tbuckley/cabot-search huggingface dataset:
ArchAlign: Coordinate-free chromatin alignment reveals novel architectures
Authors: William KM Lai, Michael J Buck
Journal: Genome biology (2010)

Abstract To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. ArchAlign is freely available at http://www.acsu.buffalo.edu/~mjbuck/ArchAlign.html .
Statin and the risk of hepatocellular carcinoma and death in a hospital-based hepatitis B-infected population: A propensity score landmark analysis
Authors: John Chen Hsiang, Grace Lai-Hung Wong, Yee-Kit Tse, Vincent Wai-Sun Wong, Terry Cheuk-Fung Yip, Henry Lik-Yuen Chan
Journal: Journal of Hepatology (2015)
Measuring sociosexuality across people and nations: Revisiting the strengths and weaknesses of cross-cultural sex research
Authors: David P. Schmitt
Journal: Behavioral and Brain Sciences (2005)

My response to the commentaries highlights three main points. First, the Sociosexual Orientation Inventory (SOI) has demonstrated adequate reliability and validity across dozens of studies, and it deserves its reputation as a useful measure of basic human mating strategies. Second, the sampling limitations of the International Sexuality Description Project (ISDP) do not negate the conclusion that sex differences in sociosexuality are likely universal across cultures. Third, the ISDP results support several theories of human sexuality, although some are based on faulty assumptions that render them less viable than others.
Effect of altered bathing pH on calcium activated force in toxin permeabilised rat portal vein and human umbilical artery
Authors: C. A Crichton, A. G B Templeton, G. L Smith
Journal: Cardiovascular Research (1994)

Journal Article Effect of altered bathing pH on calcium activated force in α toxin permeabilised rat portal vein and human umbilical artery Get access Catherine A Crichton, Catherine A Crichton Institute of Physiology, Glasgow University, Glasgow G12 8QQ, United Kingdom: C A Crichton, A G B Templeton, G L Smith. Correspondence to Dr Crichton. Search for other works by this author on: Oxford Academic PubMed Google Scholar Alison G B Templeton, Alison G B Templeton Institute of Physiology, Glasgow University, Glasgow G12 8QQ, United Kingdom: C A Crichton, A G B Templeton, G L Smith. Search for other works by this author on: Oxford Academic PubMed Google Scholar Godfrey L Smith Godfrey L Smith Institute of Physiology, Glasgow University, Glasgow G12 8QQ, United Kingdom: C A Crichton, A G B Templeton, G L Smith. Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 28, Issue 9, September 1994, Pages 1378–1384, https://doi.org/10.1093/cvr/28.9.1378 Published: 01 September 1994 Article history Received: 03 February 1994 Accepted: 31 May 1994 Published: 01 September 1994
No Effect of Depression on [<sup>15</sup>O]H<sub>2</sub>O PET Response to Intravenous<i>d</i>-Fenfluramine
Authors: Jeffrey H. Meyer, Sidney Kennedy, Gregory M. Brown
Journal: American Journal of Psychiatry (1998)

Subnormal prolactin responses to the serotonin-releasing agonist fenfluramine occur in depression. Since many measures of serotonin pathology occur in depression, abnormal responses to fenfluramine may occur in brain structures other than the hypothalamic-pituitary axis. One study compared six depressed and six healthy subjects' responses to oral d,l-fenfluramine by assessing [18F]fluorodeoxyglucose uptake as detected by positron emission tomography (PET). That study showed several abnormalities within the cortex, and the authors concluded that low responsivity to d,l-fenfluramine is widespread in depression. In this study abnormalities in regional neuromodulation by serotonin in major depression were assessed with intravenous d-fenfluramine and [(15)O]H2O PET.Changes in regional cerebral blood flow (CBF) were detected by using [(15)O]H2O PET after administration of intravenous d-fenfluramine to 13 depressed and 18 healthy women. The PET scans were done 20 and 5 minutes before and 20 and 35 minutes after d-fenfluramine administration. Differences between the depressed and healthy groups in change in regional CBF (mean postfenfluramine minus mean prefenfluramine) were analyzed by using statistical parametric mapping.There were no significant differences between depressed and healthy subjects; in fact, changes in regional CBF after intravenous d-fenfluramine were remarkably similar.Degrees of neuronal responsivity to d-fenfluramine are similar in depressed and healthy subjects. Differences between the previous and current findings may be accounted for by greater specificity of intravenous d-fenfluramine to serotonin release, timing of scans, paucity of suicidal subjects in the current study, or greater variance in regional CBF from direct vascular effects of serotonin.
Surgery in patients receiving anti-tumour necrosis factor treatment in rheumatoid arthritis: an observational study on 50 surgical procedures
Authors: D Wendling
Journal: Annals of the Rheumatic Diseases (2005)

This case illustrates the usefulness of a therapeutic trial of colchicine monitored objectively by frequent acute phase protein measurements in patients with undiagnosed periodic fever syndromes.It also raises the possibility that a low threshold for analysing the FMF gene might disclose a wider spectrum of associated disease.
Genomic Classifier Identifies Men With Adverse Pathology After Radical Prostatectomy Who Benefit From Adjuvant Radiation Therapy
Authors: Robert B. Den, Kasra Yousefi, Edouard J. Trabulsi, Firas Abdollah, Voleak Choeurng, Felix Y. Feng, Adam P. Dicker, Costas D. Lallas, Leonard G. Gomella, Elai Davicioni, R. Jeffrey Karnes
Journal: Journal of Clinical Oncology (2015)

The optimal timing of postoperative radiotherapy (RT) after radical prostatectomy (RP) is unclear. We hypothesized that a genomic classifier (GC) would provide prognostic and predictive insight into the development of clinical metastases in men receiving post-RP RT and inform decision making.
Kinship terms are not kinship
Authors: Maurice Bloch
Journal: Behavioral and Brain Sciences (2010)

Abstract The target paper claims to contribute to the conceptualisation of kinship but is, in fact, only concerned with descriptive kinship terminologies. It uses Optimal Theory to analyse this vocabulary but it is not clear if this is to be understood as a psychological phenomenon. Jones does not make clear how this special vocabulary might relate to kinship in general.
Malignant pleural mesothelioma from nonoccupational asbestos exposure in Metsovo (north-west Greece): slow end of an epidemic?
Authors: K Sakellariou, V Malamou-Mitsi, A Haritou, C Koumpaniou, C Stachouli, ID Dimoliatis, SH Constantopoulos
Journal: European Respiratory Journal (1996)

Inhabitants of the Metsovo area, north-west Greece have been exposed since childhood to inhalation of asbestos, from a material containing tremolite, used for whitewashing ("luto soil"). This has resulted in endemic pleural calcifications (47% of adult population) and increased incidence of malignant pleural mesothelioma (MPM). In 1987, we reported that the incidence of MPM between 1981-1985 was around 300 times higher than expected in a nonasbestos exposed population (seven cases in 5 yrs in a population of 4,000-5,000). The present study is an updated report regarding this "mesothelioma epidemic", in conjunction with the diminished use and final abandonment of "luto soil" in the early 1980s. It appears that the incidence of MPM in Metsovo has dropped considerably since our first report. Between 1985-1994, we diagnosed six such cases (incidence rate = 1.4 cases per 10,000 person-years), whilst between 1980-1984 eight cases had been diagnosed (incidence rate = 3.7 cases per 10,000 person-years). Although, because of the small number of cases, this did not reach statistical significance (p = 0.08), we note that the incidence is now considerably lower than before. Had it remained unchanged, we would have expected 17 cases of MPM instead of six. This drop follows the diminished use of "luto" whitewash (by 92% of the population in 1950 and only 18% in 1980). If we take into account a 30-40 year latency period for mesothelioma, we expect that the "Metsovo mesothelioma epidemic" will fade away by the year 2020-2030, since the material has not been used since 1985.
Maintenance, reduction, or withdrawal of etanercept after treatment with etanercept and methotrexate in patients with moderate rheumatoid arthritis (PRESERVE): a randomised controlled trial
Authors: Josef S Smolen, Peter Nash, Patrick Durez, Stephen Hall, Elena Ilivanova, Fedra Irazoque-Palazuelos, Pedro Miranda, Min-Chan Park, Karel Pavelka, Ronald Pedersen, Annette Szumski, Constance Hammond, Andrew S Koenig, Bonnie Vlahos
Journal: The Lancet (2013)
Mammary-Derived Growth Inhibitor Alters Traffic of EGFR and Induces a Novel Form of Cetuximab Resistance
Authors: Jonna Nevo, Elina Mattila, Teijo Pellinen, Daniel L. Yamamoto, Henri Sara, Kristiina Iljin, Olli Kallioniemi, Petri Bono, Päivi Heikkilä, Heikki Joensuu, Anni Wärri, Johanna Ivaska
Journal: Clinical Cancer Research (2009)

Abstract Purpose: Only few predictive factors for the clinical activity of anti–epidermal growth factor receptor (EGFR) therapy are available. Mammary-derived growth inhibitor (MDGI) is a small cytosolic protein suggested to play a role in the differentiation of epithelial cells. Here, we have investigated the effect of MDGI expression on the EGFR signaling and cetuximab responsiveness of cancer cells. Experimental Design: MDGI mRNA expression was investigated in clinical breast and lung cancer samples and in nontransformed and malignant cell lines. The effect of ectopic expression of MDGI on EGFR, ErbB2, and integrin function and traffic was investigated in breast and lung cancer cell lines using multiple methods. The effect of anti-EGFR agents on these cells were tested by cell proliferation measurements and by assessing tumor growth of breast cancer cells in cetuximab treated and control athymic nude mice. Results: Here, we show that although MDGI is absent in cultured cell lines because of epigenetic silencing, MDGI mRNA is expressed in 40% of clinical breast carcinomas and 85% of lung cancers. Ectopic expression of MDGI rendered breast and lung cancer cells resistant to the anti-EGFR antibody cetuximab in vitro and in an orthotopic breast cancer xenograft model in vivo. When expressed in cancer cells, MDGI induces intracellular accumulation of EGFR, but not ErbB2, and the internalized receptor is phosphorylated and not degraded. Conclusions: MDGI-driven inherent desensitization of cancer cells is a novel molecular mechanism for resistance to the anti-EGFR antibody therapy, and MDGI may be a biomarker for responsiveness to anti-EGFR antibody therapy.(Clin Cancer Res 2009;15(21):6570–81)
Differential Regulation of Estrogen Receptor α Expression in Breast Cancer Cells by Metastasis-Associated Protein 1
Authors: Hyun-Jin Kang, Min-Ho Lee, Hae-Lim Kang, Sung-Hye Kim, Jung-Ranh Ahn, Hyelin Na, Tae-Young Na, Yo Na Kim, Je Kyung Seong, Mi-Ock Lee
Journal: Cancer Research (2014)

Metastasis-associated protein 1 (MTA1) is a component of the nucleosome remodeling and histone deacetylase (HDAC) complex, which plays an important role in progression of breast cancer. Although MTA1 is known as a repressor of the transactivation function of estrogen receptor α (ERα), its involvement in the epigenetic control of transcription of the ERα gene ESR1 has not been studied. Here, we show that silencing of MTA1 reduced the level of expression of ERα in ERα-positive cells but increased it in ERα-negative cells. In both MCF7 and MDA-MB-231, MTA1 was recruited to the region +146 to +461 bp downstream of the transcription start site of ESR1 (ERpro315). Proteomics analysis of the MTA1 complex that was pulled down by an oligonucleotide encoding ERpro315 revealed that the transcription factor AP-2γ (TFAP2C) and the IFN-γ-inducible protein 16 (IFI16) were components of the complex. Interestingly, in MCF7, TFAP2C activated the reporter encoding ERpro315 and the level of ERα mRNA. By contrast, in MDA-MB-231, IFI16 repressed the promoter activity and silencing of MTA1 increased expression of ERα. Importantly, class II HDACs are involved in the MTA1-mediated differential regulation of ERα. Finally, an MDA-MB-231-derived cell line that stably expressed shIFI16 or shMTA1 was more susceptible to tamoxifen-induced growth inhibition in in vitro and in vivo experiments. Taken together, our findings suggest that the MTA1-TFAP2C or the MTA1-IFI16 complex may contribute to the epigenetic regulation of ESR1 expression in breast cancer and may determine the chemosensitivity of tumors to tamoxifen therapy in patients with breast cancer.
Pleurodesis outcome in malignant pleural mesothelioma: Table 1
Authors: Edward Thomas Hamilton Fysh, Sze Khen Tan, Catherine Ann Read, Felicity Lee, Kate McKenzie, Nola Olsen, Indunil Weerasena, Timothy Threlfall, Nicholas de Klerk, A William Musk, Y C Gary Lee
Journal: Thorax (2013)

Few data exist on the pleurodesis outcome in patients with malignant pleural mesothelioma (MPM). A retrospective review of the Western Australian Mesothelioma Registry over 5 years revealed 390 evaluable patients. Only a subset of patients (42.3%) underwent pleurodesis, surgically (n=78) or by bedside instillation of sclerosants (n=87). Surgical pleurodesis showed no advantages over bedside pleurodesis in efficacy (32% vs 31% failures requiring further drainage, p=0.98), patient survival (p=0.52) or total time spent in hospital from procedure till death (p=0.36). No clinical, biochemical or radiographic parameters tested adequately predict pleurodesis outcome.
Prediction of relapse after discontinuation of infliximab therapy in severe sarcoidosis
Authors: Adriane D.M. Vorselaars, Anouk Verwoerd, Coline H.M. van Moorsel, Ruth G.M. Keijsers, Ger T. Rijkers, Jan C. Grutters
Journal: European Respiratory Journal (2013)

Infliximab is effective as a third-line therapeutic for severe sarcoidosis; however, long-term efficacy is unknown. The aim of this study was to assess the relapse rate after discontinuation of infliximab in sarcoidosis patients and predict relapse by analysis of the activity marker soluble interleukin (IL)-2 receptor (sIL-2R) and maximum standardised uptake value (SUVmax) of (18)F-fluorodeoxyglucose positron emission tomography (FDG PET). In this retrospective cohort study, the proportion of relapse was analysed using the Kaplan-Meier method and predicting factors were studied using Cox regression. 47 sarcoidosis patients who started infliximab therapy were included in the risk analysis. Kaplan-Meier analysis revealed a median time to relapse of 11.1 months and showed that 25% of the cohort relapsed within 4 months. Both mediastinal SUVmax ≥ 6.0 on FDG PET (hazard ratio 3.77, p<0.001) and serum sIL-2R ≥ 4000 pg · mL(-1) (hazard ratio 2.24, p=0.033) at start of therapy predicted relapse. In multivariate analysis, a mediastinal SUVmax ≥ 6.0 at initiation of therapy was an independent predictor of relapse (hazard ratio 4.33, p<0.001). The majority of patients that discontinued infliximab therapy relapsed. High serum sIL-2R and high SUVmax on FDG PET at initiation of therapy were significant predictors of relapse. These results suggest close monitoring of patients in this category when they discontinue infliximab treatment.
Search for Group-Specific Antibodies of Avian Leukosis Virus in Human Leukemic Sera&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;
Authors: Frieda K. Roth, Robert M. Dougherty
Journal: JNCI Journal of the National Cancer Institute (1971)

Agar-gel precipitin and complement-fixation tests were used in a search for group-specific (gs) antibodies of avian leukosis virus (ALV) in 101 sera from leukemic patients. Although 7 human sera reacted immunologically with the virus-infected, chicken tissue-culture extracts that served as antigen, the antibodies proved to be against chicken antigens and not viral antigens. Thus there was no evidence of ALV gs antibodies in any human sera tested.
A New Central Scaffold for Metastasis: Parsing HEF1/Cas-L/NEDD9
Authors: Geraldine M. O'Neill, Sachiko Seo, Ilya G. Serebriiskii, Stuart R. Lessin, Erica A. Golemis
Journal: Cancer Research (2007)

Abstract Greater understanding of metastasis is required to improve cancer treatment outcomes. Recently, changes in expression of the scaffold protein HEF1/CAS-L/NEDD9 were found to be a potent prometastatic stimulus in melanoma and other cancers. Mechanistic studies suggest diverse cellular roles of HEF1 and highlight its importance in the response to extracellular cues that drive invasion and metastasis. As a metastatic “hub” for signaling in cancer, HEF1 may provide a useful target for drug discovery efforts. [Cancer Res 2007;67(19):8975–9]
Relevance of intraocular involvement in the management of primary central nervous system lymphomas
Authors: A.J.M. Ferreri, J.-Y. Blay, M. Reni, F. Pasini, A. Gubkin, U. Tirelli, A. Calderoni, E. Zucca, S. Cortelazzo, C. Chassagne, M. Tinguely, B. Borisch, F. Berger, M. Ponzoni, F. Cavalli
Journal: Annals of Oncology (2002)
Why Do We Eat? A Neural Systems Approach
Authors: Allen S. Levine, Charles J. Billington
Journal: Annual Review of Nutrition (1997)

▪ Abstract Neuroregulators found at various brain sites are involved in controlling food intake, a behavior that occurs for many reasons. Different neuroregulators may affect different stimuli that impact eating behavior. For example, neuropeptide Y may initiate feeding for energy needs, opioid peptides may provide the rewarding aspects of eating, and corticotropin releasing factor may affect stress-induced eating. We know that the neural networks regulating feeding also impact other components of energy balance. Neuropeptide Y not only increases eating, it also decreases energy expenditure in brown fat and increases enzymatic activity associated with fat storage in white fat, resulting in a more obese animal. What the sites of action are of these neuroregulators and how they interact with regulators at other sites are of utmost importance. Different regions of the brain, together with the periphery, communicate via signals acting in coordinated fashion, which leads to the final outcome: eating less or more and expending less or more energy.
Colorectal Cancer Models with Intrinsic Bevacizumab Resistance Show Strong Autocrine Hif-Vegf-Pvegfr Signaling and are Sensitive to Nintedanib
Authors: Paul Mésange, Virginie Poindessous, Aude Battistella, Sylvie Dumont, Fathia Merabtene, Aimery De Gramont, Annette Larsen
Journal: Annals of Oncology (2013)
Relationship Between Cardiac Output and Peripheral Resistance in Borderline Hypertension
Authors: STEVO JULIUS, ARTURO V. PASCUAL, RUNE SANNERSTEDT, CHARLES MITCHELL
Journal: Circulation (1971)

Eighty-eight observations on 77 patients with borderline hypertension and 82 single observations in healthy control subjects are reported. Hemodynamic effects of assumption of the sitting position, mild exercise, infusion of dextran, blockade with propranolol and with a combination of propranolol and atropine are evaluated. In the recumbent position, patients with borderline hypertension have increased cardiac output and "normal" peripheral resistance. Under all other experimental conditions, the peripheral resistance in patients with borderline hypertension was elevated. Increased resistance was accompanied by a decrease of the cardiac output. After administration of the atropine and propranolol combination, cardiac output in patients with borderline hypertension was significantly below the normal. Nevertheless, whether cardiac output was high or low and resistance normal or elevated, patients with borderline hypertension maintained mild elevations of the blood pressure. Consequently, borderline hypertension is not caused solely by elevations of cardiac output.
Epidemiology and outcome of cardiac arrests reported in the lay-press: an observational study
Authors: Richard A Field, Jasmeet Soar, Jerry P Nolan, Gavin D Perkins
Journal: Journal of the Royal Society of Medicine (2011)

The aims of this study were to evaluate the frequency with which cardiac arrests are reported in newspapers, assess the level of detail reported and ascertain whether this coverage gives a realistic portrayal of cardiac arrest outcomes to the lay-reader.Observational study.All UK newspaper articles published between 1 January 2010 and 30 June 2010.Articles containing the words 'cardiac arrest', 'CPR' or 'resuscitation' were screen for eligibility. Any articles not involving reference to a real cardiac arrest were excluded.Data relating to patient demographics, arrest characteristics, treatment (CPR and defibrillation) and survival using the Utstein template were extracted. The results were then compared with cardiac arrest statistics from epidemiological studies.Six hundred and forty-eight articles were reviewed, 203 of which referred to individual cardiac arrest events; 22 events occurred in-hospital and 181 occurred out-of-hospital. In the out-of-hospital cardiac arrest (OHCA) group 32 (17.7%) were reported to survive to hospital discharge, almost all with good neurological outcome. The median age group was 31-45-year-olds, 52 (28.7%) were women and 40 were children. Seventy-five percent of victims received bystander CPR with 13 being attended to by lay-responders using AEDs, eight of which presented with a shockable rhythm of which six made a full recovery.Survival to hospital discharge rate among newspaper reports was double that of complete epidemiological studies of OHCAs in urban environments. Newspapers may give readers an over-optimistic portrayal of cardiac arrest survival and neurological outcome following successful resuscitation.
FGFR3 Is Overexpressed Waldenström Macroglobulinemia and Its Inhibition by Dovitinib Induces Apoptosis and Overcomes Stroma-Induced Proliferation
Authors: Abdel Kareem Azab, Feda Azab, Phong Quang, Patricia Maiso, Antonio Sacco, Hai T. Ngo, Yang Liu, Yong Zhang, Brittany L. Morgan, Aldo M. Roccaro, Irene M. Ghobrial
Journal: Clinical Cancer Research (2011)

There is no standard of therapy for the treatment of Waldenström macroglobulinemia (WM), therefore there is a need for the development of new agents. Fibroblast growth factor receptor 3 (FGFR3) was shown to play a major role in several types in cancer. Dovitinib, an inhibitor of FGFR3, was effective in hematologic malignancies. In this study, we tested FGFR3 as a therapeutic target in WM and tested the effect of dovitinib on cell proliferation and apoptosis of WM cells in the context of BM microenvironment.The expression of FGFR3 in WM cells was tested using immunofluorescence and flow cytometry. Cell signaling in response to stimulation with FGF3 and stromal cells, and its inhibition by dovitinib was performed using immunoblotting. Cell survival and cell proliferation were assessed by MTT and BrdU assays. Apoptosis was measured by detection of APO-2.7 and cleavage of caspase-3 using flow cytometry. Cell cycle was performed by PI staining of cells and flow cytometry. The combinatory effect of dovitinib with other drugs was analyzed using Calcusyn software. The effect of dovitinib was tested in vivo.FGFR3 was overexpressed in WM cells and its activation induced cell proliferation. Inhibition of FGFR3 with dovitinib decreased cell survival, increased apoptosis, and induced cell cycle arrest. Inhibition of FGFR3 by dovitinib reduced the interaction of WM to bone marrow components, and reversed its proliferative effect. Dovitinib had an additive effect with other drugs. Moreover, dovitinib reduced WM tumor progression in vivo.We report that FGFR3 is a novel therapeutic target in WM, and suggest dovitinib for future clinical trial the treatment of patients with WM.