Applied text mining

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Lars Juhl Jensen

Ciencias

Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1
homolog) directly phosphorylated Swe1
and this modification served as a priming
step to promote subsequent Cdc5-
dependent Swe1 hyperphosphorylation
and degradation

Gene and protein names
Cue words for entity
recognition
Verbs for relation extraction
[nxexpr The expression of
[nxgene the cytochrome
genes
[nxpg CYC1 and CYC7]]]
is controlled by
[nxpg HAP1]

Letunic & Bork, Trends in Biochemical Sciences, 2008

Korbel et al., Nature Biotechnology, 2004

Jensen et al., Nature Reviews Genetics, 2012

Roque et al., PLOS Computational Biology, 2011
3262638254947
Assigned codes
Text mined codes

Roque et al., PLOS Computational Biology, 2011

EMBO Practical Course Computational Biology:
Genomesto Systems
Puerto Varas, 3-9April2014
Thank you!Thank you!

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Cotton crops are vulnerable to a variety of sucking pests, which can severely impact plant health, yield, and fiber quality. These pests primarily feed on plant sap, extracting nutrients directly from the plant's vascular system. Here's a breakdown of some of the most significant sucking pests in cotton cultivation: Aphids: Cotton aphids or melon aphids can cause direct damage by sucking sap and indirect damage by secreting honeydew, which encourages sooty mold growth. This can interfere with photosynthesis and weaken the plant. Aphids can also transmit viral diseases. Whiteflies: Two species, the silverleaf whitefly and the bandedwinged whitefly, are particularly troublesome. They not only suck sap from the underside of leaves, causing yellowing and leaf drop, but their honeydew excretion promotes sooty mold and they can transmit several plant viruses. Thrips: While thrips can chew on plants, their primary damage to cotton is through sucking. They attack the cotton plant during its seedling stage, which can stunt growth and reduce vigor. Thrips are also capable of transmitting the Cotton Bud disease. Spider Mites: These are not insects but arachnids. Spider mites, such as the two-spotted spider mite, suck cell contents from the leaves, leading to speckled discoloration and potentially significant leaf loss if infestations are severe. Leafhoppers: Including various species, leafhoppers can cause direct damage through feeding, which results in leaf curling and stunted growth. They can also be vectors for plant diseases. Mealybugs: These pests are less common but can be problematic, especially in clustered planting conditions. They suck sap and secrete honeydew, which leads to sooty mold. Mealybugs can also spread viruses. Stink Bugs: Although primarily known for their chewing mouthparts, certain stink bugs can cause damage similar to sucking pests by injecting saliva into the plant and sucking out nutrients, leading to boll damage and stained lint. Management Strategies: Cultural Controls: This includes practices such as crop rotation, using resistant varieties, and managing planting and harvesting times to avoid peak pest populations. Biological Controls: Beneficial insects like lady beetles, lacewings, and predatory mites can naturally control sucking pest populations. Parasitic wasps also play a role in controlling aphid and whitefly populations. Chemical Controls: Insecticides may be used but should be chosen carefully to minimize resistance development and preserve beneficial insects. Systemic insecticides can be particularly effective against sucking pests. Integrated Pest Management (IPM): Combining multiple control strategies based on monitoring and thresholds to apply the most effective and environmentally sensitive approach. Effective management of sucking pests in cotton requires a thorough understanding of the pest species present, their life cycles, and the ecological balance of the field environment.

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Context. WASP-76 b has been a recurrent subject of study since the detection of a signature in high-resolution transit spectroscopy data indicating an asymmetry between the two limbs of the planet. The existence of this asymmetric signature has been confirmed by multiple studies, but its physical origin is still under debate. In addition, it contrasts with the absence of asymmetry reported in the infrared (IR) phase curve. Aims. We provide a more comprehensive dataset of WASP-76 b with the goal of drawing a complete view of the physical processes at work in this atmosphere. In particular, we attempt to reconcile visible high-resolution transit spectroscopy data and IR broadband phase curves. Methods. We gathered 3 phase curves, 20 occultations, and 6 transits for WASP-76 b in the visible with the CHEOPS space telescope. We also report the analysis of three unpublished sectors observed by the TESS space telescope (also in the visible), which represents 34 phase curves. Results. WASP-76 b displays an occultation of 260±11 and 152±10 ppm in TESS and CHEOPS bandpasses respectively. Depending on the composition assumed for the atmosphere and the data reduction used for the IR data, we derived geometric albedo estimates that range from 0.05 ± 0.023 to 0.146 ± 0.013 and from <0.13 to 0.189 ± 0.017 in the CHEOPS and TESS bandpasses, respectively. As expected from the IR phase curves, a low-order model of the phase curves does not yield any detectable asymmetry in the visible either. However, an empirical model allowing for sharper phase curve variations offers a hint of a flux excess before the occultation, with an amplitude of ∼40 ppm, an orbital offset of ∼−30◦ , and a width of ∼20◦ . We also constrained the orbital eccentricity of WASP-76 b to a value lower than 0.0067, with a 99.7% confidence level. This result contradicts earlier proposed scenarios aimed at explaining the asymmetry observed in high-resolution transit spectroscopy. Conclusions. In light of these findings, we hypothesise that WASP-76 b could have night-side clouds that extend predominantly towards its eastern limb. At this limb, the clouds would be associated with spherical droplets or spherically shaped aerosols of an unknown species, which would be responsible for a glory effect in the visible phase curves.

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www.seribangash.com The Mariana Trench is one of the most remarkable geological features on Earth. Here are some details about it: Location: The Mariana Trench is located in the western Pacific Ocean, east of the Mariana Islands. It stretches for about 2,550 kilometers (1,580 miles) and is known as the deepest part of the world's oceans. Depth: The trench reaches incredible depths, with its deepest point known as the Challenger Deep, which plunges down to approximately 10,984 meters (36,037 feet) below sea level. To put this into perspective, if Mount Everest, the tallest mountain on Earth, were placed at the bottom of the Challenger Deep, its peak would still be over 2 kilometers (1.25 miles) underwater. Formation: The Mariana Trench was formed by the subduction of the Pacific Plate beneath the Mariana Plate. This process creates a deep trench as the heavier Pacific Plate is forced beneath the lighter Mariana Plate. Geological Features: The trench is characterized by steep, V-shaped valleys, and its walls are composed of highly compressed sedimentary rock. At the bottom of the trench, there are also large amounts of marine sediment. Pressure: The pressure at the bottom of the Mariana Trench is immense, reaching over 1,000 times the pressure at the surface. This extreme pressure creates a challenging environment for exploration and makes it difficult for organisms to survive. Exploration: Despite its extreme conditions, the Mariana Trench has been the subject of numerous scientific expeditions and explorations. One of the most famous explorations was the dive to the Challenger Deep by Swiss scientist Jacques Piccard and U.S. Navy Lieutenant Don Walsh in 1960. More recently, in 2012, filmmaker James Cameron made a solo dive to the bottom of the Challenger Deep in the Deepsea Challenger submersible. Biological Discoveries: Despite the harsh conditions, the Mariana Trench is home to a surprising variety of life forms, including unique species of deep-sea fish, crustaceans, and microbial life. Some organisms have adapted to survive in the extreme pressure and darkness of the trench. Environmental Importance: Studying the Mariana Trench provides valuable insights into the geology, biology, and oceanography of the deep sea. It also helps scientists better understand the processes that shape the Earth's crust and the distribution of life in the oceans. Conservation: Due to its remote location and extreme depths, the Mariana Trench has remained relatively untouched by human activity. However, there is growing concern about the potential impacts of deep-sea mining and pollution on this fragile ecosystem, highlighting the need for conservation efforts to protect this unique environment. https://seribangash.com/barber-shop-business-complete-guide-for-beginners/ https://seribangash.com/legend-virat-kohli-in-cricket-history/

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Molecular markers are identifiable DNA sequences used to locate genes associated with specific traits or genetic conditions. A molecular marker is a specific gene fragment present at a specific position called ‘locus’ (pleural loci) in the genome of a cell. In the pool of unknown DNA or in a whole chromosome, these molecular markers help in identification of particular sequence of DNA at particular location.

Molecular markers- RFLP, RAPD, AFLP, SNP etc.

Silpa

Theoretical predictions and observational data indicate a class of sub-Neptune exoplanets may have water-rich interiors covered by hydrogen-dominated atmospheres. Provided suitable climate conditions, such planets could host surface liquid oceans. Motivated by recent JWST observations of K2-18 b, we self-consistently model the photochemistry and potential detectability of biogenic sulfur gases in the atmospheres of temperate sub-Neptune waterworlds for the first time. On Earth today, organic sulfur compounds produced by marine biota are rapidly destroyed by photochemical processes before they can accumulate to significant levels. Domagal-Goldman et al. suggest that detectable biogenic sulfur signatures could emerge in Archean-like atmospheres with higher biological production or low UV flux. In this study, we explore biogenic sulfur across a wide range of biological fluxes and stellar UV environments. Critically, the main photochemical sinks are absent on the nightside of tidally locked planets. To address this, we further perform experiments with a 3D general circulation model and a 2D photochemical model (VULCAN 2D) to simulate the global distribution of biogenic gases to investigate their terminator concentrations as seen via transmission spectroscopy. Our models indicate that biogenic sulfur gases can rise to potentially detectable levels on hydrogen-rich water worlds, but only for enhanced global biosulfur flux (20 times modern Earth’s flux). We find that it is challenging to identify DMS at 3.4 μm where it strongly overlaps with CH4, whereas it is more plausible to detect DMS and companion byproducts, ethylene (C2H4) and ethane (C2H6), in the mid-infrared between 9 and 13 μm. Unified Astronomy Thesaurus concepts: Exoplanet atmospheres (487); Exoplanet

Biogenic Sulfur Gases as Biosignatures on Temperate Sub-Neptune Waterworlds

Sérgio Sacani

Applied text mining

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29. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation

30. no tool will find that

31. named entity recognition

32. identify the concepts

33. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation

34. comprehensive lexicon

35. CDC2

36. cyclin dependent kinase 1

37. orthographic variation

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67. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation

68. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation

69. Reflect

70. reflect.ws

71. information extraction

72. formalize the facts

73. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation

74. two approaches

75. the formal way

76. NLP Natural Language Processing

77. grammatical analysis

78. part-of-speech tagging

79. multiword detection

80. semantic tagging

81. sentence parsing

82. Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]

83. extract stated facts

84. high precision

85. poor recall

86. the pragmatic way

87. guilt by association

88.

89. co-mentioning

90. counting

91. within documents

92. within paragraphs

93. within sentences

94. quality score