tbuckley/cabot-search huggingface dataset:
A first-draft human protein-interaction map.
Authors: Ben Lehner, Andrew G Fraser
Journal: Genome biology (2004)

Protein-interaction maps are powerful tools for suggesting the cellular functions of genes. Although large-scale protein-interaction maps have been generated for several invertebrate species, projects of a similar scale have not yet been described for any mammal. Because many physical interactions are conserved between species, it should be possible to infer information about human protein interactions (and hence protein function) using model organism protein-interaction datasets.Here we describe a network of over 70,000 predicted physical interactions between around 6,200 human proteins generated using the data from lower eukaryotic protein-interaction maps. The physiological relevance of this network is supported by its ability to preferentially connect human proteins that share the same functional annotations, and we show how the network can be used to successfully predict the functions of human proteins. We find that combining interaction datasets from a single organism (but generated using independent assays) and combining interaction datasets from two organisms (but generated using the same assay) are both very effective ways of further improving the accuracy of protein-interaction maps.The complete network predicts interactions for a third of human genes, including 448 human disease genes and 1,482 genes of unknown function, and so provides a rich framework for biomedical research.
Long-Term Exposure to Traffic Emissions and Fine Particulate Matter and Lung Function Decline in the Framingham Heart Study
Authors: Mary B. Rice, Petter L. Ljungman, Elissa H. Wilker, Kirsten S. Dorans, Diane R. Gold, Joel Schwartz, Petros Koutrakis, George R. Washko, George T. O’Connor, Murray A. Mittleman
Journal: American Journal of Respiratory and Critical Care Medicine (2015)

Few studies have examined associations between long-term exposure to fine particulate matter (PM2.5) and lung function decline in adults.To determine if exposure to traffic and PM2.5 is associated with longitudinal changes in lung function in a population-based cohort in the Northeastern United States, where pollution levels are relatively low.FEV1 and FVC were measured up to two times between 1995 and 2011 among 6,339 participants of the Framingham Offspring or Third Generation studies. We tested associations between residential proximity to a major roadway and PM2.5 exposure in 2001 (estimated by a land-use model using satellite measurements of aerosol optical thickness) and lung function. We examined differences in average lung function using mixed-effects models and differences in lung function decline using linear regression models. Current smokers were excluded. Models were adjusted for age, sex, height, weight, pack-years, socioeconomic status indicators, cohort, time, season, and weather.Living less than 100 m from a major roadway was associated with a 23.2 ml (95% confidence interval [CI], -44.4 to -1.9) lower FEV1 and a 5.0 ml/yr (95% CI, -9.0 to -0.9) faster decline in FEV1 compared with more than 400 m. Each 2 μg/m(3) increase in average of PM2.5 was associated with a 13.5 ml (95% CI, -26.6 to -0.3) lower FEV1 and a 2.1 ml/yr (95% CI, -4.1 to -0.2) faster decline in FEV1. There were similar associations with FVC. Associations with FEV1/FVC ratio were weak or absent.Long-term exposure to traffic and PM2.5, at relatively low levels, was associated with lower FEV1 and FVC and an accelerated rate of lung function decline.
Age, Thymopoiesis, and CD4+ T-Lymphocyte Regeneration after Intensive Chemotherapy
Authors: Crystal L. Mackall, Thomas A. Fleisher, Margaret R. Brown, Mary P. Andrich, Clara C. Chen, Irwin M. Feuerstein, Marc E. Horowitz, Ian T. Magrath, Aziza T. Shad, Seth M. Steinberg, Leonard H. Wexler, Ronald E. Gress
Journal: New England Journal of Medicine (1995)

Inadequate reconstitution of CD4+ T lymphocytes is an important clinical problem complicating chemotherapy, human immunodeficiency virus infection, and bone marrow transplantation, but relatively little is known about how CD4+ T lymphocytes regenerate. There are two main possibilities: bone marrow-derived progenitors could reconstitute the lymphocyte population using a thymus-dependent pathway, or thymus-independent pathways could predominate. Previous studies have suggested that the CD45RA glycoprotein on CD4+ T lymphocytes is a marker for progeny generated by a thymus-dependent pathway.We studied 15 patients 1 to 24 years of age who had undergone intensive chemotherapy for cancer. The absolute numbers of CD4+ T lymphocytes in peripheral blood and the expression of CD45 isoforms (CD45RA and CD45RO) on these lymphocytes were studied serially during lymphocyte regeneration after the completion of therapy. Radiographic imaging of the thymus was performed concomitantly.There was an inverse relation between the patients' ages and the CD4+ T-lymphocyte counts six months after therapy was completed (r = -0.92). The CD4+ recovery correlated quantitatively with the appearance of CD45RA+CD4+ T lymphocytes in the blood (r = 0.64). There was a higher proportion of CD45RA+CD4+ T lymphocytes in patients with thymic enlargement after chemotherapy than in patients without such enlargement (two-sided P = 0.015).Thymus-dependent regeneration of CD4+ T lymphocytes occurs primarily in children, whereas even young adults have deficiencies in this pathway. Our results suggest that rapid T-cell regeneration requires residual thymic function in patients receiving high-dose chemotherapy.
Residents’ perspectives on dermatology training in Dutch university medical centres in 2006
Authors: W.H.P.M. Vissers, T. van Meurs, W.F.M. Goldschmidt, R.P.M. Ceulen, Y. Assen, N. Kuck, P. Nijboer, M. de Waard
Journal: British Journal of Dermatology (2008)

Journal Article Residents' perspectives on dermatology training in Dutch university medical centres in 2006 Get access W.H.P.M. Vissers, W.H.P.M. Vissers Department of Dermatology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, NL‐6500 HB Nijmegen, the Netherlands Search for other works by this author on: Oxford Academic Google Scholar T. Van Meurs, T. Van Meurs Free University Medical Centre, Amsterdam, the Netherlands Search for other works by this author on: Oxford Academic Google Scholar W.F.M. Goldschmidt, W.F.M. Goldschmidt Academic Medical Centre, Amsterdam, the Netherlands Search for other works by this author on: Oxford Academic Google Scholar R.P.M. Ceulen, R.P.M. Ceulen University Medical Centre, Maastricht, the Netherlands Search for other works by this author on: Oxford Academic Google Scholar Y. Assen, Y. Assen Erasmus Medical Centre, Rotterdam, the Netherlands Search for other works by this author on: Oxford Academic Google Scholar N. Kuck, N. Kuck Department of Dermatology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, NL‐6500 HB Nijmegen, the Netherlands Search for other works by this author on: Oxford Academic Google Scholar P. Nijboer, P. Nijboer University Medical Centre, Leiden, the Netherlands Search for other works by this author on: Oxford Academic Google Scholar M. De Waard M. De Waard University Medical Centre, Groningen, the Netherlands E‐mail: w.vissers@derma.umcn.nl Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 159, Issue 3, 1 September 2008, Pages 736–738, https://doi.org/10.1111/j.1365-2133.2008.08691.x Published: 01 September 2008
Effects of increasing afterload on left ventricular output in fetal lambs.
Authors: J Hawkins, G F Van Hare, K G Schmidt, A M Rudolph
Journal: Circulation Research (1989)

Fetal ventricular performance has been considered limited because ventricular output does not increase with rapid volume expansion above mean left atrial pressures (mLAPs) of 5-7 mm Hg. To explore relations between preload, afterload, and stroke volume (SV) in the fetal left ventricle, we instrumented 126-129 days gestation fetal lambs with ascending aortic electromagnetic flow transducers, vascular catheters, and inflatable occluders around the aortic isthmus (n = 8) or descending aorta (n = 7). At 24-48 hours after surgery, blood was withdrawn or infused to reach various mLAPs. The aorta was then slowly occluded as aortic flow and mean arterial pressure (MAP) were measured continuously. Isthmus constriction produced linear decreases in SV as MAP increased; mLAP was unchanged. Descending aortic constriction produced no decrease in SV until high MAPs were reached. SV decreased as MAP increased further, and mLAP rose significantly. The curve relating mLAP and SV before constriction showed little increase in SV above mLAPs of 5-7 mm Hg; however, when curves were derived relating SV and mLAP at relatively constant MAPs, SV continued to increase even above an mLAP of 8-10 mm Hg. Our studies indicate that the fetal left ventricle responds to progressive increases in mLAP to at least 10 mm Hg. The lack of increase in SV above an mLAP of 5-7 mm Hg with rapid volume expansion is related to the concomitant increase in MAP and afterload.
Radiotherapy is unnecessary in elderly patients with localized agressive non Hodgkin's lymphoma: results of the LNH 93-4 study
Authors: Christophe Bonnet, Georges Fillet, N. Mounier, C. Thieblemont, C. Fermé, B. Quesnel, C. Martin, M. Blanc, Th. Conroy, A.M. Penny, T. Petrella, F. Reyes
Journal: Blood (2002)
Combining Human and Rat Sequences in Her-2 DNA Vaccines Blunts Immune Tolerance and Drives Antitumor Immunity
Authors: Jennifer B. Jacob, Elena Quaglino, Olga Radkevich-Brown, Richard F. Jones, Marie P. Piechocki, Joyce D. Reyes, Amy Weise, Augusto Amici, Wei-Zen Wei
Journal: Cancer Research (2010)

Abstract Immune tolerance to tumor-associated self-antigens poses a major challenge in the ability to mount an effective cancer vaccine response. To overcome immune tolerance to HER-2, we formulated DNA vaccines that express both human HER-2 and heterologous rat Neu sequences in separate plasmids or as single hybrid constructs that encode HER-2/Neu fusion proteins. Candidate vaccines were tested in Her-2 transgenic (Tg) mice of BALB/c (BALB), BALB/c × C57BL/6 F1 (F1), or C57BL/6 (B6) background, which exhibit decreasing immune responsiveness to HER-2. Analysis of various cocktails or hybrid vaccines defined a requirement for particular combination of HER/2/Neu sequences to effectively prime immune effector cells in HER-2 Tg mice. In B6 HER-2 Tg mice, rejection of HER-2–positive tumors protected mice from HER-2–negative tumors, providing evidence of epitope spreading. Our findings show that a strategy of combining heterologous antigen with self-antigens could produce a potent DNA vaccine that may be applicable to other tumor-associated antigens. Cancer Res; 70(1); 119–28
Ventilation parameters in asthmatic children after one week at 1400 meters altitude
Authors: Alessandro da Ponte, Annarita Tullio, Bruno Grassi, Mario Canciani
Journal: European Respiratory Journal (2012)

Introduction and background

Bronchial asthma prevalence is increasing. Many triggers are known but little about protective factors.

Aims and objectives

To find out whether 1400 meters altitude could modify ventilation parameters, NO (Nitric Oxide) concentration and clinical symptoms in 13 children after a week of uncontrolled physical activity.

Methods

Thirteen asthmatic children were evaluated at arrival and departure from a mountain resort for: FVC, FEV1, FEF 25-75 and exhaled NO concentration. Unscheduled physical activity were encouraged for eight hours daily.

Results

All the children showed improvement of FVC, FEV1, FEF 25-75.

View this table:

Main Ventilation Parameters and NO concentation





![Figure][1] 



![Figure][1] 



Conclusions: after a week permanence at 1400 meters resort all subjects showed an improvement in ventilation parameters, together with no episode of asthma exacerbations. This study suggests that physical activity in an healthy environment can be safe and feasible for asthmatic children.

 [1]: pending:yes
Control of Cell Divisions in the Nervous System: Symmetry and Asymmetry
Authors: Bingwei Lu, Lily Jan, Yuh-Nung Jan
Journal: Annual Review of Neuroscience (2000)

The diverse cell types in the nervous system are derived from neural progenitor cells. Neural progenitors can undergo symmetric divisions to expand cell population or asymmetric divisions to generate diverse cell types. Furthermore, neural progenitors must exit the cell cycle in a developmentally regulated manner to allow for terminal differentiation. The patterns of neural progenitor divisions have been characterized in vertebrates and invertebrates. During the course of nervous system development, extrinsic and intrinsic cues dictate the division patterns of neural progenitors by influencing their cell cycle behavior and cellular polarity. The identification in Drosophila of asymmetrically distributed fate determinants, adapter molecules, and polarity organizing molecules that participate in asymmetric neural progenitor divisions should provide points of entry for studying similar asymmetric divisions in vertebrates.
THE EFFECT OF LIVER REGENERATION ON TUMOR FORMATION IN RATS FED 4-DIMETHYLAMINOAZOBENZENE
Authors: André D. Glinos, Nancy L. R. Bucher, Joseph C. Aub
Journal: The Journal of Experimental Medicine (1951)

Partial hepatectomies were performed on five groups of rats which had been maintained on a diet containing 4-dimethylaminoazobenzene for various lengths of time. The effect of regeneration on the incidence of hepatic tumors was compared with that in similarly treated non-hepatectomized controls. Regeneration, and the time of exposure to the carcinogen as well, were relatively effective in accelerating the rate of appearance of tumors, although not markedly so. These factors were without effect on final total tumor formation. These findings support the concept that during chemical carcinogenesis tumor formation proceeds in stages.
Microbial Spectrum and Antibiotic Susceptibility Profile of Gram-Positive Aerobic Bacteria Isolated From Cancer Patients
Authors: Hossam M. Ashour, Amany El-Sharif
Journal: Journal of Clinical Oncology (2007)

Cancer patients are particularly susceptible to nosocomial infections because of their compromised immune system, and because of the nature of treatment practices they experience. Recently, a shift of the microbial spectrum of cancer patients from gram-negative to gram-positive has been demonstrated. This study analyzed the distribution and the antimicrobial resistance of gram-positive bacteria isolated from cancer patients in Egypt.We examined the microbial spectrum of gram-positive bacteria in patients with hematologic malignancies and solid tumors. In addition, we also studied the antimicrobial resistance of pathogens accounting for the majority of gram-positive infections in these cancer patients.Most of gram-positive isolates from urinary tract (100%), respiratory tract (89.7%), and bloodstream infections (BSIs; 65.5%) were obtained from leukemic patients. All gram-positive isolates from skin infections were isolated from solid-tumor patients. In both leukemic and solid-tumor patients, gram-positive bacteria causing nosocomial BSI were mainly Coagulase-negative staphylococcus (CNS) and S. aureus, whereas gram-positive bacteria causing nosocomial RTI were mainly alpha-hemolytic streptococci and CNS. Gram-positive bacteria were not isolated from GI tract infections. S. aureus, CNS, and alpha-hemolytic streptococci demonstrated methicillin resistance (81.5%, 92.3%, and 90% resistance, respectively). S. aureus and CNS were susceptible to linezolid (15.4% and 0% resistance, respectively), and vancomycin (15.5% and 11% resistance, respectively).This is the first study to report the emergence of vancomycin- and linezolid-resistant S. aureus in Egypt. Newer generation quinolones (moxifloxacin and gatifloxacin) were more active than older quinolones (ciprofloxacin and ofloxacin) against S. aureus and CNS, suggesting the use of newer generation quinolones in the prophylaxis of cancer patients.
PET imaging to non-invasively study immune activation leading to antitumor responses with a 4-1BB agonistic antibody
Authors: Helena Escuin-Ordinas, Mark W Elliott, Mohammad Atefi, Michelle Lee, Charles Ng, Liu Wei, Begoña Comin-Anduix, Encarnacion Montecino-Rodriguez, Earl Avramis, Caius Radu, Leslie L Sharp, Antoni Ribas
Journal: Journal for ImmunoTherapy of Cancer (2013)

<h3>Background</h3> Molecular imaging with positron emission tomography (PET) may allow the non-invasive study of the pharmacodynamic effects of agonistic monoclonal antibodies (mAb) to 4-1BB (CD137). 4-1BB is a member of the tumor necrosis factor family expressed on activated T cells and other immune cells, and activating 4-1BB antibodies are being tested for the treatment of patients with advanced cancers. <h3>Methods</h3> We studied the antitumor activity of 4-1BB mAb therapy using [<sup>18</sup> F]-labeled fluoro-2-deoxy-2-D-glucose ([<sup>18</sup> F]FDG) microPET scanning in a mouse model of colon cancer. Results of microPET imaging were correlated with morphological changes in tumors, draining lymph nodes as well as cell subset uptake of the metabolic PET tracer <i>in vitro</i>. <h3>Results</h3> The administration of 4-1BB mAb to Balb/c mice induced reproducible CT26 tumor regressions and improved survival; complete tumor shrinkage was achieved in the majority of mice. There was markedly increased [<sup>18</sup> F]FDG signal at the tumor site and draining lymph nodes. In a metabolic probe <i>in vitro</i> uptake assay, there was an 8-fold increase in uptake of [<sup>3</sup>H]DDG in leukocytes extracted from tumors and draining lymph nodes of mice treated with 4-1BB mAb compared to untreated mice, supporting the <i>in vivo</i> PET data. <h3>Conclusion</h3> Increased uptake of [<sup>18</sup> F]FDG by PET scans visualizes 4-1BB agonistic antibody-induced antitumor immune responses and can be used as a pharmacodynamic readout to guide the development of this class of antibodies in the clinic.
Upper airway and soft tissue anatomy in normal subjects and patients with sleep-disordered breathing. Significance of the lateral pharyngeal walls.
Authors: R J Schwab, K B Gupta, W B Gefter, L J Metzger, E A Hoffman, A I Pack
Journal: American Journal of Respiratory and Critical Care Medicine (1995)

The geometry and caliber of the upper airway in apneic patients differs from those in normal subjects. The apneic airway is smaller and is narrowed laterally. Examination of the soft tissue structures surrounding the upper airway can lead to an understanding of these apneic airway dimensional changes. Magnetic resonance imaging was utilized to study the upper airway and surrounding soft tissue structures in 21 normal subjects, 21 snorer/mild apneic subjects, and 26 patients with obstructive sleep apnea. The major findings of this investigation in the 68 subjects were as follows: (1) minimum airway area was significantly smaller in apneic compared with normal subjects and occurred in the retropalatal region; (2) airway narrowing in apneic patients was predominantly in the lateral dimension; there was no significant difference in the anterior-posterior (AP) airway dimension between subject groups; and (3) distance between the rami of the mandible was equal between subject groups, and thus the narrowing of the lateral dimension was not explained by differences in bony structure; (4) lateral airway narrowing was explained predominantly by larger pharyngeal walls in apneic patients (the parapharyngeal fat pads were not closer together as one would expect if the airway walls were compressed by fat); and (5) fat pad size at the level of the minimum airway was not greater in apneic than normal subjects. At the minimum airway area, thickness of the lateral pharyngeal muscular walls rather than enlargement of the parapharyngeal fat pads was the predominant anatomic factor causing airway narrowing in apneic subjects.
Concepts and categories: What is the evidence for neural specialisation?
Authors: Lorraine K. Tyler, Helen E. Moss
Journal: Behavioral and Brain Sciences (2001)

Humphreys and Forde argue that semantic memory is divided into separate substores for different kinds of information. However, the neuro-imaging results cited in support of this view are inconsistent and often methodologically and statistically unreliable. Our own data indicate no regional specialisation as a function of semantic category or domain and support instead a distributed unitary account.
Vaccine-induced tumor-specific immunity despite severe B-cell depletion in mantle cell lymphoma
Authors: Sattva S Neelapu, Larry W Kwak, Carol B Kobrin, Craig W Reynolds, John E Janik, Kieron Dunleavy, Therese White, Linda Harvey, Robin Pennington, Maryalice Stetler-Stevenson, Elaine S Jaffe, Seth M Steinberg, Ronald Gress, Fran Hakim, Wyndham H Wilson
Journal: Nature Medicine (2005)
Noninvasive monitoring of airway inflammation
Authors: H. Magnussen, F.E. Hargreave
Journal: European Respiratory Journal (2000)

The management of asthma relies, in large measure, on subjective evaluation of the frequency and severity of symptoms as well as on obtaining objective measurements of airway caliber such as peak expired flow rates (PEFR) or the forced expiratory volume in one second (FE'It). The objective measurements are important because of a lack of sensitivity in asthmatics' perception of airway narrowing, which may be worse in patients with longstanding asthma (1). Frequent assessment of both symptoms and flow rates is often needed because of the need to achieve optimal control of asthma with minimal treatment. A characteristic form of airway inflammation has also been recognized as necessary for the presence of symptomatic asthma. This inflammation consists of activated eosinophils, lymphocytes, and an increased number of mast cells, all of which have been described both in bronchoalveolar lavage (2-4) and airway biopsies from asthmatic subjects (5, 6), as well as characteristic structural changes of the airways (7-9). These inflammatory changes have been described in patients with stable asthma and those who have died from very severe asthma. However, until recently a non-invasive method was not available to evaluate whether an exacerbation of asthma symptoms was associated with increased numbers of activated inflammatory cells in the airways. Evaluating the severity of an exacerbation and the requirement for treatment with corticosteroids has relied on indirect indices to suggest that airway inflammation has worsened. These indices have included increased symptoms, demonstrated worsening airflow obstruction, increased variability of flow rates, and airway hyperresponsiveness.