We used Bayes' theorem to calculate the probability of enteric fever in 260 patients presenting with undiagnosed fever, without recourse to blood or stool culture results. These individuals were divided into 110 patients with enteric fever (63 culture positive, 47 culture negative) and 150 patients with other causes of fever. Comparison of the frequencies of occurrence of 19 clinical and laboratory events, said to be helpful in the diagnosis of enteric fever, in the two groups revealed that only 8 events were significantly more frequent in enteric fever. These were: a positive Widal test at a screening dilution of 1:40; a peak temperature greater than = 39 degrees C; previous treatment for the fever; a white blood cell count less than 9 X 10(6)/litre; a polymorphonuclear leucocyte count less than 3.5 X 10(6)/litre; splenomegaly; fever duration greater than 7 d; and hepatomegaly. When the probability of enteric fever was determined prospectively in 110 patients, using only 6 of these discriminating events, the probability of patients with a positive prediction having enteric fever (diagnostic specificity) was 0.80 (95% confidence interval: 0.68 to 0.91) and the probability of those with a negative prediction not having enteric fever (diagnostic sensitivity) was 0.92 (0.85 to 0.99). Using all 19 events did not alter the diagnostic specificity or diagnostic sensitivity. This study shows that a small number of clinical and laboratory features can objectively discriminate enteric fever from other causes of fever in the majority of patients. Calculating the probability of enteric fever can aid in diagnosis, when culturing for salmonella is either unavailable or is negative.
An integral art of the Bayesian approach which is not present in the classical approach is the prior distribution. Different researchers may have different level of prior knowledge regarding the parameter of interest before seeing the data. Sometimes different prior distributions can result in different decisions, as such investigations have to be careful in making the choice of the prior distribution. In this paper, we compare results from the Bayesian analyses based on three possible choices of the prior distributions, which are uniform prior, lognormal prior and an improper prior, in the evaluation of the effectiveness of mini-roundabouts. Data from five before and after studies into the effect of mini-roundabouts when replacing priority junctions are used. The effects of the different prior distributions are distinguishable from the analysis of an anamolous 'desk-drawer' study. The uniform and improper prior pull the estimated treatment effect away from one more than the lognormal prior. The results based on lognormal prior depict a less worst scenario of the ineffectiveness of mini-roundabouts and this may correspond to the deficiency in engineering design at only a few sites. Consequently, it is more appropriate to use the lognormal prior in the analysis of mini-roundabouts as a road safety measure.
Satu ciri yang penting dalam kaedah Bayesian yang tidak ada dalam kaedah klasik ialah taburan prior. Sebelum melihat data, mungkin setiap penyelidik mempunyai tahap pengetahuan prior yang berbeza berkenaan sesuatu parameter yang ingin dikaji. Kadang-kala taburan prior yang berlainan boleh menghasilkan keputusan yang berlainan. Oleh itu, pengkaji perlu berhati-hati dalam memilih taburan prior. Dalam kertas-kerja ini, kami bandingkan keputusan dari analisis Bayesian berdasarkan tiga pilihan taburan prior yang menasabah iaitu prior seragam, prior lognormal dan prior tak wajar untuk menilai keberkesanan bulatan mini. Data dari kajian-kajian sebelum dan selepas terhadap kesan mengantikan persimpangan dengan bulatan mini digunakan. Kesan taburan prior yang berlainan dapat dibezakan berasaskan keputusan analisis terhadap satu kajian 'laci-meja' yang ganjil. Prior seragam dan prior fak wajar felah menyebabkan anggaran nilai kesan rawatan melebihi satu lebih dari prior lognormal. Keputusan berasaskan prior lognormal ini menunjukkan senario yang kurang teruk tentang kurang berkesannya bulatan mini dan mungkin ini boleh dikaitkan dengan rekabentuk kejuruteraan yang tidak baik di beberapa tempat sahaja. Dengan itu, prior lognormal adalah lebih sesuai digunakan untuk menilai bulatan mini sebagai langkah keselamatan jalanraya.
This paper presents a study of the application of autonomously learning multiple neural network systems to medical pattern classification tasks. In our earlier work, a hybrid neural network architecture has been developed for on-line learning and probability estimation tasks. The network has been shown to be capable of asymptotically achieving the Bayes optimal classification rates, on-line, in a number of benchmark classification experiments. In the context of pattern classification, however, the concept of multiple classifier systems has been proposed to improve the performance of a single classifier. Thus, three decision combination algorithms have been implemented to produce a multiple neural network classifier system. Here the applicability of the system is assessed using patient records in two medical domains. The first task is the prognosis of patients admitted to coronary care units; whereas the second is the prediction of survival in trauma patients. The results are compared with those from logistic regression models, and implications of the system as a useful clinical diagnostic tool are discussed.
Dengue is one of the main factors of mortality of inhabitants in the region of South East Asia. Malaysia is one of the countries which is facing a high incidence of dengue, particularly in the 70's and early 80's. The Ministry of Health has taken various measures in order to reduce the dengue epidemic. These include educating people about dengue and conducting research such as investigation of factors that influence the epidemic of dengue. In this study, a sequential Bayesian approach is applied to data of the proportion of death due to dengue over the period from 1982 to 1992. In the sequential Bayesian approach, the data for the year 1982 becomes the prior information for the 1983 data and so on. The data for the different periods are combined in a chronological manner until the final posterior distribution of the proportion of death due to dengue is obtained. It is found that the overall proportion is 0.59% and its standard deviation is 0.00002%.
Denggi adalah satu daripada faktor utama kematian bagi penduduk di rantau Asia Tenggara. Malaysia pula merupakan satu daripada negara yang sedang mengalami kadar insiden denggi yang tinggi, khususnya dalam tahun 70-an dan pada awal 80-an. Kementerian Kesihatan telah mengambil pelbagai langkah untuk mengurangkan wabak denggi. Ini termasuk memberikan pendidikan tentang denggi dan membuat kajian tentang faktor-faktor yang mempengaruhinya. Dalam kajian ini kaedah Bayesan jujukan digunakan terhadap data perkadaran yang mati akibat denggi dalam tempoh 1982 hingga 1992. Dalam kaedah ini, data tahun 1982 digunakan sebagai maklumat prior untuk data tahun 1983 dan seterusnya. Data dari tahun yang berlainan digabungkan secara kronologi sehingga diperoleh taburan posterior yang terakhir bagi perkadaran yang mati akibat denggi. Didapati bahawa perkadaran keseluruhan ialah 0.59% dan sisihan piawainya 0.00002%.
We investigate the evolution of host association in a cryptic complex of mutualistic Crematogaster (Decacrema) ants that inhabits and defends Macaranga trees in Southeast Asia. Previous phylogenetic studies based on limited samplings of Decacrema present conflicting reconstructions of the evolutionary history of the association, inferring both cospeciation and the predominance of host shifts. We use cytochrome oxidase I (COI) to reconstruct phylogenetic relationships in a comprehensive sampling of the Decacrema inhabitants of Macaranga. Using a published Macaranga phylogeny, we test whether the ants and plants have cospeciated. The COI phylogeny reveals 10 well-supported lineages and an absence of cospeciation. Host shifts, however, have been constrained by stem traits that are themselves correlated with Macaranga phylogeny. Earlier lineages of Decacrema exclusively inhabit waxy stems, a basal state in the Pachystemon clade within Macaranga, whereas younger species of Pachystemon, characterized by nonwaxy stems, are inhabited only by younger lineages of Decacrema. Despite the absence of cospeciation, the correlated succession of stem texture in both phylogenies suggests that Decacrema and Pachystemon have diversified in association, or codiversified. Subsequent to the colonization of the Pachystemon clade, Decacrema expanded onto a second clade within Macaranga, inducing the development of myrmecophytism in the Pruinosae group. Confinement to the aseasonal wet climate zone of western Malesia suggests myrmecophytic Macaranga are no older than the wet forest community in Southeast Asia, estimated to be about 20 million years old (early Miocene). Our calculation of COI divergence rates from several published arthropod studies that relied on tenable calibrations indicates a generally conserved rate of approximately 1.5% per million years. Applying this rate to a rate-smoothed Bayesian chronogram of the ants, the Decacrema from Macaranga are inferred to be at least 12 million years old (mid-Miocene). However, using the extremes of rate variation in COI produces an age as recent as 6 million years. Our inferred timeline based on 1.5% per million years concurs with independent biogeographical events in the region reconstructed from palynological data, thus suggesting that the evolutionary histories of Decacrema and their Pachystemon hosts have been contemporaneous since the mid-Miocene. The evolution of myrmecophytism enabled Macaranga to radiate into enemy-free space, while the ants' diversification has been shaped by stem traits, host specialization, and geographic factors. We discuss the possibility that the ancient and exclusive association between Decacrema and Macaranga was facilitated by an impoverished diversity of myrmecophytes and phytoecious (obligately plant inhabiting) ants in the region.
A new method for estimating the time to colonization of Methicillin-resistant Staphylococcus Aureus (MRSA) patients is developed in this paper. The time to colonization of MRSA is modelled using a Bayesian smoothing approach for the hazard function. There are two prior models discussed in this paper: the first difference prior and the second difference prior. The second difference prior model gives smoother estimates of the hazard functions and, when applied to data from an intensive care unit (ICU), clearly shows increasing hazard up to day 13, then a decreasing hazard. The results clearly demonstrate that the hazard is not constant and provide a useful quantification of the effect of length of stay on the risk of MRSA colonization which provides useful insight.
Although the kinetic behaviour of tramadol has been described, the present study is the first to our knowledge, to report specifically on the population pharmacokinetic modelling of tramadol hydrochloride.
Taxonomic relationships within the Old World fruit bat genus, Cynopterus, have been equivocal for the better part of a century. While nomenclature has been revised multiple times on the basis of phenotypic characters, evolutionary relationships among taxa representing the entire geographic range of the genus have not been determined. We used mitochondrial DNA sequence data to infer phylogenetic relationships among the three most broadly distributed members of the genus: C. brachyotis, C. horsfieldi, and C. sphinx, and to assess whether C. brachyotis represents a single widespread species, or a complex of distinct lineages. Results clearly indicate that C. brachyotis is a complex of lineages. C. sphinx and C. horsfieldi haplotypes formed monophyletic groups nested within the C. brachyotis species complex. We identified six divergent mitochondrial lineages that are currently referred to C. brachyotis. Lineages from India, Myanmar, Sulawesi, and the Philippines are geographically well-defined, while in Malaysia two lineages, designated Sunda and Forest, are broadly sympatric and may be ecologically distinct. Demographic analyses of the Sunda and Forest lineages suggest strikingly different population histories, including a recent and rapid range expansion in the Sunda lineage, possibly associated with changes in sea levels during the Pleistocene. The resolution of the taxonomic issues raised in this study awaits combined analysis of morphometric characters and molecular data. However, since both the Indian and Malaysian Forest C. brachyotis lineages are apparently ecologically restricted to increasingly fragmented forest habitat, we suggest that reevaluation of the conservation status of populations in these regions should be an immediate goal.
We investigated the genetic structure within and among Bornean orang-utans (Pongo pygmaeus) in forest fragments of the Lower Kinabatangan flood plain in Sabah, Malaysia. DNA was extracted from hair and faecal samples for 200 wild individuals collected during boat surveys on the Kinabatangan River. Fourteen microsatellite loci were used to characterize patterns of genetic diversity. We found that genetic diversity was high in the set of samples (mean H(E) = 0.74) and that genetic differentiation was significant between the samples (average F(ST) = 0.04, P < 0.001) with F(ST) values ranging from low (0.01) to moderately large (0.12) values. Pairwise F(ST) values were significantly higher across the Kinabatangan River than between samples from the same river side, thereby confirming the role of the river as a natural barrier to gene flow. The correlation between genetic and geographical distance was tested by means of a series of Mantel tests based on different measures of geographical distance. We used a Bayesian method to estimate immigration rates. The results indicate that migration is unlikely across the river but cannot be completely ruled out because of the limited F(ST) values. Assignment tests confirm the overall picture that gene flow is limited across the river. We found that migration between samples from the same side of the river had a high probability indicating that orang-utans used to move relatively freely between neighbouring areas. This strongly suggests that there is a need to maintain migration between isolated forest fragments. This could be done by restoring forest corridors alongside the river banks and between patches.
The genus Rana, notably diversified in Oriental regions from China to Southeast Asia, includes a group of cascade frogs assigned to subgenera Odorrana and Eburana. Among them, R. ishikawae and the R. narina complex represent the northernmost members occurring from Taiwan to the Ryukyu Archipelago of Japan. Relationships of these frogs with the continental members, as well as the history of their invasions to islands, have been unclear. The taxonomic status of Odorrana and related genera varies among authors and no phylogenetic reassessment has been done. Using partial sequences of mitochondrial 12S and 16S rRNA genes, we estimated phylogenetic relationships among 17 species of the section Hylarana including Odorrana and Eburana, and related species from the Ryukyus, Taiwan, China, Thailand, Malaysia, and Indonesia. We estimate that (1) Odorrana is monophyletic and encompasses species of Eburana and R. hosii, which is now placed in Chalcorana, (2) the ancestor of R. ishikawae separated from other Rana in the middle to late Miocene prior to its entry to the Ryukyu Archipelago, (3) the ancestor of the R. narina complex later diversified in continental Asia, and invaded the Ryukyu Archipelago through Taiwan, (4) the R. narina complex attained its current distribution within the Ryukyus through niche segregations, and (5) vicariance of R. hosii between Malay Peninsula and Borneo occurred much later than the divergence events in the R. narina complex. Current subgeneric classification of Rana, at least of Southeast Asian members, requires full reassessment in the light of phylogenetic relationships.
Biogeographic connections between Australia and other continents are still poorly understood although the plate tectonics of the Indo-Pacific region is now well described. Eupetes macrocerus is an enigmatic taxon distributed in a small area on the Malay Peninsula and on Sumatra and Borneo. It has generally been associated with Ptilorrhoa in New Guinea on the other side of Wallace's Line, but a relationship with the West African Picathartes has also been suggested. Using three nuclear markers, we demonstrate that Eupetes is the sister taxon of the South African genus Chaetops, and their sister taxon in turn being Picathartes, with a divergence in the Eocene. Thus, this clade is distributed in remote corners of Africa and Asia, which makes the biogeographic history of these birds very intriguing. The most parsimonious explanation would be that they represent a relictual basal group in the Passerida clade established after a long-distance dispersal from the Australo-Papuan region to Africa. Many earlier taxonomic arrangements may have been based on assumptions about relationships with similar-looking forms in the same, or adjacent, biogeographic regions, and revisions with molecular data may uncover such cases of neglect of ancient relictual patterns reflecting past connections between the continents.
Many methods have been developed to capture the biological similarity between two compounds for use in drug discovery. A variety of similarity metrics have been introduced, the Tanimoto coefficient being the most prominent. Many of the approaches assume that molecular features or descriptors that do not relate to the biological activity carry the same weight as the important aspects in terms of biological similarity. Herein, a novel similarity searching approach using a Bayesian inference network is discussed. Similarity searching is regarded as an inference or evidential reasoning process in which the probability that a given compound has biological similarity with the query is estimated and used as evidence. Our experiments demonstrate that the similarity approach based on Bayesian inference networks is likely to outperform the Tanimoto similarity search and offer a promising alternative to existing similarity search approaches.
Several anuran groups of Laurasian origin are each co-distributed in four isolated regions of the Northern Hemisphere: central/southern Europe and adjacent areas, Korean Peninsula and adjacent areas, Indo-Malaya, and southern North America. Similar distribution patterns have been observed in diverse animal and plant groups. Savage [Savage, J.M., 1973. The geographic distribution of frogs: patterns and predictions. In: Vial, J.L. (Ed.), Evolutionary Biology of the Anurans. University of Missouri Press, Columbia, pp. 351-445] hypothesized that the Miocene global cooling and increasing aridities in interiors of Eurasia and North America caused a southward displacement and range contraction of Laurasian frogs (and other groups). We use the frog genus Bombina to test Savage's biogeographical hypothesis. A phylogeny of Bombina is reconstructed based on three mitochondrial and two nuclear gene fragments. The genus is divided into three major clades: an Indo-Malaya clade includes B. fortinuptialis, B. lichuanensis, B. maxima, and B. microdeladigitora; a European clade includes B. bombina, B. pachypus, and B. variegata; and a Korean clade contains B. orientalis. The European and Korean clades form sister-group relationship. Molecular dating of the phylogenetic tree using the penalized likelihood and Bayesian analyses suggests that the divergence between the Indo-Malaya clade and other Bombina species occurred 5.9-28.6 million years ago. The split time between the European clade and the Korean clade is estimated at 5.1-20.9 million years ago. The divergence times of these clades are not significantly later than the timing of Miocene cooling and drying, and therefore can not reject Savage's hypothesis. Some other aspects of biogeography of Bombina also are discussed. The Korean Peninsula and the Shandong Peninsula might have supplied distinct southern refugia for B. orientalis during the Pleistocene glacial maxima. In the Indo-Malaya clade, the uplift of the Tibetan Plateau might have promoted the split between B. maxima and the other species.
To understand the effects of environmental factors on a social system with multilevel society in proboscis monkey units, the temporal change of the local density of sleeping sites of monkeys was investigated along the Menanggul river from May 2005 to 2006 in Malaysia. Proboscis monkeys typically return to riverside trees for night sleeping. The sleeping site locations of a one-male unit (BE-unit) were recorded and the locations of other one-male and all-male units within 500 m of the BE-unit were verified. In addition, environmental factors (food availability, the water level of the river, and the river width) and copulation frequency of BE-unit were recorded. From the analyses of the distance from the BE-unit to the nearest neighbor unit, no spatial clumping of the sleeping sites of monkey units on a smaller scale was detected. The results of a Bayesian analysis suggest that the conditional local density around the BE-unit can be predicted by the spatial heterogeneity along the river and by the temporal change of food availability, that is, the local density of monkey units might increase due to better sleeping sites with regard to predator attacks and clumped food sources; proboscis monkeys might not exhibit high-level social organization previously reported. In addition, this study shows the importance of data analysis that considers the effects of temporal autocorrelation, because the daily measurements of longitudinal data on monkeys are not independent of each other.
Insect larvae and adult insects found on human corpses provide important clues for the estimation of the postmortem interval (PMI). Among all necrophagous insects, flesh flies (Diptera: Sarcophagidae) are considered as carrion flies of forensic importance. DNA variations of 17 Malaysian, two Indonesian and one Japanese flesh fly species are analysed using the mitochondrial COI and COII. These two DNA regions were useful for identifying most species experimented. However, characterisation of the species was not sufficiently made in the case of Sarcophaga javanica. Seventeen Malaysian species of forensic importance were successfully clustered into distinct clades and grouped into the six species groups: peregrina, albiceps, dux, pattoni, princeps and ruficornis. These groups correspond with generic or subgeneric taxa of the subfamily Sarcophaginae: Boettcherisca, Parasarcophaga, Liosarcophaga, Sarcorohdendorfia-Lioproctia, Harpagophalla-Seniorwhitea and Liopygia. The genetic variations found in COI and COII can be applied not only to identify the species of forensic importance, but also to understand the taxonomic positions, generic or subgeneric status, of the sarcophagine species.
A Bayesian inference network (BIN) provides an interesting alternative to existing tools for similarity-based virtual screening. The BIN is particularly effective when the active molecules being sought have a high degree of structural homogeneity but has been found to perform less well with structurally heterogeneous sets of actives. In this paper, we introduce an alternative network model, called a Bayesian belief network (BBN), that seeks to overcome this limitation of the BIN approach. Simulated virtual screening experiments with the MDDR, WOMBAT and MUV data sets show that the BIN and BBN methods allow effective screening searches to be carried out. However, the results obtained are not obviously superior to those obtained using a much simpler approach that is based on the use of the Tanimoto coefficient and of the square roots of fragment occurrence frequencies.
By investigating genealogical relationships, we estimated the phylogenetic history and biogeography in the megophryid genus Leptobrachium (sensu lato, including Vibrissaphora) from southern China, Indochina, Thailand and the Sundaland. The genealogical relationships among the 30 named and unnamed taxa were estimated using 2009 bp of sequences from the mitochondrial DNA genes 12S rRNA, tRNA(val), and 16S rRNA using maximum parsimony, maximum likelihood, and Bayesian inference methods. The genus Leptobrachium was a well-supported monophyletic group that contained two major clades. One clade had three subclades primarily from disjunct regions including Borneo, Peninsular Malaysia and Java, and Thailand. The Bornean subclade included one species each from the Philippines and Sumatra. The other major clade consisted of two subclades, one from Indochina and the other from southern China (Vibrissaphora). Divergence times estimated an old evolutionary history of each subclade, one that could not be explained by the geohistory of Southeast Asian major landmasses.
Diabetic retinopathy (DR) is a sight threatening complication due to diabetes mellitus that affects the retina. At present, the classification of DR is based on the International Clinical Diabetic Retinopathy Disease Severity. In this paper, FAZ enlargement with DR progression is investigated to enable a new and an effective grading protocol DR severity in an observational clinical study. The performance of a computerised DR monitoring and grading system that digitally analyses colour fundus image to measure the enlargement of FAZ and grade DR is evaluated. The range of FAZ area is optimised to accurately determine DR severity stage and progression stages using a Gaussian Bayes classifier. The system achieves high accuracies of above 96%, sensitivities higher than 88% and specificities higher than 96%, in grading of DR severity. In particular, high sensitivity (100%), specificity (>98%) and accuracy (99%) values are obtained for No DR (normal) and Severe NPDR/PDR stages. The system performance indicates that the DR system is suitable for early detection of DR and for effective treatment of severe cases.
This study deals with the overcapacity problem of water treatment plants in Korea, and mainly discusses status, causes, and engineering options. To this end, we first statistically analyze the recent trend of demand, revealing that the demands of small- and mid-size systems are still increasing while that of large-size systems is now decreasing. Since the existing approach to plan capacity implicitly assumes that demand will increase at a regular rate, we estimate excess capacities and system utilizations of large-size systems. From these results it is found that the large-size systems are suffering from serious overcapacity, thus necessitating that engineers make very difficult decisions given that systems are still expanding the capacities of plants due to a lack of awareness of the current demand trend. For other systems where there is a better understanding of the transition of demand, planners have ceased to expand plants or have closed down relatively old plants in efforts to reduce O&M costs. To address this problem, quick recognition of the transition of demand is being highlighted by the concepts of integrated resources management and cybernetics. Therefore, we examined how quickly the new trend of the Seoul case could be precisely recognized and appropriately addressed. Using the Bayesian parameter estimation method, we found that a new trend can be recognized six years after the transition of demand.
In this multiple-subject study, intrinsic couplings between the primary motor (M1) and supplementary motor areas (SMA) were investigated. Unilateral (UNIright and UNIleft) self-paced tapping of hand fingers were performed to activate M1 and SMA. The intrinsic couplings were analysed using statistical parametric mapping, dynamic causal modeling (DCM) and Bayesian model analysis. Brain activation observed for UNIright and UNIleft showed contralateral and ipsilateral involvement of M1 and SMA. Ten full connectivity models were constructed with right and left M1 and SMA as processing centres. DCM indicated that all subjects prefer M1 as the intrinsic input for UNIright and UNIleft as indicated by a large group Bayes factor (GBF). Positive evidence ratio (PER) that showed strong evidence of Model 3 and Model 6 against other models in at least 12 out of 16 subjects, supported GBF results. The GBF and PER results were later found to be consistent with that of BMS for group studies with high expected posterior probability and exceedance probability. It was concluded that during unilateral finger tapping, the contralateral M1 would act as the input centre which in turn triggered the propagation of signals to SMA in the same hemisphere and to M1 and SMA in the opposite hemisphere.