Displaying publications 1 - 20 of 134 in total

Abstract:
Sort:
  1. Hotez PJ
    Acta Trop, 2020 Feb;202:105182.
    PMID: 31550453 DOI: 10.1016/j.actatropica.2019.105182
    While the East Asia Pacific (EAP) region has experienced tremendous economic growth and development, the resulting public health gains from reductions in its neglected tropical diseases (NTDs) have been less than expected due to opposing forces of urbanization, political instability, food insecurity, and climate change, together with co-morbidities with non-communicable diseases, including diabetes and hypertension. To be sure there's been progress towards the elimination of lymphatic filariasis and trachoma through mass drug administration, and there are opportunities to extend MDA to yaws and scabies, but for most of the other NTDs we'll require new biotechnologies. So far, EAP's major technology hubs in China, Japan, Malaysia, Singapore, South Korea, and Taiwan have mostly failed to shift their attention towards new innovations for the NTDs, including new drugs, diagnostics, and vaccines, and vector control. Unless this situation changes the EAP could be facing a new grim reality of unhealthy megacities beset by emerging arbovirus infections, widespread antimicrobial resistance, and urban helminth infections.
  2. Sirichai P, Anderson PJ
    Br J Oral Maxillofac Surg, 2015 Dec;53(10):938-42.
    PMID: 26130591 DOI: 10.1016/j.bjoms.2015.06.007
    Our aim was to examine the relations between type and site of the fracture, age of the patient, and the management and outcomes, among children diagnosed with orbital fractures at the Women's and Children's Hospital, Adelaide, during a 10-year period from 1 January 2003 to 31 December 2012. The records of 41 children whose ages ranged from 8 months to 15 years were analysed. There was a male predominance (n=33). Two most common fractures were orbital floor and multiwalled fractures, with medial wall as the second most common site. The most common cause of injury was sport, more often with increasing age. In contrast, falls were more common among young children. Fractures of the orbital roof were more common among young children, all of ours being in children 10 years old or less. Lateral wall fractures were also more common among young children and declined in frequency with increasing age. In contrast, fractures of the orbital floor and medial wall can occur at any age, though those of the medial wall were more common among older children. As children grow their behaviour and activities change, and the mechanism by which they become injured also changes. Growth and development of the craniofacial skeleton lead to differences in the patterns of fractures with age. Fractures of the orbital roof and lateral wall are more common among young children, while those of the orbital floor and medial wall can occur at any age.
  3. Peterson PJ, Granados A
    Environ Sci Pollut Res Int, 2002;9(3):204-14.
    PMID: 12094535
    Decision-makers require useful tools, such as indicators, to help them make environmentally sound decisions leading to effective management of hazardous wastes. Four hazardous waste indicators are being tested for such a purpose by several countries within the Sustainable Development Indicator Programme of the United Nations Commission for Sustainable Development. However, these indicators only address the 'down-stream' end-of-pipe industrial situation. More creative thinking is clearly needed to develop a wider range of indicators that not only reflects all aspects of industrial production that generates hazardous waste but considers socio-economic implications of the waste as well. Sets of useful and innovative indicators are proposed that could be applied to the emerging paradigm shift away from conventional end-of-pipe management actions and towards preventive strategies that are being increasingly adopted by industry often in association with local and national governments. A methodological and conceptual framework for the development of a core-set of hazardous waste indicators has been developed. Some of the indicator sets outlined quantify preventive waste management strategies (including indicators for cleaner production, hazardous waste reduction/minimization and life cycle analysis), whilst other sets address proactive strategies (including changes in production and consumption patterns, eco-efficiency, eco-intensity and resource productivity). Indicators for quantifying transport of hazardous wastes are also described. It was concluded that a number of the indicators proposed could now be usefully implemented as management tools using existing industrial and economic data. As cleaner production technologies and waste minimization approaches are more widely deployed, and industry integrates environmental concerns at all levels of decision-making, it is expected that the necessary data for construction of the remaining indicators will soon become available.
  4. Juanna Bahadun, Abou-Hamden, Amal, Anderson, Peter J.
    MyJurnal
    Paediatric facial traumas are often accompanied by other intracranial and non-head injuries. Use of
    Computed Tomography (CT) has increased diagnostic accuracy when compared to plain radiographs alone. Coexisting anomalies can sometimes be a chance finding from the imagings and this highlights the need of a formalreporting by a radiologist. We report a case of a traumatic unilateral condylar fracture with a coexisting life-threatening abnormality detected from careful assessment of the imagings.
  5. Mohamed IN, Helms PJ, McLay JS
    Basic Clin Pharmacol Toxicol, 2012 Dec;111(6):396-401.
    PMID: 22734606 DOI: 10.1111/j.1742-7843.2012.00917.x
    Drug switching is a common medical practice. It indicates continuation of treatment regardless of the reason why the original therapy was stopped and switched. Therefore, the aims of this study were to develop a novel method for determining drug switching from routinely acquired NHS health data and to explore the aspect of continuation of care for patients. Patients who were first prescribed ramipril, simvastatin and an angiotensin receptor blocker (ARB) between 1 March 2004 and 28 February 2007 and discontinued their medication within 6 months of the index prescription were identified from the PTI database. The identified patients were then categorized into three groups: i) patients who were switched to a different drug for the same medical condition, ii) patients who were being prescribed with other types of antihypertensive/lipid-regulating drug prior to the initiation of study; and iii) patients who were without any continuation of care or therapy. Twenty percent (808), 29%(1429) and 14%(455) of the identified patients discontinued ramipril, simvastatin and ARB, respectively, within 6 months of an index prescription. Among the ramipril discontinuation group, 36.4% of the patients were switched to another antihypertensive, while another 31.6% of them were without continuation of care. In patients discontinuing ARB, 30.6% were switched, while another 30.1% were without continuation of treatment. In patients discontinuing simvastatin, 28.8% were switched to another lipid-regulating medicine, while another 63.1% of them were without continuation of care. The results of this study confirm that primary care prescribing databases can be used to determine drug-switching information and continuation of care/therapy.
  6. Thomson PJ, Goodson ML, Smith DR
    J Oral Pathol Med, 2018 Jul;47(6):557-565.
    PMID: 29663518 DOI: 10.1111/jop.12716
    BACKGROUND: Clinically identifiable potentially malignant disorders (PMD) precede oral squamous cell carcinoma development. Oral lichenoid lesions (OLL) and proliferative verrucous leukoplakia (PVL) are specific precursor lesions believed to exhibit both treatment resistance and a high risk of malignant transformation (MT).

    METHODS: A retrospective review of 590 PMD patients treated in Northern England by CO2 laser surgery between 1996 and 2014 was carried out. Lesions exhibiting lichenoid or proliferative verrucous features were identified from the patient database and their clinicopathological features and outcome post-treatment determined at the study census date of 31 December 2014.

    RESULTS: One hundred and 98 patients were identified as follows: 118 OLL and 80 PVL, most frequently leukoplakia at ventrolateral tongue and floor of mouth sites, equally distributed between males and females. Most exhibited dysplasia on incision biopsy (72% OLL; 85% PVL) and were treated by laser excision rather than ablation (88.1% OLL; 86.25% PVL). OLL were more common in younger patients (OLL 57.1 year; PVL 62.25 years; P = .008) and more likely than PVL to present as erythroleukoplakia (OLL 15.3%; PVL 2.5%; P = .003). Whilst no significant difference was seen between OLL and PVL achieving disease-free status (69.5% and 65%, respectively; P = .55), this was less than the overall PMD cohort (74.2%). MT was identified in 2 OLL (1.7%) and 2 PVL (2.5%) during follow-up.

    CONCLUSION: One-third of PMD cases showed features of OLL or PVL, probably representing a disease presentation continuum. Post-treatment disease-free status was less common in OLL and PVL, although MT was infrequent.

  7. Goodson ML, Smith DR, Thomson PJ
    J Oral Pathol Med, 2019 Sep;48(8):662-668.
    PMID: 31125457 DOI: 10.1111/jop.12881
    BACKGROUND: Nomograms are graphical calculating devices used to predict risk of malignant transformation (MT) or response to treatment during cancer management. To date, a nomogram has not been used to predict clinical outcome during oral potentially malignant disorder (PMD) treatment. The aim of this study was to create a nomogram for use by clinicians to predict the probability of MT, thereby facilitating accurate assessment of risk and objective decision-making during individual patient management.

    METHODS: Clinico-pathological data from a previously treated cohort of 590 newly presenting PMD patients were reviewed and clinical outcomes categorized as disease free, persistent PMD or MT. Multiple logistic regression was used to predict the probability of MT in the cohort using age, gender, lesion type, site and incision biopsy histopathological diagnoses. Internal validation and calibration of the model was performed using the bootstrap method (n = 1000), and bias-corrected indices of model performance were computed.

    RESULTS: Potentially malignant disorders were predominantly leukoplakias (79%), presenting most frequently at floor of mouth and lateral tongue sites (51%); 99 patients (17%) developed oral squamous cell carcinoma during the study period. The nomogram performed well when MT predictions were compared with patient outcome data, demonstrating good bias-corrected discrimination and calibration (Dxy  = 0.58; C = 0.790), with a sensitivity of 87% and specificity 63%, and a positive predictive value of 32% and negative predictive value 96%.

    CONCLUSION: The "Newcastle Nomogram" has been developed to predict the probability of MT in PMD, based on an internally validated statistical model. Based upon readily available and patient-specific clinico-pathological data, it provides clinicians with a pragmatic diagrammatic aid for clinical decision-making during diagnosis and management of PMD.

  8. Flynn AN, Rogers PJ, Brunstrom JM
    Physiol Behav, 2023 Oct 15;270:114314.
    PMID: 37536621 DOI: 10.1016/j.physbeh.2023.114314
    Previously, we demonstrated a non-linear association between meal caloric intake and meal energy density (ED, kcal/g) in data from a controlled trial in the US and from free-living participants in the UK [1]. In both datasets, meal caloric intake increased with ED in lower energy-dense meals (below ∼1.75 kcal/g) and decreased in higher energy-dense meals (above ∼1.75 kcal/g). In the current study, we sought to explore whether this pattern extends to data from free-living participants in Argentina (N = 2738 meals) and Malaysia (N = 4658 meals). Again, a significant breakpoint was found in both the Argentinean (2.04 kcal/g (SE = 0.06)) and Malaysian (2.17 kcal/g (SE = 0.06)) datasets with mean centered meal caloric intake increasing with ED below the breakpoint and decreasing above the breakpoint. These results lend further support for our two-component theoretical model of meal size (g) in which a volume signal is dominant in lower energy-dense meals and a calorie-content signal is dominant in higher energy-dense meals. Together, our research adds to evidence supporting human sensitivity to calories and exposes a complexity in the correspondence between meal energy content and meal size in everyday (non-manipulated) meals. Further research is needed to provide causal evidence for this sensitivity and whether individual variation impacts meal size and energy balance.
  9. Williams PJ, Zipkin EF, Brodie JF
    Nat Commun, 2024 Mar 28;15(1):2457.
    PMID: 38548741 DOI: 10.1038/s41467-024-46757-z
    Biogeographic history can lead to variation in biodiversity across regions, but it remains unclear how the degree of biogeographic isolation among communities may lead to differences in biodiversity. Biogeographic analyses generally treat regions as discrete units, but species assemblages differ in how much biogeographic history they share, just as species differ in how much evolutionary history they share. Here, we use a continuous measure of biogeographic distance, phylobetadiversity, to analyze the influence of biogeographic isolation on the taxonomic and functional diversity of global mammal and bird assemblages. On average, biodiversity is better predicted by environment than by isolation, especially for birds. However, mammals in deeply isolated regions are strongly influenced by isolation; mammal assemblages in Australia and Madagascar, for example, are much less diverse than predicted by environment alone and contain unique combinations of functional traits compared to other regions. Neotropical bat assemblages are far more functionally diverse than Paleotropical assemblages, reflecting the different trajectories of bat communities that have developed in isolation over tens of millions of years. Our results elucidate how long-lasting biogeographic barriers can lead to divergent diversity patterns, against the backdrop of environmental determinism that predominantly structures diversity across most of the world.
  10. Peter JW, Chandrawathani P
    Trop Biomed, 2005 Dec;22(2):131-7.
    PMID: 16883278 MyJurnal
    There is no doubt that on a global basis, Haemonchus contortus is by far the most important parasite of small ruminants (sheep and goats). This is particularly more so now, with the development of high levels of resistance to both the broad and narrow spectrum anthelmintic drugs in H. contortus throughout the world. Epidemiological studies describe the lower environmental limits for haemonchosis to occur in sheep, as being a mean monthly temperature of 18C and approximately 50mm rainfall. Thus it has been generally recognised that H. contortus is a problem parasite restricted to the warm, wet countries where sheep and goats are raised. However, recent evidence shows that this parasite is apparently common even in northern Europe. Thus the need for sustainable control strategies for H. contortus is becoming much more pressing. This report highlights two examples of sustainable and highly efficient control programmes for H. contortus, that can be implemented in regions at the extremes of its geographic range (Malaysia and Sweden), where the authors have had direct involvement.
  11. Nadzirin N, Willett P, Artymiuk PJ, Firdaus-Raih M
    Nucleic Acids Res, 2013 Jul;41(Web Server issue):W432-40.
    PMID: 23716645 DOI: 10.1093/nar/gkt431
    We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/.
  12. Lippmann JM, Fenner PJ, Winkel K, Gershwin LA
    J Travel Med, 2011 Jul-Aug;18(4):275-81.
    PMID: 21722240 DOI: 10.1111/j.1708-8305.2011.00531.x
    Jellyfish are a common cause of injury throughout the world, with fatalities and severe systemic events not uncommon after tropical stings. The internet is a recent innovation to gain information on real-time health issues of travel destinations, including Southeast Asia.
  13. Githiori JB, Höglund J, Waller PJ, Leyden Baker R
    Vet Parasitol, 2003 Dec 30;118(3-4):215-26.
    PMID: 14729169
    Parasitic nematodes are among the most common and economically important infectious diseases of grazing livestock, especially in small ruminants in the tropics and subtropics in Kenya the control of gastrointestinal nematode infections in sheep and goats is usually made with synthetic anthelmintics but substantial levels of anthelmintic resistance have been recorded. A number of medicinal plants, that may provide possible alternatives, and are used by pastoralists and smallholder farmers in Kenya as deworming agents for their livestock and equines, namely Aframomum sanguineum, Dodonea angustifolia, Hildebrandtia sepalosa, Myrsine africana, Rapanea melanophloeos from Kenya, and Azadirachta indica from Kenya and Malaysia, together with the chemicals embelin and santonin that occur in some of these plants, were evaluated against Heligmosomoides polygyrus in mice. Commercial anthelmintics, namely ivermectin, pyrantel and piperazine, were also investigated, both to validate the mouse model system and to assess efficacy of these drugs against H. polygyrus. Pyrantel and ivermectin were highly effective in reducing the numbers of H. polygyrus worms as well as eggs in faeces of the mice, but piperazine had a lower activity. Application of santonin and M. africana significantly reduced the number of total worm counts (TWC) but not faecal egg counts (FEC). The use of embelin, R. melanophloeos and A. indica reduced FEC but not TWC. In all cases, however, reductions were well below the a priori level of 70% required for biological significance. A. sanguineum, D. angustifolia and H. sepalosa had no effect on either TWC or FEC. In conclusion, none of the plant preparations had any biologically significant anthelmintic effect in this monogastric host-parasite model system.
  14. Esro M, Kolosov O, Jones PJ, Milne WI, Adamopoulos G
    ACS Appl Mater Interfaces, 2017 01 11;9(1):529-536.
    PMID: 27933760 DOI: 10.1021/acsami.6b11214
    Silicon dioxide (SiO2) is the most widely used dielectric for electronic applications. It is usually produced by thermal oxidation of silicon or by using a wide range of vacuum-based techniques. By default, the growth of SiO2 by thermal oxidation of silicon requires the use of Si substrates whereas the other deposition techniques either produce low quality or poor interface material and mostly require high deposition or annealing temperatures. Recent investigations therefore have focused on the development of alternative deposition paradigms based on solutions. Here, we report the deposition of SiO2 thin film dielectrics deposited by spray pyrolysis in air at moderate temperatures of ≈350 °C from pentane-2,4-dione solutions of SiCl4. SiO2 dielectrics were investigated by means of UV-vis absorption spectroscopy, spectroscopic ellipsometry, XPS, XRD, UFM/AFM, admittance spectroscopy, and field-effect measurements. Data analysis reveals smooth (RRMS < 1 nm) amorphous films with a dielectric constant of about 3.8, an optical band gap of ≈8.1 eV, leakage current densities in the order of ≈10(-7) A/cm(2) at 1 MV/cm, and high dielectric strength in excess of 5 MV/cm. XPS measurements confirm the SiO2 stoichiometry and FTIR spectra reveal features related to SiO2 only. Thin film transistors implementing spray-coated SiO2 gate dielectrics and C60 and pentacene semiconducting channels exhibit excellent transport characteristics, i.e., negligible hysteresis, low leakage currents, high on/off current modulation ratio on the order of 10(6), and high carrier mobility.
  15. Sathasivam HP, Sloan P, Thomson PJ, Robinson M
    J Oral Pathol Med, 2022 Feb;51(2):180-187.
    PMID: 34797585 DOI: 10.1111/jop.13262
    INTRODUCTION: Clinical management of oral potentially malignant disorders relies on accurate histopathological assessment of the presence and grade of oral epithelial dysplasia. While adjunctive laboratory tests have provided useful prognostic information, none are in widespread clinical use. This study was performed to assess the clinical utility of two contemporary oral epithelial dysplasia grading systems.

    METHODS: Patients were identified from a clinical database. Oral epithelial dysplasia grading was performed by three oral and maxillofacial pathologists blinded to clinical outcome using the WHO 2017 system and a binary classification. The primary outcome measure was the development of oral squamous cell carcinoma, termed 'malignant transformation'.

    RESULTS: One hundred thirty-one cases satisfied the inclusion criteria, of which 23 underwent malignant transformation. There was substantial inter-rater agreement between the study pathologists for both grading systems, measured using kappa statistics (κ = 0.753 - 0.784). However, there was only moderate agreement between the consensus WHO 2017 dysplasia grade for the study against the original grade assigned by a pool of six pathologists in the context of the clinical service (κ = 0.491). Higher grade categories correlated with an increased risk of developing cancer using both grading systems.

    CONCLUSION: This study demonstrates that the WHO 2017 and binary grading systems are reproducible between calibrated pathologists and that consensus reporting is likely to improve the consistency of grading. The WHO and binary systems were prognostically comparable. We recommend that institutions implement consensus oral epithelial dysplasia grading and prospectively audit the effectiveness of risk stratifying their patients with oral potentially malignant disorders. (249 words).

  16. Pillai P, Mitchell PJ, Phan TG, Ma H, Yan B
    Cerebrovasc Dis, 2023;52(3):353-362.
    PMID: 36423598 DOI: 10.1159/000526873
    BACKGROUND: Extensive randomized controlled clinical trials for endovascular thrombectomy in anterior circulation large vessel occlusions (internal carotid arteries and M1 segment of middle cerebral arteries) have been published over the past decade, but there have not been randomized controlled trials for distal arterial occlusions to date. Distal arterial occlusion randomized controlled trials are essential to decide on patient selection, imaging criteria, and endovascular approach to improve the outcome and reduce complications.

    SUMMARY: The definition of distal arterial occlusion is however unclear, and we believe that a uniform nomenclature of distal arterial occlusions is essential for the design of robust randomized controlled studies. We undertook a systematic literature review and comprehensive analysis of 70 articles looking at distal arterial occlusions and previous attempts at classifying them as well as comparing their similarities and differences with a more selective look at the middle cerebral artery. Thirty-two articles were finally deemed suitable and included for this review. In this review article, we present 3 disparate classifications of distal arterial occlusions, namely, classical/anatomical, functional/imaging, and structural/calibre, and compare the similarities and differences between them.

    KEY MESSAGES: We propose the adoption of functional/imaging classification to guide the identification of distal arterial occlusions with the M2 segment starting at the point of bifurcation of the middle cerebral artery trunk/M1 segment. With regards to the anterior temporal artery, we propose that it will be considered a branch of the M1 and only be considered as the M2 segment if it is a holo-temporal artery. We believe that this is a practical method of classification in the time-critical decision-making period.

  17. Abu Bakar R, Hepburn KS, Keddie JL, Roth PJ
    Angew Chem Int Ed Engl, 2023 Aug 21;62(34):e202307009.
    PMID: 37378955 DOI: 10.1002/anie.202307009
    Pressure-sensitive adhesives (PSAs) are made from soft, irreversibly lightly crosslinked polymers. Even after removal from surfaces, they retain insoluble networks which pose problems during the recycling of glass and cardboard. Herein, degradable PSAs are presented that provide the required performance in use but have networks that can be degraded after use. A series of copolymers was prepared through radical copolymerization of n-butyl acrylate, 4-acryloyloxy benzophenone (ABP) photo-crosslinker, and dibenzo[c,e]oxepin-5(7H)-thione (DOT) to provide degradable backbone thioesters. The optimum tack and peel strengths were found for molar contents of 0.05 mol% ABP and 0.25 mol% DOT. Degradation of the backbone thioesters through aminolysis or thiolysis led to the full dissolution of the networks, loss of adhesive properties of films (decreases in the measured tack and peel strengths), and the quick detachment of model labels from a substrate. Inclusion of DOT into PSAs offers a viable route toward degradable and recyclable packaging labels.
  18. Sudo M, Yamaguchi Y, Späth PJ, Matsumoto-Morita K, Ong BK, Shahrizaila N, et al.
    PLoS One, 2014;9(9):e107772.
    PMID: 25259950 DOI: 10.1371/journal.pone.0107772
    Intravenous immunoglobulin (IVIG) is the first line treatment for Guillain-Barré syndrome and multifocal motor neuropathy, which are caused by anti-ganglioside antibody-mediated complement-dependent cytotoxicity. IVIG has many potential mechanisms of action, and sialylation of the IgG Fc portion reportedly has an anti-inflammatory effect in antibody-dependent cell-mediated cytotoxicity models. We investigated the effects of different IVIG glycoforms on the inhibition of antibody-mediated complement-dependent cytotoxicity. Deglycosylated, degalactosylated, galactosylated and sialylated IgG were prepared from IVIG following treatment with glycosidases and glycosyltransferases. Sera from patients with Guillain-Barré syndrome, Miller Fisher syndrome and multifocal motor neuropathy associated with anti-ganglioside antibodies were used. Inhibition of complement deposition subsequent to IgG or IgM autoantibody binding to ganglioside, GM1 or GQ1b was assessed on microtiter plates. Sialylated and galactosylated IVIGs more effectively inhibited C3 deposition than original IVIG or enzyme-treated IVIGs (agalactosylated and deglycosylated IVIGs). Therefore, sialylated and galactosylated IVIGs may be more effective than conventional IVIG in the treatment of complement-dependent autoimmune diseases.
  19. Firdaus-Raih M, Hamdani HY, Nadzirin N, Ramlan EI, Willett P, Artymiuk PJ
    Nucleic Acids Res, 2014 Jul;42(Web Server issue):W382-8.
    PMID: 24831543 DOI: 10.1093/nar/gku438
    Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac.
  20. Hamdani HY, Appasamy SD, Willett P, Artymiuk PJ, Firdaus-Raih M
    Nucleic Acids Res, 2012 Jul;40(Web Server issue):W35-41.
    PMID: 22661578 DOI: 10.1093/nar/gks513
    Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/.
Filters
Contact Us

Please provide feedback to Administrator ([email protected])

External Links