886 research outputs found
Bahumukhī mana, bahurupī prema
No full textThe document contains a novel written by the Bengali author Nirpendra Kumar Basu (1898-1979). The monograph is from the private collection of Sharmadip Basu
Outer Length Scales in Nocturnal Stable Boundary Layers
No full textRecently, Basu and Holstlag (2021) proposed a unified framework for describing outer length scales (OLS). By utilizing this framework, we document various characteristics of OLS in nocturnal boundary layers over the US Great Plains.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Atmospheric Remote Sensin
A SYSTEMATIC APPROACH TO ELUCIDATE THE CONNECTION BETWEEN GENOMIC ALTERATIONS AND METABOLIC PATHWAYS
No full text106 pagesSystems biology provides a structure to elucidate complex biological networks from multi-omic measurements. However, a limitation of systems biology is the ability to create testable hypotheses for further experimentation. Here we present two system-based methods, a coessentiality network and single-cell RNA sequencing, that are aimed to uncover metabolic functionality for uncharacterized genes and mitochondrial DNA mutations.Coessentiality mapping has been useful to systematically cluster genes into biological pathways and identify gene functions (Pan et al., 2018; Wainberg et al., 2019; Wang et al., 2017). Here, using the debiased sparse partial correlation (DSPC) method (Basu et al., 2017), we construct a functional coessentiality map for cellular metabolic processes across human cancer cell lines. This analysis reveals 35 modules associated with known metabolic pathways and further assigns metabolic functions to unknown genes. In particular, we identify C12orf49 as an essential regulator of cholesterol and fatty acid metabolism in mammalian cells. Mechanistically, C12orf49 localizes to the Golgi, binds membrane-bound transcription factor peptidase, site 1 (MBTPS1, site 1 protease) and is necessary for the cleavage of its substrates, including sterol regulatory element binding protein (SREBP) transcription factors. The electron transport chain (ETC) activity in mammalian cells is necessary for survival and proliferation. The ETC is composed of ~100 subunits mostly encoded in the nuclear genome, but 13 essential subunits are in the mitochondrial genome (mtDNA). Accumulation of mutations in the mtDNA can lead to severe genetic defects and cell death. Interestingly, we and other groups have found the occurrence of loss-of-function (LOF) mtDNA mutations across a variety of cancer types at high heteroplasmy. Heteroplasmy is defined as the proportion of mtDNA copies with a specific mutation over the total number of mtDNA copies. Furthermore, there is an enrichment for these LOF mutations suggesting that they are positively selected. Despite their prevalence, it is unclear whether these mutations have functional roles in cancer progression or are simply passenger mutations as the study of mtDNA mutations is stymied by the lack of methods to genetically modify the mtDNA. Here, we have identified a novel method that combines single-cell RNA sequencing (scRNAseq) and fluorescence-activated cell sorting (FACS) in order to create a low and high heteroplasmic mixed population of cells. The high heteroplasmic populations have severe ETC dysfunction and are morphologically, transcriptomically, and metabolomically distinct from the low heteroplasmic cells. These differences result in the high heteroplasmy cells having elevated metastatic potential compared to the low heteroplasmy cells suggesting a role for LOF mtDNA mutations in cancer progression. Altogether, our findings reveal that a combination between single-cell RNAseq and FACS can produce distinct populations that correlate with LOF heteroplasmic mutations
Cupid Joins the War
No full textThe author explores the history of love and sex in war though the ages. This monograph is from the private collection of Sharmadip Basu, Kolkata, W.B., India
AGRICULTURAL COMMODITY PRICES AND LOAN LOSSES AT A FARM CREDIT ASSOCIATION: AN AUTOREGRESSIVE DISTRIBUTED LAG ANALYSIS
No full text60 pagesThis study investigates how agricultural commodity prices affect loan loss provisions (LLP) and loan loss charge-offs (LLC) in a financial institution of the Farm Credit System. Commodity prices have an impact on farmers’ revenue generation, which might influence farmers’ ability to repay loans. This study hypothesizes that loan loss provisions are a function of loan loss charge-offs and commodity prices, and alternatively, that loss provisions and commodity prices determine charge-offs. An autoregressive distributed lagged model is estimated for a financial institution of the Farm Credit System using data from 2010 to 2019. The empirical evidence suggests that LLP is positively related to LLC and various commodity prices, with lagged components of different periods. LLC is also positively correlated with LLP and various commodity prices, with lagged components of different periods
Magnanimous Kunti by Samaresh Basu/ সমরেশ বসুর কলমে মনস্বিনী কুন্তী
No full textSamaresh Basu wrote a number of books based on Puran-Mahabharata under the pseudonym Bhramar and Kalkoot. Such as, ‘Shamba (1978)’, ‘Juddher Sesh Senapati (1984)’, ‘Prachetas (1984)’, \u27Pritha (1986)\u27, ‘Antim Pranay (1987)’ etc. ‘Pritha’ was published in the magazine \u27Prasad\u27 under the pseudonym \u27Bhramar\u27. In such books, the author analyzed the traditional story of the Puranas in a new perspective.
One of the memorable Panchakanyas in Puranas, Empress Kunti has been recreated in the light of the author\u27s spirit in this book. In the present article we will discuss how the character of Kunti has been recreated by Samaresh Basu in \u27Pritha\u27.
At the beginning of the story, before reaching the context of Kunti, the author undertakes a very realistic analysis of heaven-hell, Gods-demons, Samhita era-Puranic era, male-female relationship, marriage customs, child birth and the position of women in society. Then he explained the solitude, self-immolation and transition of Kunti from a feminist perspective.
The story of love-marriage-motherhood-heroism-restraint-pain-sacrifice of this remarkable female character of Mahabharata has been captured in a new way in the unique writing of Kalkoot. Inventing many thoughtful arguments the author tried to establish the father-son relationship between Yudhisthira-Vidura and Karna-Durbasha. How the author incarnated new contexts in the familiar story of Mahabharata and how he made it acceptable by arranging relevant arguments in favour of his new thoughts – this essay will try to elaborate these points
Metrocoris dinendrai Basu, Polhemus and Subramanian, NEW SPECIES
No full textMetrocoris dinendrai Basu, Polhemus and Subramanian, NEW SPECIES Figs. 33–44 Material examined. Holotype: Apterous male: INDIA, West Bengal, Darjeeling District, roadside cascades within Neora Valley National Park, 27.0828°N, 88.7437°E, 2006m. asl, 3.X.2012, coll. S. Basu, deposited at the Zoological Survey of India, H.Q., Kolkata (NZSI) Reg. No. 4774/H15. Paratypes: INDIA, West Bengal: 1 apterous male, 1 apterous female, 31 nymphs: same data as holotype Reg. No. 4775/H15; 2 apterous males, 1 apterous female, 1 macropterous female, 5 nymphs, Darjeeling District, stream on the way to Chengey Falls, near Lava, 27.0511°N, 88.6800°E, 1639 m. asl, 3.X. 2012, coll. S. Basu (NZSI) Reg. No. 4776/H15; 4 apterous males, 2 apterous females, 1 nymph, Darjeeling District, stream near Gorubathan, 26.96636°N, 88.7000°E, 370 m. asl., 1.X.2013, coll. S. Basu, (NZSI) Reg. No. 4777/H15. Description. Apterous male (Holotype): Fig.33 Size: Body length 5.42 mm, maximum width across mesoacetabula 2.53 mm. Colour: Dorsal body coloration yellowish to orange with dorsal black markings (Fig. 33). Interocular dark mark rectangular, bifid posteriorly, anterior margin not connected with dark mark of postclypeus, posterior portion in some individuals connected with dark inner margin of eye. Antennal segments black, with first segment yellow basally. Eyes black. Dark marks on pronotum broad T-shaped, connected to propleural margin (Fig.33). Meso- and metanota pale orange with dark markings as in Figs. 33, sublateral dark stripes broader than yellowish part on apical half, longitudinal dark stripe of mesopleuron extending nearly through its length. Abdominal terga black except segment VIII. Thoracic venter black, with a deep yellowish patch laterally (Fig. 36). Abdominal sterna II– VI black, sterna VII–VIII yellowish posteriorly. Fore femur black, basal one-fourth of ventral and dorsal surfaces yellowish, fore tibia and tarsus black. Rostrum black with pale yellowish lateral margins. Structural characteristics: Head width 1.36, length 0.73. Interocular region wider than eye, widths 0.61 and 0.25 respectively. Eye length 0.62, posterior half of eye covering anterior one fourth of propleuron. Length of antennal segments I–IV: 2.29, 0.97, 0.88, 0.65, first segment longer than combined lengths of remainder. Rostrum length 1.46, surpassing fore trochanter. Pronotum slightly bulbous in male, wider than long, width 1.61, length 0.57, slightly wider than head. Meso- and metanota 1.12 times wider than combined length, width 2.55, length 2.27. Fore femur (Fig. 39) slender and slightly curved at middle, ratio of length/width approximately 6.5, ventral surface with small constriction near middle, without indentation or tooth, with short dense hair fringe ventrally near apex, inner margin with rows of short hairs. Inner margin of fore tibia not modified, bearing rows of short hairs. Second tarsal segment long. Pretarsus with pair of sharp claws. Hind trochanter lacking modifications. Abdominal terga with prominent golden pubescence, combined length 1.83, maximum width 1.21. Abdominal sternum VIII bearing long dense hair fringe (Fig. 37). For measurements of leg segments see Table 1. Male genitalia: Male abdominal sternum VIII (Fig. 37) elongate, sub-oval, length 1.27, width 0.86, densely clothed with fringe of golden hairs. Posterior margin of abdominal tergum VIII straight. Pygophore (Fig. 42) elongate, heavily setiferous, apex truncate. Proctiger (Fig. 41) moderately elongate, lateral margins slightly convex, isolating angular basal lobes, apex broadly rounded, posterior margin with dense hair fringe. Parameres symmetrical (Fig.43) strongly curved near midpoint, apical section expanded to small head with outer margin concave, apex blunt, inner and outer margins with long distinct setae, several whitish dots distributed throughout. Endosomal sclerites as in Fig. 44. Apterous female: Fig. 34 Size: Body length 4.41–4.55, maximum width across mesoacetabula 2.29–2.31. Colour: Pattern of dark markings similar to that of male except much wider and more prominent; fore femur slender, lacking median invaginations; sterna VI–VII yellowish. Structural characteristics: Head length 0.74, width 1.21. Length of antennal segments 1–4: 1.87, 0.65, 0.60, 0.72. Eye length 0.61, width 0.24, interocular width 0.66. Length of rostrum 1.45. Pronotum wider than long, length 0.50, width 1.54. Combined lengths of meso- and metanota 2.12, width 2.21. Fore femur length/width ratio 6.3, lacking medial constriction; fore pretarsi bearing sharp, curved claws; hind trochanter lacking modifications. Abdominal sterna II–VI combined length 0.96, maximum width 1.57. For measurements of leg segments see Table 2. Female terminalia: Abdominal sternum VII semi-circular, length 0.30, width 1.07, slightly constricted laterally, clothed with short golden pubescence. Macropterous male: Unknown. Macropterous female: Fig. 35 Size: Body length 5.32, maximum width across mesoacetabula 2.67. Structural characteristics: Golden brown dorsally, marked with prominent black markings as shown in Fig.35. Median length of pronotum 2.41, humeral width 1.72, length of lateral margin from anterior angle to humerus 0.89, length of lateral margin from humerus to apex 1.76, apex of pronotum pointed, medially slightly bulged. Etymology. This name “dinendra” is a patronym dedicated to Professor Dinendra Roychoudhury of Department of Zoology of University of Calcutta, who had encouraged the first author to carry out entomological research. Habitat. This species was collected from high mountainous cascades within the Neora Valley National Park of the Darjeeling District in West Bengal. The insects were found in steep, rocky areas flooded with splashing water, and appear adapted to the cold waters. A preference for rushing, high gradient upland streams has also been observed by the second author (DP) for another currently undescribed species of the Metrocoris compar species group collected in northern Vietnam, suggesting this habitat association may be typical of the group as a whole. Comparative notes. Metrocoris dinendrai sp. nov. belongs to Metrocoris compar group based on the structure of male fore femur, which is slender and slightly curved; the strongly curved male parameres; the elongate male pygophore which bears dense dark pilosity; and the laterally constricted female terminal abdominal sterna. This new species can be recognized within this group by the distinctive shape of male paramere, which has a a slightly expanded apex that is somewhat concave on its outer margin (Fig. 43); the structure of male endosomal sclerites (Fig. 44); and the female trochanter clothed with thick black bristles. Within the Metrocoris compar group, M. dinendrai seems most similar to M. pardus from the Malay Peninsula (Zettel, 2011a), but has the distal arm of the male paramere more slender and elongate, and the outer margin of the paramere apex concave rather than convex (compare Fig. 43 to Fig. 8 in Zettel, 2011a). The basal lobes on the male proctiger also are more angular than in M. pardus, whereas the internal sclerotization of the male endosoma is similar in both species.Published as part of Basu, Srimoyee, Polhemus, D. A., Subramanian, K. A., Saha, G. K. & Venkatesan, T., 2016, Metrocoris Mayr (Insecta: Hemiptera: Gerridae) of India with descriptions of five new species, pp. 257-277 in Zootaxa 4178 (2) on pages 265-267, DOI: 10.11646/zootaxa.4178.2.5, http://zenodo.org/record/25873
Bridging Theories and Experiments: Modeling Solution X-ray Scattering of Small RNA Molecules
No full text344 pagesSolution X-ray scattering is a powerful tool to understand conformations of macromolecules in vitro.Small-angle X-ray scattering (SAXS) provides low-resolution (20 - 100 Angstrom) envelope of electron densities while wide-angle X-ray scattering (WAXS) reveals finer structural information beyond the SAXS resolution. Ribonucleic acids (RNAs), with important biological functions, exhibit both large-scale molecular arrangements and fine structural periodicity, which are revealed by SAXS and WAXS. Qualitative macromolecular behaviors can be inferred by RNA construct design and comparison of X-ray scattering profiles. However, molecular and statistical modeling of experimental SAXS or WAXS profiles is required for a quantitative interpretation on the RNA system of interest. In this work, we started by applying ab initio reconstruction and refining atomic molecular models generated by molecular dynamics (MD) simulations using experimental SAXS profiles to investigate the ion-dependent role of RNA junctions in determining the overall conformations. Furthermore, we extended both ideas to the wide-angle regime to reveal much finer structural variations that is invisible to the SAXS experiments. Our methods as well as the understanding of ion-dependent RNA behaviors are significant to the solution X-ray scattering and RNA communities
Practical Data Quality for Modern Data & Modern Uses, With Applications To America's COVID-19 Data
No full text239 pagesModern data is often assumed to be of high quality. We dismiss this assumption using examples from America’s COVID-19 data. We explore the types and origins of these issues by diving into the data production process, noting that the root causes are not particular to this dataset but are typical of modern data in general. Data quality issues are frequently surprising, sometimes baffling, and often overwritten. We recover these issues by creating data releases which enable us to replay history. Using novel visualizations, we are able to surface quality issues within and across releases. Two such issues are of particular concern: major restatements, which rewrite history, and non-retroactive changes, which restart history. Data quality is defined by use case. We explore this through two applications: allocation of finite resources and surge prediction. While doing so, we propose κ-accuracy, a practical solution to a common obstacle, and argue for quality-based data selection. Research into data quality is urgently needed. The field is young, the theory uncoordinated, and the metrics all but nonexistent. Yet, assessing data quality is essential to using data properly. Researchers have developed so many ways to use data, and so few ways to assess whether or not we should. We hope this work will inspire research and investment into data quality
LEARNING REGULATORY CONTRIBUTIONS TO GENE EXPRESSION VARIATION IN GRASSES
No full text88 pagesIn the advent of a rapidly changing climate, there is a need for rapid selection and editing of plants to develop climate resilience. To aid in these efforts, interpretable and accurate mechanistic models of gene regulation will need to be developed in a multitude of species. This dissertation presents a comprehensive exploration of computational techniques for predicting gene expression in maize, focusing on regulatory network-based machine learning and deep learning approaches. These models have significant implications for gene editing in crop plants, providing information on the regulatory mechanisms that govern gene expression. The first section investigates the integration of regulatory network information into machine learning models to predict gene expression. Through extensive experimentation, various network-based approaches are evaluated, with the aim of improving prediction accuracy by capturing the complex shared regulatory mechanisms that underlie gene expression in maize. The next study focuses on the development of PLExBench, a benchmark suite specifically tailored for predicting gene expression in plants. PLExBench encompasses multiple tasks in model plants of Arabidopsis thaliana and Zea mays, serving as a standardized platform to evaluate the performance of gene expression prediction methods. By rigorously evaluating state-of-the-art prediction algorithms using PLExBench, this work introduces an effective strategy to assess the strengths and limitations of existing methods in accurately predicting gene expression in plants. Finally, this dissertation explores the application of deep learning techniques to uncover cis-regulatory contributions to tissue-specific gene expression in maize. Using perturbation-driven experimental data, deep learning models are used to decipher the intricate regulatory mechanisms underlying tissue-specific gene expression patterns. Through systematic analysis and validation, the study elucidates the capabilities of deep learning approaches in capturing cis-regulatory elements and predicting tissue-specific gene expression profiles in maize. By combining insights from regulatory network-based machine learning, benchmarking efforts with PLExBench, and perturbation-driven assessment of deep learning, this dissertation contributes to a deeper understanding of the use of deep learning to find regulatory components of gene expression. The findings provide valuable resources and methodologies to improve gene expression prediction models in agricultural contexts and advance our understanding of plant biology, thus facilitating targeted gene editing efforts to enhance crop traits and agricultural productivity
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