MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data

Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms.

Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis.

Availability: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html.

Contact:tperkins@ohri.ca

Supplementary information:Supplementary data are available at Bioinformatics online.

Liver fibrosis: a bidirectional model of fibrogenesis and resolution

Liver fibrosis is the generic response to chronic injury of varying aetiologies. A number of common mechanisms link this response to the pathogenesis of fibrosis in other organs. While long thought to be relentlessly progressive, there is now excellent evidence in both human liver disease and animal models that hepatic fibrosis is potentially reversible. The liver therefore provides an excellent bidirectional model for the study of fibrogenesis and fibrosis resolution. In this article, we will review the evidence for the reversibility of liver fibrosis. We will highlight some of the mechanisms responsible for fibrogenesis and fibrosis regression, focussing on the role of hepatic myofibroblast activation and apoptosis, the importance of matrix metalloproteinases and their tissue inhibitors and the central involvement of hepatic macrophages in orchestrating this process. Finally, we will briefly discuss what renders liver fibrosis irreversible and how this accumulating knowledge base could lead to badly needed anti-fibrotic therapies in the future.

Indications and outcome of flexible bronchoscopy in neonates

OBJECTIVE

To analyse the indications, safety and outcome of flexible fiberoptic bronchoscopy (FOB) in neonates.

METHODS

This descriptive study was conducted in Level III neonatal unit (ICH, Chennai) and included 84 neonates with various respiratory problems admitted over a 3 y period.

RESULTS

The indications included stridor (18%), persistent radiological abnormalities (44%), unexplained wheeze/respiratory distress (21%) and others (17%). The mean age and weight were 25 d and 2.82 kg respectively. Bronchoscopy detected various anomalies like upper airway anomalies (10.7%), lower airway malacia (21%), synchronous airway malacias (19%) and miscellaneous anatomical abnormalities (18%). Bronchoalveolar lavage was done in 62% with microbiological yield in 54% cases.FOB helped in the revision of diagnosis in 57%. Resolution of atelectasis was observed in 13.5% cases. Except for transient hypoxemia in 2 neonates, no other complication was encountered.

CONCLUSIONS

Flexible bronchoscopy is safe and useful both as diagnostic and therapeutic tool in neonates with respiratory problems.

Filter-based methodology for the location of hot spots in proteins and exons in DNA

The so-called receiver operating characteristic technique is used as a tool in an optimization procedure for the improvement and assessment of a filter-based methodology for the location of hot spots in protein sequences and exons in DNA sequences. By optimizing the characteristic values of the nucleotides, high efficiency as well as improved accuracy can be achieved relative to results obtained with the electron-ion interaction potentials. On the other hand, by using the proposed filter-based methodology with binary sequences, improved accuracy can be achieved although the efficiency is somewhat compromised relative to that achieved using the optimized characteristic values. Extensive experimental results, evaluated using measures such as the g-mean, the Matthews correlation coefficient, and the chi-square statistic, show that the filter-based methodology performs much better than existing techniques using the short-time discrete Fourier transform, particularly in applications where short exons are involved.

UK consensus guidelines for the use of the protease inhibitors boceprevir and telaprevir in genotype 1 chronic hepatitis C infected patients

BACKGROUND

The nonstructural 3 serine protease inhibitors (PIs), boceprevir and telaprevir, represent the first in a new generation of directly acting antivirals against genotype 1 hepatitis C (HCV) infection. When used in combination with pegylated interferon and ribavirin, these drugs greatly improve sustained virological response rates in both treatment-naïve patients and patients who have had previous virological failure on treatment. However, the addition of these new agents will increase the complexity of therapeutic regimens, the rates of side-effects and costs.

AIMS

To review concisely the current evidence and to suggest current best practice, for the use of telaprevir and boceprevir in the management of chronic genotype 1 HCV infection.

METHODS

These guidelines for the use of boceprevir and telaprevir have been formulated following extensive review of the current literature, are based on the consensus opinion of a panel of national experts, and have been openly discussed and debated at a national meeting of HCV care providers.

RESULTS

We have made recommendations on a number of the key practical issues facing HCV care providers: (i) Which patients to treat?; (ii) Standards for the provision of care; (iii) Pre-treatment considerations; (iv) Which treatment regimens to use?; (v) Stopping rules; and (vi) Management of adverse effects. Finally, we have produced suggested algorithms for the assessment and treatment of these patients.

CONCLUSIONS

These UK Consensus guidelines indicate the current best practice for the use of boceprevir and telaprevir in the management of genotype 1 chronic HCV infection.

UK consensus guidelines for the use of the protease inhibitors boceprevir and telaprevir in genotype 1 chronic hepatitis C infected patients

BACKGROUND

The nonstructural 3 serine protease inhibitors (PIs), boceprevir and telaprevir, represent the first in a new generation of directly acting antivirals against genotype 1 hepatitis C (HCV) infection. When used in combination with pegylated interferon and ribavirin, these drugs greatly improve sustained virological response rates in both treatment-naïve patients and patients who have had previous virological failure on treatment. However, the addition of these new agents will increase the complexity of therapeutic regimens, the rates of side-effects and costs.

AIMS

To review concisely the current evidence and to suggest current best practice, for the use of telaprevir and boceprevir in the management of chronic genotype 1 HCV infection.

METHODS

These guidelines for the use of boceprevir and telaprevir have been formulated following extensive review of the current literature, are based on the consensus opinion of a panel of national experts, and have been openly discussed and debated at a national meeting of HCV care providers.

RESULTS

We have made recommendations on a number of the key practical issues facing HCV care providers: (i) Which patients to treat?; (ii) Standards for the provision of care; (iii) Pre-treatment considerations; (iv) Which treatment regimens to use?; (v) Stopping rules; and (vi) Management of adverse effects. Finally, we have produced suggested algorithms for the assessment and treatment of these patients.

CONCLUSIONS

These UK Consensus guidelines indicate the current best practice for the use of boceprevir and telaprevir in the management of genotype 1 chronic HCV infection.

Laparoscopic versus open appendicectomy for complicated appendicitis: A prospective study

AIMS

The purpose of this study was to compare open versus laparoscopic appendicectomy (LA) in complicated appendicitis.

MATERIALS AND METHODS

We prospectively analyzed all children over a 2-year period who underwent appendicectomy in a single institution and found 30 cases of complicated appendicitis diagnosed on the table and confirmed by histopathology. These children were allocated randomly into Group 1 if they had LA and Group 2 if they had open appendicectomy (OA), solely based on surgeon assessment. The parameters assessed were duration of symptoms before surgery, use of postoperative parenteral analgesia, timing of initiation of feeds after surgery, postoperative complications and duration of postoperative stay.

RESULTS

Of the 30 patients with complicated appendicitis, 12 patients in Group 1 underwent LA and 18 patients in Group 2 underwent OA. The two groups were comparable for age and sex. Children in Group 1 were found to need less parenteral analgesia (two out of 12 versus six out of 18). Postoperatively, feeds were started earlier in Group 1 than in Group 2 (2.5 days versus 3.7 days). The average postoperative hospital stay was 5 days in Group 1 and 7.5 days in Group 2. There were only minor wound infections in Group1 as against two major complications in Group 2. There was no mortality in either group.

CONCLUSIONS

In complicated appendicitis, laparoscopic approach carries definite advantages with less postoperative morbidity and hospital stay. It is a feasible and better alternative than the open approach in complicated appendicitis.

Comparative human salivary and plasma proteomes

The protein compositions, or the proteomes, found in human salivary and plasma fluids are compared. From recent experimental work by many laboratories, a catalogue of 2290 proteins found in whole saliva has been compiled. This list of salivary proteins is compared with the 2698 proteins found in plasma. Approximately 27% of the whole-saliva proteins are found in plasma. However, despite this apparent low degree of overlap, the distribution found across Gene Ontological categories, such as molecular function, biological processes, and cellular components, shows significant similarities. Moreover, nearly 40% of the proteins that have been suggested to be candidate markers for diseases such as cancer, cardiovascular disease, and stroke can be found in whole saliva. These comparisons and correlations should encourage researchers to consider the use of saliva to discover new protein markers of disease and as a diagnostic non-proximal fluid to detect early signs of disease throughout the body.

Left ventricular non compaction a tertiary care centre experience

AIM

To analyse the clinical profile of consecutive cases of Left Ventricular Non Compaction (LVNC), a condition characterized by excessive and prominent Left Ventricular (LV) trabeculations which may be associated with LV systolic dysfunction.

METHODS

Twenty six consecutive cases from January 2003 to December 2008 with echocardiographic evidence of hypertrabeculation of LV were evaluated by clinical examination, electrocardiographic (ECG) and echocardiographic features. Diagnosis was based on 3 published definitions.

RESULTS

Out of 26 cases of LVNC (18 Males: 8 Females) aged between 1 day and 63 years, isolated LVNC was seen in 16 cases and rest of the cases were associated with congenital heart disease (CHD), Rheumatic Heart Disease (RHD) and Coronary Artery Disease (CAD). All patients were previously undiagnosed cases of LVNC. Left ventricular ejection Fraction ranged from 20-60% in these cases.

CONCLUSIONS

This study demonstrates the increased detection of patients fulfilling echocardiographic criteria of LVNC and its association with other disorders. It also shows that milder phenotypes exist and the disease is detected incidentally in some cases.

Efficacy and safety of tenecteplase in Indian patients with st-segment elevation myocardial infarction

OBJECTIVE

To assess the efficacy and safety of tenecteplase in Indian patients with ST-segment elevation MI (STEMI).

METHODS

Cardiologists/physicians who had used tenecteplase for management of STEMI, recorded safety and efficacy parameters from consecutively treated patients. Tenecteplase was administered as per the prescribing information. Adjunctive therapy which included clopidogrel and UFH/LMWH was administered as routinely practiced and indicated by guidelines.

RESULTS

Five hundred and seven patients (male = 415, females = 92; mean age = 58.28 +/- 12.23 yrs; weight (kg) = 70.12 +/- 11.06) with STEMI were treated with weight-adjusted tenecteplase within median chest pain to drug interval of 120 minutes. Resolution of chest pain within median interval of 45 minutes occurred in 436 patients with median duration required for > or = 50% resolution of ST segment of 75 minutes. Clinically successful thrombolysis was reported in 80.67% patients. Five patients suffered intra-cranial hemorrhage (ICH), of which 3 patients had received Gp IIb/IIIa inhibitors. Incidence of intra-cranial hemorrhage attributable to tenecteplase was 0.39% (2 out of 507 patients). Incidence of myocardial re-infarction was 2.96% (15 out of 507 patients). There were 12 deaths (2.36%). CONCLUSION , This data shows that tenecteplase is safe and effective in Indian patients with STEMI and conforms to the international ASSENT-2 trial data.

Identification of tubulin drug binding sites and prediction of relative differences in binding affinities to tubulin isotypes using digital signal processing

Microtubules are involved in numerous cellular processes including chromosome segregation during mitosis and, as a result, their constituent protein, tubulin, has become a successful target of several chemotherapeutic drugs. In general, these drugs bind indiscriminately to tubulin within both cancerous and healthy cells, resulting in unwanted side effects. However, differences between beta-tubulin isotypes expressed in a wide range of cell types may aid in the development of anti-tubulin drugs having increased specificity for only certain types of cells. Here, we describe a digital signal processing (DSP) method that is capable of predicting hot spots for the tubulin family of proteins as well as determining relative differences in binding affinities to these hot spots based only on the primary sequence of 10 human tubulin isotypes. Due to the fact that several drug binding sites have already been characterized within beta-tubulin, we are able to correlate hot spots with the binding sites for known chemotherapy drugs. We have also verified the accuracy of this method using the correlation between the binding affinities of characterized drugs and the tubulin isotypes. Additionally, the DSP method enables the rapid estimation of relative differences in binding affinities within the binding sites of tubulin isotypes that are yet to be experimentally determined.

Morphological abnormalities in the innervation of the atretic segment of bowel in neonates with intestinal atresia

The aim of this study was to examine precisely the morphological abnormalities in the myenteric plexus at the atretic end of the bowel in jejunoileal atresia (JIA). Although changes in the myenteric plexus has been examined in the proximal and distal segments of bowel in JIA, a histochemical analysis of the atretic segment is lacking. Specimens from the atretic end of bowel were obtained from six neonates with JIA. Whole-mount preparations were made of the myenteric plexus, and the cholinergic and nitrergic components were studied by staining with acetylcholine esterase (Ach E) and NADPH diaphorase, respectively. Controls were obtained from two neonates undergoing small bowel resection for Meckel's diverticulum. At the blind end of bowel in type 3a atresia (5 neonates), the intensity of NADPH staining was comparable with controls. However, there was distortion of polygonal architecture of the primary and secondary plexuses at the blind end arranged in concentric fashion parallel to the circular muscle fibres. The ganglia were large and irregularly shaped and contained round neuronal cells. In the sausage shaped segment of bowel in multiple atresia, there was total loss of polygonal architecture with abnormal ganglia, and whorls of nerve fibers. Neuronal cells could not be made out in the ganglia. In specimens stained with Ach E, the findings were similar except that the staining intensity was markedly reduced compared with controls. The morphological abnormalities in the atretic bowel in type 3a were restricted to the architecture of the plexuses and ganglia. The neuronal cells were normal. However, the total loss of polygonal architecture and absence of neuronal cells in the ganglia in multiple atresia probably indicate a different etiology for this type of atresia.

Rectal prolapse of intussusception--a single institution's experience

AIM

The objective was to study the clinical presentation and outcome of intussusceptions prolapsing rectally.

METHODS

A retrospective analysis was done of 198 children who presented with intussusception at a single institution over a 5-year period. Of this group, the data of children with intussusception prolapsing rectally was studied.

RESULTS

The incidence of prolapsing intussusception in this series was 8%. All 16 patients were infants with an average age of 5 months. The most common presenting features were rectal bleeding and abdominal mass. Only 56% of children had abdominal pain. 4/16 children had abdominal distension and 4 had dehydration. The duration of symptoms was less than 48 hours in 14/16 patients. Air enema reduction (AER) was attempted in 14/16 patients and was successful in 8 patients. The success rate of AER was 57%. One patient developed a perforation during AER. Manual reduction was done in six patients who failed AER and in two patients in whom AER was not attempted because of prolonged duration of symptoms (> 48 hrs). There were no recurrences in this series.

CONCLUSION

The incidence of intussusceptions prolapsing rectally is high in this series. It can present in the absence of the cardinal symptoms of intussusception. A high index of clinical suspicion is necessary to make the diagnosis. AER is often successful and must be attempted in children who do not have contraindications for this procedure.

Blastomycosis in a South Indian patient after visiting an endemic area in USA

We describe a case of blastomycosis in a diabetic patient from South India who had visited Milwaukee, Wisconsin, an endemic area for blastomycosis in the USA. After his return to Bangalore, India, the patient developed intermittent fever of moderate to high grade, cough, loss of weight and appetite, and abscesses in the left cubital fossa and thigh regions. Systemic examination at our hospital revealed that he had dullness to percussion over the chest region and decreased breath sounds. Direct examination of Gram-stained smears of the pus from an abscess showed many broad-based budding yeast cells and culture yielded a dimorphic fungus later identified as Blastomyces dermatitidis. Histologic examination of the curettage tissue slides stained with hematoxylin and eosin, periodic acid Schiff's reagent, and Gomori's methenamine silver stain procedures showed many broad-based budding cells characteristic of B. dermatitidis. The patient was successfully treated, initially with amphotericin B, followed by oral itraconazole for a period of 6 months. Blastomycosis cases in India are reviewed and the likely source of infection in this patient is discussed.

Short-course chemotherapy for paediatric respiratory tuberculosis: 5-year report

This report presents the 5-year follow-up of 137 children with respiratory tuberculosis enrolled in a randomised clinical trial of two different anti-tuberculosis regimens 9HR and 2HRZ3/4RH2. Both regimens had similar cure rates, with low relapse rates and mortality. Of 134 children followed up to 5 years, 86% had normal radiographs, with more sequelae in the 9HR group (15% vs. 1.5%, P < 0.01). One patient relapsed and there was one accidental death. Short-course chemotherapy in children is safe, effective and well tolerated, and leads to excellent long-term results, with a small proportion of children left with radiological sequelae.

Balloon valvuloplasty of stenosed Carpentier-Edwards bioprosthesis at pulmonary position

Bioprostheses frequently become calcified and stenosed, especially when implanted in younger patients. The general recommendation in such cases is to repeat surgery. Balloon valvuloplasty has hitherto been attempted with mixed success. Calcification and limitation of the balloon size due to the valve ring can lead to suboptimal long-term results. We report a case where balloon dilation of the stenosed bioprosthesis at pulmonary position was successfully performed with good immediate result. Cardiac catheterization after 3 years showed only a minimal increase (5 mmHg) in the gradient.

Anterior mediastinal teratoma presenting as cardiac tamponade

Anterior mediastinal teratoma presenting clinically as cardiac tamponade is unusual. We report the case of a 58-year-old woman, with an unremarkable prior history, who was admitted with cardiac tamponade. Emergency pericardial aspiration showed a thick, yellow fluid. Computed tomography scan of the chest was suggestive of anterior mediastinal teratoma rupturing into the pericardium. Within 24 hours, just before the planned surgery could be performed, it re-ruptured, warranting emergency surgery. Histopathology confirmed the diagnosis of a teratoma. Early surgery is recommended for even asymptomatic benign mediastinal teratomas to avoid this potentially lethal complication of rupture into the pericardial cavity, and cardiac tamponade.

Turpentine-induced chemical pneumonitis with broncho-pleural fistula

Turpentine is a volatile hydrocarbon used in polishes, solvents, paints and textile industry. When hydrocarbons are aspirated into the lung, they cause chemical pneumonitis, acute respiratory distress syndrome (ARDS), and rarely pneumatoceles and pneumothorax. We report a 20-year old boy with turpentine-induced chemical pneumonitis that evolved into a bronchopleural fistula. He was treated with oxygen, steroids and intercostal tube drainage. This is the first reported case of turpentine-associated bronchopleural fistula.

Adenosine myocardial SPECT--its efficacy and safety and correlation with coronary angiogram

OBJECTIVE

The aim of this study was to determine the safety and efficacy of adenosine Tc99m sestamibi myocardial perfusion study under controlled conditions and to correlate the adenosine Tc99m sestamibi perfusion defects and the coronary angiography in patients investigated for coronary artery disease.

METHODS

This prospective study included 122 consecutive patients who underwent adenosine Tc99m sestamibi single photon emission computed tomography (SPECT) myocardial perfusion study. Seventy two patients had coronary angiographic correlation. All the patients who were referred by the cardiologists for stress myocardial perfusion scan who could not be stressed physiologically for one reason or the other were included in the study.

RESULTS

Among the coronary angiography group the overall sensitivity, specificity, positive predictive value and negative predictive value of adenosine Tc99m sestamibi single photon emission computed tomography myocardial perfusion study for detecting significant coronary obstruction (diameter > or = 50%) were 94.4%, 79%, 85% and 92% respectively. The side effects were transient and required no treatment.

CONCLUSION

We conclude adenosine Tc99m sestamibi single photon emission computed tomogram myocardial perfusion study is a reliable test with high sensitivity and specificity for the detection of coronary artery disease.

Flail aortic valve--a forme fruste of Marfan's syndrome?

Marfan's syndrome is an autosomal dominant disorder with risk of premature death from rupture of an aneurysm or aortic dissection. A case of acute severe aortic regurgitation due to flail aortic valve in a patient with family history of Marfan's syndrome which may be a form fruste of this syndrome is reported.

Pulmonary embolism: an overview

Pulmonary embolism and deep venous thrombosis account for hundreds of thousands of hospitalisation and afflict millions of individuals worldwide. A brief overview on the subject concerned is presented here.

Strangulated left paraduodenal hernia in an infant

Paraduodenal hernia is a rare cause of intestinal obstruction. It occurs typically in adults, but can also present in children. The symptoms include chronic abdominal pain and acute intestinal obstruction. Rapid evaluation must be followed by early surgery to avoid the morbidity and mortality associated with strangulation.

Grouping and comparison of Indian citrus tristeza virus isolates based on coat protein gene sequences and restriction analysis patterns

Citrus tristeza virus (CTV) is an aphid-transmitted closterovirus, which causes one of the most important citrus diseases worldwide. Isolates of CTV differ widely in their biological properties. CTV-infected samples were collected from four locations in India: Bangalore (CTV-B), Delhi (CTV-D), Nagpur (CTV-N), and Pune (CTV-P), and were maintained by grafting into Kagzi lime ( Citrus aurantifolia (Christm. Swing.). All isolates produced typical vein clearing and flecking symptoms 6-8 weeks after grafting. In addition, CTV-B and CTV-P isolates produced stem-pitting symptoms after 8-10 months. The CTV coat protein gene (CPG) was amplified by RT-PCR using CPG specific primers, yielding an amplicon of 672 bp for all the isolates. Sequence analysis of the CPG amplicon of all the four Indian isolates showed 93-94% nucleotide sequence homology to the Californian CTV severe stem pitting isolate SY568 and 92-93% homology to the Japanese seedling yellows isolate NUagA and Israeli VT p346 isolates. In phylogenetic tree analysis, Indian CTV isolates appeared far different from other isolates as they formed a separate branch. Comparison among the Indian isolates was carried out by restriction analysis and restriction fragment length polymorphism (RFLP). Specific primers to various genome segments of well-characterized CTV isolates were used to further classify the Indian CTV isolates.

A novel trigger for acute coronary syndromes: the effect of lunar cycles on the incidence and in-hospital prognosis of acute coronary syndromes--a 3-year retrospective study

Circadian variations in the incidence of hypertension and coronary events are well known with early morning surges. Effect of lunar cycles on various medical illnesses like seizures and psychiatric disturbances are documented. However, the effect of lunar cycles on coronary events has been sparsely documented. The authors studied the incidence of acute coronary events and admission patterns in the departments of emergency medicine and cardiology. Inclusion criteria included unstable angina, non-ST elevation myocardial infarction (MI) and ST elevation MI. Exclusion criteria included chest pain syndromes which were subsequently deemed non-cardiac by invasive or non-invasive investigations. Data from 1999 to 2001 were analysed. Admissions on full moon days were compared with those on new moon days. There were 30 full moon days and 30 new moon days and 223 admissions on full moon days and 266 on new moon days. This difference was statistically significant [p = .005]. Sixty-seven per cent were males and the rest were females. Subgroup analysis of mortality, postinfarction angina, effect on diabetics and hypertensives were done which showed an increased trend in new moon days. It is concluded that there is increased incidence of acute coronary events associated with new moon days.

Profile of female patients undergoing coronary angiogram at a tertiary centre

OBJECTIVE

To study clinical profile, risk factors and pattern of coronary artery involvement in females.

MATERIAL AND METHOD

Female patients undergoing coronary angiography at Apollo Hospitals, Chennai during 1996-1998 for angina were analysed for risk factors.

RESULTS

Out of 5997 angiograms, 660 (11%) were females of which 574 (88%) post-menopausal. 48% had atypical chest pain, 11% had unstable angina, 1% had acute myocardial infarction (MI). Past history of MI was present in 48%. Risks factors were hypertension in 60%, diabetes in 52%, obesity in 41%, dyslipidemia in 32%, family history in 36%. 71% patients used oral contraceptive. None of the patients were smoker, 34.8% pre-menopausal and 72.2% post-menopausal had coronary artery disease. Single vessel disease 33% vs 22.1% two vessel disease 43.3 vs 31.2%. Triple vessel 22.3 vs 46.6% and diffuse disease 10% vs 38.7% was seen in pre-menopausal vs post-menopausal females, respectively.

CONCLUSIONS

Family history was the predominant risk factor in pre-menopausal and diabetes mellitus and hypertension in post-menopausal females. Diffuse and triple vessel disease were significantly common in post-menopausal females.

Epidermal nerve innervation in impaired glucose tolerance and diabetes-associated neuropathy

The authors describe skin biopsy findings in patients with peripheral neuropathy associated with diabetes and impaired glucose tolerance (IGT). Six patients with IGT, eight with early diabetes-associated neuropathy, and five controls were recruited. Most subjects underwent nerve conduction studies (NCS) and quantitative sensory tests (QST). Skin biopsy was abnormal in all neuropathy subjects and correlated poorly with NCS. Neuropathy associated with IGT primarily affects small fibers and is similar to early diabetes-associated neuropathy.

Primary angioplasty: the past, the present and the future

Primary angioplasty (PTCA) in acute myocardial infarction has many theoretical advantages including better antegrade flow and reduced intracranial haemorrhage. However the improvement in the mortality and morbidity of primary angioplasty in the randomized trials from sophisticated centres has not been translated to the community setting. Primary PTCA is a suitable alternative to thrombolytic therapy if performed in a timely fashion by persons skilled in the procedure in a suitable laboratory. It is also recommended in patients with cardiogenic shock and in those with contraindications to thrombolytic therapy. Combination of thrombolytics and glycoprotein IIb/IIIa inhibitors with primary angioplasty may form the reperfusion strategy of the future.

Usefulness of concomitant nitrate administration for the enhancement of viability detection with myocardial perfusion imaging

Myocardial viability assessment is crucial in the evaluation of patients who had prior myocardial infarction for revascularisation procedures. Conventional methods include nuclear myocardial perfusion imaging, dobutamine stress echocardiography and positron emission tomography. Utility of nitrate in assessment of viability was assessed. Twenty-five patients with prior myocardial infarction underwent 99mTc-sestamibi single photon emission computed tomography protocol of stress, rest and post 5 mg sublingual isorbide dinitrate. The mean age of the patients was 51.28 years. Eight (32%) had reduction in perfusion defect and increased tracer uptake following nitrate administration. It is concluded that addition of nitrate adds to utility of conventional perfusion imaging in the assessment of myocardial viability.

Percutaneous transluminal septal myocardial ablation in drug-resistant hypertrophic obstructive cardiomyopathy: 18-month follow-up results

OBJECTIVE

Surgery has been the only therapeutic option in patients with hypertrophic obstructive cardiomyopathy (HOCM) who are resistant to standard treatment. Percutaneous transluminal septal myocardial ablation (PTSMA) by alcohol-induced occlusion of the septal artery for the reduction of left ventricular outflow tract (LVOT) gradient is a novel method. However, long-term clinical follow-up is insufficient. This study reports the acute and mid-term results after PTSMA in symptomatic patients with HOCM.

METHODS

Six patients (4 men and 2 women) with symptomatic HOCM and inadequate response to pharmacologic therapy had their major septal branches ablated with alcohol. Mean duration of follow-up was 1.5 years.

RESULTS

There was reduction in LVOT gradient in all patients (100%) with a mean reduction of 50 mmHg. Two patients developed complete heart block (CHB) and 3 patients developed bifascicular block. CHB persisted in 1 patient. Two patients died within 8 days of the procedure; one due to cerebrovascular accident and 1 due to asystole. The patient who died of asystole had CHB but refused permanent pacemaker implantation. CHB reverted in 1 patient and bifascicular blocks persisted in 3 patients. Clinical and echocardiographic follow-up was achieved in the 4 surviving patients after 1.5 years. All surviving patients had LVOT gradient reduction and clinical improvement.

CONCLUSION

PTSMA for HOCM is a non-surgical technique for reducing LVOT gradient. Heart blocks are one potential complication, and may require pacemaker implantation. Long-term follow-up and a larger series of patients are required to determine conclusive therapeutic significance.

Dor's endoaneurysmorrhaphy in severe heart failure due to giant cell myocarditis

Giant cell myocarditis is an unusual and frequently fatal form of myocarditis. A 37-year-old woman presented with resistant cardiac failure and left ventricular aneurysm. She underwent Dor's endoaneurymorrhaphy and was histopathologically proved to have giant cell myocarditis. She had significant improvement of symptoms and was alive 13 months after surgery. Dor's endoaneurysmorrhaphy may be a useful therapeutic modality in selected cases of giant cell myocarditis.

Evidence for Association of a Viroid with Tapping Panel Dryness Syndrome of Rubber (Hevea brasiliensis)

Tapping panel dryness (TPD) is one of the most destructive maladies affecting rubber plantations and is becoming a matter of serious concern. Reduced latex yield leading to total drying of the tapping panel is the obvious symptom. The cause of TPD syndrome is unknown but has been mostly attributed to abiotic causes. In India, the high yielding commercial clone RRII 105 is affected by TPD, leading to enormous losses. We have observed that TPD-affected trees show symptoms of bark scaling, cracking, drying, necrotic streaking, and browning of internal bark leading to the decay of internal tissues. Often prominent abnormal bulges on the lower part of tree trunks occur where the first panel begins to dry. Investigations on TPD-affected rubber samples did not reveal the association of fungus, bacterium, virus, or a protozoan. Total nucleic acid extracts purified from leaf and bark tissues of affected samples and analyzed by polyacrylamide gel electrophoresis under denaturing conditions of low salt and high temperature showed the presence of nucleic acids similar in electrophoretic mobility to low molecular weight (LMW) RNA, of ~359 nucleotides such as potato spindle tuber viroid (PSTVd). The LMW nucleic acid detected from TPD-affected samples was found to be RNA based on its sensitivity to RNase and insensitivity to DNase, phenol, and heat treatments. The LMW RNA was purified and cloned in a pUC 19-derived vector by using primers specific to PSTVd (1). The cloned DNA, when random labeled and used as probe reacted specifically to nucleic acid extracts from TPD-affected rubber trees but not from healthy tissue in dot-blot hybridization assays. Based on the above findings, a viroid etiology for TPD syndrome is proposed. Reference: (1) R. A. Owens, A. T. Candresse, and T. O. Diener. Virology 175:238, 1990.

Congenital malformations of the lung and mediastinum--a quarter century of experience from a single institution

Congenital malformations of the lung are rare and vary widely in their presentation and severity. The authors reviewed 25 years of experience with specific reference to diagnosis, treatment, and outcome. From July 1970 to June 1995, 70 patients were diagnosed with congenital malformations of the lung, which included sequestration (n = 20), foregut anomalies (n = 20), congenital lobar emphysema (CLE; n = 10), congenital cystic adenomatoid malformation (CCAM; n = 5), benign lung cysts (n = 6), lung aplasia/ hypoplasia (n = 4), and other miscellaneous disorders (n = 5). All patients with pulmonary hypoplasia presented at birth. With the exception of one patient, infants with CCAM and CLE presented before 5 months of age. All other patients presented from birth to 16 years of age. A prenatal diagnosis was accurate in two patients. Although prompt surgical management is the rule, the exceptions were children with bilateral lung involvement. Corrective surgery was delayed in some patients in whom extended respiratory support was required or in whom the delay led to an increase in pulmonary reserve. Extracorporeal membrane oxygenation (ECMO) was used in two patients pre- and postoperatively to manage persistent pulmonary hypertension. This review, representing the largest series of congenital lung lesions, showed that (1) prenatal diagnosis is useful but generally does not change the outcome; (2) computerized tomography (CT) is the optimum postnatal diagnostic imaging modality if chest radiography is not definitive; (3) ECMO can be an adjunct in treating associated pulmonary hypertension; (4) pulmonary resection (lobectomy) is the surgical procedure of choice for most lesions; (5) expected survival is good; and (6) pulmonary hypertension is the most common cause of mortality.

High performance liquid chromatographic assay of amprolium and ethopabate in chicken feed using solid-phase extraction

A method for the assay of mixtures of amprolium and ethopabate in chicken feed was developed utilizing reversed-phase high-performance liquid chromatography (HPLC) after sample clean-up of a methanolic extract by solid-phase extraction using CN cartridges. HPLC was done with benzocaine as internal standard on a C-8 column with methanol-water 40:60, containing octanesulfonic acid, triethylamine and acetic acid, as mobile phase. Eluate was monitored at 274 nm. Baseline separation was achieved with retention times of approximately 7.5, 9.4, and 10.4 min, for amprolium, benzocaine, and ethopabate respectively. Feed constituents did not give peaks after 6.5 min. Peak area ratios were linear over 10-180 ng of amprolium, and 2-18 ng of ethopabate injected. Limits of quantitation at AUFS 0.05 were 0.5 and 0.3 ng respectively. Recovery studies from spiked feed (n = 9), covering +/- 30% of usual doses in feed, gave percent recoveries (+/- SD) of 99.4 +/- 1.4% for amprolium and 100.5 +/- 2.6% for ethopabate. Applying the method to two different batches of commercial feed gave results which were comparable to those obtained by the AOAC spectrofluorometric methods.

Role of O-acetyltransferase in activation of oxidised metabolites of the genotoxic environmental pollutant 1-nitropyrene

The genotoxic environmental contaminant 1-nitropyrene is metabolised in mammalian systems by pathways more complex than the straightforward nitroreduction which accounts for most of its biological activity in bacteria. In order to evaluate the role of O-acetyltransferase (OAT) activity in generation of genotoxic intermediates from 1-nitropyrene, the mutagenicity of the major primary oxidised metabolites of 1-nitropyrene was characterised in the Ames Salmonella typhimurium plate incorporation assay with strain TA98, and with variants of TA98 deficient (TA98/1,8-DNP6) or enhanced (YG1024) in O-acetyltransferase. 1-Nitropyren-3-ol was more mutagenic in the absence than in the presence of S9, while 1-nitropyren-4-ol, 1-nitropyren-6-ol and 1-nitropyren-8-ol required S9 for maximum expression of mutagenicity. 1-Nitropyren-4-ol (176 rev/nmol without S9, 467 rev/nmol with S9 in TA98) and 1-nitropyren-6-ol (13 rev/nmol without S9, 266 rev/nmol with S9 in TA98) were overall the most potent nitropyrenol isomers assayed. 1-Acetamidopyren-8-ol and 1-acetamidopyrene 4,5-quinone were only minimally active. 1-Acetamidopyren-3-ol exhibited direct-acting mutagenicity. 1-Acetamidopyren-6-ol, previously shown to be a major contributor to mutagenicity in the urines of rats dosed with 1-nitropyrene (Ball et al., 1984b), was confirmed as a potent (359 rev/nmol) S9-dependent mutagen. Both the direct-acting and the S9-dependent mutagenicity of all the compounds studied was enhanced in the OAT-overproducing strain and much diminished (though not always entirely lost) in the OAT-deficient strain, showing that OAT amplifies expression of the genotoxicity of these compounds. 1-Acetamidopyren-6-ol required both S9 and OAT activity in order to exhibit any mutagenicity; this finding strongly implicates N-hydroxylation followed by O-esterification, as opposed to further S9-catalyzed ring oxidation, as a major route of activation for urinary metabolites of 1-nitropyrene.