Large-scale integration of data and text
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This document discusses large-scale integration of biological data and text. It describes combining heterogeneous data from many databases on topics like protein interactions, disease associations, tissue expression, and subcellular localization. It also discusses using text mining of over 10 km of text to extract information on entities, relationships, and annotations in order to supplement incomplete experimental data and facilitate updates and predictions.
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Scientific Highlights: The Reflect and NetPhorest web resources
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This document discusses using data mining and text mining techniques to link proteins, chemicals, and side effects in molecular interaction networks. It provides examples of using the STRING and STITCH databases to explore protein and chemical networks. It also discusses how text mining of biomedical literature and electronic health records can help identify molecular interactions, adverse drug reactions, and support drug repurposing efforts.
Data and text mining of Danish electronic health records
This document discusses data and text mining of Danish electronic health records. It notes that Denmark has established centralized medical registries since 1968. These registries contain data on 6.2 million patients, 45 million admissions, and 119 million diagnoses. Both structured data from registries and unstructured free-text data from medical records are analyzed. Text mining is used to extract information from the free-text data through techniques like dictionary-based coding. Studies have used this data to develop detailed disease profiles, identify adverse drug events, and study diagnosis trajectories and networks. Challenges include dealing with confounding factors and missing or unreported information.
Medical data and text mining: Linking diseases, drugs, and adverse reactions
The document discusses using Danish medical registries containing data on over 6.2 million patients and 45 million hospital admissions over 14 years to study disease trajectories and adverse drug reactions through medical data and text mining. It describes how structured data in the registries on diagnoses, treatments and prescriptions can be linked to study relationships between diseases and drugs. It also explains how natural language processing of unstructured free-text data from medical records can help identify adverse drug reactions mentioned in notes. The goal is to gain insights into diagnosis trajectories, discover new adverse drug reactions, and better estimate frequencies of adverse reactions.
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The pragmatic text miner: Itâs just another type of poorly standardized data
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Medical data and text mining - Linking diseases, drugs, and adverse reactions
Medical data and text mining - Linking diseases, drugs, and adverse reactions
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Statistics on big biomedical data - Methods and pitfalls when analyzing high-...
Statistics on big biomedical data - Methods and pitfalls when analyzing high-...
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The Literature Text Mining Approach In Cancer Research
The Literature Text Mining Approach In Cancer Research
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Large-scale data and text mining - Linking proteins, chemicals, and side effects
Large-scale data and text mining - Linking proteins, chemicals, and side effects
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Data and text mining of Danish electronic health records
Data and text mining of Danish electronic health records
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Medical data and text mining: Linking diseases, drugs, and adverse reactions
Medical data and text mining: Linking diseases, drugs, and adverse reactions
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We present the JWST discovery of SNâ2023adsy, a transient object located in a host galaxy JADES-GS
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Candidate young stellar objects in the S-cluster: Kinematic analysis of a sub...
Context. The observation of several L-band emission sources in the S cluster has led to a rich discussion of their nature. However, a definitive answer to the classification of the dusty objects requires an explanation for the detection of compact Doppler-shifted BrÎł emission. The ionized hydrogen in combination with the observation of mid-infrared L-band continuum emission suggests that most of these sources are embedded in a dusty envelope. These embedded sources are part of the S-cluster, and their relationship to the S-stars is still under debate. To date, the question of the origin of these two populations has been vague, although all explanations favor migration processes for the individual cluster members. Aims. This work revisits the S-cluster and its dusty members orbiting the supermassive black hole SgrA* on bound Keplerian orbits from a kinematic perspective. The aim is to explore the Keplerian parameters for patterns that might imply a nonrandom distribution of the sample. Additionally, various analytical aspects are considered to address the nature of the dusty sources. Methods. Based on the photometric analysis, we estimated the individual HâK and KâL colors for the source sample and compared the results to known cluster members. The classification revealed a noticeable contrast between the S-stars and the dusty sources. To fit the flux-density distribution, we utilized the radiative transfer code HYPERION and implemented a young stellar object Class I model. We obtained the position angle from the Keplerian fit results; additionally, we analyzed the distribution of the inclinations and the longitudes of the ascending node. Results. The colors of the dusty sources suggest a stellar nature consistent with the spectral energy distribution in the near and midinfrared domains. Furthermore, the evaporation timescales of dusty and gaseous clumps in the vicinity of SgrA* are much shorter ( 2yr) than the epochs covered by the observations (â15yr). In addition to the strong evidence for the stellar classification of the D-sources, we also find a clear disk-like pattern following the arrangements of S-stars proposed in the literature. Furthermore, we find a global intrinsic inclination for all dusty sources of 60 Âą 20âŚ, implying a common formation process. Conclusions. The pattern of the dusty sources manifested in the distribution of the position angles, inclinations, and longitudes of the ascending node strongly suggests two different scenarios: the main-sequence stars and the dusty stellar S-cluster sources share a common formation history or migrated with a similar formation channel in the vicinity of SgrA*. Alternatively, the gravitational influence of SgrA* in combination with a massive perturber, such as a putative intermediate mass black hole in the IRS 13 cluster, forces the dusty objects and S-stars to follow a particular orbital arrangement. Key words. stars: black holesâ stars: formationâ Galaxy: centerâ galaxies: star formation
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JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
The pathway(s) to seeding the massive black holes (MBHs) that exist at the heart of galaxies in the present and distant Universe remains an unsolved problem. Here we categorise, describe and quantitatively discuss the formation pathways of both light and heavy seeds. We emphasise that the most recent computational models suggest that rather than a bimodal-like mass spectrum between light and heavy seeds with light at one end and heavy at the other that instead a continuum exists. Light seeds being more ubiquitous and the heavier seeds becoming less and less abundant due the rarer environmental conditions required for their formation. We therefore examine the different mechanisms that give rise to different seed mass spectrums. We show how and why the mechanisms that produce the heaviest seeds are also among the rarest events in the Universe and are hence extremely unlikely to be the seeds for the vast majority of the MBH population. We quantify, within the limits of the current large uncertainties in the seeding processes, the expected number densities of the seed mass spectrum. We argue that light seeds must be at least 103 to 105 times more numerous than heavy seeds to explain the MBH population as a whole. Based on our current understanding of the seed population this makes heavy seeds (Mseed > 103 Mâ) a significantly more likely pathway given that heavy seeds have an abundance pattern than is close to and likely in excess of 10â4 compared to light seeds. Finally, we examine the current state-of-the-art in numerical calculations and recent observations and plot a path forward for near-future advances in both domains.
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MICROBIAL INTERACTION PPT/ MICROBIAL INTERACTION AND THEIR TYPES // PLANT MIC...ABHISHEK SONI NIMT INSTITUTE OF MEDICAL AND PARAMEDCIAL SCIENCES , GOVT PG COLLEGE NOIDA
Microbial interaction
Microorganisms interacts with each other and can be physically associated with another organisms in a variety of ways.
One organism can be located on the surface of another organism as an ectobiont or located within another organism as endobiont.
Microbial interaction may be positive such as mutualism, proto-cooperation, commensalism or may be negative such as parasitism, predation or competition
Types of microbial interaction
Positive interaction: mutualism, proto-cooperation, commensalism
Negative interaction: Ammensalism (antagonism), parasitism, predation, competition
I. Mutualism:
It is defined as the relationship in which each organism in interaction gets benefits from association. It is an obligatory relationship in which mutualist and host are metabolically dependent on each other.
Mutualistic relationship is very specific where one member of association cannot be replaced by another species.
Mutualism require close physical contact between interacting organisms.
Relationship of mutualism allows organisms to exist in habitat that could not occupied by either species alone.
Mutualistic relationship between organisms allows them to act as a single organism.
Examples of mutualism:
i. Lichens:
Lichens are excellent example of mutualism.
They are the association of specific fungi and certain genus of algae. In lichen, fungal partner is called mycobiont and algal partner is called
II. Syntrophism:
It is an association in which the growth of one organism either depends on or improved by the substrate provided by another organism.
In syntrophism both organism in association gets benefits.
Compound A
Utilized by population 1
Compound B
Utilized by population 2
Compound C
utilized by both Population 1+2
Products
In this theoretical example of syntrophism, population 1 is able to utilize and metabolize compound A, forming compound B but cannot metabolize beyond compound B without co-operation of population 2. Population 2is unable to utilize compound A but it can metabolize compound B forming compound C. Then both population 1 and 2 are able to carry out metabolic reaction which leads to formation of end product that neither population could produce alone.
Examples of syntrophism:
i. Methanogenic ecosystem in sludge digester
Methane produced by methanogenic bacteria depends upon interspecies hydrogen transfer by other fermentative bacteria.
Anaerobic fermentative bacteria generate CO2 and H2 utilizing carbohydrates which is then utilized by methanogenic bacteria (Methanobacter) to produce methane.
ii. Lactobacillus arobinosus and Enterococcus faecalis:
In the minimal media, Lactobacillus arobinosus and Enterococcus faecalis are able to grow together but not alone.
The synergistic relationship between E. faecalis and L. arobinosus occurs in which E. faecalis require folic acid
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Evidence of Jet Activity from the Secondary Black Hole in the OJ 287 Binary S...
Wereport the study of a huge optical intraday flare on 2021 November 12 at 2 a.m. UT in the blazar OJ287. In the binary black hole model, it is associated with an impact of the secondary black hole on the accretion disk of the primary. Our multifrequency observing campaign was set up to search for such a signature of the impact based on a prediction made 8 yr earlier. The first I-band results of the flare have already been reported by Kishore et al. (2024). Here we combine these data with our monitoring in the R-band. There is a big change in the RâI spectral index by 1.0 Âą0.1 between the normal background and the flare, suggesting a new component of radiation. The polarization variation during the rise of the flare suggests the same. The limits on the source size place it most reasonably in the jet of the secondary BH. We then ask why we have not seen this phenomenon before. We show that OJ287 was never before observed with sufficient sensitivity on the night when the flare should have happened according to the binary model. We also study the probability that this flare is just an oversized example of intraday variability using the Krakow data set of intense monitoring between 2015 and 2023. We find that the occurrence of a flare of this size and rapidity is unlikely. In machine-readable Tables 1 and 2, we give the full orbit-linked historical light curve of OJ287 as well as the dense monitoring sample of Krakow.
Methods of grain storage Structures in India.pdf
â˘Post-harvestlossesaccountforabout10%oftotalfoodgrainsduetounscientificstorage,insects,rodents,micro-organismsetc.,
â˘Totalfoodgrainproductioninindiais311milliontonnesandstorageis145mt.InIndia,annualstoragelosseshavebeenestimated14mtworthofRs.7,000croreinwhichinsectsaloneaccountfornearlyRs.1,300crores.
â˘InIndiaoutofthetotalproduction,about30%ismarketablesurplus
â˘Remaining70%isretainedandstoredbyfarmersforconsumption,seed,feed.Hence,growerneedstoragefacilitytoholdaportionofproducetosellwhenthemarketingpriceisfavourable
â˘TradersandCo-operativesatmarketcentresneedstoragestructurestoholdgrainswhenthetransportfacilityisinadequate
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BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
Ahota Beel, nestled in Sootea Biswanath Assam , is celebrated for its extraordinary diversity of bird species. This wetland sanctuary supports a myriad of avian residents and migrants alike. Visitors can admire the elegant flights of migratory species such as the Northern Pintail and Eurasian Wigeon, alongside resident birds including the Asian Openbill and Pheasant-tailed Jacana. With its tranquil scenery and varied habitats, Ahota Beel offers a perfect haven for birdwatchers to appreciate and study the vibrant birdlife that thrives in this natural refuge.
SDSS1335+0728: The awakening of a âź 106Mâ black holeâ
Context. The early-type galaxy SDSS J133519.91+072807.4 (hereafter SDSS1335+0728), which had exhibited no prior optical variations during the preceding two decades, began showing significant nuclear variability in the Zwicky Transient Facility (ZTF) alert stream from December 2019 (as ZTF19acnskyy). This variability behaviour, coupled with the host-galaxy properties, suggests that SDSS1335+0728 hosts a âź 106Mâ black hole (BH) that is currently in the process of âturning onâ. Aims. We present a multi-wavelength photometric analysis and spectroscopic follow-up performed with the aim of better understanding the origin of the nuclear variations detected in SDSS1335+0728. Methods. We used archival photometry (from WISE, 2MASS, SDSS, GALEX, eROSITA) and spectroscopic data (from SDSS and LAMOST) to study the state of SDSS1335+0728 prior to December 2019, and new observations from Swift, SOAR/Goodman, VLT/X-shooter, and Keck/LRIS taken after its turn-on to characterise its current state. We analysed the variability of SDSS1335+0728 in the X-ray/UV/optical/mid-infrared range, modelled its spectral energy distribution prior to and after December 2019, and studied the evolution of its UV/optical spectra. Results. From our multi-wavelength photometric analysis, we find that: (a) since 2021, the UV flux (from Swift/UVOT observations) is four times brighter than the flux reported by GALEX in 2004; (b) since June 2022, the mid-infrared flux has risen more than two times, and the W1âW2 WISE colour has become redder; and (c) since February 2024, the source has begun showing X-ray emission. From our spectroscopic follow-up, we see that (i) the narrow emission line ratios are now consistent with a more energetic ionising continuum; (ii) broad emission lines are not detected; and (iii) the [OIII] line increased its flux âź 3.6 years after the first ZTF alert, which implies a relatively compact narrow-line-emitting region. Conclusions. We conclude that the variations observed in SDSS1335+0728 could be either explained by a âź 106Mâ AGN that is just turning on or by an exotic tidal disruption event (TDE). If the former is true, SDSS1335+0728 is one of the strongest cases of an AGNobserved in the process of activating. If the latter were found to be the case, it would correspond to the longest and faintest TDE ever observed (or another class of still unknown nuclear transient). Future observations of SDSS1335+0728 are crucial to further understand its behaviour. Key words. galaxies: activeâ accretion, accretion discsâ galaxies: individual: SDSS J133519.91+072807.4
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- 1. Large-scale integration of data and text Lars Juhl Jensen
- 7. proteins
- 10. stitch-db.org
- 16. usage statistics
- 17. heavily used
- 19. especially in the US
- 21. data integration
- 26. many databases
- 29. variable quality
- 30. not comparable
- 31. hard work
- 33. quality scores
- 35. missing most of the data
- 36. text mining
- 37. >10 km
- 40. cyclin dependent kinase 1
- 41. CDC2
- 43. hCdc2
- 44. âblack listâ
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- 50. within sentences
- 53. text mining
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- 65. questions?