Local computational methods to improve the interpretability and analysis of cryo-EM maps.

Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However, 'over-sharpening' due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e. ab initio modelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions.

Localization and prediction of malignant potential in recurrent pheochromocytoma/paraganglioma (PCC/PGL) using 18F-FDG PET/CT.

BACKGROUND: To our knowledge, data are lacking on the role of 18F-FDG PET/CT in the localization and prediction of neuroendocrine tumors, in particular the pheochromocytoma/paraganglioma (PCC/PGL) group. PURPOSE: To evaluate the role of 18F-FDG PET/CT in localizing and predicting the malignant potential of PCC/PGL. MATERIAL AND METHODS: Twenty-three consecutive patients with a history of PCC/PGL, presenting with symptoms related to catecholamine excess, underwent 18F-FDG PET/CT. Final confirmation of the diagnosis was made using the composite references. PET/CT findings were analyzed on a per-lesion basis and a per-patient basis. Tumor SUVmax was analyzed to predict the dichotomization of patient endpoints for the local disease and metastatic groups. RESULTS: We investigated 23 patients (10 men, 13 women) with a mean age of 46.43 ± 3.70 years. Serum catecholamine levels were elevated in 82.60% of these patients. There were 136 sites (mean SUVmax: 16.39 ± 3.47) of validated disease recurrence. The overall sensitivities for diagnostic CT, FDG PET, and FDG PET/CT were 86.02%, 87.50%, and 98.59%, respectively. Based on the composite references, 39.10% of patients had local disease. There were significant differences in the SUVmax distribution between the local disease and metastatic groups; a significant correlation was noted when a SUVmax cut-off was set at 9.2 (P<0.05). CONCLUSION: In recurrent PCC/PGL, diagnostic 18F-FDG PET/CT is a superior tool in the localization of recurrent tumors. Tumor SUVmax is a potentially useful predictor of malignant tumor potential.

Crimean-Congo haemorrhagic fever outbreak investigation in the Western Region of Afghanistan in 2008

Crimean-Congo haemorrhagic fever [CCHF] is a life-threatening viral haemorrhagic fever. This paper reports on the first multifocal outbreak recorded in the Afghanistan. The outbreak was detected in 2008 in the Western Region of the country and 30 cases [17 males and 13 females] were detected between 10 July and 22 October 2008. Standard case definitions based on World Health Organization sources were used. Most of the cases [27] occurred in Herat province; 25 were aged between 18-55,1 was > 55 years and 4 were12-18 years [median age was 27 years]. The case fatality rate was 33%; 41% among males and 23% among females [P - 0.29]. Significantly more patients infected by contact with meat and body fluids died that those whose contact was through animal husbandry or ticks [P = 0.0048]. Of the 30 cases, 33 close contacts were traced; 3 were positive for CCHF IgM with no symptomatic evidence of the disease

Reliability, technical error of measurements and validity of length and weight measurements for children under two years old in Malaysia.

The National Health and Morbidity Survey III 2006 wanted to perform anthropometric measurements (length and weight) for children in their survey. However there is limited literature on the reliability, technical error of measurement (TEM) and validity of these two measurements. This study assessed the above properties of length (LT) and weight (WT) measurements in 130 children age below two years, from the Hospital Universiti Kebangsaan Malaysia (HUKM) paediatric outpatient clinics, during the period of December 2005 to January 2006. Two trained nurses measured WT using Tanita digital infant scale model 1583, Japan (0.01kg) and Seca beam scale, Germany (0.01 kg) and LT using Seca measuring mat, Germany (0.1cm) and Sensormedics stadiometer model 2130 (0.1cm). Findings showed high inter and intra-examiner reliability using 'change in the mean' and 'intraclass correlation' (ICC) for WT and LT. However, LT was found to be less reliable using the 'Bland and Altman plot'. This was also true using Relative TEMs, where the TEM value of LT was slightly more than the acceptable limit. The test instruments were highly valid for WT using 'change in the mean' and 'ICC' but was less valid for LT measurement. In spite of this we concluded that, WT and LT measurements in children below two years old using the test instruments were reliable and valid for a community survey such as NHMS III within the limits of their error. We recommend that LT measurements be given special attention to improve its reliability and validity.

Reliability, technical error of measurements and validity of instruments for nutritional status assessment of adults in Malaysia.

INTRODUCTION: The Third National Health and Morbidity Survey Malaysia 2006 includes a nutritional status assessment of children. This study aimed to assess the inter- and intra-examiner reliability, the technical error of measurement and the validity of instruments for measuring weight, height and waist circumference. METHODS: A convenience sample of 130 adults working in a selected office setting was chosen to participate in the study, subject to the inclusion and exclusion study criteria. Two public health nurses, trained to follow a standard protocol, obtained the weight, height and waist circumference measurements. The weight was measured using the Tanita HD-318 digital weighing scale to the nearest 0.1 kg, and Seca Beam Scale to the nearest 0.01 kg. The height was measured using the Seca Bodymeter 206 and Stadiometer, both to the nearest 0.1 cm. The waist circumference was measured using the Seca circumference measuring tape S 201, to the nearest 0.1 cm. RESULTS: The intra-examiner reliability in descending order was weight and height followed by waist circumference. The height measurement, on average, using the test instrument, reported a recording of 0.4 cm higher than the reference instrument, with the upper and lower limits at 2.5 cm and 1.6 cm, respectively. The technical error of measurement and coefficient of variation of weight and height for both inter-examiner and intra-examiner measurements were all within acceptable limits (below five percent). CONCLUSION: The findings of this study suggest that weight, height and waist circumference measured in adults aged 18 years and above, using the respective above mentioned instruments, are reliable and valid for use in a community survey. Limiting the number of examiners, especially for waist circumference measurements, would yield a higher degree of reliability and validity.

Nutritional Status of Children below Five Years in Malaysia: Anthropometric Analyses from the Third National Health and Morbidity Survey III (NHMS, 2006).

The Third National Health and Morbidity Survey (NHMS III) was conducted in 2006 on a nationally representative sample of population in Malaysia. Over 21,000 children aged 0-17.9 years were measured for body weight and stature according to the protocol of the World Health Organization. This article describes the nutritional status of children aged 0-59.9 months. Mean z score for weightfor-age (WAZ), height-for-age (HAZ) and BMI-for-age were compared with the z-scores tables of the WHO standards. The overall prevalence of underweight and stunting of the children were 12.9% and 17.2% respectively. These levels included 2.4% severe underweight and 6.0% severe stunting. In terms of z scores, the age group of 0-5.9 months showed the best nutritional status with mean WAZ of -0.33 (95%CI: -0.52, 0.15) and -0.40 (-0.57, 0.24) for boys and girls respectively, while mean HAZ was 0.64 (0.38, 0.89) for boys and 0.76 (0.54, 0.98) for girls. Mean HAZ and WAZ status was least satisfactory after about 6 months, suggesting a faltering in growth rate at an age that coincides with dependence on complementary feeding. Prevalence of overweight based on BMI-for-age for the sexes combined was 6.4%, while that based on WAZ was 3.4%. The NHMS III results indicate that Malaysian children have better nutritional status compared to children under 5 years in neighbouring countries. In order to meet the targets set in the National Plan of Nutrition (2006-2015), more effective intervention programmes are needed to accelerate the reduction of underweight and stunting, and to arrest the rise of overweight in young children.

Abdominal Obesity in Malaysian Adults: National Health and Morbidity Survey III (NHMS III, 2006).

Abdominal obesity (AO) is an independent risk factor for cardiovascular disease, hypertension and diabetes mellitus in adults. There is a lack of data on the magnitude and socio-demographic profile of AO among Malaysian adults at the national level. In the Third National Health and Morbidity Survey (NHMS III) conducted in 2006, AO of adults aged 18 years and above was determined based on the waist circumference as part of the nutritional status assessment. This article reports the prevalence of AO in relation to socio-economic factors and demographic characteristics of adult subjects. Out of a total of 33,465 eligible individuals 18 years and above, waist circumference was measured in 32,900 (98.3%) individuals. The prevalence of AO was assessed using the cut-off points recommended by World Health Organization. The mean waist circumference in men and women was 84.0cm [95% confidence interval (95% CI): 83.8, 84.3] and 80.3cm (95% CI: 80.1, 80.6) respectively. The national prevalence of AO was 17.4% (95% CI: 16.9, 17.9). The identified risks of AO were women (OR: 4.2, 95% CI: 3.8, 4.6), aged 50-59 years (OR: 5.6, 95% CI: 4.0, 7.7), Indians (OR: 3.0, 95% CI: 2.4, 3.8), housewives (OR: 1.4, 95% CI: 1.1, 1.7), subjects with primary education (OR: 1.3, 95% CI: 1.1, 1.5) and ever married (OR: 1.4, 95% CI: 1.2, 1.6). Being the largest population-based study on AO among Malaysians, these findings have important public health implications. There is an urgent need to revise public health policies and programmes aimed at prevention of abdominal obesity especially in the groups at risk.

Reliability and Technical Error of Calf Circumference and Mid-half Arm Span Measurements for Nutritional Status Assessment of Elderly Persons in Malaysia.

This study sought to examine the reliability of two measurements; Calf Circumference (CC) and Mid-half Arm Span (MHAS). A sample of 130 elderly persons aged 60 years and above seen consecutively in the Kuala Lumpur Hospital outpatient clinic during the period of December 2005 to January 2006, upon consent, were recruited to the study. There was a high degree of reliability for both inter- and intra-examiner (r close to 1). For inter-examiner, on average the CC measurements taken by the first examiner were 0.3 cm lower than that of the second examiner. The upper and lower limit of the differences were +0.4 to -0.9 cm respectively. Inter-examiner MHAS measurements on average by the first examiner were 0.2 cm lower than that of the second examiner. The limits were +1.7 to -2.1 cm. By comparison, the inter-examiner CC measurements were more reliable than the MHAS measurements. For intra-examiner, on average the CC measurements at Time 1 were consistent with Time 2 (mean difference=0) with limits of the difference at + 0.5 cm. MHAS measurements at Time 1 were on average 0.1 cm less than at Time 2 with limits at +1.7 and -1.8 cm. The technical error of measurement (TEM) and coefficient of variation of CC and MHAS for both interexaminer and intra-examiner measurements were within acceptable limits with the exception of MHAS TEM. This study suggests that CC and MHAS measured in elderly persons 60 years and above, using Seca Circumference Tape ® 206, Germany (0.05 cm) are reliable and can be used in a community survey.