ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses

Glucosinolates (GSLs) are plant secondary metabolites consisting of sulfur and nitrogen, commonly found in Brassicaceae crops, such as Arabidopsis thaliana. These compounds are known for their roles in plant defense mechanisms against pests and pathogens. 'Guilt-by-association' (GBA) approach predicts genes encoding proteins with similar function tend to share gene expression pattern generated from high throughput sequencing data. Recent studies have successfully identified GSL genes using GBA approach, followed by targeted verification of gene expression and metabolite data. Therefore, a GSL co-expression network was constructed using known GSL genes obtained from our in-house database, SuCComBase. DPClusO was used to identify subnetworks of the GSL co-expression network followed by Fisher's exact test leading to the discovery of a potential gene that encodes the ARIA-interacting double AP2-domain protein (ADAP) transcription factor (TF). Further functional analysis was performed using an effective gene silencing system known as CRES-T. By applying CRES-T, ADAP TF gene was fused to a plant-specific EAR-motif repressor domain (SRDX), which suppresses the expression of ADAP target genes. In this study, ADAP was proposed as a negative regulator in aliphatic GSL biosynthesis due to the over-expression of downstream aliphatic GSL genes (UGT74C1 and IPMI1) in ADAP-SRDX line. The significant over-expression of ADAP gene in the ADAP-SRDX line also suggests the behavior of the TF that negatively affects the expression of UGT74C1 and IPMI1 via a feedback mechanism in A. thaliana.

Development of An Integrated Surface and Sub-Surface Simulation Model in A Single Simulation Platform

An integrated model between surface and sub-surface is typically done by interconnecting many process modelling platforms. PROSPER and GAP are the common steady state modelling platforms for sub-surface while VMGSim and HYSYS are typical steady state surface modelling platforms. A major issue of using multiple simulation platforms is the compatibility of thermodynamic physical properties calculations among the platforms. This situation makes the simulations difficult to converge to a consistent thermo physical properties values. This is due to different interaction parameters applied in each platform that impact flashing and the physical property values even though the same property package such as Peng Robinson is used. To overcome this convergence problem, a single simulation platform within iCON (PETRONAS’s standard process simulation software, co-developed with VMG-Schlumberger) has been developed. This allows the use of one thermodynamic package across the integrated model. PROSPER sub-surface pressure-flow relationship results were automatically correlated and connected to surface models within the iCON environment. This integrated model was validated with data from operations and yielded about 1.23% average error tolerance. Based on this validated model, an optimization envelope can be developed with all possible well lineup configurations. This envelope covers set points for the operations where CAPEX free optimization can readily be applied.

MAPPING OF HIGHLY HETEROGENEOUS URBAN STRUCTURE TYPE FOR FLOOD VULNERABILITY ASSESSMENT

Abstract. Vulnerability plays an important role in risk assessment. For flood vulnerability assessment, the map and characteristics of elements-at-risk at different scales are strongly required depending on the risk and vulnerability assessment requirements. This study proposes a methodology to classify urban structure type by combining object-based image classification and different high resolution remote sensing data. In this study, a high resolution satellite image and LiDAR have been acquired over Kota Bharu, Kelantan which consists of highly heterogeneous urban structure type (UST) classes. The first stage is data pre-processing that includes orthorectification and pansharpening of Geoeye satellite image, image resampling for normalised Digital Surface Model (nDSM) and followed by image segmentation for creating meaningful objects. The second stage comprises of derivation of image features, generation of training and testing datasets, and classification of UST. The classification was based on three types of machine learning classifiers, i.e. Random Forest (RF), Support Vector Machine (SVM) and Classification and Regression Tree (CART). The results obtained from the classification processes were compared using individual omission and commission error, overcall accuracy and Kappa coefficient. The results show that Random Forest classifier with all image features achieved the highest overall accuracy (93.5%) and Kappa coefficient (0.94). This is followed by CART classifier with overall accuracy of 93.7% and Kappa coefficient of 0.92. Finally, SVM classifier produced the lowest overall accuracy and Kappa coefficient with 88.6% and 0.86, respectively. The UST classification result can be further used to assist detailed building characterisation for large scale flood vulnerability assessment.

Human intestinal parasitism in three areas of Indonesia: a survey

Stools from 1387 people were examined quantitatively for eggs of nematode parasites. The people were residents of Padangganting, near Sawahlunto, Sumatra (227 people), Sukamaju and Cibungur rubber plantations near Sukabumi, Java (831 people) and the villages of Mahima and Rabo near Reo, Manggarai, Flores (329 people). Ascaris lumbricoides, Trichuris trichiura and Necator americanus were common; Ancylostoma was not observed. Prevalence of parasitism was highest in Java and lowest in Flores. Egg counts were low, suggesting low worm burdens; intensity of infection with Ascaris and Trichuris was highest in Java, while hookworm was highest in Sumatra. Ascaris infections decreased and hookworm infections increased in prevalence and intensity with age; Trichuris was unaffected. A sex-related difference was observed only in Sumatra, where more females than males were infected with Ascaris. Village-to-village variation in prevalence of nematode infestation was observed in Flores and on the Sukamaju plantation; the topography of other areas did not allow for village comparisons. Ad hoc anthelmintic treatment of the residents of Cibungur plantation was reflected in reduced parasitism by Ascaris and Trichuris, but not hookworm, compared with neighbouring Sukamaju. Comparison of the patterns of disease in the three areas, in terms of the occurrence of single, double or triple infections, revealed marked differences. In Java most people with parasitism had triple infections. In Sumatra the most common expression of parasitism was single infection with hookworm. In Flores single infection with Ascaris prevailed. It is suggested that the clinical effects of intestinal parasitism might depend on the pattern of infection. Samples collected in Flores were also examined for protozoa which were found in about half the population; Entamoeba coli and E. histolytica were most common.

Chicken faeces garden fertilizer: possible source of human avian influenza H5N1 infection

Avian influenza H5N1 infection in humans is typically associated with close contact with infected poultry or other infected avian species. We report on human cases of H5N1 infection in Indonesia where exposure to H5N1-infected animals could not be established, but where the investigation found chicken faeces contaminated with viable H5N1 virus in the garden fertilizer. Human cases of avian influenza H5N1 warrant extensive investigations to determine likely sources of illness and to minimize risk to others. Authorities should regulate the sale and transportation of chicken faeces as fertilizer from areas where H5N1 outbreaks are reported.

Pupil dilation using a pledget sponge: a randomized controlled trial

BACKGROUND

To show that a pledget soaked in mydriatics and placed in the lower conjunctival fornix is as effective as drops in providing mydriasis for cataract surgery.

METHODS

A randomized, masked, controlled trial of 56 patients assigned to either a pledget group (n=25) or a control eye drops group (n=31) was carried out. Controls had the routine practice of repeated topical mydriatic drops: tropicamide, phenylepherine and atropine. The trial group had a 3-mm pledget trimmed, soaked in mydriatics and placed in the inferior fornix for 20 min. Pupil diameter was measured using a photographic technique with a standard scale shown in each picture. Two masked observers measured the pupils using the scale of the ruler in the developed photograph. All patients completed a 0-10 stinging score prior to surgery.

RESULTS

There were no complications. The mean pupil diameter in the control group was 7.23 (6.91-7.94 95% confidence intervals [CI]) and 7.44 (6.96-7.92 95% CI) in the pledget group. There was no statistically significant difference in pupil diameter between the two groups: difference between means 0.21 (-0.32 to 0.75 95% CI) and Student's t-test of the difference between means (t=0.8 and two-tailed) probability P=0.43. There was no significant difference in the stinging scores: Mann-Whitney test P=0.69.

CONCLUSION

The use of a pledget cellulose sponge to deliver mydriatics prior to cataract surgery is as effective as the conventional method of repeated drop administration and was not associated with any adverse effects.

The correlation between insulin resistance and left ventricular systolic function in obese women

AIM

To determine the correlation between insulin resistance and left ventricular systolic function in obese women.

METHODS

44 obese (BMI > or =25 kg/m2) and 45 normal weight women were studied. They had no other pathological conditions. Echocardiograms were undertaken in our echocardiographic laboratory following standard methods. The homeostasis model was used to assess insulin resistance (HOMA IR).

RESULTS

Ejection fraction (p =0.22) and fractional shortening (p= 0.58) were not difference between obese women and the normal group. There was no correlation between insulin resistance and left ventricular systolic function.

CONCLUSION

There was no correlation between insulin resistance and left ventricular ejection fraction.

Left ventricular diastolic dysfunction in obese women

AIM

To determine the direct effect of obesity on echocardiographic indices of diastolic left ventricular function

METHODS

44 obese (BMI > or =25 kg/m2) and 45 normal weight women were studied. They had no other pathological conditions. Echocardiographic indices of diastolic function were obtained, and dysfunction was assumed when at least two values differed by > or =2 SD from the normal weight group.

RESULTS

In obese subjects, the values of maximum velocity of active mitral filling (A) were increased and pulmonary diastolic velocity was decreased significantly (p< 0,01); all other diastolic variables were unchanged. Subclinical diastolic dysfunction tend to be more prevalent among obese subjects but it was not significantly different from non obese (p= 0.11), being present in nine obese (20.5%) and 4 normal (8.9%) subjects.

CONCLUSION

Subclinical left ventricular diastolic dysfunction is present in obese women.

Purtscher's retinopathy after fracture dislocation of shoulder joint

Purtscher described sudden blindness in patients with severe head trauma due to a remote retinopathy, characterised by bilateral retinal haemorrhages, cotton wool spots, and optic disc swelling seen on fundoscopy. A similar retinopathy has been reported in compressive chest trauma, long bone fractures, and acute pancreatitis. It is less well recognised that Purtscher's retinopathy can occur unilaterally and following less severe trauma. We present a case of unilateral remote traumatic retinal angiopathy following a fracture dislocation of the shoulder joint.

Correlation between cortisol levels and myocardial infarction mortality among intensive coronary care unit patients during first seven days in hospital

AIM

To measure cortisol level, its relationship with myocardial infarction, and to determine the correlation of elevated cortisol levels with the outcome of myocardial infarction.

METHODS

This study was designed as a pre and post study. The diagnosis of myocardial infarction was established based on the WHO criteria. The patients were followed for seven days. Blood specimens were collected on day 1, 3, 5 and 7.

RESULTS

Thirty six patients with myocardial infarction were studied. Four patients (11.1%) died and 32 patients (88.9%) survived. Nineteen patients (52.7%) had large infarcts and 23 patients (63.9%) had myocardial complications. The deceased patient's cortisol level differed significantly from those tht survived (65.68 + 29.07 vs 21350 + 15.82 microg/dl, p < 0.05). The groups with large infarcts and myocardial infarct complications had higher cortisol levels, but the difference was not significant compared with the group with small infarcts and patients without complications. Six patients (16.6%) who received thrombolytic therapy had significantly lower cortisol levels as compared to patients without thrombolytic therapy. The duration of elevation cortisol elevation in the deceased patient was longer than that among those who survived. Similar findings were also true for those with large infarcts when compared to those with small infarcts, as well as myocardial infarct patients with complications when compared to those without. However, the duration of cortisol elevation was shorter among patients who received thrombolytic therapy.

CONCLUSION

Cortisol level can be used as a prognostic marker for myocardial mortality.

Isozyme evidence for three sibling species in the Anopheles sundaicus complex from Indonesia

Electrophoretic studies of isoenzymes in three chromosomally distinct forms (A, B and C) of the mosquito Anopheles sundaicus Theobald (Diptera: Culiciae) were undertaken on wild samples collected from six geographically isolated populations in Indonesia. Analyses of 12 enzyme systems comprising 15 loci revealed significant allelic variations, genetic polymorphism, within and among the populations of the An. sundaicus complex. Phylogenetic dendrograms produced by analysis using the Biosys-1 program based on UPGMA methods show that all the populations of form A fall into one cluster, which is closely related to the form C cluster, whereas the populations of form B belong to a more distinct cluster. Allelic frequency and Wright's F statistics of Mpi (mannose phosphate isomerase) are sufficient to identify individuals of each cytological form. This isozyme data correlates with our previous cytological evidence for the existence of three isomorphic species within the taxon An. sundaicus in Indonesia. These three species of the An. sundaicus complex were found together sympatrically at one locality, Asahan in North Sumatra.

Delayed spinal cord compression in ankylosing spondylitis

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Astigmatism in Bangladeshi and white school entrants in East London: a prospective comparative study

A prospective comparative study was undertaken to determine the prevalence of significant astigmatism in school entrants living in the same area of East London. Thirty-one Bangladeshi and thirty-one white school entrants were refracted in two local state schools. In the Bangladeshi group, 7 right and 5 left eyes had more than 1 dioptre of astigmatism. Most of this astigmatism was with the rule. In the white group, 1 left eye had more than 1 dioptre of astigmatism. This study has shown a statistically significant incidence of astigmatism in an ethnic group in East London. This difference between two racial groups living in the same area of East London has not previously been documented. In our study, Bangladeshi school entrants may be at greater risk of amblyopia if their refractive error is not identified and corrected.

An unusual oronasal foreign body

An unusual case of oronasal foreign body in a child is reported. A plain lateral X-ray of the head was carried out to show the shape and position of the foreign body; it was also useful in planning removal. Ribbon gauze impregnated with vaseline was packed around the sharp end of the metal in the nostril to protect the nasal mucosa from further trauma while removing it. We recommend this technique.

Use of chitinase to facilitate detection of protozoan, helminth and single copy genes in squashed whole mosquitoes

The application of DNA probes to detect foreign DNA in whole arthropods has been limited by the inability of the probes to distinguish between small quantities of target DNA and the background signal generated by non-specific hybridization of mosquito material. We report that treatment of nitrocellulose filters upon which mosquitoes have been squashed with chitinase and proteinase K eliminates non-specific hybridization of DNA probes to mosquito components. Using this technique we have been able to detect a single larva of Brugia malayi, sporozoites of Plasmodium falciparum and Plasmodium berghei, and a single-copy gene in directly squashed vector mosquitoes. Use of this simple, rapid technique should facilitate the successful use of DNA probes in field studies.

RII and RIII type resistance of Plasmodium falciparum to combination of mefloquine and sulfadoxine/pyrimethamine in Indonesia

2 of 36 Plasmodium falciparum infections were resistant (RII and RIII) in vivo to the combination of mefloquine (M) and sulfadoxine-pyrimethamine (SP) in Jayapura, Irian Jaya, Indonesia. Expected absorption of mefloquine and pyrimethamine was confirmed in the one resistant patient from whom sera were available, and the isolate from this patient was sensitive to mefloquine in vitro. Only 2 of 41 infections studied at the same time were resistant in vivo to SP. There was no clinical advantage of MSP compared with SP, and limited observations suggest there may be a disadvantage.

Prolonged incubation improves the micro-scale in-vitro test for drug sensitivity of Plasmodium falciparum

In the standard micro-scale in-vitro test for detecting resistance of Plasmodium falciparum to chloroquine, isolates are incubated for 24-28 h in medium that does not contain serum. The effect of prolonging incubation to 48 h and of adding human AB serum to the culture medium of P falciparum from Irian Jaya, Indonesia was studied. Addition of serum was not associated with any advantages or disadvantages. Production of schizonts was increased when incubation was prolonged. This facilitated reading of the malaria smears and interpretation of the results. The percentage of successful tests (greater than or equal to 20 schizonts/200 asexual parasites in control wells) increased from 31% at 28 h incubation to 94% at 48 h. Among the 7 (44%) isolates which were chloroquine-resistant in vivo, only 1 met the criteria for a positive test at 28 h incubation, but at 48 h all 7 did. To achieve optimum results from the micro-scale in-vitro test in Jayapura, Irian Jaya, isolates should be incubated for 48 h.

Absence of malaria mortality in villagers with chloroquine-resistant Plasmodium falciparum treated with chloroquine

We carried out a series of malaria studies in Robek , Flores, Indonesia, a coastal village of 900 farmers and fishermen where malaria is hyperendemic by parasite rate and holoendemic by spleen rate. The studies showed that: (i) 28 of 31 isolates (90%) of Plasmodium falciparum were resistant to chloroquine in vitro, (ii) 3 of 12 isolates (25%) were resistant at the R-11 level in vivo, (iii) 376 P. falciparum infections occurred in 301 individuals during one year, (iv) no villagers who were treated with chloroquine for P. falciparum infections during the year died, and (v) increasing the dosage of chloroquine base from 15 to 25 to 37.5 mg/kg led to improved clearing of parasitaemia. We conclude that chloroquine can still be used as the primary antimalarial in Robek , but the dosage may have to be increased to clear parasitaemia.