RLSuite: An Integrative R-Loop Bioinformatics Framework

We recently described the development of a database of 810 R-loop mapping datasets and used this data to conduct a meta-analysis of R-loops. R-loops are three-stranded nucleic acid structures containing RNA:DNA hybrids and we were able to verify that 30% of expressed genes have an associated R-loop in a location conserved manner.. Moreover, intergenic R-loops map to enhancers, super enhancers and with TAD domain boundaries. This work demonstrated that R-loop mapping via high-throughput sequencing can reveal novel insight into R-loop biology, however the analysis and quality control of these data is a non-trivial task for which few bioinformatic tools exist. Herein we describe RLSuite, an integrative R-loop bioinformatics framework for pre-processing, quality control, and downstream analysis of R-loop mapping data. RLSuite enables users to compare their data to hundreds of public datasets and generate a user-friendly analysis report for sharing with non-bioinformatician colleagues. Taken together, RLSuite is a novel analysis framework that should greatly benefit the emerging R-loop bioinformatics community in a rapidly expanding aspect of epigenetic control that is still poorly understood.

Liquid Chromatographic Determination of Major Organic Acids in Apple Juice and Cranberry Juice Cocktail: Collaborative Study

Twelve laboratories collaboratively studied a liquid chromatographic method for determination of quinic, malic, and citric acids in cranberry juice cocktail and apple juice. Samples are passed through a disposable silica cartridge, filtered, and directly injected into the chromatograph. The mobile phase is 0.2M KH2PO4 (pH 2.4). Two reverse phase columns are used, with UV detection at 214 nm. Six samples of cranberry juice cocktail and 6 samples of apple juice were sent to each collaborator. Repeatability and reproducibility coefficients of variation ranged from 1.2 to 7.6% and from 2.9 to 14.7%, respectively, for quinic, malic, and citric acid levels above 0.10%. The precision of the method is satisfactory. The method has been adopted official first action.

A randomized controlled trial adding fluvastatin to peginterferon and ribavirin for naïve genotype 1 hepatitis C patients

Fluvastatin or simvastatin has demonstrable antiviral activity against hepatitis C virus (HCV) as monotherapy. The safety and efficacy of adding fluvastatin or simvastatin to peginterferon/ribavirin for 48 weeks was tested in HCV genotype 1 naïve-to-treatment veterans. Thirty-seven naïve-to-treatment genotype 1 HCV patients were randomized to either a control group (n = 20) to receive peginterferon alfa plus ribavirin or an experimental group (n = 18) to similarly receive peginterferon alfa plus ribavirin as well as fluvastatin 20 mg/day. In addition, seven patients who presented for HCV treatment already were on simvastatin and could not be withdrawn. These simvastatin users were not randomized but were entered into a concurrent prospective pilot arm. There were no unique safety issues with fluvastatin or simvastatin when these drugs were given with peginterferon/ribavirin for 48 weeks. Thirteen of 25 statin patients achieved sustained viral response (SVR), while 5 of 20 control patients achieved SVR. Analysis of SVR by intention-to-treat showed P = 0.078. In this phase 2 study, there were no safety issues with the addition of fluvastatin or simvastatin to peginterferon and ribavirin for 48 weeks. There was a trend towards improvement in SVR when fluvastatin or simvastatin was administered with peginterferon/ribavirin. The size of the groups did not reach the prestudy size thought needed to show significant difference (type II error). These results support the significant results of two other larger randomized controlled trials reported using the same dose of fluvastatin in naïve-to-treatment genotype 1 HCV patients.

Myth: necrotizing enterocolitis: probiotics will end the disease, and surgical intervention improves the outcome

Necrotizing enterocolitis remains an important contributor to neonatal morbidity and mortality. Recent studies suggest that probiotic supplementation may reduce the risk of the disease in premature infants, and some authors recommend that this approach is ready to be utilized as standard-of-care. Once necrotizing enterocolitis is diagnosed and progresses toward peritonitis or perforation, surgical intervention is thought to improve the outcome, and investigators have suggested that peritoneal drainage is as effective as an exploratory laparotomy. In this chapter, we review the current state of knowledge, and suggest that additional studies are necessary to confirm that probiotics will end this disease, and that surgical intervention may not significantly improve the outcome after diagnosis in these compromised patients.

Urban-rural differences in psychiatric rehabilitation outcomes

OBJECTIVE

Employing rural and urban patient populations, the aim of the study was to examine the differences in rehabilitation intervention outcomes, particularly in regard to the social and clinical determinants.

DESIGN

The study employed a retrospective, cross-sectional analysis of patient outcome and characteristics.

SETTING

Community-based psychiatric rehabilitation service in regional and rural Australia.

PARTICIPANTS

A total of 260 patients were included in the service evaluation phase of the study and 86 in the second part of the study. Participants were community-based and suffered from a chronic mental illness.

MAIN OUTCOME MEASURE(S)

Clinical and functional outcomes were measured using the Health of Nations Outcome Scale and the 16-item Life Skills Profile. The outcome score employed was the difference between scores at intake and at the last complete assessment. Clinical and sociodemographic characters were recorded using a proforma developed for the study.

RESULTS

Patients from rural Maitland had a significantly larger mean reduction in total scores and classified more often as 'Improved' on both the Health of Nations Outcome Scale and Life Skills Profile than patients from either of the urban areas (P < 0.01). Study of randomly selected patients showed that those from an urban area had a more complex illness with multiple needs and less often received family support than their rural counterparts.

CONCLUSIONS

For rural communities the improvement in rehabilitation outcomes might be attributable to a more benign form of the illness and the availability of higher levels of social capital.

Prosthetic repair of prevascular femoral herniation

INTRODUCTION

In prevascular femoral hernias the sac is situated anterior to the femoral vessels in the groin. These hernias are rare and a preoperative diagnosis is seldom considered. Traditionally the surgeon had to do the best with the situation that confronted him/her. The aim of this study was to evaluate the use of a prosthetic mesh-plug via a low anterior groin approach.

METHODS AND RESULTS

Over a nine-year period, six patients (all men, aged 46-82 year) were treated for prevascular herniation using a mesh-plug. Five patients had previous groin surgery. Follow-up ranged from 15 months to nine years, during which no recurrence, infection or vascular compromise was detected.

DISCUSSION

Prevascular herniation is rare and the diagnosis may be difficult. Our results suggest that mesh-plug repair via a low approach is feasible and safe and may provide another option for a surgeon encountering a prevascular hernia.

Temporal artery biopsy...who needs one?

OBJECTIVE

To review a 10 year period of temporal artery biopsies, using the American College of Rheumatology (ACR) 1990 criteria: a five point scoring system for the diagnosis of giant cell arteritis (GCA).

DESIGN

Population based, retrospective cohort analysis.

SETTING

One district general hospital in the United Kingdom, over one decade.

PARTICIPANTS

All patients who underwent temporal artery biopsy from July 1994 to June 2004.

MAIN OUTCOME MEASURES

ACR score and temporal artery biopsy result.

RESULTS

During the 10 year period 111 patients were identified. The median (range) age at presentation was 71 (29-85) years. Seventy five patients had an initial ACR score of three or four at presentation. There were 20 positive biopsy specimens. In 19 of these cases at least three of the other criteria were positive so there was already sufficient clinical information for a confident diagnosis. In only one case did the positive result influence the diagnosis by changing the ACR score from two to three. In our series, corticosteroid treatment before biopsy did not significantly reduce the yield of the biopsy.

CONCLUSIONS

The ACR score of three or more has a sensitivity of 93.5% and specificity of 91.2% for the diagnosis of GCA. Using these criteria, 68% of patients had sufficient clinical features when referred to make a confident diagnosis of GCA. Temporal artery biopsy was therefore unnecessary in this group. In the remaining group (ACR score < or =2) there was one positive biopsy. The biopsy only changed the diagnosis in this one case-less than 3% of the uncertain cases and less than 1% of the total cases. Using the ACR criteria and restricting biopsy to those cases in which it might change the diagnosis will reduce the number of biopsies by two thirds without jeopardising diagnostic accuracy.

Variations in the estimation of the contribution of environmental tobacco smoke (ETS) to respirable (< or = 5 microns) indoor air particulates obtained by the use of different analytical methods

Several methods are in use for the identification of the contribution of particulate associated environmental tobacco smoke (ETS) and sidestream smoke to an atmosphere. These include the measurement of respirable suspended particulates (RSP), measurements of the total UV absorption and total fluorescence emission of a methanol extract of collected particulates and the use of specific marker compounds such as solanesol and scopoletin. Use of these methods gave values for the contribution of particulate ETS to total respirable (< or = 5 microns) particulates in the ranges 8.3-124.7% for smokers' houses and 9.6-121.2% for smokers' offices, respectively. However, using what we consider to be the most reliable methodology, based on the measurement of solanesol, the average contribution of particulate ETS to total respirable (< or = 5 microns) particulates for smokers' houses was 21.7% and for smokers' offices was 23.3%.

Elderly rheumatoid arthritis patients on steroid treatment tolerate physical training without an increase in disease activity

The effects of physical training on elderly, fragile patients with rheumatoid arthritis (RA) who are on low-dose steroids were investigated. The controlled study included 24 patients who had been treated with low-dose steroids for 2 years. Each patient was assigned either to a treatment group receiving training or to an untrained control group. The training took place over a 3-month period and was based on a protocol using progressive interval training consisting of bicycle exercises, heel lifts, and step-climbing. The exercises were performed twice weekly for 45 minutes. Comparison of the two groups showed that disease activity did not increase in the trained group and that fewer, but not significantly fewer, swollen joints were observed in this group (p = 0.06). No significant changes were noticed in erythrocyte sedimentation rate, tender joints, or morning stiffness. The work capacity of the trained patients were doubled and the numbers of repetitions increased 76%. Individually adapted exercise programs can therefore be recommended for elderly rheumatoid arthritis patients on steroid treatment.

Disparity-sensitive cells in the owl have a characteristic disparity

We experience the visual world as being three-dimensional. A major source of depth information derives from the slightly different views of each eye, leading to small variations in the retinal images ('disparities'). Neurons sensitive to visual disparities are thought to form the neural basis of stereo vision. Barn owls as well as several mammalian species have neurons that are sensitive to visual disparities. But how visual disparities are represented in the brain has been a matter of discussion ever since the first disparity-sensitive neurons were found some 25 years ago. Here we adopt a new approach to this problem and study the neural computation of visual disparities with a paradigm borrowed from auditory research. The measurement of interaural time difference (ITD) has many similarities with the measurement of visual disparity on the formal, algorithmic level. We speculate that the similarities might extend to the level of neural computation. The neural representation of ITD is well understood, and we have studied the representation of disparities with visual stimuli analogous to those successfully used in acoustic experiments. For example, ITD is converted in the brain to a pathlength on an axon that, owing to the finite conduction velocity in neurons, exactly matches the external ITD. This pathlength is called 'characteristic delay'. Our results suggest that there is an analogue of the characteristic delay in stereo vision which we propose to call 'characteristic disparity'.

Specific cognitive flexibility rehabilitation in schizophrenia

A Cognitive Shift neurocognitive training module was developed in the attempt to ameliorate cognitive flexibility deficits in chronic schizophrenic patients. A procedural training approach hypothesized the exercise of specific neural network processes, identified from theories of frontal and prefrontal lobe functioning. Three male patients who underwent the intensive program demonstrated significant gains in Wisconsin Card Sorting Test performance, gains that were maintained at a six month reassessment. Expanded Brief Psychiatric Rating Scale (a measure of symptomatology) and Life Skills Profile (a measure of daily functioning) measures showed smaller improvements. The ability to improve cognitive flexibility could have important implications for the treatment of schizophrenia.

Physician recruitment in Ontario Provincial Psychiatric Hospitals

Recruitment of Physicians/Psychiatrists to staff the Ontario Provincial Psychiatric Hospitals remains an ongoing problem despite the introduction of measures such as University Affiliation and Incentive Grants. Historically there has been heavy reliance upon Foreign Medical Graduates (GOFM's) who have been denied the possibility of professional mobility and advancement because of restrictive licences. Recent changes in regulations have severely restricted the recruitment of GOFM's. During 1987, details of all physicians employed in the provincial hospitals during the preceeding five years were entered into a computerized data base. This paper presents some initial analyses which indicate that Canadian graduates have provided low levels of service, especially outside major urban centres, quite insufficient to replace the GOFM's. These findings raise urgent social and professional concerns.

Cytochrome c methylation

In this review, protein methylation is outlined in general terms, highlighting the major amino acids that are methylated and some of the proteins in which they are found. The majority of the review examines the methylation of cytochrome c at Lys-77 of lower eukaryotes as a possible model for methylation studies. Early work involving the purification and characterization of the methyltransferase responsible for this methylation indicated cytochrome c was methylated posttranslationally, yet prior to import into the mitochondria. Methylation in vitro occurred only at the in vivo methylation site and only on cytochrome c. Later studies using in vitro translated apocytochrome c revealed that methylated, as compared with unmethylated, apocytochrome c was imported preferentially into yeast, but not rat liver, mitochondria. Efforts to discover the reasons for this preference have shown that methylation of apocytochrome c dramatically lowers its isoelectric point (against a predicted increase) and decrease its Stokes radius. A possible mechanism for these differences involving the disruption of hydrogen bonds is presented here with space-filling models. Finally, the in vivo significance of this modification is also discussed.

Effect of enzymatic methylation of apocytochrome c on holocytochrome c formation and proteolysis

1. Methylation of the lysine at residue 72 of yeast apocytochrome c increases its import into mitochondria. 2. Using methylated and unmethylated apocytochrome c as substrate and intact yeast mitochondria and a solubilized mitochondrial fraction as a source of cytochrome c heme lyase, the results show that the methylation state of the apoprotein has no significant effect on its conversion to holoprotein. 3. The above result suggests that the import mechanism is separate from the heme-attaching activity. 4. Unmethylated apocytochrome c was less resistant to a yeast homogenate fraction that methylated apocytochrome c, suggesting that methylation of apocytochrome c alters the conformation of the whole protein.

Enzymatic methylation of in vitro synthesized apocytochrome c enhances its transport into mitochondria

The gene for iso-1-cytochrome c from Saccharomyces cerevisiae was recloned into a pSP65 vector containing an active bacteriophage SP promoter. The iso-1-cytochrome c gene was cloned as an 856-base pair XhoI-HindIII fragment. When the resulting plasmid was digested at the HindIII site 279 bases downstream from the termination codon of the gene and transcribed in vitro using SP6 RNA polymerase, full length transcripts were produced. The SP6 iso-1-cytochrome c mRNA was translated using a rabbit reticulocyte lysate system, and the protein products were analyzed on sodium dodecyl sulfate-polyacrylamide gels. One major band with a molecular weight of 12,000 was detected by autofluorography and coincided with the Coomassie staining band of apocytochrome c from S. cerevisiae. The product was also shown to be identical with that of standard yeast apocytochrome c on an isoelectrofocusing gel. The in vitro synthesized iso-1-apocytochrome c was enzymatically methylated by adding partially purified S-adenosyl-L-methionine:cytochrome c-lysine N-methyltransferase (protein methylase III, EC 2.1.1.59) from S. cerevisiae along with S-adenosyl-L-methionine to the in vitro translation mixtures. The methylation was shown to be inhibited by the addition of the methylase inhibitor S-adenosyl-L-homocysteine or the protein synthesis inhibitor puromycin. The principal type of methylated amino acid in the protein was found to be epsilon-N-trimethyllysine which accounted for 77% of the total. Finally, the methylation of in vitro synthesized iso-1-apocytochrome c was found to increase its import into mitochondria isolated from S. cerevisiae 2-4-fold over unmethylated protein, but not into rat liver mitochondria. This suggests that methylation facilitates the import of apocytochrome c into mitochondria by a specific receptor mechanism.

A new, rapid, high-sensitivity analysis of amino acids in food type samples

A new approach to the analysis of free amino acids and amino acids from hydrolyzed foods is described. The method is based on reaction of the free amino acids with phenylisothiocyanate to form stable derivatives which are subsequently separated by liquid chromatography. Sample preparation procedures are described and results are compared with conventional ion exchange results. Reproducibility of the new method has been determined on a typical food type sample.

Neonatal screening for sickle cell diseases in Camberwell: results and recommendations of a two year pilot study

The sickle cell diseases are a major health problem for Afro-Caribbean peoples. Neonatal detection and prophylactic management can reduce mortality and morbidity in childhood. A study was therefore conducted analysing the results of the first two years of cord blood screening in the Camberwell health area. Thirteen cases of sickle cell disease and two of haemoglobin (Hb)C disease were identified among 2202 non-white infants screened. The carrier state, sickle cell trait (HbAS), was present in 11.9% and HbC trait (HbAC) in 4.1% of Afro-Caribbean infants. The incidence of disease and of carrier states was much higher in West Africans than in Caribbeans. The wider implications of screening and the need for a comprehensive plan of care are emphasised.

Thalassaemia genes in Peninsular Arabs

The haematological indices of Peninsular Arabs (United Arab Emirate Nationals, Yemeni and Omani) have been examined. The most outstanding feature, seen in 40-50% of all subjects, was one of hypochromia, microcytosis associated with erythrocytosis. In approximately 5% the hypochromia was severe (MCH 19-22 pg) and 20% of these were found to have beta thalassaemia trait. In 10% of subjects the hypochromia was moderate (MCH 23-24 pg) and beta thalassaemia was confirmed in only 10%. The remaining 25% had a mild hypochromia (MCH 25-27 pg) and no beta thalassaemia was detected. The cause of the hypochromia in subjects with a normal Hb A2 (30% of the total population) is probably alpha thalassaemia, firstly because in those patients with an MCH of 19-24 pg the other haematological parameters are statistically the same as those with proven beta thalassaemia and, secondly, in those with an MCH of 25-27 pg iron deficiency is not common (6% of the population). The degree and pattern of the distribution of hypochromia of the three major ethnic groups of the Peninsular Arabs could be explained either by different alpha and beta thalassaemia genes being operative or by different degrees of inbreeding of the same genes.

Complications of peritoneal dialysis

Peritoneal dialysis is an easily available therapeutic procedure. The complications noted in 490 dialyses over a six-year period in a university hospital have been reviewed. Seventeen major and 624 minor complications occurred. Only four deaths could be attributed to the procedure itself. Peritoneal dialysis is an effective procedure but one with a significant incidence of complications, though few of these are associated with mortality or morbidity for the patient. Various safeguards against these are discussed.

Human visual ecology and orientation anisotropies in acuity

The visual environment of Cree Indians from the east coast of James Bay, Quebec, is different from that of city-raised Euro-Canadians. So also are their corresponding orientation anisotropies in visual acuity. A Euro-Canadian sample exhibited the usual higher resolution for vertically and horizontally oriented gratings as compared with oblique orientations, while a Cree Indian sample did not. The most parsimonious explanation of these acuity differences is that orientation-specific detectors in humans are tuned by the early visual environment.