Science Collected Works - Research Publications
Now showing items 1-12 of 101
Weighted Overlay Based Land Suitability Analysis of Agriculture Land in Azad Jammu and Kashmir Using GIS and AHP
(University of Agriculture Faisalabad, 2020-11-01)
Agriculture land suitability plays an important role in sustainable agriculture production by improving the use of current land resources and in the identification of new land that maybe prepare for agriculture. The present research aimed to focus on the agricultural land suitability of Azad Jammu and Kashmir (AJK), where the existing agriculture land is only 8% and dense forest and glaciers are covering 46.06% of the total area. Based on the literature review and local expert’s knowledge, eight different criteria have been taken to scale the available land for the suitability of agriculture practices. These parameters are soil orders, soil pH, Land-use Land-cover (LULC), slope, elevation, temperature, precipitation, and Potential Evapotranspiration (PET). Analytical Hierarchy Process (AHP) technique in integration with Geographical Information System (GIS) and Weighted Overlay Analysis (WOA) had been incorporated to classify the land for agriculture production. In AHP, weights were determined with the use of pairwise comparison matrix based on expert opinions. According to the guidelines of the United Nations Food and Agriculture Organization (FAO), the land suitability map was divided into five zones. After subtracting the areas of permanent features like mountains, forest, and glaciers, it was estimated that a highly suitable area was 13.21%, moderately suitable area was 11.61%, marginally suitable area was 13.14% and 62.05% was not suitable permanently. It is concluded that the integration of GIS and AHP in land suitability, is efficient and it will help the policymakers to improve the management of their land resources.
Annotating the biomedical literature for the human variome
(OXFORD UNIV PRESS, 2013-04-12)
This article introduces the Variome Annotation Schema, a schema that aims to capture the core concepts and relations relevant to cataloguing and interpreting human genetic variation and its relationship to disease, as described in the published literature. The schema was inspired by the needs of the database curators of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database, but is intended to have application to genetic variation information in a range of diseases. The schema has been applied to a small corpus of full text journal publications on the subject of inherited colorectal cancer. We show that the inter-annotator agreement on annotation of this corpus ranges from 0.78 to 0.95 F-score across different entity types when exact matching is measured, and improves to a minimum F-score of 0.87 when boundary matching is relaxed. Relations show more variability in agreement, but several are reliable, with the highest, cohort-has-size, reaching 0.90 F-score. We also explore the relevance of the schema to the InSiGHT database curation process. The schema and the corpus represent an important new resource for the development of text mining solutions that address relationships among patient cohorts, disease and genetic variation, and therefore, we also discuss the role text mining might play in the curation of information related to the human variome. The corpus is available at http://opennicta.com/home/health/variome.
Early Priming Minimizes the Age-Related Immune Compromise of CD8(+) T Cell Diversity and Function
(PUBLIC LIBRARY SCIENCE, 2012-02-01)
The elderly are particularly susceptible to influenza A virus infections, with increased occurrence, disease severity and reduced vaccine efficacy attributed to declining immunity. Experimentally, the age-dependent decline in influenza-specific CD8(+) T cell responsiveness reflects both functional compromise and the emergence of 'repertoire holes' arising from the loss of low frequency clonotypes. In this study, we asked whether early priming limits the time-related attrition of immune competence. Though primary responses in aged mice were compromised, animals vaccinated at 6 weeks then challenged >20 months later had T-cell responses that were normal in magnitude. Both functional quality and the persistence of 'preferred' TCR clonotypes that expand in a characteristic immunodominance hierarchy were maintained following early priming. Similar to the early priming, vaccination at 22 months followed by challenge retained a response magnitude equivalent to young mice. However, late priming resulted in reduced TCRβ diversity in comparison with vaccination earlier in life. Thus, early priming was critical to maintaining individual and population-wide TCRβ diversity. In summary, early exposure leads to the long-term maintenance of memory T cells and thus preserves optimal, influenza-specific CD8(+) T-cell responsiveness and protects against the age-related attrition of naïve T-cell precursors. Our study supports development of vaccines that prime CD8(+) T-cells early in life to elicit the broadest possible spectrum of CD8(+) T-cell memory and preserve the magnitude, functionality and TCR usage of responding populations. In addition, our study provides the most comprehensive analysis of the aged (primary, secondary primed-early and secondary primed-late) TCR repertoires published to date.
The Effect of a Hyperdynamic Circulation on Tissue Doppler Values: A Simulation in Young Adults during Exercise.
(Hindawi Limited, 2011)
Left ventricular tissue Doppler imaging (TDI) velocities are used to monitor systolic and diastolic function, but it is not known how these may change in a hyperdynamic circulation, as often occurs in anesthesia and critical care medicine. Twenty-six healthy young volunteers were recruited and left ventricular systolic and diastolic tissue Doppler velocities measured at rest, light exercise, strenuous exercise, and recovery (10 minutes after exercise). At rest, TDI velocities significantly decreased from base to apex (P < .001). Within basal, mid, and apical sections, systolic and diastolic peak velocities differed between segments (P < .05), except for systolic middle (P = .094) and late diastolic apical velocities (P = .257). Basal septal velocities differed from basal lateral, for systolic (P = .041) but not diastolic peak values. Inferobasal radial values differed from basal lateral values for both systolic and diastolic velocities (P < .05). Both systolic and diastolic TDI velocities increased significantly in all segments in a proportionate manner with a hyperdynamic circulation.
New Host Range for Hematodinium in Southern Australia and Novel Tools for Sensitive Detection of Parasitic Dinoflagellates
(PUBLIC LIBRARY SCIENCE, 2013-12-06)
Hematodinium is a parasitic dinoflagellate and emerging pathogen of crustaceans. It preferably manifests in haemolymph of marine decapod crustaceans, killing a large variety of genera with significant impacts on fisheries worldwide. There is, however, evidence that some crustacean stocks harbor high prevalence, low intensity infections that may not result in widespread host mortality and are therefore hard to detect. The most widely used methods for detection of Hematodinium are conventional blood smears and polymerase chain reaction (PCR) against ribosomal RNAs. Blood smears demand a trained investigator, are labor intensive and not readily scalable for high-throughput sampling. PCRs only detect parasite DNA and can also suffer from false negatives and positives. In order to develop alternative detection tools for Hematodinium cells in decapod crustaceans we employed an immunological approach against a newly identified, abundant dinoflagellate-specific nuclear protein--Dinoflagellate/Viral NucleoProtein (DVNP). Both immunofluorescence assay (IFA) and Western blot methods against DVNP showed high sensitivity of detection. The Western blot detects Hematodinium parasites to levels of 25 parasites per milliliter of crustacean haemolymph, with the potential for sample pooling and screening of large samples. Using both PCR and these new tools, we have identified Hematodinium cells present in three new host crab taxa, at high prevalence but with no sign of pathogenesis. This extends the known range of Hematodinium to southern Australia.
Postglacial Fringing-Reef to Barrier-Reef conversion on Tahiti links Darwin's reef types
(NATURE PUBLISHING GROUP, 2014-05-21)
In 1842 Charles Darwin claimed that vertical growth on a subsiding foundation caused fringing reefs to transform into barrier reefs then atolls. Yet historically no transition between reef types has been discovered and they are widely considered to develop independently from antecedent foundations during glacio-eustatic sea-level rise. Here we reconstruct reef development from cores recovered by IODP Expedition 310 to Tahiti, and show that a fringing reef retreated upslope during postglacial sea-level rise and transformed into a barrier reef when it encountered a Pleistocene reef-flat platform. The reef became stranded on the platform edge, creating a lagoon that isolated it from coastal sediment and facilitated a switch to a faster-growing coral assemblage dominated by acroporids. The switch increased the reef's accretion rate, allowing it to keep pace with rising sea level, and transform into a barrier reef. This retreat mechanism not only links Darwin's reef types, but explains the re-occupation of reefs during Pleistocene glacio-eustacy.
Z944, a Novel Selective T-Type Calcium Channel Antagonist Delays the Progression of Seizures in the Amygdala Kindling Model
(PUBLIC LIBRARY SCIENCE, 2015-08-14)
Temporal lobe epilepsy (TLE) is the most common form of drug resistant epilepsy. Current treatment is symptomatic, suppressing seizures, but has no disease modifying effect on epileptogenesis. We examined the effects of Z944, a potent T-type calcium channel antagonist, as an anti-seizure agent and against the progression of kindling in the amygdala kindling model of TLE. The anti-seizure efficacy of Z944 (5mg/kg, 10mg/kg, 30mg/kg and 100mg/kg) was assessed in fully kindled rats (5 class V seizures) as compared to vehicle, ethosuximide (ETX, 100mg/kg) and carbamazepine (30mg/kg). Each animal received the seven treatments in a randomised manner. Seizure class and duration elicited by six post-drug stimulations was determined. To investigate for effects in delaying the progression of kindling, naive animals received Z944 (30mg/kg), ETX (100mg/kg) or vehicle 30-minutes prior to each kindling stimulation up to a maximum of 30 stimulations, with seizure class and duration recorded after each stimulation. At the completion of drug treatment, CaV3.1, CaV3.2 and CaV3.3 mRNA expression levels were assessed in the hippocampus and amygdala using qPCR. Z944 was not effective at suppressing seizures in fully kindled rats compared to vehicle. Animals receiving Z944 required significantly more stimulations to evoke a class III (p<0.05), IV (p<0.01) or V (p<0.0001) seizure, and to reach a fully kindled state (p<0.01), than animals receiving vehicle. There was no significant difference in the mRNA expression of the T-type Ca2+ channels in the hippocampus or amygdala. Our results show that selectively targeting T-type Ca2+ channels with Z944 inhibits the progression of amygdala kindling. This could be a potential for a new therapeutic intervention to mitigate the development and progression of epilepsy.
Impaired glucose metabolism and exercise capacity with muscle-specific glycogen synthase 1 (gys1) deletion in adult mice
(ELSEVIER SCIENCE BV, 2016-03-01)
OBJECTIVE: Muscle glucose storage and muscle glycogen synthase (gys1) defects have been associated with insulin resistance. As there are multiple mechanisms for insulin resistance, the specific role of glucose storage defects is not clear. The aim of this study was to examine the effects of muscle-specific gys1 deletion on glucose metabolism and exercise capacity. METHODS: Tamoxifen inducible and muscle specific gys-1 KO mice were generated using the Cre/loxP system. Mice were subjected to glucose tolerance tests, euglycemic/hyperinsulinemic clamps and exercise tests. RESULTS: gys1-KO mice showed ≥85% reduction in muscle gys1 mRNA and protein concentrations, 70% reduction in muscle glycogen levels, postprandial hyperglycaemia and hyperinsulinaemia and impaired glucose tolerance. Under insulin-stimulated conditions, gys1-KO mice displayed reduced glucose turnover and muscle glucose uptake, indicative of peripheral insulin resistance, as well as increased plasma and muscle lactate levels and reductions in muscle hexokinase II levels. gys1-KO mice also exhibited markedly reduced exercise and endurance capacity. CONCLUSIONS: Thus, muscle-specific gys1 deletion in adult mice results in glucose intolerance due to insulin resistance and reduced muscle glucose uptake as well as impaired exercise and endurance capacity. IN BRIEF: This study demonstrates why the body prioritises muscle glycogen storage over liver glycogen storage despite the critical role of the liver in supplying glucose to the brain in the fasting state and shows that glycogen deficiency results in impaired glucose metabolism and reduced exercise capacity.
Tumour-associated neutrophils and loss of epithelial PTEN can promote corticosteroid-insensitive MMP-9 expression in the chronically inflamed lung microenvironment
(BMJ PUBLISHING GROUP, 2017-12-01)
Matrix metalloproteinase-9 (MMP-9) is increased in a number of pathological lung conditions, where the proteinase contributes to deleterious remodelling of the airways. While both lung cancer and COPD are associated with increased MMP-9 expression, the cellular and molecular drivers of MMP-9 remain unresolved. In this study, MMP-9 transcript measured within the tumour region from patients with non-small-cell lung cancer (NSCLC) and coexisting COPD was found to be uniformly increased relative to adjacent tumour-free tissue. MMP-9 gene expression and immunohistochemistry identified tumour-associated neutrophils, but not macrophages, as a predominant source of this proteinase. In addition, PTEN gene expression was significantly reduced in tumour and there was evidence of epithelial MMP-9 expression. To explore whether PTEN can regulate epithelial MMP-9 expression, a small interfering (si)RNA knockdown strategy was used in Beas-2B bronchial epithelial cells. PTEN knockdown by siRNA selectively increased MMP-9 expression in response to lipopolysaccharide in a corticosteroid-insensitive manner. In summary, tumour-associated neutrophils represent an important source of MMP-9 in NSCLC, and loss of epithelial PTEN may further augment steroid-insensitive expression.
Phylodynamic Reconstruction Reveals Norovirus GII. 4 Epidemic Expansions and their Molecular Determinants
(PUBLIC LIBRARY SCIENCE, 2010-05-01)
Noroviruses are the most common cause of viral gastroenteritis. An increase in the number of globally reported norovirus outbreaks was seen the past decade, especially for outbreaks caused by successive genogroup II genotype 4 (GII.4) variants. Whether this observed increase was due to an upswing in the number of infections, or to a surveillance artifact caused by heightened awareness and concomitant improved reporting, remained unclear. Therefore, we set out to study the population structure and changes thereof of GII.4 strains detected through systematic outbreak surveillance since the early 1990s. We collected 1383 partial polymerase and 194 full capsid GII.4 sequences. A Bayesian MCMC coalescent analysis revealed an increase in the number of GII.4 infections during the last decade. The GII.4 strains included in our analyses evolved at a rate of 4.3-9.0x10(-3) mutations per site per year, and share a most recent common ancestor in the early 1980s. Determinants of adaptation in the capsid protein were studied using different maximum likelihood approaches to identify sites subject to diversifying or directional selection and sites that co-evolved. While a number of the computationally determined adaptively evolving sites were on the surface of the capsid and possible subject to immune selection, we also detected sites that were subject to constrained or compensatory evolution due to secondary RNA structures, relevant in virus-replication. We highlight codons that may prove useful in identifying emerging novel variants, and, using these, indicate that the novel 2008 variant is more likely to cause a future epidemic than the 2007 variant. While norovirus infections are generally mild and self-limiting, more severe outcomes of infection frequently occur in elderly and immunocompromized people, and no treatment is available. The observed pattern of continually emerging novel variants of GII.4, causing elevated numbers of infections, is therefore a cause for concern.
Benefits and challenges of incorporating citizen science into university education.
(Public Library of Science (PLoS), 2017)
A common feature of many citizen science projects is the collection of data by unpaid contributors with the expectation that the data will be used in research. Here we report a teaching strategy that combined citizen science with inquiry-based learning to offer first year university students an authentic research experience. A six-year partnership with the Australian phenology citizen science program ClimateWatch has enabled biology students from the University of Western Australia to contribute phenological data on plants and animals, and to conduct the first research on unvalidated species datasets contributed by public and university participants. Students wrote scientific articles on their findings, peer-reviewed each other's work and the best articles were published online in a student journal. Surveys of more than 1500 students showed that their environmental engagement increased significantly after participating in data collection and data analysis. However, only 31% of students agreed with the statement that "data collected by citizen scientists are reliable" at the end of the project, whereas the rate of agreement was initially 79%. This change in perception was likely due to students discovering erroneous records when they mapped data points and analysed submitted photographs. A positive consequence was that students subsequently reported being more careful to avoid errors in their own data collection, and making greater efforts to contribute records that were useful for future scientific research. Evaluation of our project has shown that by embedding a research process within citizen science participation, university students are given cause to improve their contributions to environmental datasets. If true for citizen scientists in general, enabling participants as well as scientists to analyse data could enhance data quality, and so address a key constraint of broad-scale citizen science programs.