tbuckley/cabot-search huggingface dataset:
Induced sputum in the diagnosis of childhood community-acquired pneumonia
Authors: E Lahti, V Peltola, M Waris, R Virkki, K Rantakokko-Jalava, J Jalava, E Eerola, O Ruuskanen
Journal: Thorax (2008)

<h3>Background:</h3> The usefulness of induced sputum in searching for causative agents of pneumonia in children has not been studied. <h3>Methods:</h3> The study involved 101 children, aged 6 months to 15 years, treated for community-acquired pneumonia at Turku University Hospital (Turku, Finland) from January 2006 to April 2007. Nasopharyngeal aspirate samples were first collected through both nostrils. Sputum production was then induced by inhalation of 5.0% hypertonic saline for 5–10 min and a sputum sample was either aspirated or expectorated. The presence and amount of bacteria and viruses in paired nasopharyngeal aspirate and sputum specimens was analysed and compared using semiquantitative bacterial culture and quantitative PCR techniques. <h3>Results:</h3> A good quality sputum specimen was obtained from 76 children. The possible causative agent was found in 90% of cases. <i>Streptococcus pneumoniae</i> (46%) and rhinovirus (29%) were the most common microbes detected. Newly discovered viruses human bocavirus and human metapneumovirus were detected in 18% and 13% of the children, respectively. One-quarter of all bacterial findings were only detected in sputum, and the amount of bacteria in the remainder of the sputum specimens compared with nasopharyngeal aspirate was higher in 14% and equal in 70%. The amount of rhinovirus in sputum was higher than in nasopharyngeal aspirate in 82%. <h3>Conclusions:</h3> Sputum induction provides good quality sputum specimens with high microbiological yield in children with community-acquired pneumonia. Induced sputum analysis can be useful in the microbiological diagnosis of childhood community-acquired pneumonia.
Clinical Lecture on a Case of Aneurism of the Arch of the Aorta Treated by Galvano-Puncture
Authors: H. C. Bastian
Journal: BMJ (1873)

you will find them soft and pliable for use over tender surfaces, and for cleansing deep wounds otherwvise difficult of access.You will expect me to tell you, more definitely than I have as yet, the extent to which you may look for healing of a wound by primary adhesion of its surfaces.You may, I believe, reckon upon obtaining this result whenever you can keep the surfaces which are to be united in accurate apposition; if this be impracticable, the wound must be filled uip by a process of granulation.If you consider the difficulty of getting, for example, the flaps of an amputation exactly applied, you will understand tlhat, although the entire margin of an amputation-wound Nvill unite at once, you cannot reasonably anticipate that the deeper parts of the wound, save in rare cases, will be healed, except by the gradual filling up of the interstices, which must here and there exist, by some process whiclh takes time, as by granulation, and during which process you are not unlikely to have some, although it may be but little, discharge of laudable pus.It is the necessity of leaving the parts at rest for the completion of this process which chiefly compels us to keep a patient in bed, after an amputation, for three weeks or longer, for it is not prudent to allow the parts to be in the least disturbed until the repair has become what we may term consolidated.At the end of this rest-period, any sutures which have been used (and I prefer after most operations the use of silver wire, as it is little irritaling and holds bletter than catgut, which is apt to give way under any strain) should be remnoved, unless for some reason it has been necessary to take them out at aa earlier period, and, in so doing, you should be careful, if wire have heen employed, after cutting eaclh one, to turn back the end distant from the twist, so that the rnetal may be withdrawn smoothly and with- out pain.Durin(-g a11 the progress of wound-healing, carbolised oil dressings mnay be continued.I have only once had trouble from their use, and that was in a case of excision of the knee, the boy apparently suffering constitutionally from the action of the acid upon the system ; at least, .we got on much better when the use of the acid was discontinued.But
Influence of Clinical Communication on Patients' Decision Making on Participation in Clinical Trials
Authors: Terrance L. Albrecht, Susan S. Eggly, Marci E.J. Gleason, Felicity W.K. Harper, Tanina S. Foster, Amy M. Peterson, Heather Orom, Louis A. Penner, John C. Ruckdeschel
Journal: Journal of Clinical Oncology (2008)

Purpose To investigate how communication among physicians, patients, and family/companions influences patients' decision making about participation in clinical trials. Patients and Methods We video recorded 235 outpatient interactions occurring among oncologists, patients, and family/companions (if present) at two comprehensive cancer centers. We combined interaction analysis of the real-time video-recorded observations (collected at Time 1) with patient self-reports (Time 2) to determine how communication about trial offers influenced accrual decisions. Results Clinical trials were explicitly offered in 20% of the interactions. When offers were made and patients perceived they were offered a trial, 75% of patients assented. Observed messages (at Time 1) directly related to patients' self-reports regarding their decisions (2 weeks later), and how they felt about their decisions and their physicians. Specifically, messages that help build a sense of an alliance (among all parties, including the family/companions), provide support (tangible assistance and reassurance about managing adverse effects), and provide medical content in language that patients and family/companions understand are associated with the patient's decision and decision-making process. Conclusion In two urban, National Cancer Institute–designated comprehensive cancer centers, a large percentage of patients are not offered trials. When offered a trial, most patients enroll. The quality and quantity of communication occurring among the oncologist, patient, and family/companion when trials are discussed matter in the patient's decision-making process. These findings can help increase physician awareness of the ways that messages and communication behaviors can be observed and evaluated to improve clinical practice and research.
Somatic Mutation of <b> <i>p53</i> </b> Leads to Estrogen Receptor α-Positive and -Negative Mouse Mammary Tumors with High Frequency of Metastasis
Authors: Suh-Chin J. Lin, Kuo-Fen Lee, Alexander Yu. Nikitin, Susan G. Hilsenbeck, Robert D. Cardiff, Aihua Li, Keon-Wook Kang, Steven A. Frank, Wen-Hwa Lee, Eva Y-H. P. Lee
Journal: Cancer Research (2004)

Approximately 70% of human breast cancers are estrogen receptor alpha (ERalpha)-positive, but the origins of ERalpha-positive and -negative tumors remain unclear. Hormonal regulation of mammary gland development in mice is similar to that in humans; however, most mouse models produce only ERalpha-negative tumors. In addition, these mouse tumors metastasize at a low rate relative to human breast tumors. We report here that somatic mutations of p53 in mouse mammary epithelial cells using the Cre/loxP system leads to ERalpha-positive and -negative tumors. p53 inactivation under a constitutive active WAPCre(c) in prepubertal/pubertal mice, but not under MMTVCre in adult mice, leads to the development of ERalpha-positive tumors, suggesting that target cells or developmental stages can determine ERalpha status in mammary tumors. Importantly, these tumors have a high rate of metastasis. An inverse relationship between the number of targeted cells and median tumor latency was also observed. Median tumor latency reaches a plateau when targeted cell numbers exceed 20%, implying the existence of saturation kinetics for breast carcinogenesis. Genetic alterations commonly observed in human breast cancer including c-myc amplification and Her2/Neu/erbB2 activation were seen in these mouse tumors. Thus, this tumor system reproduces many important features of human breast cancer and provides tools for the study of the origins of ERalpha-positive and -negative breast tumors in mice.
Event-Related fMRI of Frontotemporal Activity During Word Encoding and Recognition in Schizophrenia
Authors: J. Daniel Ragland, Ruben C. Gur, Jeffrey Valdez, Bruce I. Turetsky, Mark Elliott, Christian Kohler, Steve Siegel, Stephen Kanes, Raquel E. Gur
Journal: American Journal of Psychiatry (2004)

Neuropsychological studies have demonstrated verbal episodic memory deficits in schizophrenia during word encoding and retrieval. This study examined neural substrates of memory in an analysis that controlled for successful retrieval.Event-related blood-oxygen-level-dependent (BOLD) functional magnetic resonance imaging (fMRI) was used to measure brain activation during word encoding and recognition in 14 patients with schizophrenia and 15 healthy comparison subjects. An unbiased multiple linear regression procedure was used to model the BOLD response, and task effects were detected by contrasting the signal before and after stimulus onset.Patients attended during encoding and had unimpaired reaction times and normal response biases during recognition, but they had lower recognition discriminability scores, compared with the healthy subjects. Analysis of contrasts was restricted to correct items. Previous findings of a deficit in bilateral prefrontal cortex activation during encoding in patients were reproduced, but patients showed greater parahippocampal activation rather than deficits in temporal lobe activation. During recognition, left dorsolateral prefrontal cortex activation was lower in the patients and right anterior prefrontal cortex activation was preserved, as in the authors' previous study using positron emission tomography. Successful retrieval was associated with greater right dorsolateral prefrontal cortex activation in the comparison subjects, whereas orbitofrontal, superior frontal, mesial temporal, middle temporal, and inferior parietal regions were more active in the patients during successful retrieval.The pattern of prefrontal cortex underactivation and parahippocampal overactivation in the patients suggests that functional connectivity of dorsolateral prefrontal and temporal-limbic structures is disrupted by schizophrenia. This disruption may be reflected in the memory strategies of patients with schizophrenia, which include reliance on rote rehearsal rather than associative semantic processing.
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophilagenome
Authors: Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin, Susan E Celniker
Journal: Genome biology (2002)

It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined. We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences. Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone.
Biomarkers With a Mechanistic Focus
Authors: Daniel S. Pine, Ellen Leibenluft
Journal: JAMA Psychiatry (2015)

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Oral mucosal neuroma-medullary thyroid carcinoma syndrome
Authors: D. MURRAY WALKER
Journal: British Journal of Dermatology (1973)

A case history of the multiple mucosal neuroma-medullary thyroid carcinoma syndrome is reported. The diagnosis first suggested by neuromas confined to the oral cavity, led to evidence of clinically unsuspected residual thyroid tumour in a patient who had undergone total thyroidectomy. The opportunity for the clinician when confronted with such oral neuromas to initiate a search for a thyroid carcinoma is emphasized, since neuromas may precede this potentially fatal thyroid tumour by as much as 10 years.
THYMUS-DERIVED CELL (T CELL) ACTIVATION BY HETEROLOGOUS ANTIGENS AS A REPLACEMENT OF SPECIFIC IMMUNE T CELLS IN THE TRANSFER OF THE SECONDARY RESPONSE TO SHEEP ERYTHROCYTES
Authors: J. J. Mond, T. Takahashi, G. J. Thorbecke
Journal: The Journal of Experimental Medicine (1972)

Spleen cells from LAF(1) mice hyperimmune to sheep erythrocytes (SE) lost their ability to transfer a secondary response to irradiated recipients after incubation with anti-theta and rabbit complement in vitro. Small numbers of specific immune cells even when taken 3 days after a primary SE injection reconstituted the direct and indirect plaque-forming cell responses. Larger numbers of cells sensitized to B. abortus (or keyhole limpet hemocyanin), and given together with the corresponding antigen, also partially reconstituted the ability to respond to SE. This property was mediated by theta-bearing cells and was interpreted as due to a nonspecific humoral factor liberated by specifically activated T cells and acting on B cell proliferation or maturation.
Relation between chest expansion, pulmonary function, and exercise tolerance in patients with ankylosing spondylitis.
Authors: L R Fisher, M I Cawley, S T Holgate
Journal: Annals of the Rheumatic Diseases (1990)

Thirty three patients with definite ankylosing spondylitis (AS) were examined to establish the relation between restriction of chest expansion, limitation of lung function, and working capacity or exercise tolerance. As in previous studies there was a significant association between chest expansion and lung vital capacity. There was also a significant association between vital capacity and exercise tolerance as measured by a subject's maximum oxygen capacity (VO2max). Both vital capacity and VO2max were expressed as a percentage of predicted normal values using patients' height before disease. In this study chest expansion did not have a significant effect on exercise tolerance. The results suggested that patients who took a modest amount of exercise regularly could maintain a satisfactory work capacity despite very restricted spinal and chest wall mobility. It is recommended that greater emphasis should be given to encouraging patients with AS to maintain cardiorespiratory fitness as well as spinal mobility.
Predicting hypoxaemia during flights in children with cystic fibrosis
Authors: R M Buchdahl
Journal: Thorax (2001)

<h3>BACKGROUND</h3> We have previously suggested that it is possible to predict oxygen desaturation during flight in children with cystic fibrosis and chronic lung disease by non-invasive measurement of oxygen saturation following inhalation of 15% oxygen—the pre-flight hypoxic challenge. This study reports on the results of measurements over 5 years. <h3>METHODS</h3> The study comprised a pre-flight hypoxic challenge measuring oxygen saturation by finger tip pulse oximetry (Spo<sub>2</sub>) during tidal breathing of 15% oxygen in nitrogen and spirometric testing 1 month before the flight followed by Spo<sub>2</sub> measurements during intercontinental flights to and from holidays abroad with children in wake and sleep states. <h3>RESULTS</h3> Pre-flight tests were completed on 87 children with cystic fibrosis. Desaturation of &lt;90% occurred in 10 children at some stage during the flight, three of whom received supplementary oxygen. Using a cut off Spo<sub>2</sub> of 90%, the pre-flight hypoxic challenge correctly predicted desaturation in only two of these children. The sensitivity and specificity of the pre-flight hypoxic challenge were 20% and 99%, respectively, compared with 70% and 96% for spirometric tests (using a cut off for forced expiratory volume in 1 second (FEV<sub>1</sub>) of &lt;50% predicted). Overall, pre-flight spirometric tests were a better predictor of desaturation during flight with the area under the Receiver Operating Characteristic (ROC) curve of 0.89 compared with 0.73 for the hypoxic challenge test. <h3>CONCLUSIONS</h3> In this group of subjects pre-flight spirometric testing was a better predictor of desaturation during flight than the pre-flight hypoxic challenge.
Small RNAs in the peripheral blood discriminate metastasized from non-metastasized seminoma
Authors: Christian G Ruf, Daniela Dinger, Matthias Port, Hans-Ulrich Schmelz, Walter Wagner, Cord Matthies, Bertram Müller-Myhsok, Viktor Meineke, Michael Abend
Journal: Molecular Cancer (2014)

We aimed to better discriminate metastasized (lymphogen/occult/both combined) from non-metastasized seminoma based on post-transcriptional changes examined in the peripheral blood. Total RNAs including small RNAs were isolated from the peripheral blood of patients suffering from metastasized testicular tumours (lymphogen, n = 5, clinical stage IIb/c; occult, n = 5, clinical stage I) and non-metastasized patients (n = 5, clinical stage I). Small RNA next generation sequencing (SOLID, Life Technologies) was employed to examine post-transcriptional changes. We searched for small RNAs showing at least 50 reads and a significant ≥ 2-fold difference using peripheral blood small RNAs of non-metastasized tumours as the reference group. Candidate small RNAs were examined in univariate logistic regression analysis and combinations of two small RNAs were further examined using support vector machines. On average 1.3x107, 1.2x107 and 1.2x107 small RNA reads were detectable in non-metastasized, lymphogen and occult metastasized seminoma, respectively of which 73-76% remained after trimming. From these between 80-82% represented annotated reads and 7.2-7.8% (1.6-1.7x104) were annotated small RNA tags. Of them 137 small RNAs showed > 50 reads and a ≥ two-fold difference to the reference. In univariate analysis we detected 33-35 different small RNAs which significantly discriminated lymphogen/occult/combined metastasized from non-metastasized seminoma and among these different comparisons it were the same small RNAs in 44-79%. Many combinations of two of these small RNAs completely discriminated metastasized from non-metastasized seminoma irrespective of the metastasis subtype. Metastasized (either lymphogen or occult) seminoma can be completely discriminated from non-metastasized seminoma with a combination of two small RNAs measured in the peripheral blood.
New insights into nevogenesis: In vivo characterization and follow-up of melanocytic nevi by reflectance confocal microscopy
Authors: Giovanni Pellacani, Alon Scope, Barbara Ferrari, Gaia Pupelli, Sara Bassoli, Caterina Longo, Anna Maria Cesinaro, Giuseppe Argenziano, Rainer Hofmann-Wellenhof, Josep Malvehy, Ashfaq A. Marghoob, Susana Puig, Stefania Seidenari, H. Peter Soyer, Iris Zalaudek
Journal: Journal of the American Academy of Dermatology (2009)
Endogenous Inhibitors of Nuclear Factor-κB, An Opportunity for Cancer Control
Authors: Fei Chen
Journal: Cancer Research (2004)

Abstract Excessive and prolonged activation of nuclear factor-κB (NF-κB) has been linked to numerous human diseases, especially cancer, because of the elevated expression of genes encoding antiapoptotic proteins, cytokines, chemokines, cell adhesion molecules, and so on. Eukaryotic cells have developed multiple mechanisms to keep this ubiquitous transcription factor in check. In addition to the inhibitor of κB family proteins, a number of endogenous molecules that negatively regulate the activation or activity of NF-κB have been identified. These molecules include A20, CYLD, cyPG15-deoxy-Δ12,14-prostaglandin J2, Foxj1, Twist proteins, and β-arrestins. The extended list of these endogenous inhibitors of NF-κB may provide new opportunities for the development of novel strategies for the intervention of malignant transformation. The question to be asked is how NF-κB is sustained activated in a number of cancers in which so many antagonists are surrounded.