locStra: Fast analysis of regional/global stratification in whole‐genome sequencing studies

locStra is an ‐package for the analysis of regional and global population stratification in whole‐genome sequencing (WGS) studies, where regional stratification refers to the substructure defined by the loci in a particular region on the genome. Population substructure can be assessed based on the genetic covariance matrix, the genomic relationship matrix, and the unweighted/weighted genetic Jaccard similarity matrix. Using a sliding window approach, the regional similarity matrices are compared with the global ones, based on user‐defined window sizes and metrics, for example, the correlation between regional and global eigenvectors. An algorithm for the specification of the window size is provided. As the implementation fully exploits sparse matrix algebra and is written in C++, the analysis is highly efficient. Even on single cores, for realistic study sizes (several thousand subjects, several million rare variants per subject), the runtime for the genome‐wide computation of all regional similarity matrices does typically not exceed one hour, enabling an unprecedented investigation of regional stratification across the entire genome. The package is applied to three WGS studies, illustrating the varying patterns of regional substructure across the genome and its beneficial effects on association testing.     

Factitious hypoglycemia due to surreptitious administration of insulin. Diagnosis, treatment, and long-term follow-up

Ten patients had factitious hypoglycemia due to surreptitious insulin injections diagnosed and were followed for up to 15 years (median, 5 years; range, 2 months to 15 years). When available, demonstration of anti-insulin antibodies was the most helpful diagnostic test. Decreased plasma C-peptide levels corroborated the diagnosis. Young women (nine of ten) with knowledge of the medical profession or relatives with diabetes mellitus predominated in the sample. Five of the patients had a history of insulin-requiring diabetes mellitus. Two patients eventually committed suicide despite the best efforts at therapy. Only three of ten patients made a successful transition into productive life after the diagnosis of factitious hypoglycemia was established. Factitious hypoglycemia remains a difficult diagnosis to make, and the long-term outcome after the diagnosis is established is unpredictable. All efforts have to be made to confirm the diagnosis before the patients are approached. The confrontation is to be made by an experienced team of health care professionals who have gained the patient's confidence through an understanding but firm manner. Long-term therapy must be planned and initiated before the patient's discharge.     

Fluid reabsorption and glucose consumption in edematous rat lungs

Solute and water uptake were studied in isolated perfused rat lungs with airspaces filled with the perfusion fluid. The albumin in this solution was labelled with Evans blue (T-1824), and uptake of fluid from the airspaces was documented by an increase in T-1824 concentration in airway fluid of 6.5 +/- 1.6% (n = 5, SEM) at 1 hour and 12.2 +/- 0.9% (n = 10) at 2 hours. The only detectable osmotic force that could have contributed to a loss of fluid from the alveolar fluid was a decrease in airspace glucose concentrations, which fell much more rapidly (from 150 mg/dl to 58.7 +/- 7.1 mg/dl, n = 10, after 2 hours) than plasma glucose (from 150 mg/dl to 128.9 +/- 3.7 mg/dl). Addition of 5 X 10(-5) M terbutaline to the perfusate and airspace solutions nearly doubled fluid reabsorption at 1 hour, an effect that was inhibited by propranolol and did not appear to be related to glucose consumption. Exposure to terbutaline for 2 hours increased epithelial permeability to 3H-mannitol and 22Na+. These observations suggest that active sodium transport and epithelial metabolism or transport of glucose in airway fluid may each play a role in the reabsorption of edema fluid.     

Tailoring Interventions: Understanding Medical Practice Culture

This article describes the results of a study that used intensive direct observations of eight medical practices to assess the factors affecting the barriers and facilitators to adult immunization for influenza and pneumonia. The study aimed to describe the culture of these practices by identifying key features that facilitate or deter the immunization process. The article presents profiles of six of the eight practices describing their cultural and organizational frameworks. Six features that are critical to an understanding of the cultures of these practices, particularly as they relate to receptivity to influenza immunization for diverse practices and patient populations, are highlighted. These include policies and procedures, funding source, physician philosophy, patient receptivity to provider recommendation, and physical environment and social environment. The article also discusses strategies for applying knowledge about the culture of each practice to introduce appropriate and feasible interventions aimed at increasing immunization rates.     

Clinical evidence for utilization of the A3 adenosine receptor as a target to treat rheumatoid arthritis: data from a phase II clinical trial

OBJECTIVE: Adenosine exerts antiinflammatory effects via activation of the A3 adenosine receptor (A3AR), a Gi protein-associated cell-surface receptor, overexpressed in synovial tissue and peripheral blood mononuclear cells (PBMC) in patients with active rheumatoid arthritis (RA). CF101 is a highly specific orally bioavailable A3AR agonist. METHODS: This was a multicenter study, blinded to dose, designed to assess the clinical activity and safety of CF101 in active RA. Seventy-four patients were randomized to receive 0.1, 1.0, or 4.0 mg CF101 bid for 12 weeks. The primary efficacy endpoint was American College of Rheumatology 20% response (ACR20) at Week 12. A3AR expression levels were analyzed in PBMC from 18 patients. RESULTS:. Maximal responses were observed with 1.0 mg bid, lower at 0.1 and 4.0 mg bid. At 12 weeks, 55.6%, 33.3%, and 11.5% of the patients receiving 1.0 mg CF101 achieved ACR20%, 50%, and 70% responses, respectively. CF101 was generally well tolerated, with mild headache (4.1%), nausea (2.7%), and rash (2.7%) being the most common treatment-related adverse events. Statistically significant correlations between A3AR overexpression at baseline and ACR50 and ACR70 responses were observed. CONCLUSION: CF101 administered bid for 12 weeks resulted in improvement in signs and symptoms of RA that did not achieve statistical significance, and was safe and well tolerated. The expression level of A3AR was directly correlated with patient responses to CF101, suggesting its utilization as a biomarker for the pharmacodynamic and therapeutic effects of this novel agent. These findings require confirmation in a double-blind randomized placebo-controlled trial, currently under way.     

Targeting RNA for degradation with a (2''-5'')oligoadenylate-antisense chimera.

Antisense oligonucleotides hold considerable promise both as research tools for inhibiting gene expression and as agents for the treatment of a myriad of human diseases. However, targeted destruction of RNA has been difficult to achieve in a versatile, efficient, and reliable manner. We have developed an effective strategy for cleaving unique RNA sequences with 2-5A-dependent RNase, an endoribonuclease that mediates inhibitory effects of interferon on virus infection and is activated by 5'-phosphorylated 2'-5'-linked oligoadenylates known as 2-5A [pn5' A2'(p5' A2')mp5'A], resulting in the cleavage of single-stranded RNA predominantly after UpUp and UpAp sequences. To direct 2-5A-dependent RNase to cleave unique RNA sequences, p5' A2' p5' A2'p5'A was covalently linked to an antisense oligonucleotide to yield a chimeric molecule (2-5A:AS). The antisense oligonucleotide component of 2-5A:AS bound a specific RNA sequence while the accompanying 2-5A component activated 2-5A-dependent RNase, thereby causing the cleavage of the RNA in the targeted sequence. This strategy was demonstrated by inducing specific cleavage within a modified human immunodeficiency virus type 1 vif mRNA in a cell-free system from human lymphoblastoid cells. Because 2-5A-dependent RNase is present in most mammalian cells, the control of gene expression based on this technology--including therapies for cancer, viral infections, and certain genetic diseases--can be envisioned.     

Acute endocarditis in drug addicts: surgical treatment for multiple valve infection

In 72 drug abusers surgically treated for acute infective endocarditis, 14 patients (19%) required surgical procedures on two valves. The predominant infecting organisms were Staphylococcus aureus and Pseudomonas aeruginosa (29%). In contrast to single valve infection, congestive heart failure was the most common operative indication (86%, p less than 0.05) and was uniformly present when both left-sided valves were involved. Surgery was performed 20 +/- 13 days after initiation of antibiotic therapy, yet 7 of the 14 patients had perivalvular abscess formation. In nine patients with solely left-sided infection, aortic and mitral valve replacements were performed. In five patients with bilateral infection, partial or complete tricuspid valvectomy was performed in conjunction with one aortic and four mitral valve replacements. Tricuspid valve competence was reestablished by valve insertion or anuloplasty in two patients, and these patients experienced less perioperative heart failure than did those with tricuspid excision alone. There was no early (less than 30 day) mortality. However, long-term follow-up revealed a reoperative incidence of 21% and a 36% late mortality rate due to prosthetic valve infection with or without dehiscence at 3 to 18 months (mean 7.2 +/- 6) after the initial operation. These late infectious complications were not related to infecting organism or prosthetic material in the tricuspid anulus, but did occur in four (57%) of seven patients with intracardiac abscess. The data indicate that multiple valve infection does not preclude successful early surgical therapy, maintaining tricuspid competence may be hemodynamically preferable, and reinfection in this addict population increases late mortality.     

Antibodies to carbonic anhydrase in patients with immune cholangiopathies

Bile duct epithelia contain an abundance of carbonic anhydrase. Antibodies to this enzyme have been described in autoimmune disorders. Serum from patients with immune-mediated liver diseases was studied to determine whether antibodies to carbonic anhydrase II and/or pyruvate dehydrogenase could distinguish autoimmune cholangitis as immunologically distinct from primary biliary cirrhosis. Antibody assays to carbonic anhydrase II (Western blot) and pyruvate dehydrogenase (flow cytometry) were performed on the sera of patients with autoimmune cholangitis (6), primary biliary cirrhosis (12), primary sclerosing cholangitis (12), autoimmune hepatitis (12), and control (Gilbert syndrome; 8). Reactivity to carbonic anhydrase II was detected in 5 of 6 patients with autoimmune cholangitis, 1 of 12 patients with primary biliary cirrhosis, 1 of 12 patients with autoimmune hepatitis, and no other patients. Individuals with autoimmune cholangitis were more likely than the other patients to be reactive to carbonic anhydrase II (P < 0.001). Patients with primary biliary cirrhosis were more reactive to pyruvate dehydrogenase compared with all other groups (P < 0.001). An antibody to human carbonic anhydrase II is frequently detected in the sera of patients with autoimmune cholangitis and is uncommon or not present in other cholangiopathies. These data provide evidence that autoimmune cholangitis and primary biliary cirrhosis represent distinct entities with unique patterns of immunoreactivity.     

Complete deletion of the androgen receptor gene: definition of the null phenotype of the androgen insensitivity syndrome and determination of carrier status.

The molecular basis of androgen insensitivity was investigated in a family with the complete form of the syndrome. Polymerase chain reaction amplification and Southern blot analysis of genomic DNA revealed a deletion of the entire androgen receptor (AR) gene in affected individuals. The carrier status of female members of this family was examined using a HindIII restriction fragment length polymorphism associated with the AR gene. Obligate carriers were hemizygous for one of the two alleles at this locus, while heterozygosity for the polymorphic alleles, implying the presence of two copies of the AR gene, indicated noncarrier status. This conclusion was supported by gene dosage studies using comparative densitometric analysis of Southern blots hybridized simultaneously with an AR cDNA probe and a control cDNA probe from an unrelated gene. Finally, the pattern of inheritance of another X-linked DNA polymorphism allowed us to conclude that the original mutation had occurred in the germ line of the maternal great-grandfather of the index patient. Although rare, complete deletion of the AR gene is of particular importance in terms of correlation between molecular defect and phenotype, as it represents the quintessential form of complete androgen insensitivity, the null phenotype.