High Throughput Primer Walking of cDNA Clones

Primer walking of cloned DNA is a standard research tool. It has been used in the past to determine the sequence of individual clones of interest. With the expansion of DNA sequencing capacity the need to be able to walk larger numbers of clones has become necessary. Our laboratory is a mid-sized genomics facility. In conjunction with the Advanced Biomedical Computing Center (ABCC) we have developed methods for automating the primer selection, DNA sequencing, contig assembly and sequence analysis for clones arrayed in microtiter format. This approach has allowed us to walk 475 clones (five microtiter plates) selected from a cDNA library.     

Single-Threaded vs. Multithreaded: Where Should We Focus?

Today, with the increasing popularity of multicore processors, one approach to optimizing the processor's performance is to reduce the execution times of individual applications running on each core by designing and implementing more powerful cores. Another approach, which is the polar opposite of the first, optimizes the processor's performance by running a larger number of applications on a correspondingly larger number of cores, albeit simpler ones. The difference between these two approaches is that the former focuses on reducing the latency of individual applications or threads (it optimizes the processor's single-threaded performance), whereas the latter focuses on reducing the latency of the applications' threads taken as a group (it optimizes the processor's multithreaded performance). The panel, from the 2007 Workshop on Computer Architecture Research Directions, discusses the relevant issues.     

Intermittent Phenomena in Switched Systems With High Coupling Strengths

In this paper, one kind of intermittency generated by a discontinuous system is studied. Although this system, which is composed of two switched subsystems coupled with a high strength, is nonsmooth, the mechanism of this kind of intermittency can be analyzed with several explicit relations between the intermittency characteristics and the system control parameters. In particular, estimates of "steady-state" values of the system (in the laminar phases) and a critical value for this intermittency can be derived, which are helpful in relevant control systems design. Moreover, some power laws for the observed intermittency are obtained and discussed     

Abnormal mucosal glycoprotein synthesis in inflammatory bowel diseases is not related to cigarette smoking

Patients with ulcerative colitis are usually non- or ex-smokers in contrast to Crohn's disease where smoking is common. Abnormalities of quantity and quality of intestinal mucus have been postulated in the pathogenesis of these diseases. It is possible that smoking habit may exert its effects via changes in mucus in inflammatory bowel disease. We have therefore studied incorporation of N-acetylglucosamine into synthesized colonic mucin in explants from 85 controls with normal colonoscopic appearances and histology, including 27 smokers and 58 nonsmokers, 36 patients with ulcerative colitis and 19 with ileocolonic Crohn's disease over 24 h in tissue culture. Incorporation of N-acetylglucosamine into normal explants was 31.3 +/- (SD) 7.1 dpm/microgram biopsy protein, incorporation was increased in patients with active Crohn's disease (mean 41.2 +/- (SD) 10.4 dpm/microgram biopsy protein, p = 0.003), decreased in inactive ulcerative colitis (mean 24.1 +/- 7.8 dpm/microgram biopsy protein, p = 0.0006) but normal in active ulcerative colitis (mean 35.0 +/- 13.8 dpm/microgram biopsy protein, p = 0.44). No significant relationship was found between cigarette smoking habits and mucus synthesis in controls with normal mucosa (nonsmokers, n = 58, mean 31.0 +/- (SD) 7.52 dpm/microgram biopsy protein; smokers, n = 27, mean 31.8 +/- (SD) 6.1 dpm/microgram biopsy protein, p = 0.9). This study shows that mucus glycoprotein synthesis is reduced in inactive ulcerative colitis, rising to normal levels in active disease and that synthesis is increased in Crohn's disease. There is no effect of smoking on mucus synthesis by control biopsies suggesting that the differences seen in inflammatory bowel disease are not related to cigarette smoking.     

Postoperative arachnoiditis diagnosed by high resolution fast spin-echo MRI of the lumbar spine

Concentrations of 11 trace elements were determined in 56 control and 98 Alzheimer's disease (AD) olfactory bulb, olfactory tract, olfactory trigone, piriform cortex and amygdala specimens by instrumental neutron activation analysis. Iron and zinc were significantly elevated and bromine was significantly depleted in olfactory regions of AD patients, compared with normal age-matched control subjects. Elevated iron could possibly play a role in neuronal degeneration in AD by enhancing reactive free radical formation.     

Protective effects of green tea extracts (polyphenon E and EGCG) on human cervical lesions

We investigated clinical efficacy of green tea extracts (polyphenon E; poly E and (-)-epigallocatechin-3-gallate [EGCG]) delivered in a form of ointment or capsule in patients with human papilloma virus (HPV) infected cervical lesions. Fifty-one patients with cervical lesions (chronic cervicitis, mild dysplasia, moderate dysplasia and severe dysplasia) were divided into four groups, as compared with 39 untreated patients as a control. Poly E ointment was applied locally to 27 patients twice a week. For oral delivery, a 200 mg of poly E or EGCG capsule was taken orally every day for eight to 12 weeks. In the study, 20 out of 27 patients (74%) under poly E ointment therapy showed a response. Six out of eight patients under poly E ointment plus poly E capsule therapy (75%) showed a response, and three out of six patients (50%) under poly E capsule therapy showed a response. Six out of 10 patients (60%) under EGCG capsule therapy showed a response. Overall, a 69% response rate (35/51) was noted for treatment with green tea extracts, as compared with a 10% response rate (4/39) in untreated controls (P<0.05). Thus, the data collected here demonstrated that green tea extracts in a form of ointment and capsule are effective for treating cervical lesions, suggesting that green tea extracts can be a potential therapy regimen for patients with HPV infected cervical lesions.     

Recording of the saphenous vein compliance by an ultrasonic echo-tracking device in the dog: effects of S 18149

BACKGROUND AND PURPOSE: Studies on risk factors for stroke have been less intensive than those for coronary disease. Only a few studies have addressed the question of the role of heredity in the occurrence of stroke. We analyzed whether a positive parental history of cardiovascular disease predicts the risk of stroke independently from other risk factors and whether the role of parental history varies by age and stroke subtypes. METHODS: This study was a prospective follow-up of 14371 middle-aged men and women. A positive parental history of cardiovascular disease was defined as either stroke or coronary disease before the age of 60 years. The end point of the follow-up was an incident case of stroke. Multivariate analyses were performed with the Cox proportional hazards model. RESULTS: The risk ratio of stroke after multifactorial adjustment (age, smoking, blood pressure, cholesterol, diabetes, and education) associated with a positive parental history of stroke was 1.89 (P = .004) in men and 1.80 (P = .007) in women. The association between parental history of stroke and the risk of stroke was stronger among subjects aged 25 to 49 years than among older subjects. Parental history of coronary disease was not associated with the risk of stroke in men, but in women it had a borderline significant association with the risk of ischemic stroke. CONCLUSIONS: A positive parental history of stroke predicted the risk of stroke independently from the other risk factors.