Search results for: sequence diagram merging

Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: Asma Omri, Iheb Sifaoui, Sofiane Sayahi, Hichem Besbes

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Future vehicle systems demand advanced capabilities, notably in-cabin life detection and driver monitoring systems, with a particular emphasis on drowsiness detection. To meet these requirements, several techniques employ artificial intelligence methods based on real-time vital sign measurements. In parallel, Frequency-Modulated Continuous-Wave (FMCW) radar technology has garnered considerable attention in the domains of healthcare and biomedical engineering for non-invasive vital sign monitoring. FMCW radar offers a multitude of advantages, including its non-intrusive nature, continuous monitoring capacity, and its ability to penetrate through clothing. In this paper, we propose a system utilizing the AWR6843AOP radar from Texas Instruments (TI) to extract precise vital sign information. The radar allows us to estimate Ballistocardiogram (BCG) signals, which capture the mechanical movements of the body, particularly the ballistic forces generated by heartbeats and respiration. These signals are rich sources of information about the cardiac cycle, rendering them suitable for heart rate estimation. The process begins with real-time subject positioning, followed by clutter removal, computation of Doppler phase differences, and the use of various filtering methods to accurately capture subtle physiological movements. To address the challenges associated with FMCW radar-based vital sign monitoring, including motion artifacts due to subjects' movement or radar micro-vibrations, Long Short-Term Memory (LSTM) networks are implemented. LSTM's adaptability to different heart rate patterns and ability to handle real-time data make it suitable for continuous monitoring applications. Several crucial steps were taken, including feature extraction (involving amplitude, time intervals, and signal morphology), sequence modeling, heart rate estimation through the analysis of detected cardiac cycles and their temporal relationships, and performance evaluation using metrics such as Root Mean Square Error (RMSE) and correlation with reference heart rate measurements. For dataset construction and LSTM training, a comprehensive data collection system was established, integrating the AWR6843AOP radar, a Heart Rate Belt, and a smart watch for ground truth measurements. Rigorous synchronization of these devices ensured data accuracy. Twenty participants engaged in various scenarios, encompassing indoor and real-world conditions within a moving vehicle equipped with the radar system. Static and dynamic subject’s conditions were considered. The heart rate estimation through LSTM outperforms traditional signal processing techniques that rely on filtering, Fast Fourier Transform (FFT), and thresholding. It delivers an average accuracy of approximately 91% with an RMSE of 1.01 beat per minute (bpm). In conclusion, this paper underscores the promising potential of FMCW radar technology integrated with artificial intelligence algorithms in the context of automotive applications. This innovation not only enhances road safety but also paves the way for its integration into the automotive ecosystem to improve driver well-being and overall vehicular safety.

Keywords: ballistocardiogram, FMCW Radar, vital sign monitoring, LSTM

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Authors: Sajeli A. Begum, Ameer Basha, Kirti Hira, Rukaiyya Khan

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Cyclic dipeptides are simple diketopiperazine derivatives being investigated by several scientists for their biological effects which include anticancer, antimicrobial, haematological, anticonvulsant, immunomodulatory effect, etc. They are potentially active microbial metabolites having been synthesized too, for developing into drug candidates. Cultures of Pseudomonas species have earlier been reported to produce cyclic dipeptides, helping in quorum sensing signals and bacterial–host colonization phenomena during infections, causing cell anti-proliferation and immunosuppression. Fluorescing Pseudomonas species have been identified to secrete lipid derivatives, peptides, pyrroles, phenazines, indoles, aminoacids, pterines, pseudomonic acids and some antibiotics. In the present work, results of investigation on the cyclic dipeptide metabolites secreted by the culture broth of Pseudomonas species as potent pro-inflammatory cytokine inhibitors are discussed. The bacterial strain was isolated from the rhizospheric soil of groundnut crop and identified as Pseudomonas aeruginosa by 16S rDNA sequence (GenBank Accession No. KT625586). Culture broth of this strain was prepared by inoculating into King’s B broth and incubating at 30 ºC for 7 days. The ethyl acetate extract of culture broth was prepared and lyophilized to get a dry residue (EEPA). Lipopolysaccharide (LPS)-induced ELISA assay proved the inhibition of tumor necrosis factor-alpha (TNF-α) secretion in culture supernatant of RAW 264.7 cells by EEPA (IC50 38.8 μg/mL). The effect of oral administration of EEPA on plasma TNF-α level in rats was tested by ELISA kit. The LPS mediated plasma TNF-α level was reduced to 45% with 125 mg/kg dose of EEPA. Isolation of the chemical constituents of EEPA through column chromatography yielded ten cyclic dipeptides, which were characterized using nuclear magnetic resonance and mass spectroscopic techniques. These cyclic dipeptides are biosynthesized in microorganisms by multifunctional assembly of non-ribosomal peptide synthases and cyclic dipeptide synthase. Cyclo (Gly-L-Pro) was found to be more potentially (IC50 value 4.5 μg/mL) inhibiting TNF-α production followed by cyclo (trans-4-hydroxy-L-Pro-L-Phe) (IC50 value 14.2 μg/mL) and the effect was equal to that of standard immunosuppressant drug, prednisolone. Further, the effect was analyzed by determining mRNA expression of TNF-α in LPS-stimulated RAW 264.7 macrophages using quantitative real-time reverse transcription polymerase chain reaction. EEPA and isolated cyclic dipeptides demonstrated diminution of TNF-α mRNA expression levels in a dose-dependent manner under the tested conditions. Also, they were found to control the expression of other pro-inflammatory cytokines like IL-1β and IL-6, when tested through their mRNA expression levels in LPS-stimulated RAW 264.7 macrophages under LPS-stimulated conditions. In addition, significant inhibition effect was found on Nitric oxide production. Further all the compounds exhibited weak toxicity to LPS-induced RAW 264.7 cells. Thus the outcome of the study disclosed the effectiveness of EEPA and the isolated cyclic dipeptides in down-regulating key cytokines involved in pathophysiology of autoimmune diseases.In another study led by the investigators, microbial cyclic dipeptides were found to exhibit excellent antimicrobial effect against Fusarium moniliforme which is an important causative agent of Sorghum grain mold disease. Thus, cyclic dipeptides are emerging small molecular drug candidates for various autoimmune diseases.

Keywords: cyclic dipeptides, cytokines, Fusarium moniliforme, Pseudomonas, TNF-alpha

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Authors: S. Fadda, M. Fiori, C. Matzuzzi

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Mineralized formations in the bottom sediments of a Miocene transgression have been discovered in Sardinia. The mineral assemblage consists of copper sulphides and oxidates suggesting fluctuations of redox conditions in neutral to high-pH restricted shallow-water coastal basins. Azurite/malachite has been observed as authigenic and occurs as loose spheroidal crystalline particles associated with the transitional-littoral horizon forming the bottom of the marine transgression. Many field observations are consistent with a supergenic circulation of metals involving terrestrial groundwater-seawater mixing. Both clastic materials and metals come from Tertiary volcanic edifices while the main precipitating anions, carbonates, and sulphides species are of both continental and marine origin. Formation of Cu carbonates as a supergene secondary 'oxide' assemblage, does not agree with field evidences, petrographic observations along with textural evidences in the host-rock types. Samples were collected along the sedimentary sequence for different analyses: the majority of elements were determined by X-ray fluorescence and plasma-atomic emission spectroscopy. Mineral identification was obtained by X-ray diffractometry and scanning electron microprobe. Thin sections of the samples were examined in microscopy while porosity measurements were made using a mercury intrusion porosimeter. Cu-carbonates deposited at a temperature below 100 C° which is consistent with the clay minerals in the matrix of the host rock dominated by illite and montmorillonite. Azurite nodules grew during the early diagenetic stage through reaction of cupriferous solutions with CO₂ imported from the overlying groundwater and circulating through the sandstones during shallow burial. Decomposition of organic matter in the bottom anoxic waters released additional carbon dioxide to pore fluids for azurite stability. In this manner localized reducing environments were also generated in which Cu was fixed as Cu-sulphide and sulphosalts. Microscopic examinations of textural features of azurite nodules give evidence of primary malachite/azurite deposition rather than supergene oxidation in place of primary sulfides. Photomicrographs show nuclei of azurite and malachite surrounded by newly formed microcrystalline carbonates which constitute the matrix. The typical pleochroism of crystals can be observed also when this mineral fills microscopic fissures or cracks. Sedimentological evidence of transgression and regression indicates that the pore water would have been a variable mixture of marine water and groundwaters with a possible meteoric component in an alternatively exposed and subaqueous environment owing to water-level fluctuation. Salinity data of the pore fluids, assessed at random intervals along the mineralised strata confirmed the values between about 7000 and 30,000 ppm measured in coeval sediments at the base of Miocene falling in the range of a more or less diluted sea water. This suggests a variation in mean pore-fluids pH between 5.5 and 8.5, compatible with the oxidized and reduced mineral paragenesis described in this work. The results of stable isotopes studies reflect the marine transgressive-regressive cyclicity of events and are compatibile with carbon derivation from sea water. During the last oxidative stage of diagenesis, under surface conditions of higher activity of H₂O and O₂, CO₂ partial pressure decreased, and malachite becomes the stable Cu mineral. The potential for these small but high grade deposits does exist.

Keywords: sedimentary, Cu-carbonates, authigenic, tertiary, Sardinia

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Authors: Qiaosi Li, Frankie Kwan Kit Wong, Tung Fung

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Lightweight unmanned aerial vehicle (UAV) loading with novel sensors offers a low cost approach for data acquisition in complex environment. This study established a framework for applying UAV system in complex environment quick mapping and assessed the performance of UAV-based hyperspectral image and digital surface model (DSM) derived from photogrammetric point clouds for 13 species classification in wetland area Mai Po Inner Deep Bay Ramsar Site, Hong Kong. The study area was part of shallow bay with flat terrain and the major species including reedbed and four mangroves: Kandelia obovata, Aegiceras corniculatum, Acrostichum auerum and Acanthus ilicifolius. Other species involved in various graminaceous plants, tarbor, shrub and invasive species Mikania micrantha. In particular, invasive species climbed up to the mangrove canopy caused damage and morphology change which might increase species distinguishing difficulty. Hyperspectral images were acquired by Headwall Nano sensor with spectral range from 400nm to 1000nm and 0.06m spatial resolution image. A sequence of multi-view RGB images was captured with 0.02m spatial resolution and 75% overlap. Hyperspectral image was corrected for radiative and geometric distortion while high resolution RGB images were matched to generate maximum dense point clouds. Furtherly, a 5 cm grid digital surface model (DSM) was derived from dense point clouds. Multiple feature reduction methods were compared to identify the efficient method and to explore the significant spectral bands in distinguishing different species. Examined methods including stepwise discriminant analysis (DA), support vector machine (SVM) and minimum noise fraction (MNF) transformation. Subsequently, spectral subsets composed of the first 20 most importance bands extracted by SVM, DA and MNF, and multi-source subsets adding extra DSM to 20 spectrum bands were served as input in maximum likelihood classifier (MLC) and SVM classifier to compare the classification result. Classification results showed that feature reduction methods from best to worst are MNF transformation, DA and SVM. MNF transformation accuracy was even higher than all bands input result. Selected bands frequently laid along the green peak, red edge and near infrared. Additionally, DA found that chlorophyll absorption red band and yellow band were also important for species classification. In terms of 3D data, DSM enhanced the discriminant capacity among low plants, arbor and mangrove. Meanwhile, DSM largely reduced misclassification due to the shadow effect and morphological variation of inter-species. In respect to classifier, nonparametric SVM outperformed than MLC for high dimension and multi-source data in this study. SVM classifier tended to produce higher overall accuracy and reduce scattered patches although it costs more time than MLC. The best result was obtained by combining MNF components and DSM in SVM classifier. This study offered a precision species distribution survey solution for inaccessible wetland area with low cost of time and labour. In addition, findings relevant to the positive effect of DSM as well as spectral feature identification indicated that the utility of UAV-borne hyperspectral and photogrammetry deriving 3D data is promising in further research on wetland species such as bio-parameters modelling and biological invasion monitoring.

Keywords: digital surface model (DSM), feature reduction, hyperspectral, photogrammetric point cloud, species mapping, unmanned aerial vehicle (UAV)

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Authors: Rohini Das, Subhasish Das, Smruti Rekha Sahoo, Shagupta Yesmin

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The Paleoproterozoic Kolhan Group (Purana) ensemble constitutes the youngest lithostratigraphic 'outlier' in the Singhbhum Archaean craton. The Kolhan unconformably overlies both the Singhbhum granite and the Iron Ore Group (IOG). Representing a typical sandstone-shale ( +/- carbonates) sequence, the Kolhan is characterized by the development of thin and discontinuous patches of basal conglomerates draped by sandstone beds. The IOG-fault limits the western 'distal' margin of the Kolhan basin showing evidence of passive subsidence subsequent to the initial rifting stage. The basin evolved as a half-graben under the influence of an extensional stress regime. The assumption of a tectonic setting for the NE-SW trending Kolhan basin possibly relates to the basin opening to the E-W extensional stress system that prevailed during the development of the Newer Dolerite dyke. The Paleoproterozoic age of the Kolhan basin is based on the consideration of the conformable stress pattern responsible both for the basin opening and the development of the conjugate fracture system along which the Newer Dolerite dykes intruded the Singhbhum Archaean craton. The Kolhan sandstones show progressive change towards greater textural and mineralogical maturity in its upbuilding. The trend of variations in different mineralogical and textural attributes, however, exhibits inflections at different lithological levels. Petrological studies collectively indicate that the sandstones were dominantly derived from a weathered granitic crust under a humid climatic condition. Provenance-derived variations in sandstone compositions are therefore a key in unraveling regional tectonic histories. The basin axis controlled the progradation direction which was likely driven by climatically induced sediment influx, a eustatic fall, or both. In the case of the incongruent shift, increased sediment supply permitted the rivers to cross the basinal deep. Temporal association of the Kolhan with tectonic structures in the belt indicates that syn-tectonic thrust uplift, not isostatic uplift or climate, caused the influx of quartz. The sedimentation pattern in the Kolhan reflects a change from braided fluvial-ephemeral pattern to a fan-delta-lacustrine type. The channel geometries and the climate exerted a major control on the processes of sediment transfer. Repeated fault controlled uplift of the source followed by subsidence and forced regression, generated multiple sediment cyclicity that led to the fluvial-fan delta sedimentation pattern. Intermittent uplift of the faulted blocks exposed fresh bedrock to mechanical weathering that generated a large amount of detritus and resulted to forced regressions, repeatedly disrupting the cycles which may reflect a stratigraphic response of connected rift basins at the early stage of extension. The marked variations in the thickness of the fan delta succession and the stacking pattern in different measured profiles reflect the overriding tectonic controls on fan delta evolution. The accumulated fault displacement created higher accommodation and thicker delta sequences. Intermittent uplift of fault blocks exposed fresh bedrock to mechanical weathering, generated a large amount of detritus, and resulted in forced closure of the land-locked basin, repeatedly disrupting the fining upward pattern. The control of source rock lithology or climate was of secondary importance to tectonic effects. Such a retrograding fan delta could be a stratigraphic response of connected rift basins at the early stage of extension.

Keywords: Kolhan basin, petrology, sandstone, tectonics

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Authors: Lolwa Alansari, Abdelhamid Azhaghdani, Sufia Athar, Hanen Mrabet, Annaliza Cruz, Tamara Alshadafat, Almunzer Zakaria

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Introduction: Improving the patient experience is a fundamental pillar of healthcare's quadruple aims. Recognizing the importance of patient experiences and perceptions in healthcare interactions is pivotal for driving quality improvement. This abstract centers around the Patient Experience Program, an endeavor crafted with the purpose of comprehending and elevating the experiences of patients in the Obstetrics & Gynecology Emergency Department (OB/GYN ED). Methodology: This comprehensive endeavor unfolded through a structured sequence of phases following Plan-Do-Study-Act (PDSA) model, spanning over 12 months, focused on enhancing patient experiences in the Obstetrics & Gynecology Emergency Department (OB/GYN ED). The study meticulously examined the journeys of patients with acute obstetrics and gynecological conditions, collecting data from over 100 participants monthly. The inclusive approach covered patients of different priority levels (1-5) admitted for acute conditions, with no exclusions. Historical data from March and April 2022 serves as a benchmark for comparison, strengthening causality claims by providing a baseline understanding of OB/GYN ED performance before interventions. Additionally, the methodology includes the incorporation of staff engagement surveys to comprehensively understand the experiences of healthcare professionals with the implemented improvements. Data extraction involved administering open-ended questions and comment sections to gather rich qualitative insights. The survey covered various aspects of the patient journey, including communication, emotional support, timely access to care, care coordination, and patient-centered decision-making. The project's data analysis utilized a mixed-methods approach, combining qualitative techniques to identify recurring themes and extract actionable insights and quantitative methods to assess patient satisfaction scores and relevant metrics over time, facilitating the measurement of intervention impact and longitudinal tracking of changes. From the themes we discovered in both the online and in-person patient experience surveys, several key findings emerged that guided us in initiating improvements, including effective communication and information sharing, providing emotional support and empathy, ensuring timely access to care, fostering care coordination and continuity, and promoting patient-centered decision-making. Results: The project yielded substantial positive outcomes, significantly improving patient experiences in the OB/GYN ED. Patient satisfaction levels rose from 62% to a consistent 98%, with notable improvements in satisfaction with care plan information and physician care. Waiting time satisfaction increased from 68% to a steady 97%. The project positively impacted nurses' and midwives' job satisfaction, increasing from 64% to an impressive 94%. Operational metrics displayed positive trends, including a decrease in the "left without being seen" rate from 3% to 1%, the discharge against medical advice rate dropping from 8% to 1%, and the absconded rate reducing from 3% to 0%. These outcomes underscore the project's effectiveness in enhancing both patient and staff experiences in the healthcare setting. Conclusion: The use of a patient experience questionnaire has been substantiated by evidence-based research as an effective tool for improving the patient experience, guiding interventions, and enhancing overall healthcare quality in the OB/GYN ED. The project's interventions have resulted in a more efficient allocation of resources, reduced hospital stays, and minimized unnecessary resource utilization. This, in turn, contributes to cost savings for the healthcare facility.

Keywords: patient experience, patient survey, person centered care, quality initiatives

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Authors: Almas Rajguru

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The Oligocene succession of the Tapti- Daman area is one of the established petroleum plays in Tapti-Daman block of the Mumbai Offshore Basin. Despite good control and production history, the sand geometry and continuity of reservoir character of these sediments are less understood as most reservoirs are thin and fall below seismic resolution. The present work focuses on a detailed analysis of the Early Oligocene Mahuva Formation at the reservoir scale through laboratory studies (sedimentology and biostratigraphy) of core and sidewall cores in integration with electro logs for firming up facies’ distribution, micro-depositional environment and sequence stratigraphy, diagenesis and reservoir characterization from seventeen wells from North Tapti-C-37 area in Tapti Daman Block, WOB. The thick shale/claystone with thin interbeds of sandstone and siltstones of deeper marine in the lower part of Mahuva Fm represents deposition in a transgressive regime. The overlying interbedded sandstone, glauconitic-siltstone/fine-grained sandstone, and thin beds of packstone/grainstone within highly fissile shale were deposited in a prograding tide-dominated delta during late-rise normal regression. Nine litho facies (F1-F9) representing deposition in various microenvironments of the tide-dominated delta are identified based on their characteristic sediment texture, structure and microfacies. Massive, gritty sandstone (F1) with poorly sorted sands lithic fragments with calcareous and Fe-rich matrix represents channel fill sediments. High-angle cross-stratified sandstone (F2) deposited in rapidly shifting/migrating bars under strong tidal currents. F3 records the laterally accreted tidal-channel point bars. F3 (low-angle cross-stratified to parallel bedded sandstone) and F4 (Clean sandstone) are often associated with F2 in a tidal bar complex. F5 (interbedded thin sand and mud) and F6 (bioturbated sandstone) represent tidal flat deposits. High energy open marine carbonate shoals (F8) and fossiliferous sandstone in offshore bars (F7) represent deepening up facies. Shallow marine standstill conditions facilitated the deposition of thick shale (F9) beds. The reservoir facies (F1-F6) are commonly poorly to moderately sorted; bimodal, immature sandstone represented by quartz-wacke. The framework grains are sub-angular to sub-rounded, medium to coarse-grained (occasionally gritty) embedded within argillaceous (kaolinite/chlorite/chamosite) to highly Fe-rich matrix (sideritic). The facies F7 and F8, representing the sandy packstone and grainstone facies, respectively, exhibit poor reservoir characteristics due to sanitization, diagenetic compaction and matrix-filled intergranular spaces. The various diagenetic features such as the presence of authigenic clays (kaolinite/dickite/smectite); ferruginous minerals like siderite, pyrite, hematite and other iron oxides; bioturbations; glauconite; calcite and quartz cementation, precipitation of gypsum, pressure solution and other compaction effects are identified. These diagenetic features, wherever present, have reduced porosity and permeability thereby adversely affecting reservoir quality. Tidal bar sandstones possess good reservoir characteristics such as moderate to good sorting, fair to good porosity and geometry that facilitates efficient lateral extension and vertical thickness of reservoir. The sand bodies of F2, F3 and F4 facies of Well L, M and Q deposited in a tidal bar complex exhibit good reservoir quality represented by relatively cleaner, poorly burrowed, loose, friable sandstone with good porosity. Sandstone facies around these wells could prove a potential hydrocarbon reservoir and could be considered for further exploration.

Keywords: reservoir sedimentology, facies analysis, HST, tide dominated delta, tidal bars

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