GuiTope: an application for mapping random-sequence peptides to protein sequences

BACKGROUND: Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. RESULTS: GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. CONCLUSIONS: GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net

Cardiac transplantation in patients over 50 years of age

Sixty-two patients underwent cardiac transplantation at the University of Arizona from March 1979 to March 1985. Thirteen patients (11 men and 2 women) were over 50 years of age at the time of transplantation and 49 were under the age of 50. The mean age (± SEM) of the patients over 50 was 53 ± 1 years. Eight of these patients were treated with conventional immunosuppressive therapy (azathioprine, prednisone and rabbit antithymocyte globulin) and Ave, beginning in January 1983, were treated with cyclosporine, prednisone and rabbit antithymocyte globulin.Early mortality (0 to 90 days) was 16% in the group over 50 versus 18% for those under 50. The late mortality (> 90 days) was 36 and 33%, respectively. In both groups, rejection and infection were the principal causes of death. The incidence of infection was 1.9 ± 0.5 episodes per patient in those patients over 50 and 1.9 ± 0.4 in those under 50. The incidence of rejection was 1.3 episodes per patient-year in patients over 50 and 1.7 episodes per patient-year in those under 50. Actuarial survival at 1 year was 72 ± 14% in the group over 50 and 66 ± 7% in the group under 50 years of age.These data indicate that the results of cardiac transplantation for patients over 50 do not differ significantly from those for patients under 50. Therefore, it is concluded that a rigidly defined age criterion for cardiac transplant recipients is not acceptable. Each potential recipient must be evaluated in terms of individual risk and benefit from the procedure

Susceptibility Provision Enhances Effective De-escalation (SPEED): utilizing rapid phenotypic susceptibility testing in Gram-negative bloodstream infections and its potential clinical impact

Abstract Objectives We evaluated the performance and time to result for pathogen identification (ID) and antimicrobial susceptibility testing (AST) of the Accelerate Pheno™ system (AXDX) compared with standard of care (SOC) methods. We also assessed the hypothetical improvement in antibiotic utilization if AXDX had been implemented. Methods Clinical samples from patients with monomicrobial Gram-negative bacteraemia were tested and compared between AXDX and the SOC methods of the VERIGENE® and Bruker MALDI Biotyper® systems for ID and the VITEK® 2 system for AST. Additionally, charts were reviewed to calculate theoretical times to antibiotic de-escalation, escalation and active and optimal therapy Results ID mean time was 21 h for MALDI-TOF MS, 4.4 h for VERIGENE® and 3.7 h for AXDX. AST mean time was 35 h for VITEK® 2 and 9.0 h for AXDX. For ID, positive percentage agreement was 95.9% and negative percentage agreement was 99.9%. For AST, essential agreement was 94.5% and categorical agreement was 93.5%. If AXDX results had been available to inform patient care, 25% of patients could have been put on active therapy sooner, while 78% of patients who had therapy optimized during hospitalization could have had therapy optimized sooner. Additionally, AXDX could have reduced time to de-escalation (16 versus 31 h) and escalation (19 versus 31 h) compared with SOC. Conclusions By providing fast and reliable ID and AST results, AXDX has the potential to improve antimicrobial utilization and enhance antimicrobial stewardship

Mean field analysis of a model for superconductivity in an antiferromagnetic background

We study a lattice fermion model for superconductivity in the presence of an antiferromagnetic background, described as a fixed external staggered magnetic field. We discuss the possibility that our model provides an effective description of coexistence of antiferromagnetic correlations and superconductivity, and its possible application to high temperature superconductivity. We also argue that, under certain conditions, this model describes a variant of the periodic Anderson model for heavy fermions. Using a path integral formulation we construct mean field equations, which we study in some detail. We evaluate the superconducting critical temperature and show that it is strongly enhanced by antiferromagnetic order. We also evaluate the superconducting gap, the superconducting density of states, and the tunneling conductivity, and show that the most stable channel usually has a $d_{x^2-y^2}$-wave gap.Comment: 26 pages, 9 ps figures included via epsf. Published versio

Direct antimicrobial susceptibility testing of positive blood cultures: A comparison of the accelerate Pheno™ and VITEK® 2 systems

Objectives To compare the performance and time-to-result (TTR) for antimicrobial susceptibility testing (AST) of positive blood cultures (PBC) using the Accelerate Pheno™ system (AXDX) and both a direct VITEK® 2 card inoculation workflow (DV2) and traditional FDA-approved VITEK® 2 workflow using subcultured isolates (V2). Methods Patient samples with monomicrobial Gram-negative rod bacteremia were tested on AXDX and DV2 in tandem, and compared to V2 AST results. Categorical agreement (CA) errors were adjudicated using broth microdilution. Instrumentation times and AST TTR were compared. Results AXDX and DV2 had a CA of 91.5% and 97.4%, respectively, compared to V2. Post-adjudication, AXDX, DV2, and V2 had CA of 94.7%, 95.7% and 96.5%, respectively. Instrument run times were 6.6 h, 9.4 h, and 9.2 h, and AST TTR were 8.9 h, 12.9 h and 35.5 h, respectively. Conclusions AXDX and DV2 AST is fast and reliable, which may have significant antimicrobial stewardship implications

On Four-Point Functions of Half-BPS Operators in General Dimensions

We study four-point correlation functions of half-BPS operators of arbitrary weight for all dimensions d=3,4,5,6 where superconformal theories exist. Using harmonic superspace techniques, we derive the superconformal Ward identities for these correlators and present them in a universal form. We then solve these identities, employing Jack polynomial expansions. We show that the general solution is parameterized by a set of arbitrary two-variable functions, with the exception of the case d=4, where in addition functions of a single variable appear. We also discuss the operator product expansion using recent results on conformal partial wave amplitudes in arbitrary dimension.Comment: The discussion of the case d=6 expanded; references added/correcte

The Lantern Vol. 46, No. 2, April 1980

• The Voyage to Man\u27s Destiny • If I Could Keep the Times • Barstool Blues • I Didn\u27t Know • Felonious, Friend • Cool Ride • Georgia • Let Us Eat and Drink • In a Field • New Born Foal • Union to Freedom • In the Woods • Anthropomorphism • Runner • C.C. • Lake Attempt • A Fuzzy Blue Line • Trust Me • Haven\u27t We Met Before? • Rationality • Expecting Me • Short Storyhttps://digitalcommons.ursinus.edu/lantern/1116/thumbnail.jp

International criteria for electrocardiographic interpretation in athletes: Consensus statement.

Sudden cardiac death (SCD) is the leading cause of mortality in athletes during sport. A variety of mostly hereditary, structural or electrical cardiac disorders are associated with SCD in young athletes, the majority of which can be identified or suggested by abnormalities on a resting 12-lead electrocardiogram (ECG). Whether used for diagnostic or screening purposes, physicians responsible for the cardiovascular care of athletes should be knowledgeable and competent in ECG interpretation in athletes. However, in most countries a shortage of physician expertise limits wider application of the ECG in the care of the athlete. A critical need exists for physician education in modern ECG interpretation that distinguishes normal physiological adaptations in athletes from distinctly abnormal findings suggestive of underlying pathology. Since the original 2010 European Society of Cardiology recommendations for ECG interpretation in athletes, ECG standards have evolved quickly, advanced by a growing body of scientific data and investigations that both examine proposed criteria sets and establish new evidence to guide refinements. On 26-27 February 2015, an international group of experts in sports cardiology, inherited cardiac disease, and sports medicine convened in Seattle, Washington (USA), to update contemporary standards for ECG interpretation in athletes. The objective of the meeting was to define and revise ECG interpretation standards based on new and emerging research and to develop a clear guide to the proper evaluation of ECG abnormalities in athletes. This statement represents an international consensus for ECG interpretation in athletes and provides expert opinion-based recommendations linking specific ECG abnormalities and the secondary evaluation for conditions associated with SCD