Using the Food and Drug Administration´s Sentinel System for surveillance of TB infection

BACKGROUND: We examined patterns in care for individuals treated for latent TB infection (LTBI) in the US Food and Drug Administration´s Sentinel System.METHODS: Using administrative claims data, we identified patients who filled standard LTBI treatment prescriptions during 2008-2019. In these cohorts, we assessed LTBI testing, clinical management, and treatment duration.RESULTS: Among 113,338 patients who filled LTBI prescriptions, 80% (90,377) received isoniazid (INH) only, 19% (21,235) rifampin (RIF) only, and 2% (1,726) INH + rifapentine (RPT). By regimen, the proportion of patients with documented prior testing for TBI was 79%, 54%, and 91%, respectively. Median therapy duration was 84 days (IQR 35-84) for the 3-month once-weekly INH + RPT regimen, 60 days (IQR 30-100) for the 6- to 9-month INH regimen, and 30 days (IQR 2-60) for the 4-month RIF regimen.CONCLUSIONS: Among the cohorts, INH-only was the most commonly prescribed LTBI treatment. Most persons who filled a prescription for LTBI treatment did not have evidence of completing recommended treatment duration. These data further support preferential use of shorter-course regimens such as INH + RPT.

Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood

BACKGROUND

Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization.

METHODS

Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT), 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS) and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms.

RESULTS

Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder).

CONCLUSION

The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.

Corticosteroid effects on blood gene expression in Duchenne muscular dystrophy

Though Deflazacort and prednisone improve clinical endpoints in Duchenne muscular dystrophy (DMD) patients, Deflazacort produces fewer side effects. As mechanisms of improvement and side effect differences remain unknown, we evaluated effects of corticosteroid administration on gene expression in blood of DMD patients. Whole blood was obtained from 14 children and adolescents with DMD treated with corticosteroids (DMD-STEROID) and 20 DMD children and adolescents naïve to corticosteroids (DMD). The DMD-STEROID group was further subdivided into Deflazacort and prednisone groups. Affymetrix U133 Plus 2.0 expression microarrays were used to evaluate mRNA expression. Expression of 524 probes changed with corticosteroids, including genes in iron trafficking and the chondroitin sulfate biosynthesis pathway. Deflazacort compared with prednisone yielded 508 regulated probes, including many involved in adipose metabolism. These genes and pathways help explain mechanisms of efficacy and side effects of corticosteroids, and could provide new treatment targets for DMD and other neuromuscular disorders.

Validation of a commercially available immunoassay for the measurement of bovine cardiac troponin I

BACKGROUND

Commercially available cardiac troponin I (cTnI) assays developed for use in humans have not yet been validated for use in cattle.

HYPOTHESES

The ADVIA Centaur TnI-Ultra immunoassay can be used for the detection of bovine cTnI. In healthy cattle, serum cTnI is undetectable or is present only in trace amounts.

METHODS

Purified bovine cTnI and cTnI-free bovine serum were used for the evaluation of assay performance including intra- and inter-assay precision, sensitivity, interference, linearity, and recovery. Effects of storage at 23, 4, -20, and -80 degrees C for 2 days, and at -20 and -80 degrees C for 7 and 14 days and repeated freeze-thaw cycles on recovery of cTnI were analyzed. Serum cTnI concentrations in 30 healthy dairy cows were determined.

RESULTS

Intra- and inter-assay precisions (mean +/- SD) were 4.48 +/- 2.26 and 13.36 +/- 6.59%, respectively. The assay demonstrated linearity at 0.5, 2, 15, and 30 ng/mL cTnI. Mean recovery was 100.81, 85.26, 87.72, and 114.42%, respectively. Skeletal muscle homogenate added to serum of known cTnI concentration did not alter the concentration of the analyte (P > .05). Concentration of cTnI significantly decreased when samples were stored at 4 and 23 degrees C for 2 days (P < .05). Repeated freeze-thaw cycles and storage at -20 degrees C for 7 days had no significant influence on cTnI concentration (P > .05). Serum cTnI concentration in healthy cattle was <or=0.03 ng/mL.

CONCLUSION AND CLINICAL IMPORTANCE

ADVIA Centaur can be used reliably for the detection of serum cTnI concentration in cattle.

Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients

Background

Non-biological experimental error routinely occurs in microarray data collected in different batches. It is often impossible to compare groups of samples from independent experiments because batch effects confound true gene expression differences. Existing methods can correct for batch effects only when samples from all biological groups are represented in every batch.

Results

In this report we describe a generalized empirical Bayes approach to correct for cross-experimental batch effects, allowing direct comparisons of gene expression between biological groups from independent experiments. The proposed experimental design uses identical reference samples in each batch in every experiment. These reference samples are from the same tissue as the experimental samples. This design with tissue matched reference samples allows a gene-by-gene correction to be performed using fewer arrays than currently available methods. We examine the effects of non-biological variation within a single experiment and between experiments.

Conclusion

Batch correction has a significant impact on which genes are identified as differentially regulated. Using this method, gene expression in the blood of patients with Duchenne Muscular Dystrophy is shown to differ for hundreds of genes when compared to controls. The numbers of specific genes differ depending upon whether between experiment and/or between batch corrections are performed.

A proteomic study of serum from children with autism showing differential expression of apolipoproteins and complement proteins

Modern methods that use systematic, quantitative and unbiased approaches are making it possible to discover proteins altered by a disease. To identify proteins that might be differentially expressed in autism, serum proteins from blood were subjected to trypsin digestion followed by liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) on time-of-flight (TOF) instruments to identify differentially expressed peptides. Children with autism 4-6 years of age (n=69) were compared to typically developing children (n=35) with similar age and gender distributions. A total of 6348 peptide components were quantified. Of these, five peptide components corresponding to four known proteins had an effect size >0.99 with a P<0.05 and a Mascot identification score of 30 or greater for autism compared to controls. The four proteins were: Apolipoprotein (apo) B-100, Complement Factor H Related Protein (FHR1), Complement C1q and Fibronectin 1 (FN1). In addition, apo B-100 and apo A-IV were higher in children with high compared to low functioning autism. Apos are involved in the transport of lipids, cholesterol and vitamin E. The complement system is involved in the lysis and removal of infectious organisms in blood, and may be involved in cellular apoptosis in brain. Despite limitations of the study, including the low fold changes and variable detection rates for the peptide components, the data support possible differences of circulating proteins in autism, and should help stimulate the continued search for causes and treatments of autism by examining peripheral blood.

A novel method of Multiplexed Competitive Antibody Binning for the characterization of monoclonal antibodies

We have developed a novel method of high-throughput Multiplexed Competitive Antibody Binning (MCAB). Using only a small amount of antibody and antigen, this method enables the sorting of a large, complex panel of monoclonal antibodies into different bins based on cross-competition for antigen binding. The MCAB assay builds on Luminex multiplexing bead-based technology to detect antibody competition. Because of its high sensitivity, the MCAB method is immediately applicable after identification of antigen-positive mAbs, providing information useful for advancing mAb candidates into further testing. The MCAB assay also can be used for sorting mAbs into binding groups after screening for functional activity.

Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.

Progress in the design of DNA sequence-specific lexitropsins

Sequence-specific polyamides that bind in the minor groove of DNA are attractive candidates for antibiotics, cancer chemotherapeutics, and transcriptional antagonists. This paper reviews the progress of structure-based design of minor-groove-binding polyamides, from the first structure of netropsin with DNA, to the effective linked polyamides currently under study. A theory of polyamide specificity is also reviewed, introducing methods to determine the optimal strategies for targeting a given DNA sequence within a genome of competing sequences.

Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles

Genome-wide transcript profiling was used to monitor signal transduction during yeast pheromone response. Genetic manipulations allowed analysis of changes in gene expression underlying pheromone signaling, cell cycle control, and polarized morphogenesis. A two-dimensional hierarchical clustered matrix, covering 383 of the most highly regulated genes, was constructed from 46 diverse experimental conditions. Diagnostic subsets of coexpressed genes reflected signaling activity, cross talk, and overlap of multiple mitogen-activated protein kinase (MAPK) pathways. Analysis of the profiles specified by two different MAPKs-Fus3p and Kss1p-revealed functional overlap of the filamentous growth and mating responses. Global transcript analysis reflects biological responses associated with the activation and perturbation of signal transduction pathways.

Coevolution and subsite decomposition for the design of resistance-evading HIV-1 protease inhibitors

Drug resistance sharply limits the effectiveness of human immunodeficiency virus (HIV) protease inhibitors in acquired immunodeficiency syndrome therapy. In previous work, we presented methods for design of resistance-evading inhibitors using a computational coevolution technique. Here, we report subsite decomposition experiments that examine the relative importance and roles of each subsite in HIV protease, and the constraints on robust inhibitor design that are imposed by possible resistance mutations in each subsite. The results identify several structural features of robust resistance-evading inhibitors for use in drug design, and show their basis in the constraints imposed by the range of allowable mutation in the protease. In particular, the results identify the P3 and P3' sites as being particularly sensitive to protease mutation: inhibitors designed to fill the S3 and S3' sites of the wild-type protease will be susceptible to viral resistance, but inhibitors with side-chains smaller than a phenylalanine residue at P3 and P3', preferably medium-sized amino acids in the range from valine to leucine and isoleucine residues, will be more robust in the face of protease resistance mutation.

An analysis of a class of DNA sequence reading molecules

Linked polyamides are a class of designed molecules that bind in the minor groove of double-stranded DNA in a partially sequence-specific manner but have limited sequence discriminatory abilities. This suggests a need for design alternatives to create molecules with enhanced sequence specificity. In this report we present formal proofs of the theoretical limits of the DNA sequence specificity of hypothetical sequence reading molecules as a function of their base recognition properties and sequence content and length of their target sequence. We prove that molecules containing nonspecific readers at critical positions within the molecule may have enhanced sequence specificity over molecules composed entirely of base specific reading elements. We also determine optimal patterns of base recognition for molecules in order to optimize their target sequence specificity. We also examine the effect of the length of a polyamide (i.e., the number of base pairs it binds) on its sequence discriminatory ability and determine necessary concentration dependent constraints on the binding free energies in order for longer polyamides to have greater sequence specificity than shorter ones. We show that unless the discriminatory ability of a ring for its preferred base is very strong, longer polyamides do not necessarily have greater sequence specificity over shorter ones when compared at the same molar concentration.

The theoretical limits of DNA sequence discrimination by linked polyamides

Linked polyamides bind in the minor groove of double-stranded DNA in a partially sequence-specific manner. This report analyzes the theoretical limits of DNA sequence discrimination by linked polyamides composed of two to four different types of heterocyclic rings, determining (i) the optimal choice of base-binding specificity for each ring and (ii) the optimal design for a polyamide composed of these rings to target a given DNA sequence and designed to maximize the fraction of the total polyamide binding to the specified target sequence relative to all other sequences. The results show that, fortuitously, polyamides composed of pyrrole, a naturally occurring G-excluding element, and imidazole, a rationally designed G-favoring element, have features similar to the theoretical optimum design for polyamides composed of two different rings. The results also show that, in polyamides composed of two or three types of heterocyclic rings, choosing a nonspecific "placeholder" ring, which binds equally strongly to each of the four bases, along with one or two base-specific rings will often enhance sequence specificity over a polyamide composed entirely of base-specific rings.

Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method

We report the design of optimal linker geometries for the synthesis of stapled DNA-minor-groove-binding molecules. Netropsin, distamycin, and lexitropsins bind side-by-side to mixed-sequence DNA and offer an opportunity for the design of sequence-reading molecules. Stapled molecules, with two molecules covalently linked side-by-side, provide entropic gains and restrain the position of one molecule relative to its neighbor. Using a free-atom simulated annealing technique combined with a discrete mutable atom definition, optimal lengths and atomic composition for covalent linkages are determined, and a novel hydrogen bond 'zipper' is proposed to phase two molecules accurately side-by-side.

Estimation of the DNA sequence discriminatory ability of hairpin-linked lexitropsins

Three- and four-ring polyamides containing N-methylimidazole and N-methylpyrrole, and their hairpin-linked derivatives, bind side-by-side in the minor groove of DNA in a sequence-specific manner. The sequences recognized by side-by-side molecules are dependent on the pairings of the polyamide rings to the bases. In this study we report a mathematical model for estimating the free energies of binding for gamma-aminobutyric acid-linked polyamides to 5- and 6-bp DNA sequences. The model parameters are calibrated by a least-squares fit to 35 experimental binding constants. The model performs well in cross-validation experiments and the parameters are consistent with previously proposed empirical rules of polyamide-DNA binding. We apply the model to the design of targeted polyamides, evaluating the ability of the proposed polyamides to bind to a DNA sequence of interest while minimizing binding to the remaining DNA sequences.

Drug delivery to brain tumors

We develop a macroscopic model for delivering drug to brain tumors. The model accounts for bulk convective and diffusive transport across the blood-brain barrier and through the interstitial space. Through mathematical analysis and simulations, we assess the effects of changing parameters (within physiological bounds) on drug delivery. We find that there is an optimal treatment for convective drug delivery to the center of the tumor. We interpret this phenomenon in terms of traffic flow. The implications of our analyses on existing chemotherapeutic protocols are discussed.

Time of ovulation relative to mounting activity in dairy cattle

Time of ovulation was determined for Holstein cows (n = 51) for estruses occurring spontaneously (n = 33) or those induced by PGF2 alpha (n = 86). Ultrasound examination of ovaries was conducted 42 to 49 d postpartum, followed by administration of 25 mg of PGF2 alpha if a corpus luteum was observed. In the absence of a corpus luteum, ovaries were reexamined weekly, and PGF2 alpha was administered upon observation of the presence of a corpus luteum. Onset of estrus was determined by HeatWatch, an electronic pressure-sensing system that recorded each mount associated with estrus. To determine ovulation in relation to first detected mount, ultrasound examinations were conducted at 12, 20, and 24 h after the initial mount and then every 2 h until 40 h. Cows were assigned randomly to receive one of two treatments: 1) the cow received 25 mg of PGF2 alpha 8 to 13 d later or 2) the cow was allowed to cycle spontaneously and then was switched to alternate treatment at a third cycle. The mean estrus period, determined from mounting activity recorded by HeatWatch, consisted of 10.1 mounts over 9.5 h (6.0 mounts were > or = 2 s) for a total 24.1 s of mounting activity. Estrus characteristics were extremely variable and were not different for estruses induced by PGF2 alpha or for those occurring spontaneously. Mean ovulation time relative to first mount was 27.6 +/- 5.4 h and was not different between spontaneous and induced estruses. Knowing the time of ovulation in reference to the first mount of estrus and being able to identify the first mount consistently and accurately with the HeatWatch system allows for accurate timing of AI.

Design of B-DNA cross-linking and sequence-reading molecules

We report the design of hybrid molecules to bind in the minor groove of B-DNA, which combine DNA alkylating and cross-linking ability for increased chemotherapeutic efficacy, with sequence specificity, to minimize side effects. Optimal linkage geometries have been determined for the synthesis of bis-anthramycin and anthramycin-netropsin hybrid molecules. Earlier studies on linked drugs have typically been based on molecular mechanics calculations. This work, in contrast, uses the observed crystal structures of a netropsin/DNA complex and a new anthramycin/DNA complex to determine the exact spacing between two individual drugs when bound in the minor groove of B-DNA. Molecular linkers then are designed and tested between these two experimental positions, to form a chimeric or bis-linked compound molecule. A linked anthramycin-netropsin molecule has been designed specifically to target the polypurine tract second-strand primer site of the reverse transcriptase of HIV-1.

Timing of artificial insemination of dairy cows: fixed time once daily versus morning and afternoon

Nonreturn rates to professional technician service of 7240 first AI Holstein cows were calculated to evaluate differences between once daily and a.m.-p.m. AI. To determine whether management practices affected nonreturn rates, participating herd owners were surveyed for methods used for detection of estrus. Nonreturn rates for once daily and a.m.-p.m. AI were 64.6 and 65.6% for 60-d, 60.1 and 60.6% for 75-d, and 58.4 and 57.8% for 90-d nonreturn periods. Signs of estrus for AI and interval from detection of estrus to AI were related to nonreturn rates. Nonreturn rate was highest, 63.4%, when cows were in standing estrus. Nonreturn rates were lowest, 36%, when cows were bred after treatment with PGF2 alpha without being detected in estrus or bred strictly on veterinary advice based on palpation. Nonreturn rates were similar for different times of the day when once daily AI was practiced. However, AI in the midmorning may have some advantages. The highest nonreturn rate for a 3-h period was 68.2% for 0800 and 1100 h; the lowest was 54.7% for 1300 to 1600 h. Movement before observation for estrus and an observation period > 15 min improved nonreturn rates for once daily AI. Once daily AI can be used effectively with no difference from the traditional a.m.-p.m. system; results are best when AI is based on standing estrus and performed between 0800 and 1100 h.

Surgical management of gastric ulcer

The charts of 139 patients operated on for benign gastric ulcer between 1976 and 1980 were reviewed. Indications for surgery included failure of medical management, bleeding, perforation and inability to differentiate benign from malignant disease. Surgical management included hemigastrectomy 29%, vagotomy with antrectomy 27%, vagotomy with pyloroplasty 13%, wedge resection 7% and highly selective vagotomy 4%. Eighty-four patients (60%) were available for a minimum 4-year follow-up. Recurrence rates were highest in those treated by highly selective vagotomy (33%) and wedge resection (30%). The overall death rate was 4.3%, and 70% of the patients were classified as Visick grades I or II (no or minimal symptoms). Of the 30 patients with acute perforation, 21 were treated by omental patching; 1 died and 3 had recurrent ulcer. Of six patients treated by vagotomy with antrectomy, there were no deaths and no recurrences. The authors conclude that lesser procedures are associated with an unacceptable recurrence rate and that gastric resection is the procedure of choice for both elective and emergency management of gastric ulcer.

Change in unconscious concern with body image following treatment for obesity

The Secord Homonym Test was used to elicit unconscious concerns about the body in one normal and two obese samples. The first sample of nonobese subjects was used to gather baseline data and also to examine the discriminant validity of the test as a measure of unconscious rather than conscious body concern. In a second sample of obese subjects a significantly greater concern with the body was observed. A third sample of obese subjects was tested before and after weight reduction counseling. Initial measures showed them to have similar levels of concern to the second sample; however, following treatment the levels matched those of the nonobese subjects.

Behavioural sciences in medicine at the University of Sydney

The two-year preclinical course in Behavioural Sciences in Medicine at the University of Sydney is described. A brief history of the development of the department is followed by a description of the course objectives, and the way that these objectives are translated into course content. The supervision of assignment work in the community is considered to be an essential part of the department's work. Ongoing evaluation of the course contributes to its development and refinement.

The uses of hypnotically produced emotional responses in therapy

This paper outlines a specialised use of hypnosis as a complement to counselling or interpretive psychotherapy in suitable cases. The techniques capitalise on the ease of manipulating emotions and on the vividness of fantasy experience in hypnosis, to allow patients to learn more adaptive patterns of affective response and to rehearse more adequate repertoires of social behaviour. Implications of the authors' work with a sample of 37 non-psychotic patients is discussed.

The psychiatric ward in a children's hospital: a review of the first two years

The history of in-patient units for the psychiatric treatment of children in the United Kingdom is largely confined to recent years. Their number is now slowly expanding, and there are approximately 60 in-patient psychiatric units for children and adolescents (R.M.P.A. 1970; Department of Health and Social Security, 1970).

Factors affecting the outcome of conjugal bereavement

Following the classic study of Lindemann (1944) on the various forms and possible outcomes of the reaction to bereavement, little systematic work was done in this field until the last decade. Marris (1958), in a thoughtful but uncontrolled study, interviewed 72 widows whose husbands had died at least 11 months earlier, the mean lapse of time between bereavement and interview being two years and two months. Only 14 of his subjects considered themselves to have recovered completely; 31 reported a lasting deterioration in their health, and 57 reported a continuing difficulty with sleep. More recently, Parkes (1964a), in a study of patients admitted to a psychiatric hospital, has demonstrated that the number of patients whose illness followed the death of a spouse was six times greater than expected, suggesting that bereavement must be one causative factor in the development of the illness. He has also shown (Parkes, 1964b) that widows under the age of 65 consulted their general practitioner because of psychiatric symptoms more than three times as frequently during the six months after the bereavement than they had done during a control period prior to the bereavement. The consultation rate for non-psychiatric symptoms increased by nearly a half in both older and younger widows.