Relevant bibliographies by topics / Phenotying

Academic literature on the topic 'Phenotying'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Phenotying"

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Evans, R. T., A. Walker, and K. M. Bowness. "Improved accuracy of cholinesterase phenotyping after participation in a proficiency survey." Clinical Chemistry 33, no. 6 (June 1, 1987): 823–25. http://dx.doi.org/10.1093/clinchem/33.6.823.

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Abstract We report results of an investigation into the proficiency of cholinesterase (EC 3.1.1.8) phenotying, assessed in 13 laboratories between 1983 and 1986. Thirty-two specimens of serum were distributed for analysis: two, each in duplicate, from the eight genotypes that can be recognized by differential enzyme inhibitor numbers. The accuracy of genotype ascription was markedly improved over that observed in an earlier study in which 12 of these laboratories took part, although the proportion of clinically significant errors did not change. Consequently, although participation in a proficiency testing program can lead to a considerable enhancement of performance, we still recommend the use of reference centers for detailed cholinesterase studies.
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Hund, A., S. Trachsel, and P. Stamp. "Growth of axile and lateral roots of maize: I development of a phenotying platform." Plant and Soil 325, no. 1-2 (April 8, 2009): 335–49. http://dx.doi.org/10.1007/s11104-009-9984-2.

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Sagan, Vasit, Maitiniyazi Maimaitijiang, Paheding Sidike, Kevin Eblimit, Kyle Peterson, Sean Hartling, Flavio Esposito, et al. "UAV-Based High Resolution Thermal Imaging for Vegetation Monitoring, and Plant Phenotyping Using ICI 8640 P, FLIR Vue Pro R 640, and thermoMap Cameras." Remote Sensing 11, no. 3 (February 7, 2019): 330. http://dx.doi.org/10.3390/rs11030330.

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The growing popularity of Unmanned Aerial Vehicles (UAVs) in recent years, along with decreased cost and greater accessibility of both UAVs and thermal imaging sensors, has led to the widespread use of this technology, especially for precision agriculture and plant phenotyping. There are several thermal camera systems in the market that are available at a low cost. However, their efficacy and accuracy in various applications has not been tested. In this study, three commercially available UAV thermal cameras, including ICI 8640 P-series (Infrared Cameras Inc., USA), FLIR Vue Pro R 640 (FLIR Systems, USA), and thermoMap (senseFly, Switzerland) have been tested and evaluated for their potential for forest monitoring, vegetation stress detection, and plant phenotyping. Mounted on multi-rotor or fixed wing systems, these cameras were simultaneously flown over different experimental sites located in St. Louis, Missouri (forest environment), Columbia, Missouri (plant stress detection and phenotyping), and Maricopa, Arizona (high throughput phenotyping). Thermal imagery was calibrated using procedures that utilize a blackbody, handheld thermal spot imager, ground thermal targets, emissivityand atmospheric correction. A suite of statistical analyses, including analysis of variance (ANOVA), correlation analysis between camera temperature and plant biophysical and biochemical traits, and heritability were utilized in order to examine the sensitivity and utility of the cameras against selected plant phenotypic traits and in the detection of plant water stress. In addition, in reference to quantitative assessment of image quality from different thermal cameras, a non-reference image quality evaluator, which primarily measures image focus that is based on the spatial relationship of pixels in different scales, was developed. Our results show that (1) UAV-based thermal imaging is a viable tool in precision agriculture and (2) the three examined cameras are comparable in terms of their efficacy for plant phenotyping. Overall, accuracy, when compared against field measured ground temperature and estimating power of plant biophysical and biochemical traits, the ICI 8640 P-series performed better than the other two cameras, followed by FLIR Vue Pro R 640 and thermoMap cameras. Our results demonstrated that all three UAV thermal cameras provide useful temperature data for precision agriculture and plant phenotying, with ICI 8640 P-series presenting the best results among the three systems. Cost wise, FLIR Vue Pro R 640 is more affordable than the other two cameras, providing a less expensive option for a wide range of applications.
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Genkel, Vadim, Ilya Dolgushin, Irina Baturina, Albina Savochkina, Alla Kuznetsova, Lubov Pykhova, and Igor Shaposhnik. "Associations between Hypertriglyceridemia and Circulating Neutrophil Subpopulation in Patients with Dyslipidemia." International Journal of Inflammation 2021 (May 26, 2021): 1–8. http://dx.doi.org/10.1155/2021/6695468.

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Background. There is strong evidence to suggest that the negative influence of triglyceride-rich lipoproteins (TRLs) on atherosclerosis development and progression is at least partially mediated by their proinflammatory effects. However, the effect of hypertriglyceridemia (HTG) on the subpopulation composition of circulating neutrophils has not been studied so far. The aim of this study was to examine correlations between the level of triglycerides (TGs) and the subpopulation composition of circulating neutrophils in middle-aged patients with dyslipidemia without established atherosclerotic cardiovascular diseases (ASCVDs). Methods. Ninety-one patients with dyslipidemia, including 22 (24.2%) patients with HTG, were enrolled in the study. Phenotying of neutrophil subpopulations was performed through flow cytometry (Navios 6/2, Beckman Coulter, USA). For phenotyping of neutrophil subpopulations, conjugated monoclonal antibodies were used: CD16, PE-Cyanine7 (Invitrogen, USA); CD11b-FITC (Beckman Coulter, USA); CD62L-PE (Beckman Coulter, USA); and CD184 (CXCR4)-PE-CF594 (BD Biosciences, USA). Results. Following the correlation analysis, the TG level directly correlated with the number of circulating leukocytes (r = 0.443; p < 0.0001 ) and neutrophils (r = 0.311; p = 0.008 ). HTG patients displayed a significantly high number of circulating neutrophils with CD16hiCD11bhiCD62Lhi and CD16hiCD11bloCD62Lbr phenotypes. TG levels directly correlated with the number of circulating neutrophils having CD16hiCD11bhiCD62Lhi and CD16hiCD11bloCD62Lbr phenotypes. Following the linear regression analysis, statistically significant correlations between TG levels and neutrophil subpopulations having CD16hiCD11bloCD62Lbr and CD16hiCD11bbrCD62LloCXCR4hi phenotypes were established. Changes in TG levels could explain up to 19.1% of the variability in the number of studied neutrophil subpopulations. Conclusion. Among middle-aged patients without established ASCVDs, patients with HTG demonstrated a significantly higher overall number of neutrophils and neutrophils having CD16hiCD11bhiCD62Lhi (mature neutrophils) and CD16hiCD11bloCD62Lbr (immunosuppressive neutrophils) than patients with normal TG levels. The TG level was associated with an increase in the number of CD16hiCD11bloCD62Lbr and CD16hiCD11bbrCD62LloCXCR4hi (ageing neutrophils) neutrophils, adjusted for the sex and age of the patients.
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Washko, George R. "Chest Computed Tomography for Phenotying Chronic Obstructive Pulmonary Disease. A Pathway and a Challenge for Personalized Medicine." Annals of the American Thoracic Society 12, no. 7 (July 2015): 966–67. http://dx.doi.org/10.1513/annalsats.201504-239ed.

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Helali, Asadul Mazid. "Pharmacogenetics and polymorphism: future tools for optimizing therapeutic efficacy." Bangladesh Journal of Physiology and Pharmacology 26, no. 1-2 (August 12, 2014): 34–42. http://dx.doi.org/10.3329/bjpp.v26i1-2.19966.

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Individual variation in drug response is a major problem in clinical practice and drug development, which ranges from therapeutic failure to adverse drug reaction as well as drug interaction in multidrug therapy. Pharmacogenetics is relevant in this aspects and mainly concern with the study of genetic variation, which influence individuals’ responses to drug. Again, polymorphism (variation) in the genes which are involved in encoding drug metabolizing enzymes, transporters of drug and ion channels can play role in the adverse drug reaction in an individual or can interfere with the therapeutic efficacy. By studying pharmacogenetics one can apply genotyping of polymorphic alleles that encodes drug metabolizing enzymes to identify individual’s drug metabolism phenotype and correlating this knowledge to dosing or drug selection, avoidance of many adverse effect of drug and therapeutic failure is possible as well as economic burden to the patient will be reduced. It is true that one drug will not effective for everyone and everyone will not response to a single drug in a similar fashion. It is almost impossible to test every drug in whole population in respect of investment and time. From this point of view, pharmacogenetic screening, such as phenotying test can be useful to identify patients who have inherent risk factor for a specific adverse drug reaction. Recently pharmacogenetic testing is performed for only a few drugs e.g. mercaptopurine, thioguanine, azathriopine and tacrine and the facility is also available in a limited number of teaching hospital but the days are not so far, when it may be considered as unethical if pharmacogenetics test is not done routinely before prescribing a drug to a patient. http://dx.doi.org/10.3329/bjpp.v26i1-2.19966 Bangladesh J Physiol Pharmacol 2010; 26(1&2) : 34-42
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ÁLVAREZ DE NEYRA KAPPLER, Susana. "EL FENOTIPADO FORENSE." IUS ET SCIENTIA 2, no. 4 (2018): 63–86. http://dx.doi.org/10.12795/iestscientia.2018.i02.05.

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Delage, Clément, Léa Darnaud, Bruno Etain, Marina Vignes, Tu-Ky Ly, Alexia Frapsauce, Marc Veyrier, et al. "Cytochromes P450 and P-Glycoprotein Phenotypic Assessment to Optimize Psychotropic Pharmacotherapy: A Retrospective Analysis of Four Years of Practice in Psychiatry." Journal of Personalized Medicine 12, no. 11 (November 8, 2022): 1869. http://dx.doi.org/10.3390/jpm12111869.

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Altered cytochromes P450 enzymes (CYP) and P-glycoprotein transporter (P-gp) activity may explain variabilities in drug response. In this study, we analyzed four years of phenotypic assessments of CYP/P-gp activities to optimize pharmacotherapy in psychiatry. A low-dose probe cocktail was administered to evaluate CYP1A2, 2B6, 2D6, 2C9, 2C19, 3A4, and P-gp activities using the probe/metabolite concentration ratio in blood or the AUC. A therapeutic adjustment was suggested depending on the phenotyping results. From January 2017 to June 2021, we performed 32 phenotypings, 10 for adverse drug reaction, 6 for non-response, and 16 for both reasons. Depending on the CYP/P-gp evaluated, only 23% to 56% of patients had normal activity. Activity was decreased in up to 57% and increased in up to 60% of cases, depending on the CYP/P-gp evaluated. In 11/32 cases (34%), the therapeutic problem was attributable to the patient’s metabolic profile. In 10/32 cases (31%), phenotyping excluded the metabolic profile as the cause of the therapeutic problem. For all ten individuals for which we had follow-up information, phenotyping allowed us to clearly state or clearly exclude the metabolic profile as a possible cause of therapeutic failure. Among them, seven showed a clinical improvement after dosage adaptation, or drug or pharmacological class switching. Our study confirmed the interest of CYP and P-gp phenotyping for therapeutic optimization in psychiatry.
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Sarkar, Sayantan, Joseph Oakes, Alexandre-Brice Cazenave, Mark D. Burow, Rebecca S. Bennett, Kelly D. Chamberlin, Ning Wang, et al. "Evaluation of the U.S. Peanut Germplasm Mini-Core Collection in the Virginia-Carolina Region Using Traditional and New High-Throughput Methods." Agronomy 12, no. 8 (August 18, 2022): 1945. http://dx.doi.org/10.3390/agronomy12081945.

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Peanut (Arachis hypogaea L.) is an important food crop for the U.S. and the world. The Virginia-Carolina (VC) region (Virginia, North Carolina, and South Carolina) is an important peanut-growing region of the U.S and is affected by numerous biotic and abiotic stresses. Identification of stress-resistant germplasm, along with improved phenotyping methods, are important steps toward developing improved cultivars. Our objective in 2017 and 2018 was to assess the U.S. mini-core collection for desirable traits, a valuable source for resistant germplasm under limited water conditions. Accessions were evaluated using traditional and high-throughput phenotyping (HTP) techniques, and the suitability of HTP methods as indirect selection tools was assessed. Traditional phenotyping methods included stand count, plant height, lateral branch growth, normalized difference vegetation index (NDVI), canopy temperature depression (CTD), leaf wilting, fungal and viral disease, thrips rating, post-digging in-shell sprouting, and pod yield. The HTP method included 48 aerial vegetation indices (VIs), which were derived using red, blue, green, and near-infrared reflectance; color space indices were collected using an octocopter drone at the same time, with traditional phenotyping. Both phenotypings were done 10 times between 4 and 16 weeks after planting. Accessions had yields comparable to high yielding checks. Correlation coefficients up to 0.8 were identified for several Vis, with yield indicating their suitability for indirect phenotyping. Broad-sense heritability (H2) was further calculated to assess the suitability of particular VIs to enable genetic gains. VIs could be used successfully as surrogates for the physiological and agronomic trait selection in peanuts. Further, this study indicates that UAV-based sensors have potential for measuring physiologic and agronomic characteristics measured for peanut breeding, variable rate input application, real time decision making, and precision agriculture applications.
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James, Paula, and Barry S. Coller. "Phenotyping bleeding." Current Opinion in Hematology 19, no. 5 (September 2012): 406–12. http://dx.doi.org/10.1097/moh.0b013e32835673ab.

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Dissertations / Theses on the topic "Phenotying"

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Zhou, Felix. "Phenotyping cellular motion." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:9fb6a57d-2e16-43c9-92e6-895330353e51.

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In the development of multicellular organisms, tissue development and homeostasis require coordinated cellular motion. For example, in conditions such as wound healing, immune and epithelial cells need to proliferate and migrate. Deregulation of key signalling pathways in pathological conditions causes alterations in cellular motion properties that are critical for disease development and progression, in cancer it leads to invasion and metastasis. Consequently there is strong interest in identifying factors, including drugs that affect the motion and interactions of cells in disease using experimental models suitable for high-content screening. There are two main modes of cell migration; individual and collective migration. Currently analysis tools for robust, sensitive and comprehensive motion characterisation in varying experimental conditions for large extended timelapse acquisitions that jointly considers both modes are limited. We have developed a systematic motion analysis framework, Motion Sensing Superpixels (MOSES) to quantitatively capture cellular motion in timelapse microscopy videos suitable for high-content screening. MOSES builds upon established computer vision approaches to deliver a minimal parameter, robust algorithm that can i) extract reliable phenomena-relevant motion metrics, ii) discover spatiotemporal salient motion patterns and iii) facilitate unbiased analysis with little prior knowledge through unique motion 'signatures'. The framework was validated by application to numerous datasets including YouTube videos, zebrafish immunosurveillance and Drosophila embryo development. We demonstrate two extended applications; the analysis of interactions between two epithelial populations in 2D culture using cell lines of the squamous and columnar epithelia from human normal esophagus, Barrett's esophagus and esophageal adenocarcinoma and the automatic monitoring of 3D organoid culture growth captured through label-free phase contrast microscopy. MOSES found unique boundary formation between squamous and columnar cells and could measure subtle changes in boundary formation due to external stimuli. MOSES automatically segments the motion and shape of multiple organoids even if present in the same field of view. Automated analysis of intestinal organoid branching following treatment agrees with independent RNA-seq results.
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Ericksen, Daniel S. (Daniel Southwick) 1977. "High-throughput genomic phenotyping." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/28527.

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Thesis (S.M.)--Massachusetts Institute of Technology, Biological Engineering Division, 2004.
Includes bibliographical references (p. 63-65).
In the wake of the development of technology to sequence the complete genome of an organism, it has become expedient to generate methodologies to elucidate and characterize the function of all genes constituting the complete genetic makeup of an organism, whereby the knowledge of the genetic code may be for scientific and intellectual profit. This work consists of an investigation into two possible methods for determining the role of genes involved in the DNA and cellular damage response, though the methods are generally applicable to investigating a wide variety of biological pathways and responses. A library of approximately 4,800 yeast (Saccharomyces cerevisiae) deletion strains produced by the Saccharomyces Genome Deletion Project and consisting essentially of all possible mutants having one non-essential gene deleted (and replaced with unique identification tags called "bar codes") from the genome are employed in this endeavor. The methods focus on gathering phenotype data in a high-throughput manner and in response to the alkylating agent methyl methanesulfonate (MMS). The first method makes use of a new technology called the Living ChipTM, which can hold libraries of compounds or cell cultures in an array of 50-nl channels and which could ideally accommodate all deletion strains on a single array. The second method involves pooling all strains together in a single culture and allowing them to grow competitively to determine their relative fitness based on a specific treatment.
by Daniel S. Ericksen.
S.M.
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Singh, Shantanu. "Quantitative Phenotyping in Tissue Microenvironments." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1306940222.

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Tikhomirova, Victoria E., Olga A. Kost, Olga V. Kryukova, Elena Z. Golukhova, Naida I. Bulaeva, Aigerim Z. Zholbaeva, Leo A. Bokeria, Joe G. N. Garcia, and Sergei M. Danilov. "ACE phenotyping in human heart." PUBLIC LIBRARY SCIENCE, 2017. http://hdl.handle.net/10150/625490.

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Aims Angiotensin-converting enzyme (ACE), which metabolizes many peptides and plays a key role in blood pressure regulation and vascular remodeling, is expressed as a type-1 membrane glycoprotein on the surface of different cells, including endothelial cells of the heart. We hypothesized that the local conformation and, therefore, the properties of heart ACE could differ from lung ACE due to different microenvironment in these organs. Methods and results We performed ACE phenotyping (ACE levels, conformation and kinetic characteristics) in the human heart and compared it with that in the lung. ACE activity in heart tissues was 10-15 lower than that in lung. Various ACE effectors, LMW endogenous ACE inhibitors and HMW ACE-binding partners, were shown to be present in both heart and lung tissues. "Conformational fingerprint" of heart ACE (i.e., the pattern of 17 mAbs binding to different epitopes on the ACE surface) significantly differed from that of lung ACE, which reflects differences in the local conformations of these ACEs, likely controlled by different ACE glycosylation in these organs. Substrate specificity and pH-optima of the heart and lung ACEs also differed. Moreover, even within heart the apparent ACE activities, the local ACE conformations, and the content of ACE inhibitors differ in atria and ventricles. Conclusions Significant differences in the local conformations and kinetic properties of heart and lung ACEs demonstrate tissue specificity of ACE and provide a structural base for the development of mAbs able to distinguish heart and lung ACEs as a potential blood test for predicting atrial fibrillation risk.
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Wang, Xin. "Inferring cellular networks from phenotyping screens." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648275.

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Edelman, Nicholas (Nicholas A. ). "Automated phenotyping of mouse social behavior." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/76810.

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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (p. 66-68).
Inspired by the connections between social behavior and intelligence, I have developed a trainable system to phenotype mouse social behavior. This system is of immediate interest to researchers studying mouse models of social disorders such as depression or autism. Mice studies provide a controlled environment to begin exploring the questions of how to best quantify social behavior. For the purposes of evaluating this system and to encourage further research, I introduce a new video dataset annotated with five social behaviors: nose-to-nose sniffing, nose-to-head sniffing, nose-to-anogenital sniffing, crawl under / crawl over, and upright head contact. These four behaviors are of particular importance to researchers characterizing mouse social avoidance [9]. To effectively phenotype mouse social behavior, the system incorporates a novel mice tracker, and modules to represent and to classify social behavior. The mice tracker addresses the challenging computer vision problem of tracking two identical, highly deformable mice through complex occlusions. The tracker maintains an ellipse model of both mice and leverages motion cues and shape priors to maintain tracks during occlusions. Using these tracks, the classification system represents behavior with 14 spatial features characterizing relative position, relative motion, and shape. A regularized least squares (RLS) classifier, trained over representative instances of each behavior, classifies the behavior present in each frame. This system demonstrates the enormous potential for building automated systems to quantitatively study mouse social behavior.
by Nicholas Edelman.
M.Eng.
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Ghadieh, Rachelle. "Phenotyping and heritability of constitutional thinness." Thesis, Lyon, 2021. https://tel.archives-ouvertes.fr/tel-03789601.

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Cette thèse est divisée en deux parties l'une consiste une revue de la littérature et la deuxième comprend quatre manuscrits. Peu d'études sur la MC ont été réalisées en Europe, aucune donnée n'est actuellement disponible sur les aspects cliniques et biologiques de la MC au Liban ou dans la région du Moyen-Orient. La pathologie MC reste mal recherchée et mal comprise. Cette première étude évaluant l'héritabilité du MC est menée dans deux cohortes de familles françaises et libanaises de MC a démontré que MC est un caractère héritable. La transmission génétique de ce caractère semble le plus souvent être autosomique récessive.La deuxième étude visée a caractériser plusieurs caractéristiques métaboliques et nutritionnelles dans une cohorte libanaise de sujets MC. L'étude est la première du genre dans la région du Moyen-Orient et peut être considérée comme une base pour une comparaison multinationale de cet état de sous-poids. Il a démontre pour la première fois que les libanaises n'ont pas de signes de déficit et confirme les principales caractéristiques nutritionnelles décrites précédemment dans les cohortes françaises. Les petites différences décrites doivent être confirmées par des cohortes plus grandes.La troisième étude était la première étude validant la forme arabe du DEBQ. Ce n'est pas un simple travail de validation, les facteurs associés au DEBQ ont également été étudiés. DEBQ est un outil pratique pour catégoriser les facteurs comportementaux liés aux habitudes alimentaires individuelles, y compris ceux impliqués dans les troubles de l'alimentation. Le manuscrit de la revue de la littérature a été construit et structuré comme complément au manuscrit évaluant l'héritage de la MC. Finalement, la MC est un nouveau sujet et la plupart des études ont été menées sur les jeunes femmes CT à Saint-Etienne, France. Il est de grande importance de conduire plus de recherches sur la MC pour comprendre les mécanismes et l'héritabilité de l'extrême minceur et trouver l'explication de ce phénomène pourrait être une étape dans le traitement de l'obésité et pour répondre à la demande de la MC et satisfaire leur désir de prendre du poids
This thesis is divided into two parts one consisting of a review of the literature and the second one involves four manuscripts. few studies on CT were done in Europe, no data is currently available on clinical and biological aspects of constitutional thinness in Lebanon or the middle east region. CT pathology remains poorly researched and understood. This first study evaluating the heritability of CT and conducted in two cohorts of french and lebanese CT families demonstrated that CT runs in families and is a heritable trait. The genetic transmission of this trait seem to be most often autosomal recessive. The second study aimed to characterize several metabolic and nutritional features in a lebanese cohort of CT subjects. the study is the first of its kind in the middle east region and can be considered as a base for a multinational comparison of this underweight state. It demonstrated for the first time that lebanese CT persons have no signs of deficits and confirmed the major nutrition features previously described in french cohorts. Small differences described for the first time need to be confirmed by larger cohorts. The third study was the first study validating the arabic form of DEBQ. It’s not just a simple validation work, factors associated with DEBQ were also studied. DEBQ is a convenient tool to categorize behavioral factors related to individual eating patterns, including those implicated in eating disorders.The literature review manuscript was constructed and structured as a complement to the manuscript evaluating the inheritability in constitutional thinness. Overall, CT is a new topic and most studies were conducted on CT young women in Saint-Etienne - France. It is of high importance to conduct more research on CT to understand the mechanisms and heritability of extreme thinness and finding the explanation behind this phenomenon might be a step in the treatment of obesity and to meet the ct's demand and satisfy their desire to gain weight
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Barker, Jared W. III. "Development of a field-based high-throughput mobile phenotyping platform." Thesis, Kansas State University, 2014. http://hdl.handle.net/2097/17543.

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Master of Science
Department of Biological and Agricultural Engineering
Naiqian Zhang
In order to meet food, fiber, and bio-fuel needs of a growing world population, crop-breeding methods must be improved and new technologies must be developed. One area under focus is the decoding of the genetic basis of complex traits, such as yield and drought stress tolerance, and predicting these traits from genetic composition of lines or cultivars. In the last three decades, significant advances in genotyping methods have resulted in a wealth of genomic information; however, little improvement has occurred for methods of collecting corresponding plant trait data, especially for agronomic crops. This study developed a mobile, field-based, high-throughput sensor platform for rapid and repeated measurement of plant characteristics. The platform consisted of three sets of sensors mounted on a high-clearance vehicle. Each set of sensors contained two infrared thermometers (IRT), one ultrasonic sensor, one Crop Circle, and one GreenSeeker. Each sensor set measured canopy temperature, crop height, and spectral reflectance. In addition to the sensors, the platform was equipped with an RTK-GPS system that provided precise, accurate position data for georeferencing sensor measurements. Software for collecting, georeferencing, and logging sensor data was developed using National Instruments LabVIEW and deployed on a laptop computer. Two verification tests were conducted to evaluate the phenotyping system. In the first test, data timestamps were analyzed to determine if the system could collect data at the required rate of 10 Hz and 5 Hz for sensor data and position data, respectively. The determination was made that, on average, IRT, ultrasonic, and Crop Circle data are received in intervals of 100 ms (SD = 10 ms), GreenSeeker data are received in intervals of 122 ms(SD=10 ms), and position data are received in intervals of 200 ms (SD = 32 ms). The second test determined that a statistically significant relationship exists between sensor readings and ambient light intensity and ambient temperatures. Whether the relationship is significant from a practical stand point should be determined based on specific application of the sensors.
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Pari, Marco. "Image Analysis Methods for Sugar Beet Phenotyping." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/10533/.

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In un mondo che richiede sempre maggiormente un'automazione delle attività della catena produttiva industriale, la computer vision rappresenta uno strumento fondamentale perciò che viene già riconosciuta internazionalmente come la Quarta Rivoluzione Industriale o Industry 4.0. Avvalendomi di questo strumento ho intrapreso presso l'azienda Syngenta lo studio della problematica della conta automatica del numero di foglie di una pianta. Il problema è stato affrontato utilizzando due differenti approcci, ispirandosi alla letteratura. All'interno dell'elaborato è presente anche la descrizione progettuale di un ulteriore metodo, ad oggi non presente in letteratura. Le metodologie saranno spiegate in dettaglio ed i risultati ottenuti saranno confrontati utilizzando i primi due approcci. Nel capitolo finale si trarranno le conclusioni sulle basi dei risultati ottenuti e dall'analisi degli stessi.
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Thomas, Shery. "Phenotyping and genotyping of idiopathic infantile nystagmus." Thesis, University of Leicester, 2010. http://hdl.handle.net/2381/7973.

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Background: Nystagmus can be a manifestation of ocular or systemic disorders. However, it may represent a separate disease entity by itself as in idiopathic infantile nystagmus (IIN). In 2004, Kerrison et al. localised the gene causing X-linked IIN to Xq26-27 (NYS1); however, the gene/genes causing IIN had not been identified. Aims and Objectives: The aims of this study were threefold. 1. To ascertain families and singletons (sporadic subjects) with IIN. 2. To further refine the locus NYS1 and to identify the gene causing X-linked IIN 3. To describe and compare the phenotype of subjects with IIN Methods: 39 families and 78 singletons with nystagmus were recruited and phenotyped. Genotyping with microsatellite markers were performed in the X-linked families to refine the genetic interval at Xq26-27. Gene sequencing was carried out by our collaborators (not by the author) at the Sanger Institute. The clinical features and eye movement recordings of 90 subjects with mutations in the FRMD7 gene were compared to 48 subjects with IIN not associated with mutations in this gene (non-FRMD7 group). Results: I: 149 familial subjects and 78 sporadic subjects with IIN were phenotyped. 121 subjects from 30 families were diagnosed to have X-linked IIN while 28 subjects from 9 families had other diagnosis such as albinism and aniridia. II: Genetic mapping in 16 families with X-linked IIN, refined the critical interval at Locus NYS1 (Xq26-17) to a 9mB region between markers DXS8072 and DXS8094 which contained about 80 genes. High throughput DNA sequencing was carried out at the Sanger Institute which led to the discovery of FRMD7, mutations in which is associated with X-linked IIN. III: The median visual acuity in subjects with a FRMD7 mutation was log MAR 0.301. The number of subjects with good stereopsis (Lang positive) was higher in the FRMD7 group (93.4%) compared to subjects in the non- FRMD7 group (78.4%). None of the subjects in the FRMD7 group had severe (>15˚) anomalous head posture (AHP) while 27% of subjects in the non-FRMD7 group had AHP more than 15˚. 52.17% of obligate female carriers of a FRMD7 mutation were clinically affected. Discussion: This study identified the first gene causing idiopathic infantile nystagmus. The phenotypic characteristics of these subjects will help in clinically identifying subjects with IIN due to mutations in FRMD7. In addition it has generated a stage for further research into the mechanisms behind ocular motor control.
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Books on the topic "Phenotying"

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Tanimoto, Naoyuki, ed. Mouse Retinal Phenotyping. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7720-8.

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Zhou, Jianfeng, and Henry T. Nguyen, eds. High-Throughput Crop Phenotyping. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-73734-4.

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Lorence, Argelia, and Karina Medina Jimenez, eds. High-Throughput Plant Phenotyping. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2537-8.

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Panguluri, Siva Kumar, and Are Ashok Kumar, eds. Phenotyping for Plant Breeding. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-8320-5.

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Martin, Hrabé de Angelis, Chambon Pierre, and Brown Stephen D. M, eds. Standards of mouse model phenotyping. Weinheim: Wiley-VCH, 2006.

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Montag, Christian, and Harald Baumeister, eds. Digital Phenotyping and Mobile Sensing. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-030-98546-2.

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Normanly, Jennifer, ed. High-Throughput Phenotyping in Plants. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-995-2.

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Baumeister, Harald, and Christian Montag, eds. Digital Phenotyping and Mobile Sensing. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-31620-4.

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Samal, Ashok, and Sruti Das Choudhury. Intelligent Image Analysis for Plant Phenotyping. Edited by Ashok Samal and Sruti Das Choudhury. First edition. | Boca Raton, FL : CRC Press, 2021.: CRC Press, 2020. http://dx.doi.org/10.1201/9781315177304.

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Tucci, Valter, ed. Handbook of Neurobehavioral Genetics and Phenotyping. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2017. http://dx.doi.org/10.1002/9781118540770.

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Book chapters on the topic "Phenotying"

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Bodner, Gernot, Mouhannad Alsalem, and Alireza Nakhforoosh. "Root System Phenotying of Soil-Grown Plants via RGB and Hyperspectral Imaging." In Methods in Molecular Biology, 245–68. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1201-9_17.

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Boopathi, N. Manikanda. "Phenotyping." In Genetic Mapping and Marker Assisted Selection, 229–51. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-2949-8_6.

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Boopathi, N. Manikanda. "Phenotyping." In Genetic Mapping and Marker Assisted Selection, 109–15. India: Springer India, 2012. http://dx.doi.org/10.1007/978-81-322-0958-4_5.

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Naccache, David. "Phenotyping." In Encyclopedia of Cryptography and Security, 927. Boston, MA: Springer US, 2011. http://dx.doi.org/10.1007/978-1-4419-5906-5_894.

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Tyrer, Peter J., Mark Slifstein, Joris C. Verster, Kim Fromme, Amee B. Patel, Britta Hahn, Christer Allgulander, et al. "Behavioral Phenotyping." In Encyclopedia of Psychopharmacology, 214. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_3100.

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Lootens, P., T. De Swaef, I. Roldán-Ruiz, and T. Altmann. "Workshop “Phenotyping”." In Breeding in a World of Scarcity, 301–2. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-28932-8_45.

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Li, Chun, and Nataraj Kalyanaraman. "Reaction Phenotyping." In ADME-Enabling Technologies in Drug Design and Development, 189–212. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118180778.ch13.

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O’Brien, Emmet, Frank C. Sciurba, and Jessica Bon. "COPD Phenotyping." In Precision in Pulmonary, Critical Care, and Sleep Medicine, 225–39. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-31507-8_15.

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Tariq, Muhammad, Mukhtar Ahmed, Pakeeza Iqbal, Zartash Fatima, and Shakeel Ahmad. "Crop Phenotyping." In Systems Modeling, 45–60. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-4728-7_2.

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Qiu, Quan, Man Zhang, Ning Wang, Ruicheng Qiu, and Yanlong Miao. "Plant Phenotyping." In Agriculture Automation and Control, 185–250. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-70432-2_7.

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Conference papers on the topic "Phenotying"

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Fu, Tianfan, Trong Nghia Hoang, Cao Xiao, and Jimeng Sun. "DDL: Deep Dictionary Learning for Predictive Phenotyping." In Twenty-Eighth International Joint Conference on Artificial Intelligence {IJCAI-19}. California: International Joint Conferences on Artificial Intelligence Organization, 2019. http://dx.doi.org/10.24963/ijcai.2019/812.

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Predictive phenotyping is about accurately predicting what phenotypes will occur in the next clinical visit based on longitudinal Electronic Health Record (EHR) data. Several deep learning (DL) models have demonstrated great performance in predictive phenotyping. However, these DL-based phenotyping models requires access to a large amount of labeled data, which are often expensive to acquire. To address this label-insufficient challenge, we propose a deep dictionary learning framework (DDL) for phenotyping, which utilizes unlabeled data as a complementary source of information to generate a better, more succinct data representation. With extensive experiments on multiple real-world EHR datasets, we demonstrated DDL can outperform the state of the art predictive phenotyping methods on a wide variety of clinical tasks that require patient phenotyping such as heart failure classification, mortality prediction, and sequential prediction. All empirical results consistently show that unlabeled data can indeed be used to generate better data representation, which helps improve DDL's phenotyping performance over existing baseline methods that only uses labeled data.
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Zhang, Qianwei, and Reza Fotouhi. "Vibration Analysis of a Long Boom for a Farm Machine." In ASME 2018 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/detc2018-86188.

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Crop phenotyping is frequently used by breeders and crop scientists to monitor growth of plants and to relate them to plants genotypes. Seemingly, this contributes to better crop growth and results in higher yield. Instead of traditional crop monitoring, which is labor intensive, high-throughput phenotyping (HTP) platforms using ground-based vehicle have several advantages (in speed, efficiency, and cost) over manual methods. A wheeled mobile platform for HTP was developed, and automated data collection were performed for different traits of canola and wheat. These data were compared with manual measured data. In this paper, vibration analysis of a relatively long cantilever boom attached to a vehicle is reported. The paper investigates how different factors influence the boom attached to a regular farming machine, its vibration, and effects on phenotyping sensors attached to the boom.
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Che, Zhengping, David Kale, Wenzhe Li, Mohammad Taha Bahadori, and Yan Liu. "Deep Computational Phenotyping." In KDD '15: The 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2783258.2783365.

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Delgado, Cristhian, Hernan Benitez, Maribel Cruz, and Michael Selvaraj. "Digital Disease Phenotyping." In IGARSS 2019 - 2019 IEEE International Geoscience and Remote Sensing Symposium. IEEE, 2019. http://dx.doi.org/10.1109/igarss.2019.8897854.

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Zhang, QianWei, Reza Fotouhi, Joshua Cote, and Majid Khak Pour. "Lightweight Long-Reach 5-DOF Robot Arm for Farm Application." In ASME 2019 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/detc2019-98366.

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Abstract Crop monitoring is frequently used by crop scientists to observe growth of plants and to relate plants phenotypes to their genotypes. Instead of traditional crop monitoring, which is labor intensive, high-throughput plant phenotyping (HTP) platforms using ground-based vehicle have several advantages over manual methods. Existing HTP platforms with robot arms has limited reach and payload, and they are sometimes not appropriate for monitoring large fields. In this research, a 5-DOF robot arm is developed and analyzed for monitoring several crops growth. This robot arm is a hybrid of both prismatic and rotational joints. This new mobile manipulator is light, has a compact structure, suitable for plant phenotyping, and doesn’t exist commercially. To investigate the performance of the robot arm, kinematics and dynamics analyses using Newton-Euler iterative method and MATLAB simulations are performed. Results matched with each other very well.
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Ozeki, Yasuyuki, Yuta Suzuki, and Keisuke Goda. "Label-free multicolor imaging flow cytometry with stimulated Raman scattering." In JSAP-OSA Joint Symposia. Washington, D.C.: Optica Publishing Group, 2019. http://dx.doi.org/10.1364/jsap.2019.18p_e208_7.

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By combining the strength of flow cytometry with optical imaging and digital image analysis, imaging flow cytometry is a powerful tool in diverse fields of biology and medicine [1]. However, its applications are constrained by its requirement of fluorescent labeling for phenotyping.
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Kumar, Pankaj, Matheyarasu Raghupathi, Nanthi S. Bolan, and Stan Miklavcic. "Phenotyping earthworm by image analysis." In 2014 13th International Conference on Control Automation Robotics & Vision (ICARCV). IEEE, 2014. http://dx.doi.org/10.1109/icarcv.2014.7064305.

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Laga, Hamid, Fahimeh Shahinnia, and Delphine Fleury. "Image-based plant stornata phenotyping." In 2014 13th International Conference on Control Automation Robotics & Vision (ICARCV). IEEE, 2014. http://dx.doi.org/10.1109/icarcv.2014.7064307.

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HUNTER, LAWRENCE. "COMPUTATIONAL CHALLENGES OF MASS PHENOTYPING." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2012. http://dx.doi.org/10.1142/9789814447973_0045.

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Rooksby, John, Alistair Morrison, and Dave Murray-Rust. "Student Perspectives on Digital Phenotyping." In CHI '19: CHI Conference on Human Factors in Computing Systems. New York, NY, USA: ACM, 2019. http://dx.doi.org/10.1145/3290605.3300655.

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Reports on the topic "Phenotying"

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Herman, Gail E. Comprehensive Clinical Phenotyping & Genetic Mapping for the Discovery of Autism Susceptibility Genes. Fort Belvoir, VA: Defense Technical Information Center, December 2012. http://dx.doi.org/10.21236/ada607156.

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Herman, Gail E., Emily Hansen, Wolfgang Sadee, Ray Smith, Mary Beth Dewitt, and Eric Seiber. Comprehensive Clinical Phenotyping and Genetic Mapping for the Discovery of Autism Susceptibility Genes. Fort Belvoir, VA: Defense Technical Information Center, March 2013. http://dx.doi.org/10.21236/ada585946.

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Vessella, Robert L. Does the Phenotyping of Disseminated Prostate Cancer Cells in Blood and Bone Marrow Prior to Radical Prostatectomy Provide Prognostic Information? Fort Belvoir, VA: Defense Technical Information Center, July 2004. http://dx.doi.org/10.21236/ada435227.

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Vessella, Robert L. Does the Phenotyping of Disseminated Prostate Cancer Cells in Blood and Bone Marrow Prior to Radical Prostatectomy Provide Prognostic Information? Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada412293.

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Vessella, Robert. Does the Phenotyping of Disseminated Prostate Cancer Cells in Blood and Bone Marrow Prior to Radical Prostatectomy Provide Prognostic Information? Fort Belvoir, VA: Defense Technical Information Center, July 2003. http://dx.doi.org/10.21236/ada418201.

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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.
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"Clinical phenotyping for interstitial cystitis and bladder pain syndrome: using the UPOINT system". BJUI Knowledge, April 2016. http://dx.doi.org/10.18591/bjuik.0065.

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