tbuckley/cabot-search huggingface dataset:
Mosaic Structure and Retropositional Dynamics During Evolution of Subfamilies of Short Interspersed Elements in African Cichlids
Authors: Kazuhiko Takahashi, Norihiro Okada
Journal: Molecular Biology and Evolution (2002)

The African cichlid (AFC) family of short interspersed elements (SINEs) is found in the genomes of cichlid fish. The alignment of the sequences of 70 members of this family, isolated from such fish in Africa, revealed the presence of correlated changes in specific nucleotides (diagnostic nucleotides) that allowed us to categorize the various members into six subfamilies, which were designated Af1 through Af6. Dividing the SINE consensus sequence into a 5′-head and 3′-tail region, these subfamilies were defined by various combinations of four types of head region (A–D) and three types of tail region [X, Y, and (YX)], with each region of each type including unique diagnostic nucleotides. The observed structures of the subfamilies Af1 through Af6 were AX, AY, CY, A(YX), BY, and DX, respectively. The formation of such structures might have involved the shuffling of head or tail regions among preexisting and existing (or both) subfamilies of the AFC family (and, probably, even another SINE family or a pseudogene for a tRNA in the case of the Af6 subfamily) by recombination at the so-called core region during the course of evolution. By plotting the timing of the retroposition of individual members of each subfamily on a phylogenetic tree of AFCs, we found that the Af3 and Af6 subfamilies became active only recently in the evolutionary history of these fish. The integrity of the 3′-tails of SINEs, which are, apparently, recognized by reverse transcriptase, has been reported to be indispensable for retention of retropositional activity. Therefore, we postulate that recombination might have been involved in the apparent recent activation of the retroposition of the Af3 and Af6 subfamilies via introduction of active tails (types Y and X, respectively) into potential ancestral sequences that might have had inactive tails. If this hypothesis is correct, shuffling of tail regions among subfamilies by recombination at the core region might have played a role in the recycling of dead copies of AFC SINEs.
Adequacy of Antidepressant Treatment After Discharge and the Occurrence of Suicidal Acts in Major Depression: A Prospective Study
Authors: Maria A. Oquendo, Masoud Kamali, Steven P. Ellis, Michael F. Grunebaum, Kevin M. Malone, Beth S. Brodsky, Harold A. Sackeim, J. John Mann
Journal: American Journal of Psychiatry (2002)

OBJECTIVE: Suicide attempts predict repeat attempts and suicide completion. Major depression requiring hospitalization is a risk factor for suicidal acts, particularly in the 2 years following discharge. The authors prospectively studied the adequacy of antidepressant treatment and its impact on suicidal acts in the 2 years after hospitalization for major depression. METHOD: Patients (N=136) with major depression were interviewed at 3 months, 1 year, and 2 years after admission. At each interview, the presence of major depression and suicidal acts and the adequacy of antidepressant treatment were assessed. Cox's proportional hazards analysis with time-varying covariates was used to model the risk of a suicide attempt during the follow-up period. RESULTS: Major depression in the follow-up period increased the risk of a suicide attempt sevenfold. For each suicide attempt in a subject's history, the risk for an attempt in the follow-up period increased by 30%. Antidepressant treatment during the follow-up period was mostly inadequate. Consequently, a relationship between adequacy of antidepressant treatment during follow-up and the risk of a suicide attempt could not be found. Furthermore, subjects with a history of a suicide attempt at baseline were not treated more vigorously than nonattempters. CONCLUSIONS: Antidepressant treatment of depressed patients is strikingly inadequate, even in suicide attempters, known to be at higher risk for suicidal acts. This deficiency undermines the ability to measure the antisuicidal effects of antidepressants in naturalistic studies. Controlled studies of antidepressants are needed to evaluate effects on suicidal acts.
Accelerated Evolution of Functional Plastid rRNA and Elongation Factor Genes Due to Reduced Protein Synthetic Load After the Loss of Photosynthesis in the Chlorophyte Alga Polytoma
Authors: Dawne Vernon, Robin R. Gutell, Jamie J. Cannone, Robert W. Rumpf, C. William Birky Jr
Journal: Molecular Biology and Evolution (2001)

Polytoma obtusum and Polytoma uvella are members of a clade of nonphotosynthetic chlorophyte algae closely related to Chlamydomonas humicola and other photosynthetic members of the Chlamydomonadaceae.Descended from a nonphotosynthetic mutant, these obligate heterotrophs retain a plastid (leucoplast) with a functional protein synthetic system, and a plastid genome (lpDNA) with functional genes encoding proteins required for transcription and translation.Comparative studies of the evolution of genes in chloroplasts and leucoplasts can identify modes of selection acting on the plastid genome.Two plastid genes-rrn16, encoding the plastid small-subunit rRNA, and tufA, encoding elongation factor Tu-retain their functions in protein synthesis after the loss of photosynthesis in two nonphotosynthetic Polytoma clades but show a substantially accelerated rate of base substitution in the P. uvella clade.The accelerated evolution of tufA is due, at least partly, to relaxed codon bias favoring codons that can be read without wobble, mainly in three amino acids.Selection for these codons may be relaxed because leucoplasts are required to synthesize fewer protein molecules per unit time than are chloroplasts (reduced protein synthetic load) and thus require a lower rate of synthesis of elongation factor Tu. Relaxed selection due to a lower protein synthetic load is also a plausible explanation for the accelerated rate of evolution of rrn16, but the available data are insufficient to test the hypothesis for this gene.The tufA and rrn16 genes in Polytoma oviforme, the sole member of a second nonphotosynthetic clade, are also functional but show no sign of relaxed selection.
Efficacy of antihistamine pretreatment in the prevention of adverse reactions to Hymenoptera immunotherapy: A prospective, randomized, placebo-controlled trial☆☆☆★★★
Authors: Knut Brockow, Margaret Kiehn, Claudia Riethmüller, Dieter Vieluf, Jürgen Berger, Johannes Ring
Journal: Journal of Allergy and Clinical Immunology (1997)
Cancer of the head and neck. Nasopharyngeal cancer. Radiologic diagnosis
Authors: H. C. Ho
Journal: JAMA (1972)

The majority of malignant tumors occurring in the nasopharynx are carcinomas usually of the epidermoid type, either undifferentiated or of varying degree of differentiation. Lymphoepithelioma is now accepted by most authorities as a poorly differentiated variant of epidermoid carcinoma. The diagnosis of nasopharyngeal carcinoma is often made after a long delay when the disease has already become advanced. This is largely because nasopharyngoscopy is a difficult procedure except in the hands of the expert. It is not possible to perform this procedure in the presence of trismus (not a rare complication resulting from the lateral spread of the carcinoma to the pterygoid muscles), or when there is a hyperactive pharyngeal reflex, in which case general anesthesia is required. Therefore, if a method which offers simplicity of execution and an acceptable degree of reliability in demonstrating nasopharyngeal lesions could be found, it would go a long way to minimize the diagnostic
THE TREATMENT OF LOBAR PNEUMONIA IN A GENERAL HOSPITAL
Authors: LEO KESSEL
Journal: JAMA (1927)

Since November, 1925, all patients with lobar pneumonia admitted to the Mount Sinai Hospital have been studied by a pneumonia commission. The "pneumonia routine" employed in this series consisted of the following orders: (1) in bed; (2) forced fluids (milk, 1,000 cc., fruit drinks, broth, coffee, tea); (3) sponge for 103 F.; (4) enema daily; (5) turpentine stupes when needed; (6) tincture of digitalis, 1 drop per pound on admission, and 45 minims daily thereafter; (7) morphine sulphate, one-fourth grain (16 mg.) on admission; (8) blood pressure daily; (9) leukocyte count and differential determination every two days; (10) blood culture; (11) sputum for culture and typing as soon as obtainable. As an expectorant, when needed, anisated spirit of ammonia, 30 drops every two hours, was used. For pain or restlessness or harassing cough, codeine sulphate, 1 grain (0.065 Gm.) hypodermically was used, to be repeated in four hours if necessary.
Sodium Gentisate in the Treatment of Acute Rheumatic Fever
Authors: LOUIS E. SCHAEFER, IRA A. RASHKOFF, RAYMOND S. MEGIBOW
Journal: Circulation (1950)

Five patients with acute rheumatic fever were treated with gentisate, the biologic oxidation product of salicylate. The clinical course of this group was contrasted with that of five patients who received salicylate. It was found that, in the doses employed, gentisate had an effect on the symptoms of acute rheumatic fever equal to that of salicylate, but that it produced none of the toxic reactions which were commonly found after salicylate administration. An oral dose of 2.0 Gm. of gentisate, every three hours, continued for at least ten days after the temperature became normal, was sufficient to control the symptoms of the disease.
Clue to a more serious diagnosis
Authors: B Abboud
Journal: Gut (2005)

Background and aims: Acid gastro-oesophageal reflux is one of the most important causes of chronic cough.The response to acid suppression in these patients is not as good as in patients with heartburn but improvement with antireflux surgery has been reported, suggesting the involvement of a non-acidic gastric component in the refluxate.Less acidic reflux may produce symptoms such as regurgitation or chest pain.We investigated whether chronic cough might be associated with weakly acidic reflux.Methods: We studied 28 patients with chronic cough using 24 hour ambulatory pressure-pH-impedance monitoring.Manometry was used for precise recognition of cough and impedance-pHmetry to detect acid (pH ,4), weakly acidic (pH 7-4), and weakly alkaline (impedance drops, pH >7) reflux.A symptom association probability (SAP) analysis was performed for each type of reflux.Results: Analysis was completed in 22 patients with 24 cough events (5-92)/patient.The majority of cough events (69.4%) were considered ''independent'' of reflux whereas 30.6% occurred within two minutes of a reflux episode.Half of these (49%) were ''reflux cough'' sequences, involving acid (65%), weakly acidic (29%), and weakly alkaline (6%) reflux.Ten patients (45%) had a positive SAP between reflux and cough: five with acid, two with acid and weakly acidic, and three only with weakly acidic reflux.Conclusions: Ambulatory pressure-pH-impedance monitoring with SAP analysis allowed precise determination of the temporal association between cough and gastro-oesophageal reflux (acid, weakly acidic, and weakly alkaline) and identification of a subgroup of patients with chronic cough clearly associated with weakly acidic gastro-oesophageal reflux.
Alendronate-loaded nanoparticles deplete monocytes and attenuate restenosis
Authors: Einat Cohen-Sela, Ohad Rosenzweig, Jianchuan Gao, Hila Epstein, Irith Gati, Reuven Reich, Haim D. Danenberg, Gershon Golomb
Journal: Journal of Controlled Release (2006)
Detection Of Causative Drugs Using Measurement Of Interferon-ãwith Quantiferon-TB Gold Test In Severe Drug Allergy: Preliminary Study
Authors: Young-Hee Nam, Kyeong-Hee Kim, Dong Sub Jeon, Hye-Won Lee, Hee-Joo Nam, Soo-Keol Lee
Journal: Journal of Allergy and Clinical Immunology (2014)
CHRONIC NEPHRITIS TERMINATING WITH HAEMORRHAGE FROM THE BOWEL AND PERFORATION OF THE BOWEL
Authors: L. G. J. Mackey
Journal: BMJ (1909)

im"x .om clearly of great imprtance that.his conclusion as to the occurrence of blood infection in every case of tuberculosis should be tested.To mention one matter-if it be com- pletely proved that living tubercle bacilli occur in the blood of practically every tuberculous patient, no matter how eaxly or circumscribed the lesion appears to be, it is without doubt that our ideas as to the use of vaccine.therapy-tuberculin-must be considerably modified.Using to some extent his methods, I have examined the blood in 12 cases of pulmonary tuberculosis.The.method of examination is simple, and is, shortlyi as follows:Method.The skin of the front of the forearm is thoroughly cleansed with liquid soap, alcohol, and ether.A tourniquet is applied, and, with a sterile syringe fitted with a platino-iridium needle previously flamed, about 5 c.cm. of blood are drawn from any convenient vein.The blood is at once mixed with about an equal volume of sterile citrated salt solution.The mixture is placed in a swift-running centrifuge for twenty minutes, and some of the deposit taken up on a slide to form a thick film.This is dried in an oven at 600 C., and is then placed in sterile distilled water to lake the blood., Thereafter the film is fixed and stained in the usual way.
Combination Cytotoxic Chemotherapy With Cisplatin or Doxorubicin and Photodynamic Therapy in Murine Tumors1
Authors: M. Y. Nahabedian, R. A. Cohen, M. F. Contino, T. M. Terem, W. H. Wright, M. W. Berns, A. G. Wile
Journal: JNCI Journal of the National Cancer Institute (1988)

This study was designed to evaluate the interaction of photodynamic therapy (PDT) and chemotherapy in an animal model. PDT is based on the interaction of hematoporphyrin derivative and red light of the appropriate wavelength (630 nm) and intensity. Two tumor models were utilized: C3H/Km mice bearing the RIF-1 tumor and BALB/c mice bearing the EMT-6 tumor. Tumor-bearing mice were treated with either cisplatin (DDP), doxorubicin (ADM), PDT, or a combination of drug and PDT. It was demonstrated that the RIF-1 tumor was sensitive to DDP and insensitive to both PDT and ADM. There was no additional antitumor effect when either drug was combined with PDT. The EMT-6 tumor was moderately sensitive to PDT and mildly sensitive to both DDP and ADM. Although the addition of DDP did not potentiate tumor destruction, the addition of ADM significantly enhanced the effect of PDT (P = .01). The enhanced activity of the combination of PDT and ADM appeared to be the result of increased activity of ADM alone, when illuminated with red (630 nm) light. This potentiation may be due to a photochemical process or may be secondary to the mild hyperthermia generated by illumination with the laser. This study demonstrates that PDT combined with cytotoxic chemotherapy is well tolerated in these animals and that certain combinations of PDT and chemotherapy may result in an enhanced tumoricidal effect. [J Natl Cancer Inst 1988;80:739–743]
Efficacy and Safety of the Novel Oral Anticoagulants in Atrial Fibrillation
Authors: Francesco Dentali, Nicoletta Riva, Mark Crowther, Alexander G.G. Turpie, Gregory Y.H. Lip, Walter Ageno
Journal: Circulation (2012)

Novel oral anticoagulants (NOACs) have been proposed as alternatives to vitamin K antagonists for the prevention of stroke and systemic embolism in patients with atrial fibrillation. Individually, NOACs were at least noninferior to vitamin K antagonists, but a clear superiority in overall and vascular mortality was not consistently proven.We performed a meta-analysis of phase II and phase III randomized, controlled trials comparing NOACs with vitamin K antagonists in patients with atrial fibrillation. The MEDLINE and EMBASE databases, supplemented with conference abstract books and www.clinicaltrials.gov, were searched up to the first week of July 2012 with no language restriction. Two reviewers performed independent article review and study quality assessment. Data on overall and cardiovascular mortality, stroke or systemic embolism, ischemic stroke, major and intracranial bleeding, and myocardial infarction were collected. NOACs were pooled to perform a comparison with vitamin K antagonists, calculating pooled relative risks (RRs) and associated 95% confidence intervals (CIs). We retrieved 12 studies (3 administering dabigatran, 4 administering rivaroxaban, 2 administering apixaban, and 3 administering edoxaban) enrolling a total of 54 875 patients. NOACs significantly reduced total mortality (5.61% versus 6.02%; RR, 0.89; 95% CI, 0.83-0.96), cardiovascular mortality (3.45% versus 3.65%; RR, 0.89; 95% CI, 0.82-0.98), and stroke/systemic embolism (2.40% versus 3.13%; RR, 0.77; 95% CI, 0.70-0.86). There was a trend toward reduced major bleeding (RR, 0.86; 95% CI, 0.72-1.02) with a significant reduction of intracranial hemorrhage (RR, 0.46; 95% CI, 0.39-0.56). No difference in myocardial infarction was observed.NOACs are associated with an overall clinical benefit compared with vitamin K antagonists. Additional research is required to confirm these findings outside the context of randomized trials.
Patterns of mortality among migrants to England and Wales from the Indian subcontinent.
Authors: R Balarajan, L Bulusu, A M Adelstein, V Shukla
Journal: BMJ (1984)

Causes of deaths in immigrants to England and Wales from the Indian subcontinent were assessed by ethnic subgroup. Observed and expected deaths for 1975-7 were aggregated to calculate proportional mortality ratios. Observed mortality due to infective and parasitic diseases, endocrine diseases (notably diabetes), diseases of the circulatory system (notably ischaemic heart disease and cerebrovascular disease, in males), and diseases of the digestive system (notably cirrhosis of the liver) exceeded expected mortality. Fewer than expected deaths were due to malignant neoplasms (notably lung cancer and chronic bronchitis); proportional mortality ratios for cancer were lower for Hindu groups than for Moslems and were lowest for Punjabis. Mortality due to ischaemic heart disease, high in all groups, was highest in Moslems. Significantly more Punjabi males died from cerebrovascular disease and cirrhosis of the liver. Diabetes was commonest among Gujaratis. The variation seen in the patterns of mortality in the different ethnic groups indicates the need for further epidemiological and health service research centred on these communities.
Measles and stroke show why healthcare must innovate
Authors: T. Jackson
Journal: BMJ (2013)

The question society has to answer is whether it is ethically acceptable to tolerate any serious complication, or death, from measles when an effective vaccine is available."So say public health specialists Felix Greaves and Liam Donaldson in their editorial reflecting on the recent epidemic of measles in south Wales and the prospect of large outbreaks in England (doi:10.1136/bmj.f2793).With large cohorts of children and teenagers unvaccinated against measles, mumps, and rubella, health systems have been playing catch up as measles cases soar.Greaves and Donaldson turn the spotlight on the public health sector as it undergoes fundamental change.
Allergen-selective redirection of immunoregulatory responses in ragweed-allergic humans using dynavex Amb a 1 immunostimulatory oligodeoxyribonucleotide conjugate (AIC)
Authors: F.E.R. Simons, Y. Shikishima, G. van Nest, J.J. Eiden, K.T. Hay-Glass
Journal: Journal of Allergy and Clinical Immunology (2003)
Generation and characterization of two human alpha/beta T cell clones. Recognizing autologous breast tumor cells through an HLA- and TCR/CD3-independent pathway.
Authors: P Nisticò, P De Berardinis, S Morrone, T Alonzi, C Buono, I Venturo, P G Natali
Journal: Journal of Clinical Investigation (1994)

Cell-mediated immune response to breast tumor has only been marginally investigated. To gain insight into this issue we have developed two clones of distinct phenotype, CD3+ alpha/beta, CD4+, CD8-, CD16-, and CD3+ alpha/beta, CD4-, CD8+, CD16-, respectively, from peripheral blood lymphocytes (PBL) of a breast cancer patient. These effectors, selected on the basis of their cytolytic activity against autologous tumor cells and lack of lysis on NK-sensitive cell lines, preferentially recognize autologous tumor cells. The two clones' cytotoxic activity, while inhibited by anti-LFA-1 mAb, could not be abolished by mAbs to CD3, to class I and class II MHC molecules, and by mAbs to molecules involved in T cell function (i.e., CD4, CD8, CD2). The molecular structure of the alpha and beta T cell receptor chains of the two effector cells, confirmed their clonality and showed that, despite an overlapping killing pattern, they possess distinct TCR alpha and beta chains. These findings demonstrate that breast tumor-specific CTL clones can be generated through current technology and that a alpha/beta effector cell population operating through a HLA-unrestricted and TCR/CD3-independent pathway may be involved in the identification and killing of this tumor.
Experts call for close scrutiny of new cancer centres
Authors: Lynn Eaton
Journal: BMJ (2007)

Community based units that provide care for patients with cancer, which are likely to emerge over the coming years in the United Kingdom, should have formal links to at least one established cancer centre, advises a joint report from the Royal College of Radiologists and the Royal College of Physicians. The staff in such units should participate in the working groups of their local cancer networks, it says.

The colleges also want the units to submit data on activity, complications, and outcomes to …
Changing Concepts of Common Bile Duct Anatomy and Physiology
Authors: Bernard T. Daniels
Journal: JAMA (1961)

Preliminary evidence shows the possibility of intrinsic activity of the common bile duct and indicates that such activity may be separate from the physiologic activity of the sphincter of Oddi and the duodenal musculature. The suggestion is made that such activity could contribute to the symptomatology in biliary dyskinesia. The evidence comes from histologic studies of the common duct wall, a consideration of the anatomic relationships of the musculature of the sphincter of Oddi and the muscle fibers of the common bile duct wall, and from physiologic studies made through operative cinefluorographic cholangiography with simultaneous pressure tracings.
FEEDING THE YOUNG.Read in the Section of Diseases of Children at the Forty-first Annual Meeting of the American Medical Association, at Nashville, Tenn., May, 1890.
Authors: O. H. PHELPS
Journal: JAMA (1890)

the upper end of a hollow hard rubber handle, through which runs a piece of rubber tubing at¬ tached at its upper end to the reservoir, while the lower is armed with a curved gold nozzle which fits firmly into the lower end of the handle and is removable at pleasure.The current, whose force