tbuckley/cabot-search huggingface dataset:
Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers
Authors: Bilal Wajid, Erchin Serpedin
Journal: Genomics Proteomics & Bioinformatics (2012)

Abstract In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity.
Experimental congestive heart failure produced by rapid ventricular pacing in the dog: cardiac effects.
Authors: J R Wilson, P Douglas, W F Hickey, V Lanoce, N Ferraro, A Muhammad, N Reichek
Journal: Circulation (1987)

Chronic rapid ventricular pacing in the dog reportedly produces a useful preparation of low-output heart failure. However, little information is available regarding cardiac changes in this preparation. Accordingly, we evaluated the effects of both short-term (3 weeks) and prolonged (2 months) rapid ventricular pacing on cardiac hemodynamics, mass, and chamber size. The effects of short-term pacing on left ventricular wall thickening, blood flow, and metabolism were also examined. Compared with 16 control dogs, dogs paced for either 3 weeks (n = 8) or 2 months (n = 13) exhibited reduced cardiac outputs (control 130 +/- 20 ml/min/kg, 3 week pacing 112 +/- 19 ml/min/kg, 2 month pacing 116 +/- 14 ml/min/kg) and elevated pulmonary wedge pressures (control 10 +/- 3 mm Hg, 3 week pacing 26 +/- 5 mm Hg, 2 month pacing 26 +/- 8 mm Hg) and right atrial pressures (control 4 +/- 1 mm Hg, 3 week pacing 13 +/- 3 mm Hg, 2 month pacing 9 +/- 3 mm Hg) (all p less than .01 vs control). At the postmortem examination, both groups of paced dogs also exhibited increased left ventricular volumes (control 13 +/- 6 ml, 3 week pacing 27 +/- 6 ml, 2 month pacing 26 +/- 8 ml), right ventricular volumes (control 13 +/- 5 ml, 3 week pacing 27 +/- 9, 2 month pacing 24 +/- 7 ml), and right ventricular mass (control 27 +/- 5 g, 3 week pacing 32 +/- 6 g, 2 month pacing 34 +/- 6 g) (all p less than .03 vs control) but had normal left ventricular mass. Three weeks of pacing also decreased percent left ventricular shortening (34 +/- 6% to 17 +/- 7%) associated with a disproportionate deterioration of posterior wall thickening (58 +/- 16% to 17 +/- 18%) (both p less than .01), as assessed by echocardiography. This left ventricular dysfunction was associated with no change in myocardial lactate extraction (prepacing 40 +/- 10%, 3 week pacing 36 +/- 10%), myocardial arteriovenous O2 difference, or myocardial histology, suggesting that it was not due to myocardial ischemia. These data indicate that rapid ventricular pacing in the dog produces a useful experimental preparation of low-output heart failure characterized by biventricular pump dysfunction, biventricular cardiac dilation, and nonischemic impairment of left ventricular contractility.
1044-56 Paclitaxel-eluting stent in complicated lesions or patient subsets: A subanalysis from the TAXUS II study
Authors: Leo Finci, Sigmund Silber, Eberhard Grube, Jorge Belardi, John Ormiston, Bradley Strauss, Giuglio Guagliumi, Mary Russell, Antonio Colombo, Antonio Colombo
Journal: Journal of the American College of Cardiology (2004)
807-1 Genetic and biophysical basis for sudden death in the short QT syndrome
Authors: Kui Hong, Robert Dumaine, Jonathan Cordeiro, Florenzo Gaita, Martin Borggrefe, Josep Brugada, Guido Pollevick, Christian Wolpert, Elena Burashnikov, Kiyotaka Matsuo, Yue Sheng Wu, Alejandra Guerchicoff, Francesca Bianchi, Carla Giustetto, Rainer Schimpf, Pedro Brugada, Charles Antzelevitch, Ramon Brugada
Journal: Journal of the American College of Cardiology (2004)
Etiology of Postneonatally Acquired Cerebral Palsy
Authors: M. A. Perlstein, Philip N. Hood
Journal: JAMA (1964)

In a retrospective study of 4,946 cerebral palsied patients, 624 (14%) had acquired the disease. This varied with the type of cerebral palsy, from 5% in athetoids to 30% in spastic hemiplegics. Encephalopathies accounted for 57% of acquired cerebral palsy, skull traumas for 18%, meningitis for 12%, vascular accidents for 8%, and all others for 5%. Sixty-five percent was acquired before the age of 2 years and 92% before 8 years. The type of cerebral palsy varies with etiology, spastic hemiplegia being most common in the vascular group. Males predominate except in the vascular accidents group. Acquired juvenile cerebral palsy is a connecting link between the congenital forms and those acquired in adult and senile life.
Ill equipped hospitals can't cope with casualties from Sri Lankan crisis
Authors: B. Bland
Journal: BMJ (2009)

Sri Lanka is facing a humanitarian crisis, as casualties from the worsening conflict between the army and the separatist Tamil Tigers overwhelm the “understaffed and ill equipped medical facilities” in the northern Vanni region, the International Committee of the Red Cross has said.

Hundreds of people have been killed and many wounded, while hospitals and ambulances have been hit by artillery attacks, and a number of aid workers have been injured, the Red Cross said.

About 250 000 civilians have been trapped by the fighting in a 250 square kilometre area in the far north of the island nation, where the Sri Lankan army is trying to end the Tigers’ long running insurgency. …
Royal college demands 2000 more NHS consultant physicians
Authors: R. Woodman
Journal: BMJ (1999)

Consultant physicians are being urged to make “firm and, if necessary, vociferous” requests to secure the extra 2000 posts that their college estimates are needed to provide safe and effective care throughout England, Wales, and Northern Ireland.

A college report says that there should be one consultant per 80000 population in all major medical specialties except geriatrics, where the pressures are such that there should be one consultant per 50000 patients. The report …
Leptin responses to short term exercise in college level male rowers
Authors: J Jürimäe, T Jürimäe
Journal: British Journal of Sports Medicine (2004)

To investigate plasma leptin response to short term exercise in college level male rowers.Thirteen rowers performed a 30 minute maximal rowing ergometer test. Venous blood samples were obtained before, immediately after, and after 30 minutes of recovery. Concentrations of leptin, insulin, growth hormone, insulin-like growth factor-I (IGF-I), and IGF binding protein-3 (IGFBP-3) were measured.Plasma leptin was significantly (p<0.05) decreased (from a mean (SD) of 2.7 (0.6) to 2.1 (0.8) ng/ml) and growth hormone significantly increased (from 0.6 (0.9) to 4.6 (5.4) microIU/l) immediately after the 30 minute maximal rowing exercise session (distance covered 7870.4 (443.3) m; blood lactate immediately after the test 14.9 (4.3) mmol/l). All other blood variables measured were not significantly changed as a result of the ergometer test. A positive relation was observed between the decreased plasma leptin concentration immediately after the test and the distance covered (R(2) = 0.645; p<0.05). Changes in leptin and IGF-I concentrations immediately after the test were also related (R(2) = 0.390; p<0.05). Percentage body fat explained 89.6% (p<0.05) of the variance (R(2) x 100) in basal leptin concentration. After normalisation for body fat, basal leptin was related (p<0.05) to basal insulin (r = 0.82) and training history (r = -0.60).Leptin is sensitive to relatively short term intense exercise when all major muscles are involved.
ELECTROLYSIS IN THE TREATMENT OF DETACHED RETINA.
Authors: W. T. MONTGOMERY
Journal: JAMA (1896)

Within the past few years various remedial agents have been advocated with more or less enthusiasm in the treatment of detachment of the retina. One of the more recent of these agents, and one which from its action and the nature of the disease seemed to promise as much or more than any other treatment, is electrolysis. One of the most full and encouraging reports on the application of electrolysis in detachment of the retina, is by Dr. Terson, and was published in the last July number of the<i>Annales d'Oculistique</i>. Dr. Terson reports twelve cases treated with one recovery which had lasted nine months, and five improvements which had persisted for from two to nine months. Within the last six months four cases of detachment of the retina have been treated in the Illinois Charitable Eye and Ear Infirmary, two by myself and two by Dr. B. Bettman. In
American Legislative Exchange Council
Authors: Jane Cassidy
Journal: BMJ (2011)

The American Legislative Exchange Council (ALEC) is a major US lobbying organisation for big business. It is linked to big tobacco, oil, food, drink, and drug companies.

Its board of directors is made up of Republican politicians opposed to public healthcare. They also promote the ideas of those people who deny that climate change is happening. Their slogan is “limited government, free market, federalism.”

One ALEC member, John Campbell, a California congressman, said that it was “nuts” of President Barack Obama to seek to emulate the NHS through his healthcare reforms. He attacked the UK health service as “enormously inefficient, wasteful, and costly.”1

It emerged during the recent Liam Fox and Adam Werritty scandal that ALEC funded a charity founded by the former defence secretary and run by his adviser and personal friend.

The Atlantic Bridge was set …
OBSTRUCTIVE HYDROCEPHALUS FOLLOWING CEREBROSPINAL MENINGITIS, WITH INTRAVENTRICULAR INJECTION OF ANTIMENINGITIS SERUM (FLEXNER)
Authors: Harvey Cushing, Frank J. Sladen
Journal: The Journal of Experimental Medicine (1908)

Despite the ultimate fatality and the failure to secure a postmortem examination in the case of this unfortunate patient, the interest, from a therapeutic standpoint, of finding, long after the primary infection, the meningococcus still viable in the cerebral ventricles in association with an obstructure hydrocephalus, whereas the spinal fluid retained no trace of organisms, makes it seem desirable to place upon record even this single experience with the intraventricular injection of serum.History.---A baby six months old was brought by its mother to the children's
Antibiotic prophylaxis of subacute bacterial endocarditis for adult patients by dentists in Dade County, Florida.
Authors: T Hashway, L J Stone
Journal: Circulation (1982)

To determine compliance with 1977 American Heart Association (AHA) recommendations for antibiotic prophylaxis (AbP) of subacute bacterial endocarditis (SBE), we mailed a questionnaire to 1019 licensed dentists from Dade County, Florida. Of the 614 practicing dentists who responded, 97.7% believe that AbP prevents SBE and 94.2% always obtain a cardiac history from new patients. AbP is given to patients with known rheumatic or other valvular heart disease by 98.9% of responders and to patients with known prosthetic heart valves by 81.5%. The majority of dentists prescribe the antibiotics recommended by the AHA, but the dosage, route, frequency and duration of therapy are usually not according to AHA guidelines. AbP completely consistent with these guidelines is prescribed by 15.4% of dentists for patients with heart disease and by only 6.7% of dentists for patients with prosthetic heart valves. The AHA recommends parenteral AbP for most patients with prosthetic heart valves, but approximately 80% of dentists use only oral agents for these patients. We conclude that most dental patients predisposed to SBE receive AbP, but not in accordance with AHA guidelines. The widest deviation occurs among patients with prosthetic heart valves.
Etude d'une Corticostimuline Hypophysaire
Authors: F. Coste, F. Delbarre
Journal: Annals of the Rheumatic Diseases (1950)

A la Clinique Rhumatologique de la Faculte de Medecine de Paris, nous avons, mis en route une preparation de " corticostimuline hypophysaire " par un procede simplifie.Ce procede se fonde sur la remarque suivante: " L'ACTH est, de toutes les hormones antehypophysaires, la plus resistante, tant a la chaleur qu'aux variations du pH vers J'alcalinite."Utilisant cette propriete, il est possible, sans soumettre l'extrait antehypo- physaire brut a des extractions longues et cofuteuses-qui consomment une grande quantite de solvant, et entrainent, probablement, des pertes notables de la sub- stance active qu'on desire isoler-d'obtenir, par simple inactivation des stimulines parasites, une preparation contenant toute l'activite ACTH de l'extrait ante- hypophysaire.Elle est donc moins pure que les preparations americaines (qui, elles-memes, d'ailleurs, ne contiennent qu'une fraction variable de l'echantillon standard d'Armour).Cette corticostimuline a ete etalonnee dans notre Service par divers procede's, en particulier sur l'animal par le test de Sayers (1943), et, sur l'homme, par les variations de l'eosinophilie et de l'uraturie.Elle s'est montree d'une activite assez analogue 'a celle qu'ont utilisee habituelle- ment les auteurs americains, et, en Suisse, Mach et al. (1950).L'experience clinique a confirme son efficacite therapeutique et biologique.On a traite 29 malades, dont: 8 polyarthrites chroniques evolutives (4 masculines et 4 feminines).5 maladies de Bouillaud. 1 spondylarthrite ankylosante.I grand rhumatisme psoriasique. 3gouttes.1 lupus erythemateux aigu. 1 dermatomyosite. 4asthmes.I leucose chronique en poussee lymphoblastique aigue. 2 rectoc6lite hemorragique. 1polyomyelite aigue.
The General Medical Council and doctors' financial interests
Authors: K. Adlington, K. Abbasi, F. Godlee
Journal: BMJ (2015)

A failure of regulation

Doctors are not supposed to allow personal financial gain to influence or appear to influence their clinical decisions. And in the UK, the public relies on the General Medical Council to pursue claims that doctors may have behaved unethically. But an investigation by The BMJ has found that the GMC failed to act when a leading insurance firm presented it with evidence of widespread payment of “incentives” to doctors in return for referrals to private hospital groups.1 These inducements were not disclosed to patients and seem to contravene GMC guidance.2 3 Some London based doctors benefited by tens, sometimes hundreds, of thousands of pounds.

The Competition and Markets Authority closed loopholes in the law last year, but the GMC has still not responded formally to the evidence presented to it in 2012. A senior doctor who works for the insurance firm and brought the evidence to The BMJ said, “It’s a sad day for the medical profession when a competition regulator has had to issue an order … because our own regulator [the GMC] has failed to do so.”

The GMC says that it didn’t receive a formal complaint against individual doctors and so could not investigate further. Its Good Medical Practice does set standards on financial arrangements and conflicts of interest. …
Poly(N-isopropylacrylamide)-graft-polypropylene membranes containing adsorbed antibody for cell separation
Authors: Aiko Okamura, Midori Itayagoshi, Taeko Hagiwara, Manae Yamaguchi, Toshiyuki Kanamori, Toshio Shinbo, Pi-Chao Wang
Journal: Biomaterials (2004)
Usefulness of Home BP Determination in Treating Borderline Hypertension
Authors: Christopher Cottier, Stevo Julius, Subhash V. Gajendragadkar, M. Anthony Schork
Journal: JAMA (1982)

This study explores whether home BP self-determination can be used to assess the effect of treatment in patients with borderline hypertension. Sixteen untreated patients underwent a double-blind trial of propranolol hydrochloride (average dose, 105 mg), clonidine hydrochloride (0.24 mg), and placebo. Home BP readings decreased with both active compounds (-8/-5 with propranolol and -11/-7 with clonidine). During placebo, the readings increased to levels identical to untreated values. This study demonstrates that patients with borderline hypertension are consistently capable of detecting small average changes in home BP. It is also shown that sympatholytic monotherapy can be effectively used to lower the BP in such patients.
Multiple myeloma: Relationship between survival and cellular morphology
Authors: Paolo Pasqualetti, Raffaele Casale, Antonio Collacciani, Benjamin P. Abruzzo, Domenico Colantonio
Journal: American Journal of Hematology (1990)

Abstract Myeloma cells in bone marrow aspirates from 121 patients with multiple myeloma at time of diagnosis were evaluated, by assigning them into morphological categories. Cox's model was used to calculate the coefficients for total myeloma cells and “plasmablasts” in respect to survival. Applying these coefficients, the Multiple Myeloma Cellular Score (MMCS) was calculated. MMCS significantly divides the patients into three stages. In fact, there are significant differences both between mean survivals ( P &lt; 0.001) and between survival curves ( P &lt; 0.00001). There is also a significant correlation ( P &lt; 0.00001) between the calculated MMCS and survival in the whole patient group.
NEED OF CAMPAIGN TO AROUSE INTEREST IN TRAINED NURSING
Authors: J. M. Mason
Journal: JAMA (1918)

<h3>To the Editor:</h3> —An editorial inThe Journal(June 8, 1918, p. 1768) under the title, "Nurses Needed by the Red Cross," calls attention to the campaign now under way for the enrolment of 25,000 nurses for the Army and Navy, in addition to those already in service, between 10,000 and 12,000. In this locality the earlier responses have been prompt and the enrolment so heavy that it is difficult to see where our proportion is to come from. Hospital service has been seriously impaired, and there are but few nurses available for work in private homes. The "practical" nurse to whom the editor refers has been so displaced in recent years by the trained nurse that she cannot be counted on for much help in the present emergency. A most serious aspect of the situation is the shortage of pupil nurses in the training schools. Young women are going
Essential role of EBF1 in the generation and function of distinct mature B cell types
Authors: Bojan Vilagos, Mareike Hoffmann, Abdallah Souabni, Qiong Sun, Barbara Werner, Jasna Medvedovic, Ivan Bilic, Martina Minnich, Elin Axelsson, Markus Jaritz, Meinrad Busslinger
Journal: The Journal of Experimental Medicine (2012)

The transcription factor EBF1 is essential for lineage specification in early B cell development. In this study, we demonstrate by conditional mutagenesis that EBF1 is required for B cell commitment, pro–B cell development, and subsequent transition to the pre–B cell stage. Later in B cell development, EBF1 was essential for the generation and maintenance of several mature B cell types. Marginal zone and B-1 B cells were lost, whereas follicular (FO) and germinal center (GC) B cells were reduced in the absence of EBF1. Activation of the B cell receptor resulted in impaired intracellular signaling, proliferation and survival of EBF1-deficient FO B cells. Immune responses were severely reduced upon Ebf1 inactivation, as GCs were formed but not maintained. ChIP- and RNA-sequencing of FO B cells identified EBF1-activated genes that encode receptors, signal transducers, and transcriptional regulators implicated in B cell signaling. Notably, ectopic expression of EBF1 efficiently induced the development of B-1 cells at the expense of conventional B cells. These gain- and loss-of-function analyses uncovered novel important functions of EBF1 in controlling B cell immunity.
Allergic Models and Cytokines
Authors: David B. Bittleman, Thomas B. Casale
Journal: American Journal of Respiratory and Critical Care Medicine (1994)

Cytokines are proinflammatory protein mediators produced by many cells, including mast cells, T lymphocytes, eosinophils, airway epithelial cells, and macrophages. There are numerous in vitro and in vivo animal and human studies showing that cytokines are released as a result of allergic reactions. Cytokines mediate allergic inflammation by activating eosinophils, promoting mast cell development, regulating immunoglobulin isotype switching to immunoglobulin E, modulating adhesion molecule regulation, and promoting both neutrophil and eosinophil chemotaxis. Furthermore, there are data that show the pro-inflammatory effects of cytokines may be blocked by cytokine antagonists. This report reviews the in vitro and in vivo animal and human studies of allergic models of cytokine production and regulation. It also discusses the specific roles of cytokines in the allergic inflammatory response and asthma.
Augmenting Transgene Expression from Carcinoembryonic Antigen (CEA) Promoter via a GAL4 Gene Regulatory System
Authors: Patricia E. Koch, Z.Sheng Guo, Shunsuke Kagawa, Jian Gu, Jack A. Roth, Bingliang Fang
Journal: Molecular Therapy (2001)

Though extensively studied, the use of tissue- or cell-type-specific promoters to target transgene expression is hampered by their weak activity. We hypothesized that this problem could be addressed by using a GAL4 gene regulatory system, wherein a weak, tissue-specific promoter would drive expression of the GAL4/VP16 fusion protein (GV16), which in turn would transactivate a minimal synthetic promoter, GAL4/TATA (GT), upstream of a transgene. To test this hypothesis, we constructed adenoviral vectors expressing a lacZ or GV16 gene driven by a carcinoembryonic antigen (CEA) promoter (Ad/CEA-LacZ or Ad/CEA-GV16) and evaluated levels of transgene expression they produced in cultured cells and in subcutaneous tumors after intratumoral administration. In CEA-positive cells, treatment with Ad/CEA-GV16 + Ad/GT-LacZ versus Ad/CEA-LacZ increased transgene expression 20- to 100-fold. In CEA-negative cells, treatment with Ad/CEA-GV16 + Ad/GT-LacZ increased transgene expression to a much lower degree (6- to 8-fold). In addition, analysis of Bax gene-mediated cell death revealed that this system can be used to avoid Bax's toxic effects on CEA-negative cells without compromising its ability to kill CEA-positive cells in vitro and in vivo. Thus, the combination of a tissue-specific promoter with the GAL4 gene regulatory system could be useful for targeting transgene expression.