 (2.6), p=0.0027), appetite 4.2(2.7) and 3.9 (2.7, p&lt;0.0001), sleep 4.2 (2.6) and 3.8 (2.6, p&lt;0.0001) and well being 4.3 (2.5) and 3.9 (2.3, p&lt;0.0001). During the follow- up the symptom clusters varied from a 3 factor to a 2 factor model, reflecting the impact of the IDT on symptom burden. CAGE positive and CAGE negative patients had a significantly different symptom cluster model. Conclusions: Cluster composition differs when patients are assessed and managed by an IDT and among patients who screen positive for alcoholism. [Table: see text] No significant financial relationships to disclose.
Abstract 19063: TGF-β Levels Are Associated with Aortic Root Dilatation, Aortic Root Growth Rate and Clinical Events in Patients with Marfan Syndrome
Authors: Romy Franken, Leo J Engele, Alexander W den Hartog, Janneke Timmermans, Arthur J Scholte, Maarten P van den Berg, Aeilko H Zwinderman, Barbara J Mulder, Maarten Groenink
Journal: Circulation (2012)

Background: Marfan syndrome (MFS) is a connective tissue disorder with variable aortic root dilatation. Recently, increased transforming growth factor beta (TGF-β) signalling emerged as a new potential biochemical pathway leading to aortic disease. The aim of this study was to investigate whether TGF-β is correlated with aortic root dilatation, exploring the role of TGF-β as a prognostic biomarker in MFS. Methods: In this correlation study between aortic root diameters and TGF-β, 86 MFS patients were included. Twenty-five patients had previously undergone aortic root replacement. Total plasma TGF-β was assessed at baseline in patients and 22 healthy controls. Aortic root diameters were measured by means of echocardiography with a mean follow-up of 32 months. Clinical events, including aortic dissection and aortic root replacement were evaluated. Results: At baseline TGF-β levels were higher in MFS patients as compared to controls (112.6 vs 33.5 pg/ml, p=0.019). Patients with previous aortic root replacement had significantly higher TGF-β levels compared to patients without aortic root repair (168.7 vs 89.7 pg/ml, p=0.008). Higher plasma TGF-β levels correlated with larger aortic root diameter at baseline (p=0.047) and at follow-up (p=0.006). Moreover, there is a correlation between higher TGF-β levels and faster aortic root growth rate (p=0.022). After 32 months of follow-up 17 events were observed: aortic root replacement in 13 patients and type b dissection in four patients. Patients with an event had higher aortic root diameters at baseline (45.6 vs 39.6 mm, p=&lt;0.0001) and higher TGF-β levels (160 vs 100 pg/ml, p=0.014) compared to patients without event. Conclusion: TGF-β levels are higher in MFS patients than in healthy controls. Higher TGF-β plasma levels were correlated with larger aortic root diameters, faster aortic root growth and aortic root replacements or type b dissections. Plasma TGF-β might serve as a prognostic biomarker in Marfan syndrome.
Bevacizumab, temozolomide, and radiotherapy for newly diagnosed glioblastoma: comprehensive safety results during and after first-line therapy
Authors: Frank Saran, Olivier L. Chinot, Roger Henriksson, Warren Mason, Wolfgang Wick, Timothy Cloughesy, Sunita Dhar, Emanuela Pozzi, Josep Garcia, Ryo Nishikawa
Journal: Neuro-Oncology (2016)

The proposed use of bevacizumab with radiotherapy/temozolomide for newly diagnosed glioblastoma raised potential safety concerns. Bevacizumab has been linked with stroke, bleeding events, and wound-healing complications in other tumor types; these events are of particular concern for glioblastoma (highly vascular tumors that are usually resected). Published data on the interaction of bevacizumab with radiotherapy/temozolomide are also limited. We report safety data from a phase III randomized trial (Avastin in Glioblastoma), focusing on these considerations.Eligible patients received: radiotherapy and temozolomide plus bevacizumab/placebo, 6 cycles; a 4-week treatment break; temozolomide plus bevacizumab/placebo, 6 cycles; and bevacizumab/placebo until progression. Data on adverse events (AEs) were collected throughout.Bevacizumab-treated patients (n = 461) had a longer median safety follow-up time (12.3 vs 8.5 mo), and a higher proportion completed 6 cycles of maintenance temozolomide (64.6% vs 36.9%) versus placebo (n = 450). The incidences of relevant AEs (bevacizumab vs placebo, respectively) were: arterial thromboembolic events (5.9% vs 1.6%); cerebral hemorrhage (3.3% vs 2.0%); wound-healing complications (6.9% vs 4.7%); thrombocytopenia (34.1% vs 27.3%); radiotherapy-associated skin injury (8.2% vs 9.3%); alopecia (39.0% vs 36.0%); gastrointestinal perforation (including gastrointestinal abscesses and fistulae, 1.7% vs 0.4%); and radiotherapy-associated injury (0.4% vs 0.0%). Overall, 15.8% and 23.8% of bevacizumab- and placebo-treated patients had surgery (including biopsy) after progression. Within 30 days of postprogression surgery, AE incidence was 10.9% (bevacizumab) and 23.4% (placebo).The safety profile was consistent with that expected from radiotherapy/temozolomide plus bevacizumab. The increased AE incidence with bevacizumab did not impact patients' ability to receive standard-of-care treatment or to undergo further surgery.
The needs of older women are just as great
Authors: S. Randall, C. Lewis
Journal: BMJ (1995)

promote contraception through safer sex cam- paigns have undoubtedly been successful in increasing the proportion of teenagers who use condoms.Most people have assumed that increas- ing the use of contraception leads to a reduction in unplanned teenage pregnancies.4Yet my analysis shows that this has not happened.A plausible explanation is that the main factor in unplanned teenage conceptions is contraceptive failure, not the lack of contraceptive knowledge and availability.The findings of Pearson and colleagues support this view.A further question is whether increasing the availability of contraception leads to an increase in sexual activity.If this is the case-and the national survey of sexual behaviour reports a large increase over the past two decades in the proportion of teenagers who are sexually active-then it is not surprising that the rate of teenage conceptions continues to increase.The answer is not more contraception or emergency contraception but a change in attitude towards sexual behaviour.
Fetal Rat Keratinizing Epidermal Cells in Culture: Effects of Long-Term Treatment by Benzo[a]pyrene on Their Growth Characteristics23
Authors: Katsuhiko Indo, Richard B. Wilson
Journal: JNCI Journal of the National Cancer Institute (1977)

Journal Article Fetal Rat Keratinizing Epidermal Cells in Culture: Effects of Long-Term Treatment by Benzo[a]pyrene on Their Growth Characteristics Get access Katsuhiko Indo, Katsuhiko Indo Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard B. Wilson Richard B. Wilson Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 59, Issue 3, September 1977, Pages 867–880, https://doi.org/10.1093/jnci/59.3.867 Published: 01 September 1977 Article history Received: 08 June 1976 Revision received: 28 February 1977 Accepted: 17 March 1977 Published: 01 September 1977
Multi drug resistant tuberculosis in a tertiary university hospital
Authors: Abdalla Khoury, Omar Balash, Lina Kayalli, Ahmad Touma
Journal: European Respiratory Journal (2011)

Objective: The interest of this study was to evaluate the rate of recovery and the mean time to detection (TTD) of mycobacterium tuberculosis in clinical specimens with two culture systems, the BACTEC MGIT 960 and Lowenstein-Jensen (LJ) medium. and determinate the type and rate of anti tuberculosis drug resistance.

Methods: We studied 325 specimens decontaminated with NaLC-NaOH then inoculated onto Bactec MGIT960, and L.J. medium. We compared, the rate of recovery, mean time to detection, contamination rates of MGIT and L.J. –(Lowenstein-Jensen)medium. We did identification to all positive specimen then we did susceptibility test to all Mycobactruim Tuberculosis samples.

Results: A total of 209 Mycobacterial isolates (161Mycobactruim tuberculosis, and 48 NTB (non tuberculos bacilli) were detected. The recovery rates were 64.3% with MGIT and 55.7% with L.J. the rates of contamination for each of the systems were 6.5% with MGIT and 4% with L.J.

The TTDs for mycobacteria were 13.1 days with BACTEC MGIT 960 and 27.3 days with LJ.

Resistance to STR was found in 7 (4.5%) patients, INH in13 (8.6%), ETH in 3 (1.8%), RIF in 5 (3.1%) and resistance to PYR in 6 (3.7%)

Conclusion: The Bactec MGIT system is a sensitive, rapid, mycobacterial culturing system. However, the high contamination rate is a concern that should be carefully evaluated in the clinical setting. Drug resistance was associated with a history of previous anti-TB treatment (p = 0.017). Monoresistance to a single first-line agent was found in 22 (13.6%), while polyresistance was noted in4 (2.5)%. Multidrug-resistant M. tuberculosis was noted in 0.6% of all MTB isolates. X-MDR TB was not detected in our specimens.
Smoking and prognostic factors in an observational setting in patients with advanced non-small cell lung carcinoma (NSCLC; B9E-AA-B004)
Authors: S. Altug, C. Li, M. Marek, S. Z. Güçlü, Y. Kim, M. M. Meshref, S. Qin, K. Krejcy, W. H. Reece
Journal: Journal of Clinical Oncology (2008)

7588 Background: Previous studies have assessed prognostic factors for advanced NSCLC. This international observational study quantifies the effect of a set of clinically relevant prognostic markers into a single model that tests continued smoking during therapy on survival, and allows for an evidence-based approach to determining prognosis in patients (pts) with advanced NSCLC receiving first-line chemotherapy with a gemcitabine-platinum combination. Methods: Eligibility criteria included: Stage IIIB/IV NSCLC, no prior chemotherapy, and ECOG performance status (PS) 0 or 1. A Cox regression model was constructed and validated by splitting the data at random into two datasets in a ratio of 3:1 (Construction [C]: Validation [V]). Country, disease stage, hypercalcemia, “N” factor, weight reduction, PS, and superior vena caval obstruction (SVCO) were pre-defined variables that were forced into the model. Other variables were selected based on significance at P<0.1 or clinical opinion. Continued smoking was then tested with adjustment for these variables. Results: 1,214 (C=891 and V=323) pts were enrolled. The primary model was estimable on 544 pts, with Hazard Ratios (* implies P<0.05): Country vs. Taiwan: China 1.04, Egypt* 1.91, Israel 1.48, Pakistan 1.37, Poland/Romania 1.30, Sth Korea 0.87, Turkey 1.28; disease stage* IV vs. IIIB: 1.59; hypercalcemia: 0.51; N-staging vs. N0: N1 1.51, N2 1.18, N3 1.49, NX 2.01, weight loss >10% 1.08, PS* 1 vs. 0: 1.66, SVCO 1.77, carboplatin vs. cisplatin*: 1.51, T-staging* vs. T1: T2 2.52, T3* 3.75, T4* 4.01, TX* 7.32, sex F vs. M 0.78, brain metastasis 1.38, and histopathology vs. adenocarcinoma: large cell* 1.77, mixed 0.62, squamous 1.19, NSCLC 1.13, COPD 1.33. Smoking during therapy was not significantly associated with survival (46/508 assessable pts smoked), HR: 1.06 (95% CI: 0.68, 1.65), P=0.78. The model performed well under validation in different centers (P=0.0008). Conclusions: After adjusting for other prognostic markers, continued smoking during therapy did not statistically significantly effect survival, though too few smoked to rule out a clinically important effect. This model forms an evidence-based approach to assessing prognosis in advanced stage NSCLC. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Eli Lilly Eli Lilly Eli Lilly