tbuckley/cabot-search huggingface dataset:
An Assessment of Accuracy, Error, and Conflict with Support Values from Genome-Scale Phylogenetic Data
Authors: D. J. Taylor
Journal: Molecular Biology and Evolution (2004)

Despite the importance of molecular phylogenetics, few of its assumptions have been tested with real data. It is commonly assumed that nonparametric bootstrap values are an underestimate of the actual support, Bayesian posterior probabilities are an overestimate of the actual support, and among-gene phylogenetic conflict is low. We directly tested these assumptions by using a well-supported yeast reference tree. We found that bootstrap values were not significantly different from accuracy. Bayesian support values were, however, significant overestimates of accuracy but still had low false-positive error rates (0% to 2.8%) at the highest values (>99%). Although we found evidence for a branch-length bias contributing to conflict, there was little evidence for widespread, strongly supported among-gene conflict from bootstraps. The results demonstrate that caution is warranted concerning conclusions of conflict based on the assumption of underestimation for support values in real data.
Financial Incentives for Organ Donation: The Perspectives of Health Care Professionals
Authors: J. S. Altshuler, M. J. Evanisko
Journal: JAMA (1992)

<h3>To the Editor.</h3> —The persistent shortage of donor organs for transplantation has lead to novel approaches for increasing the "yield" of potential donors, with the idea of offering financial incentives for organ donation among the most controversial. A proposal for a pilot study in which cash payments would be offered to families considering donation was recently published in<i>JAMA</i>.<sup>1</sup> The attitudes of those who most often request donation from families have not yet entered into the discussion about financial incentives. Since most families faced with the decision to donate have not considered the issue in advance,<sup>2</sup>the skill, attitude, and comfort level of the individual requesting donation will strongly influence whether the family will con sent to donation. At least one study has shown that uncomfortable requesters are less likely to obtain consent for donation.<sup>3</sup>Clearly, the perspectives of these "gatekeepers" of the donation process should weigh
A centrally funded health service, free at the point of delivery
Authors: Tony Delamothe
Journal: BMJ (2008)

The acute or chronic harmful use of alcohol is among the top five risk factors for disease, disability and death worldwide.1 Monitoring alcohol consumption is an important aspect of the management of alcohol-use disorders and may include subjective self-reported questionnaires or objective tests.1,2–6 Such tests include measuring alcohol or alcohol metabolite levels or biomarkers such as liver enzymes or red cell indices.2–6 Carbohydrate deficient transferrin (CDT) is a biomarker used for assessing chronic alcohol misuse.6 Here, we review CDT and its place in the assessment of chronic alcohol use.
Ventilatory function as a predictor of fatal stroke.
Authors: D. P. Strachan
Journal: BMJ (1991)

To investigate the relation between ventilatory function and subsequent mortality due to cerebrovascular disease.Prospective longitudinal study.A total of 18,403 male civil servants aged 40-64 years at entry examination for the Whitehall study.Mortality from cerebrovascular disease (ICD8 430-438) after 18 years of follow up.In all, 262 men with sinus rhythm at entry died due to stroke during the 18 years of follow up. Compared with men with a forced expiratory volume in one second of greater than or equal to 3.5 litres those with a value of less than 3.0 litres were almost twice as likely to die of cerebrovascular disease (rate ratio adjusted for age and systolic blood pressure = 1.88, 95% confidence interval 1.32 to 2.69). This increased risk occurred within each tertile of systolic blood pressure. Nested case-control analyses were used to control precisely for confounding effects of age, height, and smoking (by matching) and employment grade and physiological risk factors (by modelling). The effect of forced expiratory volume in one second was independent of age, height, smoking habits, employment grade, blood pressure, weight, cholesterol concentration, glucose tolerance, electrocardiographic abnormalities, history of chest pain, and history of intermittent claudication.Measurements of ventilatory function may assist clinical decisions about whether to treat mild hypertension. Impaired ventilatory function and stroke may share common causes.
Population Trends of Alaska Natives and the Need for Planning
Authors: JOSEPH D. BLOOM
Journal: American Journal of Psychiatry (1972)

The author discusses some of the factors that have affected the population distribution of Alaska Natives, particularly the recent population explosion and the skewing toward youth. Of prime importance is the role played by the government's system of medical care. The author points out the need for examining all aspects of the policies of a medical care system so that a properly balanced program can be provided.
The Effect of a Public Hospital's Transfer Policy on Patient Care
Authors: William Gary Reed, Karen A. Cawley, Ron J. Anderson
Journal: New England Journal of Medicine (1986)

As the health care system becomes increasingly competitive, one of the country's most critical health issues — how to ensure access to care for the indigent — will continue to plague policy makers and health care providers alike. The problem of uncompensated care will not remain an issue only for the public hospitals, since the demand for uncompensated care far exceeds the capabilities of these providers.In Texas, where approximately one third of the hospitals are owned by investors, the public hospitals clearly bear a disproportionate share of the burden of uncompensated care. Analysis of a 1984 survey of 476 . . .
Double-Hairpin Elements in the Mitochondrial DNA of Allomyces: Evidence for Mobility
Authors: Bruno Paquin, Marie-Josée Laforest, B. Franz Lang
Journal: Molecular Biology and Evolution (2000)

The mitochondrial DNA (mtDNA) of the chytridiomycete fungus Allomyces macrogynus contains 81 G+C-rich sequence elements that are 26–79 bases long and can be folded into a unique secondary structure consisting of two stem-loops. At the primary sequence level, the conservation of these double-hairpin elements (DHEs) is variable, ranging from marginal to complete identity. Forty of these DHEs are inserted in intergenic regions, 35 in introns, and 6 in variable regions of rRNA genes. Ten DHEs are inserted into other DHE elements (twins); two even form triplets. A comparison of DHE sequences shows that loop regions contain more sequence variation than helical regions and that the latter often contain compensatory base changes. This suggests a functional importance of the DHE secondary structure. We further identified nine DHEs in a 4-kb region of Allomyces arbusculus, a close relative of A. macrogynus. Eight of these DHEs are highly similar in sequence (90%–100%) to those in A. macrogynus, but only five are inserted at the same positions as in A. macrogynus. Interestingly, DHEs are also found in the mtDNAs of other chytridiomycetes, as well as certain zygomycete and ascomycete fungi. The overall distribution pattern of DHEs in fungal mtDNAs suggests that they are mobile elements.
Endoscopic ultrasonography in differentiating pancreatic cancer coexisting with chronic pancreatitis compared with other imaging examinations
Authors: Wang Wei, Jin Zhen-Dong, Wang Luo-Wei, Liu Yan, Wang Dong, Xue Pan, Chen Jie, Xu Can, Zhan Xian-Bao, Zou Duo-Wu, Li Zhao-Shen
Journal: Endoscopy (2011)

It is intrinsically difficult to diagnose pancreatic cancer in the background of chronic pancreatitis (CP) because the malignancy may coexist, precede, or follow CP. Endoscopic ultrasonography (EUS) has been shown to be very accurate in the diagnosis and staging of pancreatic cancer.
Polymyalgia rheumatica and corticosteroids: how much for how long?
Authors: A R Behn, T Perera, A B Myles
Journal: Annals of the Rheumatic Diseases (1983)

In a prospective study of 176 patients in whom polymyalgia rheumatica (PMR) or giant cell arteritis (GCA) had been diagnosed between 1968 and 1980 the effect of corticosteroid treatment was studied. In those with PMR alone an initial regimen of 10 mg prednisolone daily and for the majority of those with GCA 20 mg daily were adequate to control symptoms. No patient suffered a serious disease complication after starting treatment. Regular follow-up enabled the minimum effective corticosteroid dose to be used. Complications of treatment were infrequent. Corticosteroid treatment has been withdrawn from 72 patients after a mean of 31 months treatment (range 3-103 months). Thirty subsequently relapsed, all within 21 months of withdrawal. No clinical feature predicted those who were more likely to relapse. No rigid treatment schedule should be used in these diseases.
Overview of the protein-protein interaction annotation extraction task of BioCreative II
Authors: Martin Krallinger, Florian Leitner, Carlos Rodriguez-Penagos, Alfonso Valencia
Journal: Genome biology (2008)

The biomedical literature is the primary information source for manual protein-protein interaction annotations. Text-mining systems have been implemented to extract binary protein interactions from articles, but a comprehensive comparison between the different techniques as well as with manual curation was missing. We designed a community challenge, the BioCreative II protein-protein interaction (PPI) task, based on the main steps of a manual protein interaction annotation workflow. It was structured into four distinct subtasks related to: (a) detection of protein interaction-relevant articles; (b) extraction and normalization of protein interaction pairs; (c) retrieval of the interaction detection methods used; and (d) retrieval of actual text passages that provide evidence for protein interactions. A total of 26 teams submitted runs for at least one of the proposed subtasks. In the interaction article detection subtask, the top scoring team reached an F-score of 0.78. In the interaction pair extraction and mapping to SwissProt, a precision of 0.37 (with recall of 0.33) was obtained. For associating articles with an experimental interaction detection method, an F-score of 0.65 was achieved. As for the retrieval of the PPI passages best summarizing a given protein interaction in full-text articles, 19% of the submissions returned by one of the runs corresponded to curator-selected sentences. Curators extracted only the passages that best summarized a given interaction, implying that many of the automatically extracted ones could contain interaction information but did not correspond to the most informative sentences. The BioCreative II PPI task is the first attempt to compare the performance of text-mining tools specific for each of the basic steps of the PPI extraction pipeline. The challenges identified range from problems in full-text format conversion of articles to difficulties in detecting interactor protein pairs and then linking them to their database records. Some limitations were also encountered when using a single (and possibly incomplete) reference database for protein normalization or when limiting search for interactor proteins to co-occurrence within a single sentence, when a mention might span neighboring sentences. Finally, distinguishing between novel, experimentally verified interactions (annotation relevant) and previously known interactions adds additional complexity to these tasks.
ACTIVE IMMUNIZATION AGAINST TETANUS AND DIPHTHERIA IN INFANTS AND CHILDREN
Authors: JOHN A. BIGLER
Journal: JAMA (1941)

Prevention of certain infectious diseases by immunization has become an established part of medical practice. Active immunity produced by the introduction of an organism or its products into the body predisposes to the more rapid development of the formation of antibodies on subsequent exposure to that particular antigen. This is preferable to passive immunity because of its long duration and because usually no animal serum is used to which the recipient might be sensitive or sensitized. Passive immunity, although highly effective, has definite limitations because of its nature. It is of temporary duration, it must be given at the proper time or interval, it usually sensitizes the recipient to the serum of the animal from which it is derived or the recipient may already be an allergic person. Active immunization of infants and children against diphtheria is now generally performed. The practical value of this procedure is so well known
THE NATURE AND SIGNIFICANCE OF LEUCOCYTOSIS.
Authors: A. MANSFIELD HOLMES
Journal: JAMA (1905)

When Cohnheim demonstrated that inflammation and suppuration are due to an emigration of the white corpuscles, a great advance was made in pathology. Since then the importance of the white blood corpuscles has been increasing with each year. <h3>CELL TYPES.</h3> If leucocytes consisted of but a single variety of cells, with common functions, the study of leucocytosis would be reduced to a simple process. It would then be sufficient simply to ascertain the degree of leucocytosis by estimating the total number of leucocytes to a cubic millimeter of blood. It is well known, however, that the white blood corpuscles consist of several more or less distinct varieties. Many attempts have been made to differentiate these types, resulting in not a little confusion in the nomenclature thus introduced. 1. A classification has been based on the nature of the behavior of the cells to microchemic reagents, giving us acidophile, basophile and
Development aid: the way forward
Authors: E A S Nelson
Journal: BMJ (1994)

The British Overseas Development Administration aims to direct aid to the poorest people in the poorest countries, but it does not provide figures on how much aid is “poverty focused.” Aid is often equated with charity, but it is more about the self interest of the giver. It benefits the donors and their exporters more than the recipients. In 1986 an estimated $37bn (pounds sterling 24.6bn) of development aid was given by the rich industrialised donor countries to developing countries. But little monetary aid reaches the poor and aid is maldistributed: the richer 40% of the developing world's people get twice the aid of the poorer 40%. Almost half of America's aid over the past decade was for Egypt and Israel. Nearly half of all aid is tied to the purchase of goods and services from the donor country.

Development aid has mainly been directed to developing infrastructure - dams, roads, airports, large scale agricultural schemes, universities, and hospitals. Although some projects were successful, many were not, and debt has accumulated - rich countries now receive over $21bn (pounds sterling 14bn) annually from poor countries. Structural adjustment programmes, which are now imposed on developing countries to recover this debt, have had adverse social and medical consequences.

Donors may contend that they are now moving …
Changing Concepts of the Mechanism of Pulmonary Atelectasis
Authors: Guenter Corssen
Journal: JAMA (1963)

This study is an attempt to challenge the generally accepted concept that the human lung is merely an elastic sponge with no musculature existing beyond the terminal bronchioles. Photomicrographs of human lung tissue taken in situ, and specifically stained, reveal minute smooth muscle fibers in the most distally located portion of the air passage including alveolar sacs. While such smooth muscle elements are present in the normal lung tissue, a marked increase of these structures is noted in the lungs of individuals with bronchitis, emphysema, and, particularly, pulmonary hypertension. The existence of alveolar musculature can explain the ability of the human lung to contract actively, as may be the case in nonobstructive pulmonary collapse or "contraction atelectasis."
Comparison of the microvasculature of basal cell carcinoma and actinic keratosis using intravital microscopy and immunohistochemistry
Authors: B. Newell, A.J. Bedlow, S. Cliff, S.B. Drysdale, A.W.B. Stanton, P.S. Mortimer
Journal: British Journal of Dermatology (2003)

Summary Background Angiogenesis is a prerequisite for growth of invasive tumours. We hypothesized that angiogenesis would be present in invasive basal cell carcinoma (BCC) but not in a noninvasive tumour such as actinic keratosis (AK). Objectives To investigate both types of tumour for evidence of angiogenesis. Methods Patients with BCC or AK underwent intravital videocapillaroscopy. Three regions were examined: the tumour, perilesional skin and a control site. Microvessel width, area fraction and length density were determined from capillaroscopy images. Biopsies were stained for CD34 and a microvessel count was performed. Results Capillaroscopy demonstrated a grossly disorganized tumour microcirculation in BCC. Compared with control skin, microvessel width was increased 2·4-fold, area fraction was increased 4·9-fold and length density was increased 5·9-fold. In AK, microvessel width was increased 1·7-fold, area fraction 2·5-fold and length density 3·4-fold. Vessel width and area fraction were significantly greater in BCC than AK. Biopsies showed significant increases in microvessel length density for both BCC and AK compared with control skin, with BCC significantly greater than AK. Conclusions Angiogenesis was demonstrated in BCC in humans in vivo, and to a lesser extent in AK.
Influence of treatment on muscle sympathetic nerve activity in sleep apnea.
Authors: N V Waradekar, L I Sinoway, C W Zwillich, U A Leuenberger
Journal: American Journal of Respiratory and Critical Care Medicine (1996)

Obstructive sleep apnea (OSA) is a common disorder associated with systemic hypertension, myocardial infarction, stroke, and premature death. Elevated sympathetic tone has been documented previously in OSA and may contribute to the cardiovascular risk. As OSA therapy appears to reduce mortality, we wondered if decreased apnea activity would attenuate the sympathetic hyperactivity of untreated patients. Muscle sympathetic nerve activity (MSNA) was measured during wakefulness via peroneal microneurography in seven patients with documented OSA before and at least 1 mo after compliance-monitored nasal continuous positive airway pressure (CPAP) therapy. Before institution of CPAP therapy, MSNA was high in all patients and decreased after CPAP therapy (baseline versus CPAP: 69.4 +/- 15.3 versus 53.9 +/- 10.5 bursts/min, mean +/- SD; p<0.01). However, the decrease in MSNA was limited to the four patients with the greatest nightly use of CPAP (> or = 4.5 h/night), whereas it remained unchanged in the three patients who were less compliant. There was a direct linear correlation between the decrease in MSNA (bursts/min) and the average hours of CPAP use per night (r = 0.87, p = 0.01). We conclude that in patients with OSA effective reduction in apnea activity with CPAP therapy diminishes the high sympathetic tone present during resting wakefulness.
Gonadal Activity and Chemotherapy-Induced Gonadal Damage-Reply
Authors: Scott A. Rivkees
Journal: JAMA (1988)

<h3>In Reply.—</h3> Dr Glode's and Drs Redman and Bajorunas' comments reflect the fact that the early promise that chemotherapy-induced gonadal damage might be prevented by suppressing germ cell activity during cytotoxic therapy has yet to be clinically fulfilled. Although it was not the purpose of our report to give a detailed review of this subject, we disagree with Drs Redman and Bajorunas' inference that the clinical utility of the germ cell suppression hypothesis can be judged by the reports they cite, and we agree with Dr Glode that further investigation is necessary. As pointed out by Dr Glode, the failure of the administration of luteinizing hormone releasing hormone agonist during chemotherapy to preserve testicular function in humans<sup>1</sup>may in part be attributable to inadequate doses of agonist. The short duration of luteinizing hormone releasing hormone therapy prior to chemotherapy also appears to have had a role in its failure
THE IMPORTANCE OF A LEUCOCYTE COUNT IN DOUBTFUL CASES OF APPENDICITIS
Authors: G. F. Aldous
Journal: BMJ (1914)

LEUCOCYTE COUNT IN APPE NDICITIS.rJAN. 3 I9}4 frienids were at.first amused, and did niot realize that it was niot part of the enitertainment.Thiey tlheni camne to hiis help andl gav-e hiim a glass of water, which he was iuinable to swallow, the filuid reyurgitating through the nlose.This was followed the next day l)v paralysis of the left leg, left arm, anid left side of the face, including the upper part, and,.for a monitlh lie lhad to l)e fed with a tube.This hiappened in Japan; the doctor treated him by in-unction, anid after a montl lie was able to swallow anid speak.He vas senit to me on hiis returni from Japan suffering wvith the remaitns of a left-sided paralysis, including the uIpper facial muscles, anid there was also paresis of the left vocal cord anid soft palate.He atten(led my practice for some years witliout fuirther symptoms, and gradulally
Glucocorticoid Receptor α and β in Glucocorticoid Dependent Asthma
Authors: ROSALIA GAGLIARDO, PASCAL CHANEZ, ANTONIO M. VIGNOLA, JEAN BOUSQUET, ISABELLE VACHIER, PHILIPPE GODARD, GIOVANNI BONSIGNORE, PASCAL DEMOLY, MARC MATHIEU
Journal: American Journal of Respiratory and Critical Care Medicine (2000)

Patients with glucocorticoid (GC)-dependent asthma present an ongoing inflammation of the airways despite chronic long-term treatment with oral GC. Interleukin (IL)-8 and granulocyte/macrophage colony-stimulating factor (GM-CSF) have been implicated in airway inflammation in severe asthma and their synthesis is normally repressed by GC. To further characterize the inflammatory process in GC-dependent asthma, we measured the release of IL-8 and GM-CSF by peripheral blood mononuclear cells (PBMC) of eight normal subjects, six untreated controlled asthmatics, six untreated uncontrolled asthmatics, and nine GC-dependent asthmatics. We show that PBMC from GC-dependent asthmatics released high amounts of these cytokines despite chronic in vivo exposure to GC (p < 0.001 versus normal subjects). In contrast, when untreated uncontrolled asthmatics were given a short course of oral GC, IL-8 and GM-CSF production was inhibited (p = 0.0078). Release of IL-8 and GM-CSF by PBMC of GC-dependent asthmatics was reduced after in vitro GC treatment (p < 0.002). We investigated whether the incapacity of GC to inhibit production of these cytokines in vivo was the result of a dysregulation of the glucocorticoid receptor (GR) in GC-dependent asthma. GR α and GR β are, respectively, the functional receptor and a putative dominant negative form of the receptor. Western blot and polymerase chain reaction (PCR) analyses indicated that GR α was expressed at similar level in all groups and was largely predominant over GR β . Thus, persistent release of IL-8 and GM-CSF in GC-dependent asthma is not associated with low expression of GR α or overexpression of GR β .