tbuckley/cabot-search huggingface dataset:
A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Authors: Maha R Farhat, B Jesse Shapiro, Samuel K Sheppard, Caroline Colijn, Megan Murray
Journal: Genome Medicine (2014)

Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little has been published on how and how many pathogen strains should be selected for studies associating phenotype and genotype. There are specific challenges when identifying genetic associations in bacteria which often comprise highly structured populations. Here we consider general methodological questions related to sampling and analysis focusing on clonal to moderately recombining pathogens. We propose that a matched sampling scheme constitutes an efficient study design, and provide a power calculator based on phylogenetic convergence. We demonstrate this approach by applying it to genomic datasets for two microbial pathogens: Mycobacterium tuberculosis and Campylobacter species.
90Y-ibritumomab tiuxetan, fludarabine, busulfan and antithymocyte globulin reduced-intensity allogeneic transplant conditioning for patients with advanced and high-risk B-cell lymphomas
Authors: K. Bouabdallah, S. Furst, J. Asselineau, P. Chevalier, O. Tournilhac, P. Ceballos, S. Vigouroux, R. Tabrizi, A. Doussau, R. Bouabdallah, M. Mohty, S. Le Gouill, D. Blaise, N. Milpied
Journal: Annals of Oncology (2014)
A MAJOR GENETIC LOCUS AFFECTING RESISTANCE TO INFECTION WITH MURINE LEUKEMIA VIRUSES
Authors: Theodore Pincus, Wallace P. Rowe, Frank Lilly
Journal: The Journal of Experimental Medicine (1971)

The N-B locus affecting tissue culture infectivity with naturally occurring murine leukemia viruses appears to be identical to the Fv-1 locus described for sensitivity to Friend leukemia virus. Results of tissue culture studies were parallel to results of studies in vivo and indicate that the F-S virus is N-tropic and the F-B virus is NB-tropic. Inbred and partially congenic mouse strains sensitive at Fv-1 show N-type sensitivity; strains resistant at Fv-1 show B-type sensitivity. The Fv-2 locus does not appear to exert significant effect in tissue culture. Knowledge of N-B type has been useful in predicting Fv-1 sensitivity.
Results of the baseline positron emission tomography can customize therapy of localized esophageal adenocarcinoma patients who achieve a clinical complete response after chemoradiation
Authors: A. Suzuki, L. Xiao, T. Taketa, K. Sudo, R. Wadhwa, M.A. Blum, H. Skinner, R. Komaki, B. Weston, J.H. Lee, M.S. Bhutani, D.C. Rice, D.M. Maru, J. Erasmus, S.G. Swisher, W.L. Hofstetter, J.A. Ajani
Journal: Annals of Oncology (2013)
The Brussels Declaration: the need for change in asthma management
Authors: S. Holgate, H. Bisgaard, L. Bjermer, T. Haahtela, J. Haughney, R. Horne, A. McIvor, S. Palkonen, D. B. Price, M. Thomas, E. Valovirta, U. Wahn
Journal: European Respiratory Journal (2008)

Asthma is a highly prevalent condition across Europe and numerous guidelines have been developed to optimise management. However, asthma can be neither cured nor prevented, treatment choices are limited and many patients have poorly controlled or uncontrolled asthma. The Brussels Declaration on Asthma, sponsored by The Asthma, Allergy and Inflammation Research Charity, was developed to call attention to the shortfalls in asthma management and to urge European policy makers to recognise that asthma is a public health problem that should be a political priority. The Declaration urges recognition and action on the following points: the systemic inflammatory component of asthma should be better understood and considered in assessments of treatment efficacy; current research must be communicated and responded to quickly; the European Medicines Agency guidance note on asthma should be updated; “real world” studies should be funded and results used to inform guidelines; variations in care across Europe should be addressed; people with asthma should participate in their own care; the impact of environmental factors should be understood; and targets should be set for improvement. The present paper reviews the evidence supporting the need for change in asthma management and summarises the ten key points contained in the Brussels Declaration.
Azithromycin and severe asthma
Authors: David L Hahn
Journal: Thorax (2013)

Brusselle et al 1 performed an interesting academic-based randomised controlled trial Azithromycin for Prevention of Exacerbations in Severe Asthma (AZISAST) of azithromycin 250 mgm taken thrice weekly versus placebo as add-on therapy for 26 weeks in non-smoking patients with severe asthma, defined as Global Initiative for Asthma (GINA) steps 4–5, taking high dose inhaled corticosteroids/long-acting bronchodilators and with at least …
Use of Patient-Controlled Analgesia for Management of Acute Pain
Authors: P F White
Journal: JAMA (1988)

Patient-controlled analgesia (PCA) provides improved titration of analgesic drugs, thereby minimizing individual pharmacokinetic and pharmacodynamic differences. Patient-controlled analgesia decreases patient anxiety resulting from delays in receiving pain-relieving medication and from the slow onset of analgesic action when these drugs are administered either intramuscularly or in the extradural space. With PCA therapy, patients are reportedly able to maintain a near optimal state of analgesia with minimal sedation and few side effects. The potential for overdose can be minimized if small bolus doses are used with a mandatory lockout interval between successive doses. Finally, studies of the cost-effectiveness of PCA therapy are important if this therapeutic approach is to achieve more widespread acceptance. (<i>JAMA</i>1988;259:243-247)
Effect of periodontal treatment on preterm birth rate: a systematic review of meta‐analyses
Authors: Néstor J. López, Sergio Uribe, Benjamín Martinez
Journal: Periodontology 2000 (2014)

Preterm birth is a major cause of neonatal morbidity and mortality in both developed and developing countries. Preterm birth is a highly complex syndrome that includes distinct clinical subtypes in which many different causes may be involved. The results of epidemiological, molecular, microbiological and animal-model studies support a positive association between maternal periodontal disease and preterm birth. However, the results of intervention studies carried out to determine the effect of periodontal treatment on reducing the risk of preterm birth are controversial. This systematic review critically analyzes the methodological issues of meta-analyses of the studies to determine the effect of periodontal treatment to reduce preterm birth. The quality of the individual randomized clinical trials selected is of highest relevance for a systematic review. This article describes the methodological features that should be identified a priori and assessed individually to determine the quality of a randomized controlled trial performed to evaluate the effect of periodontal treatment on pregnancy outcomes. The AMSTAR and the PRISMA checklist tools were used to assess the quality of the six meta-analyses selected, and the bias domain of the Cochrane Collaboration's Tool was applied to evaluate each of the trials included in the meta-analyses. In addition, the methodological characteristics of each clinical trial were assessed. The majority of the trials included in the meta-analyses have significant methodological flaws that threaten their internal validity. The lack of effect of periodontal treatment on preterm birth rate concluded by four meta-analyses, and the positive effect of treatment for reducing preterm birth risk concluded by the remaining two meta-analyses are not based on consistent scientific evidence. Well-conducted randomized controlled trials using rigorous methodology, including appropriate definition of the exposure, adequate control of confounders for preterm birth and application of effective periodontal interventions to eliminate periodontal infection, are needed to confirm the positive association between periodontal disease and preterm birth.
Forward Genetic Dissection of Immunity to Infection in the Mouse
Authors: S.M. Vidal, D. Malo, J.-F. Marquis, P. Gros
Journal: Annual Review of Immunology (2007)

Forward genetics is an experimental approach in which gene mapping and positional cloning are used to elucidate the molecular mechanisms underlying phenotypic differences between two individuals for a given trait. This strategy has been highly successful for the study of inbred mouse strains that show differences in innate susceptibility to bacterial, parasitic, fungal, and viral infections. Over the past 20 years, these studies have led to the identification of a number of cell populations and critical biochemical pathways and proteins that are essential for the early detection of and response to invading pathogens. Strikingly, the macrophage is the point of convergence for many of these genetic studies. This has led to the identification of diverse pathways involved in extracellular and intracellular pathogen recognition, modification of the properties and content of phagosomes, transcriptional response, and signal transduction for activation of adaptive immune mechanisms. In models of viral infections, elegant genetic studies highlighted the pivotal role of natural killer cells in the detection and destruction of infected cells.
Role of Helicobacter pylori in ulcer healing and recurrence of gastric and duodenal ulcers in longterm NSAID users. Response to omeprazole dual therapy.
Authors: G Bianchi Porro, F Parente, V Imbesi, F Montrone, I Caruso
Journal: Gut (1996)

BACKGROUND: The relation between Helicobacter pylori infection and non-steroidal anti-inflammatory drug (NSAID)-associated peptic ulcers remains unclear; in particular, it is not known whether H pylori plays a part in the healing and recurrence of these ulcers. AIMS: To evaluate prospectively in a consecutive series of arthritis patients receiving longterm NSAID treatment the prevalence of peptic ulcer as well as the effect of H pylori eradication on the healing and recurrence of gastric and duodenal ulcer found. PATIENTS: Some 278 consecutive patients underwent gastroscopy with multiple biopsies of the gastric antrum and corpus for histological examination and rapid urease test. One hundred peptic ulcers (59 gastric ulcers, 39 duodenal ulcers, and two gastric ulcers concomitant with a duodenal ulcer) were found. Seventy per cent of these ulcers were H pylori positive. METHODS: According to their H pylori status, ulcer patients were randomised to one of the following treatments: H pylori negative ulcers received omeprazole 20 mg twice daily for four to eight weeks, whereas H pylori positive lesions were treated with omeprazole 20 mg twice daily plus amoxycillin 1 g twice daily (the second of these for the first two weeks) or omeprazole alone for four to eight weeks while continuing NSAID therapy. Patients with healed ulcers were endoscopically followed up for six months after stopping antiulcer therapy while continuing NSAIDs. RESULTS: Endoscopic healing rates for gastric and duodenal ulcers in the three different groups were similar both at four and eight weeks. H pylori eradication did not influence healing, which occurred in 14 of 20 (70%) of patients in whom H pylori was eradicated, compared with 14 of 17 (82%) of patients with persistent infection. Cumulative recurrence rates at six months did not statistically differ among the three different groups (27% in H pylori negative, 46% in H pylori positive, and 31% in those where H pylori was eradicated during the healing phase), although a numerical trend in favour of a higher recurrence rate in infected patients was evident. CONCLUSIONS: H pylori eradication does not confer any significant advantage on the healing of gastric and duodenal ulcers associated with longterm NSAID use. It remains to be established with certainty whether eradication may be helpful in the reduction of recurrence in a specific subset of NSAID associated ulcer.
Bioenergetic and Functional Consequences of Bone Marrow–Derived Multipotent Progenitor Cell Transplantation in Hearts With Postinfarction Left Ventricular Remodeling
Authors: Lepeng Zeng, Qingsong Hu, Xiaohong Wang, Abdul Mansoor, Joseph Lee, Julia Feygin, Ge Zhang, Piradeep Suntharalingam, Sherry Boozer, Abner Mhashilkar, Carmelo J. Panetta, Cory Swingen, Robert Deans, Arthur H.L. From, Robert J. Bache, Catherine M. Verfaillie, Jianyi Zhang
Journal: Circulation (2007)

The present study examined whether transplantation of adherent bone marrow-derived stem cells, termed pMultistem, induces neovascularization and cardiomyocyte regeneration that stabilizes bioenergetic and contractile function in the infarct zone and border zone (BZ) after coronary artery occlusion.Permanent left anterior descending artery occlusion in swine caused left ventricular remodeling with a decrease of ejection fraction from 55+/-5.6% to 30+/-5.4% (magnetic resonance imaging). Four weeks after left anterior descending artery occlusion, BZ myocardium demonstrated profound bioenergetic abnormalities, with a marked decrease in subendocardial phosphocreatine/ATP (31P magnetic resonance spectroscopy; 1.06+/-0.30 in infarcted hearts [n=9] versus 1.90+/-0.15 in normal hearts [n=8; P<0.01]). This abnormality was significantly improved by transplantation of allogeneic pMultistem cells (subendocardial phosphocreatine/ATP to 1.34+/-0.29; n=7; P<0.05). The BZ protein expression of creatine kinase-mt and creatine kinase-m isoforms was significantly reduced in infarcted hearts but recovered significantly in response to cell transplantation. MRI demonstrated that the infarct zone systolic thickening fraction improved significantly from systolic "bulging" in untreated animals with myocardial infarction to active thickening (19.7+/-9.8%, P<0.01), whereas the left ventricular ejection fraction improved to 42.0+/-6.5% (P<0.05 versus myocardial infarction). Only 0.35+/-0.05% donor cells could be detected 4 weeks after left anterior descending artery ligation, independent of cell transplantation with or without immunosuppression with cyclosporine A (with cyclosporine A, n=6; no cyclosporine A, n=7). The fraction of grafted cells that acquired an endothelial or cardiomyocyte phenotype was 3% and approximately 2%, respectively. Patchy spared myocytes in the infarct zone were found only in pMultistem transplanted hearts. Vascular density was significantly higher in both BZ and infarct zone of cell-treated hearts than in untreated myocardial infarction hearts (P<0.05).Thus, allogeneic pMultistem improved BZ energetics, regional contractile performance, and global left ventricular ejection fraction. These improvements may have resulted from paracrine effects that include increased vascular density in the BZ and spared myocytes in the infarct zone.
SCANNING ELECTRON MICROSCOPY OF HUMAN LYMPHOCYTE-SHEEP ERYTHROCYTE ROSETTES
Authors: A. Polliack, Shu Man Fu, S. D. Douglas, Z. Bentwich, N. Lampen, E. De Harven
Journal: The Journal of Experimental Medicine (1974)

Human lymphocytes of known B or T derivation were examined by scanning electron microscopy (SEM) before and after rosetting with SRBC. After collection of the cells onto silver membranes the samples were prepared for SEM by the critical point drying method. Sheep RBC frequently underwent sphero-echinocyte transformation and multiple projections extended from their surfaces. This was readily noticeable after storage of SRBC in the cold and washing in Hanks, but more prominent after rosetting. These erythrocyte surface alterations were less apparent when freshly withdrawn cells were used. Spontaneous sheep erythrocyte rosettes (E-R), a marker for human T lymphocytes, were prepared with normal peripheral blood lymphocytes (PBL), thymic cells, and cultured T cells. EAC-rosettes (EAC-R), used to identify B lymphocytes with complement receptors, were prepared with normal PBL and cultured B cells. The majority of rosetting T lymphocytes had generally smooth surfaces while about 20% had an intermediate number of microvilli and 15% were more villous and indistinguishable from villous B cells. Studies of rosetting thymocytes and cultured T cells however indicated that the surface of some T cells alters on rosetting, becoming more villous and thus account for the higher numbers of villous T cells seen in E-rosettes. Point to point contact sites between SRBC and T lymphocytes were more frequent than broad zones of attachment. The majority of rosetting B lymphocytes had multiple microvilli, about 25% had a moderate number of microvilli and less than 10% had smooth surfaces similar to those of most T cells. Areas of contact between EAC and B lymphocytes were frequently broad zones of attachment. The study confirms that in many cases B and T lymphocytes can be distinguished by their surface architecture as seen under the SEM; however, about 20% of rosetting B and T cells have similar surfaces with intermediate numbers of surface microvilli and cannot be distinguished by SEM without parallel immunologic identification.
Sleep-stage regulation of ventricular arrhythmias in the unanesthetized pig.
Authors: J E Skinner, D N Mohr, P Kellaway
Journal: Circulation Research (1975)

In two groups of purebred juvenile Hampshire pigs, left anterior descending coronary occluders were implanted. The pigs were then adapted to the recording chamber until they would manifest a criterion pattern of sleep while in it. In group A, permanent coronary artery occlusions were produced, and the effects of various sleep stages on the resultant cardiac arrhythmias were observed. Sleep intervals during which transitional and slow wave (SW) sleep alternated were correlated with increased arrhythmias relative to the awake state (P less than 0.04). The increase was maximum during sustained periods of SW sleep. Intervals during which rapid eye movement (REM) sleep predominated were correlated with a reduction in arrhythmias. In group B, temporary occlusions were made during both an awake condition and after criterion patterns of either SW or REM sleep. Occlusions after SW sleep reduced the ventricular fibrillation latency compared with that during the awake control state (P less than 0.05), whereas occlusions after REM sleep increased ventricular fibrillation latency (P less than 0.05). We conclude that SW SLEEP, BUT NOT REM sleep, has a deleterious effect on the ischemic myocardium. REM sleep may have a beneficial effect, since it increases ventricular fibrillation latency. Heart rate changes do not appear to be correlated with the effects of either sleep stage.
AN ULTRASTRUCTURAL STUDY OF THE MECHANISMS OF PLATELET-ENDOTOXIN INTERACTION
Authors: Arthur R. Spielvogel
Journal: The Journal of Experimental Medicine (1967)

Electron microscopy has confirmed previous studies and has provided much new information on the mechanism of endotoxin-platelet interaction. The Boivin lipopolysaccharide preparation is particulate, and on electron microscope examination appears as a three-layered structure, morphologically similar to bacterial cell wall. In vitro and in vivo experiments have demonstrated that these endotoxin particles adhere to platelets. In some species, particularly the rabbit, this is associated with loss of platelet contents, due to lysosomal and cell membrane lysis, resulting in platelet sphering and apparent cell death. Serial observation of degranulating platelets and metabolic studies indicate that although some platelet engulfment of endotoxin occurs, degranulation is not dependent upon phagocytosis. Several observations suggest that these endotoxin effects are mediated through immune mechanisms: (1) Inactivation of complement in the suspending plasma by heating to 56 degrees C, anticoagulation with EDTA, a reaction temperature of 5 degrees C, ammonium hydroxide incubation, and adsorption with either zymosan or washed antigen-antibody complexes, inhibits both endotoxin adherence and platelet degranulation. (2) The reaction requires a plasma cofactor, possibly antibody, which can be adsorbed out by endotoxin. (3) Endotoxin adheres selectively to nonprimate platelets and primate red cells, a pattern conforming to immune adherence, a phenomenon requiring antigen, antibody, and complement. It is suggested that endotoxin-induced platelet damage is dependent upon the intimate contact provided by immune adherence. We have not established whether degranulation is an endotoxin or complement effect. The species variation in susceptibility to endotoxin also merits further investigation.
Comparison of Single-Mother and Two-Parent Families on Metabolic Control of Children With Diabetes
Authors: Sanna J. Thompson, Wendy F. Auslander, Neil H. White
Journal: Diabetes Care (2001)

OBJECTIVE— To understand the impact of family structure on the metabolic control of children with diabetes, we posed two research questions: 1) what are the differences in sociodemographic, family, and community factors between single-mother and two-parent families of diabetic children? and 2) to what extent do these psychosocial factors predict metabolic control among diabetic children from single-mother and two-parent families? RESEARCH DESIGN AND METHODS— This cross-sectional study included 155 diabetic children and their mothers or other female caregivers. The children were recruited if they had been diagnosed with diabetes for at least 1 year, had no other comorbid chronic illnesses, and were younger than 18 years of age. Interviews and self-report questionnaires were used to assess individual, family, and community variables. RESULTS— The findings indicate that diabetic children from single-mother families have poorer metabolic control than do children from two-parent families. Regression models of children's metabolic control from single-mother families indicate that age and missed clinic appointments predicted HbAlc levels; however, among two-parent families,children's ethnicity and adherence to their medication regimen significantly predicted metabolic control. CONCLUSIONS— This study suggests that children from single-mother families are at risk of poorer metabolic control and that these families have more challenges to face when raising a child with a chronic illness. Implications point to a need for developing strategies sensitive to the challenges of single mothers.
Adverse reactions after administration of indocyanine green
Authors: T. R. Garski
Journal: JAMA (1978)

To the Editor.—  Sterile indocyanine green (Cardio-Green) has established clinical value in cardiac dye-dilution study, liver function and blood flow determination, and ophthalmic angiography. Early after its introduction, adverse reactions noted in patients with iodide sensitivity were attributed to the solubilizing iodide component of the pharmaceutical product and led to the incorporation of an appropriate warning in the accompanying package insert.  Four more recent reactions (including one death) having a temporal relationship to the administration of sterile indocyanine green have been reported to its manufacturer. None of the patients were thought to have received indocyanine green previously. Each reaction was reported from a different institution, and each involved a different lot number of product. In each case the product was reported to have been used promptly after proper reconstitution in doses consistent with currently recommended levels.  Report of Cases.—Case 1.—  A 70-year-old woman who had undergone a radical