tbuckley/cabot-search huggingface dataset:
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution
Authors: Bryan A. Moyers, Jianzhi Zhang
Journal: Molecular Biology and Evolution (2016)

The source of genetic novelty is an area of wide interest and intense investigation. Although gene duplication is conventionally thought to dominate the production of new genes, this view was recently challenged by a proposal of widespread de novo gene origination in eukaryotic evolution. Specifically, distributions of various gene properties such as coding sequence length, expression level, codon usage, and probability of being subject to purifying selection among groups of genes with different estimated ages were reported to support a model in which new protein-coding proto-genes arise from noncoding DNA and gradually integrate into cellular networks. Here we show that the genomic patterns asserted to support widespread de novo gene origination are largely attributable to biases in gene age estimation by phylostratigraphy, because such patterns are also observed in phylostratigraphic analysis of simulated genes bearing identical ages. Furthermore, there is no evidence of purifying selection on very young de novo genes previously claimed to show such signals. Together, these findings are consistent with the prevailing view that de novo gene birth is a relatively minor contributor to new genes in genome evolution. They also illustrate the danger of using phylostratigraphy in the study of new gene origination without considering its inherent bias.
Progesterone and Synthetic Progestin Controversies—Reply
Authors: Purna A. Joshi, Pamela J. Goodwin, Rama Khokha
Journal: JAMA Oncology (2015)

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 Oncology HomeNew OnlineCurrent IssueFor Authors Podcast 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 Oncology journal
重症大動脈弁狭窄症例におけるEnergy loss coefficientの有用性に関する検討
Authors: 久米輝善, 大倉宏之, 川元隆弘, 渡邉望, 豊田英嗣, 根石陽二, 宮本欣倫, 今井孝一郎, 山田亮太郎, 吉田清
Journal: Circulation (2008)
Two-fold illumination in topical 5-aminolevulinic acid (ALA)-mediated photodynamic therapy (PDT) for superficial basal cell carcinoma (sBCC): A retrospective case series and cohort study
Authors: Janneke Kessels, Jolanda Hendriks, Patty Nelemans, Klara Mosterd, Nicole Kelleners-Smeets
Journal: Journal of the American Academy of Dermatology (2016)
High-dose cytarabine and total body irradiation with or without cyclophosphamide as a preparative regimen for marrow transplantation for acute leukemia.
Authors: S Riddell, F R Appelbaum, C D Buckner, P Stewart, R Clift, J Sanders, R Storb, K Sullivan, E D Thomas
Journal: Journal of Clinical Oncology (1988)

Twenty-nine patients were conditioned for allogeneic marrow transplant with cytarabine (ara-C) (3 g/m2 every 12 hours for 12 doses) and total body irradiation (TBI) (200 cGy daily for six days) with or without cyclophosphamide (CY) (60 mg/kg) to determine toxicity and efficacy. Four patients had chronic myelogenous leukemia (CML) in accelerated phase or blast crisis, and 25 patients had acute leukemia, 24 at stages later than first remission. Three patients (10%) had fatal regimen-related toxicity and another 10% experienced severe toxicity in at least one organ system. The addition of CY to the ara-C and TBI regimen was not associated with an increase in the frequency of severe toxicity. Twenty-five of 29 patients engrafted eight to 33 days posttransplant: three died early before engraftment, and one patient failed to engraft. Ten of 29 patients are alive without disease, and the actuarial probability of disease-free survival for the entire group at 3 years is 33%. Three of ten patients with acute nonlymphocytic leukemia (ANL), six of 15 with acute lymphocytic leukemia (ALL), and one of four with CML are alive and disease free 25 to 42 months (median, 30 months) after transplant. High-dose ara-C (HDara-C) and TBI with or without CY can be administered with approximately the same toxicity as CY plus TBI. Phase III studies appear warranted to determine if these newer regimens provide improved results compared with currently used regimens.
Dual HER2 Targeting with Trastuzumab and Liposomal-Encapsulated Doxorubicin (MM-302) Demonstrates Synergistic Antitumor Activity in Breast and Gastric Cancer
Authors: Christopher W. Espelin, Shannon C. Leonard, Elena Geretti, Thomas J. Wickham, Bart S. Hendriks
Journal: Cancer Research (2016)

Trastuzumab is the standard of care for HER2-positive breast cancer patients, markedly improving disease-free and overall survival. Combined with chemotherapy, it enhances patient outcomes, but cardiotoxicity due to the trastuzumab treatment poses a serious adverse effect. MM-302 is a HER2-targeted PEGylated liposome that encapsulates doxorubicin to facilitate its delivery to HER2-overexpressing tumor cells while limiting exposure to nontarget tissues, including the heart. In this study, we evaluated the feasibility and preclinical activity of combining MM-302 with trastuzumab. MM-302 and trastuzumab target different domains of the HER2 receptor and thus could simultaneously bind HER2-overexpressing tumor cells in vitro and in vivo. Furthermore, trastuzumab did not disrupt the mechanism of action of MM-302 in delivering doxorubicin to the n0ucleus and inducing DNA damage. Reciprocally, MM-302 did not interfere with the ability of trastuzumab to block prosurvival p-Akt signaling. Interestingly, coadministration of the two agents acutely increased the deposition of MM-302 in human xenograft tumors and subsequently increased the expression of the DNA damage marker p-p53. Finally, the combination of MM-302 and trastuzumab induced synergistic antitumor activity in HER2-overexpressing xenograft models of breast and gastric cancer. Collectively, our findings highlight a novel combination therapy that efficiently targets HER2-overexpressing cells through multiple mechanisms and support the ongoing investigation of combined MM-302/trastuzumab therapy for HER2-positive metastatic breast cancer in a randomized phase II clinical trial.
Effect of YOCAS yoga on circadian rhythm, anxiety, and mood: A URCC CCOP randomized, controlled clinical trial among 410 cancer survivors.
Authors: K. M. Mustian, L. Sprod, L. J. Peppone, S. G. Mohile, M. C. Janelsins, O. Palesh, K. Devine, P. S. Reddy, M. Melnik, J. K. Giguere, G. R. Morrow
Journal: Journal of Clinical Oncology (2011)

9034 Background: Cancer treatments disrupt circadian rhythm exacerbating the anxiety and mood disorders experienced by survivors, ultimately, impairing recovery and quality of life. We conducted a nationwide, multi-site, phase III randomized, controlled, clinical trial examining the efficacy of yoga for improving circadian rhythm, anxiety and mood among cancer survivors through the University of Rochester (UR) Cancer Center Community Clinical Oncology Program (CCOP) Research Base. Methods: Cancer survivors with non-metastatic disease, between 2-24 months post adjuvant therapy who reported no participation in yoga during the prior 3 months were randomized into 2 arms: 1) standard care, and 2) standard care plus the 4-week (wk) yoga intervention (2 x’s/wk; 75 min./session). The yoga intervention utilized the UR Yoga for Cancer Survivors (YOCAS) program consisting of pranayama (breathing exercises), 18 gentle Hatha and Restorative yoga asanas (postures) and meditation. Circadian rhythm, anxiety and mood were assessed pre- and post-intervention. Results: 410 survivors were accrued (96% female, mean age = 54, 75% breast cancer). Multi-oscillator modeling revealed a 12-hour, ultradian rhythm model fit the circadian rhythm better than a single-oscillator, 24-hour model and demonstrated significant rhythm differences between groups post-intervention (p<0.05) with a more favorable rhythm in the yoga group. ANCOVAs showed a lower 24-hour amplitude and a delayed 12-hour acrophase in the yoga group (all p<0.05). ANCOVAs with baseline values as covariates revealed significant differences between groups on anxiety and mood (p<0.05) with yoga participants demonstrating greater improvements in anxiety (CS=-0.80, SE=0.21) and mood (CS=-6.7, SE=1.08) from pre- to post-intervention compared to controls (anxiety CS=-0.20, SE=0.24; mood CS=-1.6, SE=0.96). Conclusions: The brief community-based YOCAS intervention favorably alters circadian rhythm and improves anxiety and mood among survivors. Clinicians should consider prescribing the YOCAS program for survivors reporting anxiety and mood disorders. Funding: NCI U10CA37420 and K07CA120025.
Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With Recurrent<i>Clostridium difficile</i>Infection
Authors: Christine H. Lee, Theodore Steiner, Elaine O. Petrof, Marek Smieja, Diane Roscoe, Anouf Nematallah, J. Scott Weese, Stephen Collins, Paul Moayyedi, Mark Crowther, Mark J. Ropeleski, Padman Jayaratne, David Higgins, Yingfu Li, Neil V. Rau, Peter T. Kim
Journal: JAMA (2016)

IMPORTANCE Clostridium difficile infection (CDI) is a major burden in health care and community settings.CDI recurrence is of particular concern because of limited treatment options and associated clinical and infection control issues.Fecal microbiota transplantation (FMT) is a promising, but not readily available, intervention.OBJECTIVE To determine whether frozen-and-thawed (frozen, experimental) FMT is noninferior to fresh (standard) FMT in terms of clinical efficacy among patients with recurrent or refractory CDI and to assess the safety of both types of FMT.DESIGN, SETTING, AND PARTICIPANTS Randomized, double-blind, noninferiority trial enrolling 232 adults with recurrent or refractory CDI, conducted between July 2012 and September 2014 at 6 academic medical centers in Canada.INTERVENTIONS Patients were randomly allocated to receive frozen (n = 114) or fresh (n = 118) FMT via enema. MAIN OUTCOMES AND MEASURESThe primary outcome measures were clinical resolution of diarrhea without relapse at 13 weeks and adverse events.Noninferiority margin was set at 15%.RESULTS A total of 219 patients (n = 108 in the frozen FMT group and n = 111 in the fresh FMT group) were included in the modified intention-to-treat (mITT) population and 178 (frozen FMT: n = 91, fresh FMT: n = 87) in the per-protocol population.In the per-protocol population, the proportion of patients with clinical resolution was 83.5% for the frozen FMT group and 85.1% for the fresh FMT group (difference, -1.6% [95% CI, -10.5% to ϱ]; P = .01for noninferiority).In the mITT population the clinical resolution was 75.0% for the frozen FMT group and 70.3% for the fresh FMT group (difference, 4.7% [95% CI, -5.2% to ϱ]; P < .001for noninferiority).There were no differences in the proportion of adverse or serious adverse events between the treatment groups.CONCLUSIONS AND RELEVANCE Among adults with recurrent or refractory CDI, the use of frozen compared with fresh FMT did not result in worse proportion of clinical resolution of diarrhea.Given the potential advantages of providing frozen FMT, its use is a reasonable option in this setting.
Electron Microscopy of Human Malignant Melanoma&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: S. Robert Wellings, Benjamin V. Siegel
Journal: JNCI Journal of the National Cancer Institute (1960)

The fine structure of human malignant melanoma cells was studied by electron microscopy. The melanoma cells were characterized by dense melanin granules within their cytoplasm. These granules averaged 300 mµ in diameter, were made up of granular and rod-shaped internal units, and appeared to originate in the Golgi apparatus. Mitochondria and ergastoplasm were moderately abundant and their structure was similar to that described for other cell types. Stromal macrophages were characterized by large conglomerate granules averaging 1100 mµ in diameter and were readily distinguishable from the melanocytes.
Cancer statistics, 2016
Authors: Rebecca L. Siegel, Kimberly D. Miller, Ahmedin Jemal
Journal: CA A Cancer Journal for Clinicians (2016)

Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States in the current year and compiles the most recent data on cancer incidence, mortality, and survival. Incidence data were collected by the National Cancer Institute (Surveillance, Epidemiology, and End Results [SEER] Program), the Centers for Disease Control and Prevention (National Program of Cancer Registries), and the North American Association of Central Cancer Registries. Mortality data were collected by the National Center for Health Statistics. In 2016, 1,685,210 new cancer cases and 595,690 cancer deaths are projected to occur in the United States. Overall cancer incidence trends (13 oldest SEER registries) are stable in women, but declining by 3.1% per year in men (from 2009‐2012), much of which is because of recent rapid declines in prostate cancer diagnoses. The cancer death rate has dropped by 23% since 1991, translating to more than 1.7 million deaths averted through 2012. Despite this progress, death rates are increasing for cancers of the liver, pancreas, and uterine corpus, and cancer is now the leading cause of death in 21 states, primarily due to exceptionally large reductions in death from heart disease. Among children and adolescents (aged birth‐19 years), brain cancer has surpassed leukemia as the leading cause of cancer death because of the dramatic therapeutic advances against leukemia. Accelerating progress against cancer requires both increased national investment in cancer research and the application of existing cancer control knowledge across all segments of the population. CA Cancer J Clin 2016;7–30. © 2015 American Cancer Society.
Tamoxifen-associated eye disease. A review.
Authors: S G Nayfield, M B Gorin
Journal: Journal of Clinical Oncology (1996)

PURPOSE The oral antiestrogen tamoxifen has demonstrated efficacy in the treatment of metastatic breast cancer and as adjuvant therapy in early-stage disease. Clinical trials of tamoxifen in chemoprevention of breast cancer among high-risk women have focused attention on potential adverse effects of long-term tamoxifen use, including the possibility of ocular toxicity. This review evaluates the published case reports, clinical series, and clinical trial data on ocular toxicities attributed to tamoxifen. Clinical issues of surveillance, differential diagnosis, and management of tamoxifen-related eye disease are discussed. DESIGN National Library of Medicine online bibliographic services were used to identify case reports and clinical studies of ocular adverse effects that occurred in patients receiving tamoxifen published through the fall of 1994. The medical literature relevant to issues raised by the reports and studies was similarly identified and reviewed. RESULTS Case reports and case series identify crystalline retinal deposits, macular edema, and corneal changes as potential tamoxifen ocular toxicities. Extensive retinal lesions and macular edema with visual impairment have been reported in a few patients receiving high-dose tamoxifen. Less extensive retinal changes may occur in patients receiving low doses for long periods, and isolated retinal crystals may be observed in patients without visual symptoms. CONCLUSION Ocular toxicity is uncommon in the current clinical setting of long-term, low-dose tamoxifen use. Physicians should be aware of the potential for ocular toxicity among patients receiving the drug and should assure appropriate surveillance and prompt evaluation of visual complaints.
The International Association for the Study of Lung Cancer Lung Cancer Staging Project
Authors: Hisao Asamura, Kari Chansky, John Crowley, Peter Goldstraw, Valerie W. Rusch, Johan F. Vansteenkiste, Hirokazu Watanabe, Yi-Long Wu, Marcin Zielinski, David Ball, Ramon Rami-Porta
Journal: Journal of Thoracic Oncology (2015)
Relation between literacy, race, and stage of presentation among low-income patients with prostate cancer.
Authors: C L Bennett, M R Ferreira, T C Davis, J Kaplan, M Weinberger, T Kuzel, M A Seday, O Sartor
Journal: Journal of Clinical Oncology (1998)

PURPOSE Diagnosis of advanced prostate cancer is a major health problem, especially among low-income men. Opportunities vary for early detection of prostate cancer for low-income black and white men because of financial, cultural, and social factors. In this study, we evaluated the association of poor literacy skills with higher rates of presentation of advanced stages of prostate cancer among low-income black and white men who received care in equal-access medical systems. PATIENTS AND METHODS Literacy and stage at diagnosis of prostate cancer were evaluated in 212 low-income men who received medical care in Shreveport, LA, and Chicago, IL. The patients' literacy was assessed with the Rapid Estimate of Adult Literacy in Medicine (REALM), an individually administered reading screening test designed specifically for use in the medical setting. Logistic regression models were used to evaluate predictors of metastatic disease at presentation as a function of patient age, race, literacy, and city. RESULTS Whereas black men were almost twice as likely to present with stage D prostate cancer (49.5% v 35.9%; P &lt; .05), they were significantly more likely to have literacy levels less than sixth grade (52.3% v 8.7%; P &lt; .001). However, after adjustment for differences in literacy, age, and city, race was not a significant predictor of advanced-stage prostate cancer. CONCLUSION Low literacy may be an overlooked but significant barrier to the diagnosis of early-stage prostate cancer among low-income white and black men. The development of culturally sensitive, low-literacy educational materials may improve patient awareness of prostate cancer and improve the frequency of diagnosis of early-stage cancer.
Abstract P154: Pericardial Adiposity Predicts Incident Diabetes: The Multi-Ethnic Study of Atherosclerosis
Authors: Amy C Alman, David R Jacobs, Matthew A Allison, John J Carr, Fang-Chi Hsu, James G Terry, Janet K Snell-Bergeon, Cora E Lewis, Alain G Bertoni, David C Goff, Jingzhong Ding
Journal: Circulation (2015)

Pericardial adipose tissue (PAT) is ectopic fat deep (epicardial adipose tissue) and superficial (paracardial adipose tissue) to the pericardium of the heart. PAT has been cross-sectionally associated with diabetes, but the association with development of diabetes is unclear. Using data from the Multi-Ethnic Study of Atherosclerosis (MESA), we tested whether PAT at baseline was associated with incident diabetes over nearly 10 years of follow-up. The baseline visit (visit 1) was conducted between 2000-2002. Four follow-up visits were conducted at 2 year intervals with visit 5 between 2010 and 2012. Diabetes was defined as a fasting glucose ≥126 mg/dl or the use of antidiabetic medication. Diabetes-free participants at baseline were followed for incident diabetes at any subsequent visit (visits 2-5). Volume of PAT was measured from computed tomographic (CT) scans taken at visits 1 - 4. CT scans were completed on all participants at baseline. Repeat scans were performed on random halves at visits 2 and 3, and a subset at visit 4. Multivariable Cox proportional hazards models were used to assess the association between PAT and incident diabetes. The figure presents the mean PAT by visit and the mean PAT at baseline among those without diabetes at any time during the study period and those that develop diabetes over the 10 years of follow-up. In Cox regression models adjusted for age, race, and sex, each SD increment of baseline PAT (42.0 mL) was associated with a hazard ratio (HR) for incident diabetes of 1.6 (95% CI 1.5-1.7, p&lt;0.0001). After adjusting for baseline BMI and waist-to-hip ratio, the HR was attenuated somewhat, but remained significant: HR 1.3 (95% CI 1.2-1.4, p&lt;0.0001). Addition of waist circumference to the model did not alter PAT results further. We found that PAT was highly stable over time, accumulating very slowly. Its baseline value strongly predicts incident diabetes independent of overall body mass and central fatness.
Allogeneic bone marrow transplantation for patients with high-risk acute lymphoblastic leukemia.
Authors: J R Wingard, S Piantadosi, G W Santos, R Saral, H M Vriesendorp, A M Yeager, W H Burns, R F Ambinder, H G Braine, G Elfenbein
Journal: Journal of Clinical Oncology (1990)

Seventy-four consecutive patients with high-risk acute lymphoblastic leukemia (ALL) were given cyclophosphamide (CY; 50 mg/kg on each of 4 days) plus total body irradiation (TBI; 300 rad on each of 4 days) followed by a human leukocyte antigen (HLA)-identical allogeneic bone marrow transplant (BMT). Eighteen patients in first complete remission (CR1), 36 in CR2, 16 in CR3, and four in CR4 were transplanted. Patients in CR1 were transplanted 1 to 8 months (median, 3 months) after attaining CR. All 18 patients in CR1 had one or more poor risk factors: age more than 18 (N = 17), initial leukocyte count greater than or equal to 20,000 (N = 11), Ph 1 chromosome (N = 2), delay in attaining CR more than 6 weeks (N = 8), or extramedullary disease (N = 1). Of those transplanted in CR2, 72% had relapsed on therapy. The 5-year event-free survival (EFS) rates for patients transplanted in CR1, CR2, and CR3 are 42%, 43%, and 25%, respectively, at median follow-up times of 57, 54, and 72 months, respectively. Children aged less than 18 years transplanted in CR2 have a 5-year EFS rate of 54%. All CR4 patients died early after transplant. The actuarial probability of relapse is 20%, 26%, and 48% for those transplanted in CR1, CR2, and CR3, respectively. Although there was substantial transplant-associated mortality, it decreased over the decade of the study (P = .01). This study indicates that BMT offers an attractive alternative to postremission chemotherapy in patients in CR1 with poor prognostic factors and in patients in second remission.