Revisiting Medical Entity Recognition through the Guidelines of the Aurora Initiative

Praveen Kumar,Sabah Mohammed,Arnold Kim,Jinan Fiaidhi 보안공학연구지원센터 2016 International Journal of Bio-Science and Bio-Techn Vol.8 No.4

Clinical Document Processing is growing importance because of unstructured nature of clinical notes as well as limitation of crucial time of clinical professionals to analyses the unstructured clinical notes. Named entity recognition (NER) is a subtask of Clinical documentation processing which is important not only for text analysis but knowledge extraction. Although there are a number of clinical named entity recognition systems, they lack user flexibility and NER scalability. Clinical NER is a challenging work which required consistent research to improve clinical documentation. Accordingly, in this paper, keeping an eye on user’s flexibility, we combined the NER technique with DSL (Domain Specific Language) based user queries. This research focused to produce a prototype system which allows the user to input their queries about a clinical text in a syntax free language which will be reformulate into DSL format in background. The reformulated query then matches against the rules defined by using the DSL to get the matched rule-type. The DSL is created using Xtext framework specifically to create NER rules easily. Then NER is done as per the found NER rule-types. We used the lingpipe API to do the NER using unsupervised technique (dictionary based approach). Again considering user flexibility, research also focused on graphical visualization of the annotated recognized entities, flexibility to store the annotated document into database for later use as well as can conversion the recognized entities into CDA (Clinical Document Architecture) format for interoperability. This research is initiated and inspired by the Aurora research initiative which is an ongoing attempt lead by Dr. Arnold Kim to integrate the design of clinical documentation workflows from the physician perspective that starts with variety DSLs and ends with series of interpretations and analytics in the background

Dimethyl carbonate synthesis via transesterification of propylene carbonate with methanol by ceria-zinc catalysts: Role of catalyst support and reaction parameters

Praveen Kumar,Vimal Chandra Srivastava,Indra Mani Mishra 한국화학공학회 2015 Korean Journal of Chemical Engineering Vol.32 No.9

Ceria and zinc oxide catalyst were impregnated onto various oxide supports, namely Al2O3, TiO2 and SiO2, individually by deposition-coprecipitation method. The synthesized catalysts (CZA, CZS and CZT having supports Al2O3, TiO2 and SiO2, respectively) were characterized by X-ray diffraction (XRD), NH3- and CO2-temperature programmed desorption (TPD) and N2 adsorption. These catalysts were used for synthesis of dimethyl carbonate (DMC) from methanol and propylene carbonate in a batch reactor. CZS was found to have larger average grain size as compared to CZA and CZT. Composite oxides (catalysts) were found to contain individual phases of ZnO, CeO2 and some spinel forms of Zn, Ce along with their supports. CZS having highest basicity and surface area showed better catalytic activity as compared to CZA and CZT. Effect of reaction temperature and methanol/PC molar ratio on DMC yield was studied and a reaction mechanism has been discussed. Maximum DMC yield of 77% was observed with CZS catalyst at 170 oC with methanol/PC molar ratio of 10.

Lesion-Wise Comparison of Pre-Therapy and Post-Therapy Effective Half-Life of Iodine-131 in Pediatric and Young Adult Patients with Differentiated Thyroid Cancer Undergoing Radioiodine Therapy

Praveen Kumar,Chandrasekhar Bal,Nishikant Avinash Damle,Sanjana Ballal,S. N. Dwivedi,Sandeep Agarwala 대한핵의학회 2019 핵의학 분자영상 Vol.53 No.3

Purpose The effective half-life of radioiodine is an important parameter for dosimetry in differentiated thyroid cancer patients, particularly in children. We determined the pre-therapy and post-therapy effective half-life in different types of lesions, i.e., remnant, node, or lung metastases. Methods Of 84 patients recruited, 27 were < 18 years (group 1) and the remaining 57 were between 18 and 21 years (group 2). A total of 114 studies were conducted and 253 lesions were analyzed. Serial whole-body scans were acquired at 24, 48, and ≥ 72 h after administration of iodine-131. Region of interests was drawn over lesions to determine counts in the lesion. Time versus counts graphs were plotted and mono-exponentially fitted to determine effective half-life. Results The post-therapy effective half-life was found to be lesser than pre-therapy effective half-life in all types of lesions and in all groups. Median effective half-life was found maximum in intact lobe, minimum in the lung, and intermediate in remnant and nodes. In the assessment of all lesions together, pre- and post-therapy median and interquartile range (IQR) effective half-life were 59.8 (37–112) h and 48.6 (35.2–70.8) h (p < 0.0001) in group 1, 73.9 (46.2–112.7) h and 60 (57.4–85.9) h (p < 0.0001) in group 2, and 68.6 (41.53–112.36) h and 54.7 (36–80.6) h (p < 0.0001) in combined group, respectively. Importantly, the pre- and post-therapy median effective half-life serially dropped after each successive cycles of iodine-131. Conclusions There was a significant difference in pre-therapy and post-therapy effective half-life in all types of lesions. These results may have implications in calculating the correct therapeutic dose in children and in young adults.

Breaking dormancy: an energy-efficient means of recovering astaxanthin from microalgae

Praveenkumar, Ramasamy,Lee, Kyubock,Lee, Jiye,Oh, You-Kwan The Royal Society of Chemistry 2015 GREEN CHEMISTRY Vol.17 No.2

<P><I>Haematococcus pluvialis</I>, in the dormant aplanospore (cyst) status after 30 d of cultivation, accumulates high levels of a superpotent antioxidant, astaxanthin, which has been demonstrated to have enormous therapeutic benefits. However, owing to the robust structure of its trilayered cell wall, the recovery of astaxanthin from the cyst cells remains an energy-intensive process. In the present study, a novel strategy utilizing a short-period germination based on the natural life cycle of <I>H. pluvialis</I> was developed as an energy-efficient pretreatment for the extraction of astaxanthin using ionic liquids (ILs) as green solvents. The germination resulted in damage and deconstruction of the cyst cell wall, and thereby facilitated the extraction of astaxanthin by ILs at room temperature. By this natural pretreatment with 1-ethyl-3-methylimidazolium ethylsulfate for a very short reaction time of 1 min, a high astaxanthin yield of 19.5 pg per cell was obtained, which was about 82% of a conventional volatile organic solvent extraction by strong, 30 000 psi French-pressure-cell homogenization. The maximal astaxanthin-extraction yield from <I>H. pluvialis</I> cells was observed for 12–18 h germination. The germination rate furthermore could be improved by manipulating the nutritional composition (especially the nitrate concentration) of the culture medium. In light of these results, it can be posited that natural germination following the principles of green chemistry can be a uniquely simple method of robust microalgal cyst cell pretreatment and extraction of astaxanthin with room-temperature ILs.</P> <P>Graphic Abstract</P><P>A highly energy-efficient natural pretreatment process of germination to assist ionic liquid-based extraction of astaxanthin from <I>Haematococcus pluvialis</I> is developed. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c4gc01413h'> </P>

Regenerative Astaxanthin Extraction from a Single Microalgal (<i>Haematococcus pluvialis</i>) Cell Using a Gold Nano-Scalpel

Praveenkumar, Ramasamy,Gwak, Raekeun,Kang, Mijeong,Shim, Tae Soup,Cho, Soojeong,Lee, Jiye,Oh, You-Kwan,Lee, Kyubock,Kim, Bongsoo American Chemical Society 2015 ACS APPLIED MATERIALS & INTERFACES Vol.7 No.40

<P>Milking of microalgae, the process of reusing the biomass for continuous production of target compounds, can strikingly overcome the time and cost constraints associated with biorefinery. This process can significantly improve production efficiency of highly valuable chemicals, for example, astaxanthin (AXT) from <I>Haematococcus pluvialis</I>. Detailed understanding of the biological process of cell survival and AXT reaccumulation after extraction would be of great help for successful milking. Here we report extraction of AXT from a single cell of <I>H. pluvialis</I> through incision of the cell wall by a gold nanoscalpel (Au-NS), which allows single-cell analysis of wound healing and reaccumulation of AXT. Interestingly, upon the Au-NS incision, the cell could reaccumulate AXT at a rate two times faster than the control cells. Efficient extraction as well as minimal cellular damage, keeping cells alive, could be achieved with the optimized shape and dimensions of Au-NS: a well-defined sharp tip, thickness under 300 nm, and 1–3 μm of width. The demonstration of regenerative extraction of AXT at a single cell level hints toward the potential of a milking process for continuous recovery of target compounds from microalgae while keeping the cells alive.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/aamick/2015/aamick.2015.7.issue-40/acsami.5b07651/production/images/medium/am-2015-07651u_0008.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/am5b07651'>ACS Electronic Supporting Info</A></P>

Mild pressure induces rapid accumulation of neutral lipid (triacylglycerol) in Chlorella spp.

Praveenkumar, R.,Kim, B.,Lee, J.,Vijayan, D.,Lee, K.,Nam, B.,Jeon, S.G.,Kim, D.M.,Oh, Y.K. Elsevier Applied Science 2016 Bioresource technology Vol.220 No.-

Effective enhancement of neutral lipid (especially triacylglycerol, TAG) content in microalgae is an important issue for commercialization of microalgal biorefineries. Pressure is a key physical factor affecting the morphological, physiological, and biochemical behaviors of organisms. In this paper, we report a new stress-based method for induction of TAG accumulation in microalgae (specifically, Chlorella sp. KR-1 and Ch. sp. AG20150) by very-short-duration application of mild pressure. Pressure treatments of 10-15bar for 2h resulted in a considerable, ~55% improvement of the 10-100g/Lcells' TAG contents compared with the untreated control. The post-pressure-treatment increase of cytoplasmic TAG granules was further confirmed by transmission electron microscopy (TEM). Notwithstanding the increased TAG content, the total lipid content was not changed by pressurization, implying that pressure stress possibly induces rapid remodeling/transformation of algal lipids rather than de novo biosynthesis of TAG.

Selecting optimized mix proportion of bagasse ash blended high performance concrete using analytical hierarchy process (AHP)

S. Praveenkumar,G. Sankarasubramanian,S. Sindhu 사단법인 한국계산역학회 2019 Computers and Concrete, An International Journal Vol.23 No.6

Apart from strength properties, durability, toughness and workability are also important criteria in defining the performance of a concrete structure. Hence “High Performance Concrete (HPC)” is introduced. It is different from high strength concrete and can have various applications. In this paper, the properties (Mechanical and Durability) of High Performance Concrete blended with bagasse ash at 5%, 10%, 15% and 20% are studied. However, it is difficult to analyze the performance based on different properties obtained from different experiments. Hence it is necessary to combine all the criteria/properties into a single value to obtain a result by a technique called Analytical Hierarchy Process (AHP).It is an effective tool for dealing with complex decision making, and may aid the decision maker to set priorities and make the best decision. In addition, the AHP incorporates a useful technique for checking the consistency of the decision maker‟s evaluations, thus reducing the bias in the decision making process.

Mixotrophic cultivation of Chlorella sp. under fed-batch cultivation system with pulse feeding of glycerol

Ramasamy Praveenkumar,Kyu-Bock Lee,Bo-Hwa Kim,Eunji Choi,You-Kwan Oh 한국신재생에너지학회 2013 한국신재생에너지학회 학술대회논문집 Vol.2013 No.05

Comparison of User-generated Tags with Subject Descriptors, Author Keywords, and Title Terms of Scholarly Journal Articles: A Case Study of Marine Science

Vaidya, Praveenkumar,Harinarayana, N.S. Korea Institute of Science and Technology Informat 2019 Journal of Information Science Theory and Practice Vol.7 No.1

Information retrieval is the challenge of the Web 2.0 world. The experiment of knowledge organisation in the context of abundant information available from various sources proves a major hurdle in obtaining information retrieval with greater precision and recall. The fast-changing landscape of information organisation through social networking sites at a personal level creates a world of opportunities for data scientists and also library professionals to assimilate the social data with expert created data. Thus, folksonomies or social tags play a vital role in information organisation and retrieval. The comparison of these user-created tags with expert-created index terms, author keywords and title words, will throw light on the differentiation between these sets of data. Such comparative studies show revelation of a new set of terms to enhance subject access and reflect the extent of similarity between user-generated tags and other set of terms. The CiteULike tags extracted from 5,150 scholarly journal articles in marine science were compared with corresponding Aquatic Science and Fisheries Abstracts descriptors, author keywords, and title terms. The Jaccard similarity coefficient method was employed to compare the social tags with the above mentioned wordsets, and results proved the presence of user-generated keywords in Aquatic Science and Fisheries Abstracts descriptors, author keywords, and title words. While using information retrieval techniques like stemmer and lemmatization, the results were found to enhance keywords to subject access.

Simulatory Effect of Fungicide on Triacylglycerol Content in Chlorella sp.

Ramasamy Praveenkumar,Bohwa Kim(김보화),Kyubock Lee(이규복),You-Kwan Oh(오유관) 한국신재생에너지학회 2015 한국신재생에너지학회 학술대회논문집 Vol.2015 No.6