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Yang C Mills D Mathee K Wang Y Jayachandran K Sikaroodi M Gillevet P Entry J Narasimhan G 《Journal of microbiological methods》2006,65(1):49-62
Support vector machines (SVM) and K-nearest neighbors (KNN) are two computational machine learning tools that perform supervised classification. This paper presents a novel application of such supervised analytical tools for microbial community profiling and to distinguish patterning among ecosystems. Amplicon length heterogeneity (ALH) profiles from several hypervariable regions of 16S rRNA gene of eubacterial communities from Idaho agricultural soil samples and from Chesapeake Bay marsh sediments were separately analyzed. The profiles from all available hypervariable regions were concatenated to obtain a combined profile, which was then provided to the SVM and KNN classifiers. Each profile was labeled with information about the location or time of its sampling. We hypothesized that after a learning phase using feature vectors from labeled ALH profiles, both these classifiers would have the capacity to predict the labels of previously unseen samples. The resulting classifiers were able to predict the labels of the Idaho soil samples with high accuracy. The classifiers were less accurate for the classification of the Chesapeake Bay sediments suggesting greater similarity within the Bay's microbial community patterns in the sampled sites. The profiles obtained from the V1+V2 region were more informative than that obtained from any other single region. However, combining them with profiles from the V1 region (with or without the profiles from the V3 region) resulted in the most accurate classification of the samples. The addition of profiles from the V 9 region appeared to confound the classifiers. Our results show that SVM and KNN classifiers can be effectively applied to distinguish between eubacterial community patterns from different ecosystems based only on their ALH profiles. 相似文献
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Kateel G. Shetty Diana V. Rivadeneira Krish Jayachandran Donald M. Walker 《Mycological Progress》2016,15(9):977-986
Fungal endophytes are the most ubiquitous and highly diverse microorganisms that inhabit the interior of healthy plants. They are important in plant ecology and offer untapped potential to improve plant health and productivity in agroecosystems. The endophytic assemblage of avocado is poorly understood; therefore, surveys of fungal endophytes of Persea americana Mill. (Avocado) in South Florida organic and conventional orchards were conducted. A total of 17 endophytic fungal species were recovered from healthy avocado terminal branches. Endophytic fungal species were identified by rDNA sequencing of the internal transcribed spacer (ITS) region, using UNITE Species Hypotheses to reliably assign a taxon name, and determined as belonging to the genera Alternaria, Cladosporium, Colletotrichum, Corynespora, Diaporthe, Lasiodiplodia, Neofusicoccum, Neopestalotiopsis, Phyllosticta, and Strelitziana. Endophyte community assemblage differed between organic and conventional agroecosystems. This is the first report of Alternaria eichhorniae, Cladosporium tenuissimum, Corynespora cassiicola, Colletotrichum alatae, Diaporthe fraxini-angustifoliae, Lasiodiplodia gonubiensis, Neofusicoccum algeriense, Neofusicoccum andinum, Neopestalotiopsis foedans, Phyllosticta capitalensis, and Strelitziana africana as endophytes of avocado. Evaluation using pathogenicity tests on avocado leaves and terminal branches showed that endophytic fungal isolates did not cause disease symptoms. 相似文献
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Hofer SO Dhar BK Robinson PH Goorhuis-Brouwer SM Nicolai JP 《Plastic and reconstructive surgery》2002,110(6):1393-7; discussion 1398-1400
A 10-year retrospective study was undertaken to investigate perioperative complications in pharyngeal flap surgery in one institution using inferiorly and superiorly based flaps. In this fashion the current practice of surgical technique based on local findings and perioperative care, through regular monitoring by experienced nurses on the ward, was evaluated for adequacy. The charts of 275 patients who had 287 pharyngeal flap procedures were studied. Demographics, type and duration of operation, associated procedures, surgeon, anesthetist, duration of hospital stay, associated medical conditions, and perioperative complications such as bleeding, respiratory insufficiency, or flap dehiscence were evaluated. In this series a total complication rate of 6 percent was found, with 2.4 percent early (<6 weeks) and 3.8 percent late (>6 weeks) complications. Only two patients (0.7 percent) had postoperative bleeding requiring reoperation, and one patient (0.3 percent) needed reintubation. The most frequent complication was flap dehiscence in nine patients (3.1 percent), which occurred early in three and late in six. Pharyngeal flap surgery can be performed safely with very few complications provided the correct experience and infrastructure are present. Careful surgery, in conjunction with adequate anesthesia and postoperative monitoring, makes these procedures safe and rewarding. 相似文献
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Caryn S. Ross-Innes Irene Debiram-Beecham Maria O'Donovan Elaine Walker Sibu Varghese Pierre Lao-Sirieix Laurence Lovat Michael Griffin Krish Ragunath Rehan Haidry Sarmed S. Sami Philip Kaye Marco Novelli Babett Disep Richard Ostler Benoit Aigret Bernard V. North Pradeep Bhandari Adam Haycock Danielle Morris Stephen Attwood Anjan Dhar Colin Rees Matthew D. D. Rutter Peter D. Sasieni Rebecca C. Fitzgerald 《PLoS medicine》2015,12(1)
BackgroundBarrett''s esophagus (BE) is a commonly undiagnosed condition that predisposes to esophageal adenocarcinoma. Routine endoscopic screening for BE is not recommended because of the burden this would impose on the health care system. The objective of this study was to determine whether a novel approach using a minimally invasive cell sampling device, the Cytosponge, coupled with immunohistochemical staining for the biomarker Trefoil Factor 3 (TFF3), could be used to identify patients who warrant endoscopy to diagnose BE.ConclusionsThe Cytosponge-TFF3 test is safe and acceptable, and has accuracy comparable to other screening tests. This test may be a simple and inexpensive approach to identify patients with reflux symptoms who warrant endoscopy to diagnose BE. 相似文献
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Hernan D. Gonorazky Sergey Naumenko Arun K. Ramani Viswateja Nelakuditi Pouria Mashouri Peiqui Wang Dennis Kao Krish Ohri Senthuri Viththiyapaskaran Mark A. Tarnopolsky Katherine D. Mathews Steven A. Moore Andres N. Osorio David Villanova Dwi U. Kemaladewi Ronald D. Cohn Michael Brudno James J. Dowling 《American journal of human genetics》2019,104(3):466-483
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Hernan D. Gonorazky Sergey Naumenko Arun K. Ramani Viswateja Nelakuditi Pouria Mashouri Peiqui Wang Dennis Kao Krish Ohri Senthuri Viththiyapaskaran Mark A. Tarnopolsky Katherine D. Mathews Steven A. Moore Andres N. Osorio David Villanova Dwi U. Kemaladewi Ronald D. Cohn Michael Brudno James J. Dowling 《American journal of human genetics》2019,104(5):1007