101 research outputs found
Calculation of Metal Pollution Index and Enrichment Factor in Sodic Soil from Salt Production Area
No full textIn the present paper, the sodic soil samples were collected from the salt production area of Thakhauttaw, Hanlin, Sataung Gyi and Paline, Shwebo District, Sagaing Region. These samples were studied on the elemental analysis using the energy dispersive x ray fluorescence EDXRF spectroscopy. In order to evaluate the contamination status of metals, assessment indices such as metal pollution index MPI and enrichment factors EFs have been calculated by using the metal concentrations from the EDXRF results. The values of metal pollution index MPI for all samples were less than 1. This indicating the sodic soil was no significant of metal pollution. The results of enrichment factors show that Ca and Mn considerable enriched levels in the soil. According to health physics point of view, the overall study suggests that the sodic soil from salt production area were not metal contaminated and long term consumption cannot be cause potential health risks to consumers. Tin Htun Naing | Kyaw Kyaw Naing | Hla Win Aung | Wunna Ko | Khin Maung Htwe "Calculation of Metal Pollution Index and Enrichment Factor in Sodic Soil from Salt Production Area" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-3 | Issue-5 , August 2019, URL: https://www.ijtsrd.com/papers/ijtsrd26771.pd
Creation of characters in Kantkaw a novel of Linkar Yi Kyaw
No full textThis research paper is about creation of characters in Kantkaw a novel of Linkar Yi Kyaw. In this research paper the way the author created the characters is studied the dialogues, the manners of the characters and their thought. In doing so, the novel creation skill of the author is revealed
Taguchi Approach to Process Design Optimization for Quality Improvement Effect of Parameters on Milk Kefir Fermentation
No full textEntrain_example_brain_dataset
No full textSingle-cell RNA sequencing dataset of the developing mouse brain at E10 and E11, produced by [1], and processed by [2]. Data has been subset to E10 and E11 and subsampled to 5% of original cells.
RNA Velocity matrix has been run on this dataset, using scvelo [3] workflow.
Also attached, for convenience, is the required NicheNet database on intercellular regulation [4].
[1] La Manno G, Siletti K, Furlan A, Gyllborg D, Vinsland E, Mossi Albiach A, Mattsson Langseth C, Khven I, Lederer AR, Dratva LM, et al: Molecular architecture of the developing mouse brain. Nature 2021, 596:92-96.
[2] Abdelaal T, Lelieveldt BPF, Reinders MJT, Mahfouz A: SIRV: Spatial inference of RNA velocity at the single-cell resolution. bioRxiv 2021:2021.2007.2026.453774.
[3] Bergen V, Lange M, Peidli S, Wolf FA, Theis FJ: Generalizing RNA velocity to transient cell states through dynamical modeling. Nature Biotechnology 2020, 38:1408-1414.
[4] Browaeys R, Saelens W, Saeys Y: NicheNet: modeling intercellular communication by linking ligands to target genes. Nat Methods 2020, 17:159-16
Modelling Environmental Influences on Cell Phenotype with Mechanistic and Machine Learning Approaches
No full textMicroenvironmental conditions are critical in shaping cell phenotype. Recent advances in two modalities, single-cell transcriptomics and live imaging, have revealed that environmental conditions influence both gene expression and cellular morphology, respectively. In this PhD thesis, I develop and describe two computational models targeting each modality, both of which evaluate the extent to which environmental factors govern cell morphology and transcriptomic states. The two models, described in Chapters 3 and 4 respectively, differ in the level of embedded biological assumptions, which allows for both hypothesis-driven and data-driven exploration of environmental influences on cell phenotype.
The first model consists of an agent-based mechanistic model that examines how local environmental conditions influences the morpho-spatial phenotype of tingible body macrophages (TBMs) during the germinal centre reaction in mice. Subsequent in silico perturbation of various parameters reveals that the TBM choice of morpho-spatial phenotype maximizes the clearance rate for the local density and motility of apoptotic fragments.
The second model consists of an agnostic machine learning model, called ENTRAIN, which prioritizes ligand-receptor pairs in cellular differentiation. By integrating trajectory analysis with ligand-receptor-transcription factor networks, the first known method to do this, ENTRAIN identifies ligand-receptor pairs most likely to be influencing cell differentiation trajectories. ENTRAIN’s results are strongly concordant with published literature yet orthogonal to existing methods, demonstrating that the recovered signals are overlooked by traditional cell-cell communication methods. In contrast to the hypothesis-driven model in chapter 3, ENTRAIN operates without relying on strong prior assumptions.
Collectively, the two models illustrate the versatility of computational methods across contexts with varying levels of biological assumptions. While Chapter 3’s method embeds numerous mechanistic assumptions, Chapter 4 is a data-first method, operating in the absence of predefined rules. I then conclude this thesis in Chapter 5 with a discussion on a logical extension of this work: developing models that predict transcriptomic states in response to environmental perturbations. Such models have potential applications in combinatorial drug-response prediction, cell-state engineering, and whole-cell modelling
Hemiphyllodactylus tonywhitteni Grismer & Wood Jr & Kyaw Thura & Zin & Quah & Murdoch & Grismer & Li & Kyaw & Lwin 2017, sp. nov.
No full textHemiphyllodactylus tonywhitteni sp. nov. Phapant dwarf gecko (Figures 5 and 6) Holotype Adult male (LSUHC 13026) collected on 18 October 2016 at 1600 hours by Evan S. H. Quah, Perry L. Wood, Jr., Matthew L. Murdoch, Thaw Zin, Myint Kyaw Thura, Htet Kyaw, Marta S. Grismer, and L. Lee Grismer from Phapant Cave, 25.2 km north-east of Taunggyi, Taunggyi District, Shan State, Myanmar (21°11.472N, 96°33.214E; 1270 m). Paratypes Adult females (LSUHC 13027 and 13030) and juvenile female (LSUHC 13028) and juvenile male (LSUHC 13029) bear the same data as the holotype. Diagnosis Hemiphyllodactylus tonywhitteni sp. nov. can be separated from all other species of Hemiphyllodactylus by possessing the unique combination of having a maximum SVL of 38.8 mm; 5–8 chin scales; enlarged postmentals; 3–5 circumnasal scales; 2–4 scales between supranasals (=postrostrals); eight or nine supralabials; eight infralabials; 13–16 longitudinally arranged dorsal scales at midbody contained within one eye diameter and 7–9 ventral scales; varied digital formulae (Table 3); three subdigital lamellae on the first finger; three or four subdigital lamellae on the first toe; 20–26 continuous pore-bearing femoroprecloacal scales; no plate-like subcaudal scales; dark postorbital stripe not extending onto trunk; pairs of paravertebral light spots on trunk; dorsal body pattern not unicolour; postsacral marking bearing light-coloured anteriorly projecting arms; and caecum and gonads unpigmented. These characters are scored across all species of Hemiphyllodactylus from clades 3 and 4 (Table 3). Description of holotype Adult male; head triangular in dorsal profile, depressed, distinct from neck; lores and interorbital regions flat; rostrum moderate in length (NarEye/HeadL 0.33); prefrontal region flat to weakly concave; canthus rostralis smoothly rounded, barely discernible; snout moderate, rounded in dorsal profile; eye large; ear opening round, small; eye to ear distance greater than diameter of eye; rostral wider than high, bordered posteriorly by small supranasals; three internasals (=postnasal); external nares bordered anteriorly by rostral, dorsally by supranasal, posteriorly by two postnasals, ventrally by first supralabial (=circumnasals); 8 (R,L) rectangular supralabials tapering to below posterior margin of orbit; 8 (R,L) rectangular infralabials tapering to below posterior margin of orbit; scales of rostrum, lores, top of head, and occiput small, granular, those of rostrum largest and slightly raised; dorsal superciliaries flat, mostly square, subimbricate, largest anteriorly; mental triangular, bordered laterally by first infralabials and posteriorly by two large postmentals; each postmental bordered laterally by a single large, sublabial; seven chin scales; gular scales small, subimbricate, grading posteriorly into slightly larger, subimbricate, throat and pectoral scales which grade into slightly larger, subimbricate ventrals. Body somewhat elongate (Trunk/SVL 0.48), dorsoventrally compressed; ventrolateral folds absent; dorsal scales small, granular, 14 dorsal scales at midbody contained within one eye diameter; ventral scales, flat, subimbricate much larger than dorsal scales, seven ventral scales contained within one eye diameter; precloacal scales slightly larger than abdominal scales; pore-bearing precloacal scales continuous with pore-bearing femoral scales, totalling 26; forelimbs short, robust in stature, covered with flat, subimbricate scales dorsally and ventrally; palmar scales flat, subimbricate; all digits except digit I well developed; digit I vestigial, clawless; distal, subdigital lamellae of digits II–V undivided, angular and U-shaped; lamellae proximal to these transversely expanded; lamellar formula of digits II–V 4-4-4-4 (R,L); three transversely expanded lamellae on digit I; claws on digits II–V well developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; hind limbs short, more robust than forelimbs, covered with flat, juxtaposed scales dorsally and by larger, flat subimbricate scales ventrally; plantar scales low, flat, subimbricate; all digits except digit I well developed; digit I vestigial, clawless; distal, subdigital lamellae of digits II–V undivided, angular and U-shaped; lamellae proximal to these transversely expanded; lamellar formula of digits II–V 4-4-4-4 (R,L); three transversely expanded lamellae on digit I; claws on digits II–V well developed, unsheathed; distal portions of digits strongly curved, terminal joint free, arising from central portion of lamellar pad; dorsal caudal scales small, square, subimbricate; tail regenerated, covered with flat imbricate scales. Morphometric data are presented in Table 5. Coloration before preservation (Figure 5) Top of head, body, limbs, and tail grey, overlain with darker, broken bands on trunk appearing as paravertebral markings highlighted posteriorly by light-coloured, diffuse blotches; poorly defined dark, lineate markings extend from occipital region to shoulder; spotting or striping on trunk absent; diffuse, dark, preorbital stripe; dark, postorbital stripe irregularly shaped, extending to shoulder region; limbs bearing irregularly shaped, dark markings; tail generally unicolour; gular region generally immaculate, except for darker lateral areas and faint stippling in scales; and pigmentation density increases posteriorly with the abdomen being generally grey. Variation (Figures 5 and 6) The colour patterns of the paratypes generally match that of the holotype. LSUHC 13027 is darker overall and the colour pattern is less distinct. The light-coloured, paravertebral blotches in LSUHC 13029 are salmon coloured. The dark dorsal pattern of LSUHC 13028 is more speckled and that of the adult female LSUHC 13030 is more reticulate. LSUHC 13030 has an original tail lacking enlarged subcaudal plates and bearing a weak, ventrolateral fringe and a distinct banding pattern. The tail is oval in cross-section and the underside is dull orange. The intensity of coloration and contrast in pattern changes with mood and activity. Differences in scales counts are presented in Table 5. Distribution Hemiphyllodactylus tonywhitteni sp. nov. is known only from the type locality of Phapant Cave, Taunggyi District, Shan State, Myanmar (Figure 1). Natural history Phapant Cave is a complex of three caves situated around a small depression along a narrow river. The karstic ridge and outcroppings surround a small monastery which incorporates the caves for worship. The hilly area connecting the caves is composed of highly eroded limestone walls bearing many cracks and pores. Large limestone boulders that have broken away from the cliff face line the base of the shallow escarpment (Figure 7). We believe Hemiphyllodactylus tonywhitteni sp. nov. is a karst-adapted species. A specimen of H. tonywhitteni sp. nov. was found just inside a small opening of one of the caves nearly 4 m above the cave entrance. More specimens were found on the boulders at the base of the cliff and one on one of the cement buildings of the monastery. Syntopic with H. tonywhitteni sp. nov. on both the karst outcroppings and the cement building was an undescribed species of Hemidactylus. Hemidactylus sp. nov. was also found on wooden structures and vegetation where H. tonywhitteni sp. nov. was absent. Etymology This specific epithet ‘ tonywhitteni ’ honours Dr Tony Whitten of Fauna & Flora International who has championed a broad range of conservation efforts in Indonesia and the Asia Pacific for well over a quarter of a century. His tireless efforts to conserve and help manage karst ecosystems have been a great inspiration to the senior author (LLG) herein. Comparisons The molecular analyses indicate that Hemiphyllodactylus tonywhitteni sp. nov. is embedded within clade 4 of the typus group and is the sister species of H. montawaensis sp. nov. It can be distinguished from H. jinpingensis, H. chiangmaiensis and the species of clade 3 by lacking dark, dorsolateral stripes on the trunk and transverse, dorsal blotches. The PCA analysis shows that it occupies a unique morphospace with respect to H. montawaensis sp. nov. and H. linnwayensis sp. nov. with PC1 and PC2 accounting for 49% of the variation in the concatenated dataset (Figure 3). PC1 accounted for 29% of the variation and loaded most heavily for trunk length and the number of subdigital lamellae on the first toe (Table 6). PC2 accounted for an additional 20% of the variation and loaded most heavily for the number of dorsal scales. The first four components of the PCA were retained for the DAPC which shows that not only are all three species distinct but all individuals of each species fall very close to or within the 95% confidence ellipses (Figure 4). Uncorrected pair-wise sequence divergence between H. tonywhitteni sp. nov. and all other species of clades 3 and 4 ranges from 6.4–18.7% (Table 7). Hemiphyllodactylus tonywhitteni sp. nov. is most similar to its sister species H. montawaensis sp. nov. but differs in having more femoroprecloacal pores (20–26 versus 19–21) and a relatively wider head (0.17–0.19 versus 0.16–0.17) throughout its growth trajectory (Figure 8) and a statistically significantly wider head (p <0.24, n = 5) as an adult.Published as part of Grismer, L. Lee, Wood Jr, Perry L., Kyaw Thura, Myint, Zin, Thaw, Quah, Evan S. H., Murdoch, Matthew L., Grismer, Marta S., Li, Aung, Kyaw, Htet & Lwin, Ngwe, 2017, Phylogenetic taxonomy of Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) with descriptions of three new species from Myanmar, pp. 881-915 in Journal of Natural History 52 (13 - 16) on pages 891-898, DOI: 10.1080/00222933.2017.1367045, http://zenodo.org/record/478004
Coordinated Design of PSS and STATCOM for Power System Stability Improvement Using Bacteria Foraging Algorithm
No full textThis paper presents the coordinated controller design of static synchronous compensator (STATCOM) and power system stabilizers (PSSs) for power system stability improvement. Coordinated design problem of STATCOM-based controller with multiple PSSs is formulated as an optimization problem and optimal controller parameters are obtained using bacteria foraging optimization algorithm. By minimizing the proposed objective function, in which the speed deviations between generators are involved; stability performance of the system is improved. The nonlinear simulation results show that coordinated design of STATCOM-based controller and PSSs improve greatly the system damping oscillations and consequently stability improvement
Study and Analysis of Machine Parameters Effect on Power System Stability
No full textThe stability study of a power system is an important factor in the planning or increasing of facilities. The studies are helpful in determining such thing as nature of the relaying system needed, critical clearing time of circuit breakers, voltage level, and transfer capability between systems. In this paper, the effects of machine parameters (inertia constant, damping constant and transient reactance) on the critical clearing time of the power system stability have been analyzed. These parameters are the main contribution to the angular acceleration and power transfer capability that affected the power system stability. The analysis has been done for two types of power system: single machine infinite bus system and multi-machine system. From the analysis, it is found that the stability of the system is affected by studied parameters and important in the design of the improving power system stability and protection system
Evaluation of RT-LAMP and Dry Swab RNA Extraction Free Method for Detection of SARS-CoV-2 Infection
No full textBackground: A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in December 2019 in Wuhan, China. Due to high infectious rate of SARS-CoV-2, detection of positive patients is one of the key points to controlling the outbreak. The gold standard for diagnosis of SARS-CoV-2 remains RT-PCR. In the current pandemic, a more rapid and high throughput method is in growing concern.
Objectives: To evaluate the RT-LAMP and dry swab RNA extraction free method in diagnosing SARS-CoV-2 infection, using reverse transcription polymerase chain reaction (RT-PCR) as gold standard.
Methods: A laboratory based cross-sectional descriptive study was carried out from September 2022 to October 2022 at molecular laboratory of No (1) Defence Services General Hospital. Ninety-four nasopharyngeal swabs were collected and tested for the presence of SARS-CoV-2 infection by RT-PCR (gold standard), RT-LAMP and dry swab method.
Result: In this study, 68 (72.3%) out of 94 patients were positive for SARS CoV-2 infection by RT-PCR. The overall sensitivity, specificity, positive predictive value and negative predictive value of RT-LAMP was 76.5%, 100%, 100% and 62%. The overall sensitivity, specificity, positive predictive value and negative predictive value of dry swab method was 66%, 100%, 100% and 53%. Hundred percent sensitivity was occurred in RT-LAMP and Dry swab method with Ct<20. In Ct 20-30, sensitivity of RT-LAMP and Dry swab method was 94.8% and 89.7%.
Conclusions: RT-PCR method exist as a gold standard for diagnosis of SARS CoV-2, it required molecular laboratory; RT-PCR machine and reagents; they are expensive; trained technician; and it takes several hours to get the results. Although sensitivity and specificity of RT-LAMP and dry swab methods are inferior to RT-PCR, they can be performed easily in the short period of time (less than 2 hours). Therefore, faster, cheaper and easier alternative molecular diagnostic methods should be considered for diagnosis of SARs CoV-2 infection
Ultrasound signal processing and imaging
No full textReverberation and multi-path reflection artifacts are common problems in ultrasound
imaging. In this study, the low image quality problem of medical ultrasound imaging in the term of reverberation artifact is addressed, and subsequently a model based on which the reduction technique of reverberation artifacts is proposed.
Reverberation caused by reflections of ultrasound signal between two interfaces gives rise to multiple copies of the anatomy at the interface, significantly degrading image quality and accuracy. This study is an extension of the method for the identification of reverberation echoes in multilayered media, based on the comparison of their power spectra (estimated via Fast Fourier Transform) through a least mean square approach, and linear combination of the temporal relationship (based on time-of-flight). To provide a systematic approach, the author investigated the nature of reverberation artifacts formation, and proposed a mathematical model to express reverberations concisely and accurately.Bachelor of Engineerin
- …
