Image Analysis and Machine Learning in Agricultural Research

Agricultural research has been a focus for academia and industry to improve human well-being. Given the challenges in water scarcity, global warming, and increased prices of fertilizer, and fossil fuel, improving the efficiency of agricultural research has become even more critical. Data collection by humans presents several challenges including: 1) the subjectiveness and reproducibility when doing the visual evaluation, 2) safety when dealing with high toxicity chemicals or severe weather events, 3) mistakes cannot be avoided, and 4) low efficiency and speed. Image analysis and machine learning are more versatile and advantageous in evaluating different plant characteristics, and this could help with agricultural data collection. In the first chapter, information related to different types of imaging (e.g., RGB, multi/hyperspectral, and thermal imaging) was explored in detail for its advantages in different agriculture applications. The process of image analysis demonstrated how target features were extracted for analysis including shape, edge, texture, and color. After acquiring features information, machine learning can be used to automatically detect or predict features of interest such as disease severity. In the second chapter, case studies of different agricultural applications were demonstrated including: 1) leaf damage symptoms, 2) stress evaluation, 3) plant growth evaluation, 4) stand/insect counting, and 5) evaluation for produce quality. Case studies showed that the use of image analysis is often more advantageous than visual rating. Advantages of image analysis include increased objectivity, speed, and more reproducibly reliable results. In the third chapter, machine learning was explored using romaine lettuce images from RD4AG to automatically grade for bolting and compactness (two of the important parameters for lettuce quality). Although the accuracy is at 68.4 and 66.6% respectively, a much larger data base and many improvements are needed to increase the model accuracy and reliability. With the advancement in cameras, computers with high computing power, and the development of different algorithms, image analysis and machine learning have the potential to replace part of the labor and improve the current data collection procedure in agricultural research. Advisor: Gary L. Hei

Buchstaben und Wörter im Kontext

Acknowledgments VI Zusammenfassung VIII Summary XIV General Introduction 1 Extending the theoretical base: Interactive Activation Models 2 The original interactive activation model and the identification of letters 3 The Multiple Read-Out Model and the recognition of words 5 Dual-route models and phonological representations in visual word recognition and reading aloud 11 How to model (semantic) associations during word recognition? 17 Overview of the present studies and their methods 22 Study 1: Sub-lexical frequency measures provided by corpus analyses 22 Study 2: Word frequency, lexicality and optical imaging 24 Study 3: Modeling electrophysiological responses to conflicting lexical representations 29 Study 4: Affective connotation of lexical representations, ERPs, and pupillometry 31 Study 5: Modeling associations between lexical representations and Receiver Operation Characteristics 34 Study 1: Sub-lexical frequency measures for orthographic and phonological units in German 41 Introduction 42 Grain sizes, domains, databases, and measures 46 Grain sizes: Syllable, dual unit, or single unit 47 Processing domains: Orthography or phonology 49 Databases: Lemma or word form 50 Measures: Type or token 51 Method 53 Results 55 Syllable frequencies of the lemma database 56 Syllable frequencies of the word form database 56 Dual unit frequencies of the lemma database 57 Dual unit frequencies of the word form database 58 Single unit frequencies of the lemma database 58 Single unit frequencies of the word form database 59 Discussion 60 Study 2: Differential activation of frontal and parietal regions during visual word recognition: An optical topography study 65 Introduction 67 Methods 71 Participants 71 Materials 71 Experimental procedure 72 Data acquisition 73 Data analysis 73 Results 76 Behavioral results 76 fNIRS (optical topography) 78 Discussion 82 The lexicality effect 83 The word frequency effect 85 Optical topography as a tool to investigate word recognition 86 Appendix 90 Study 3: Conflict monitoring engages the mediofrontal cortex during nonword processing 91 Introduction 92 Methods 95 Participants 95 Materials 95 Procedure 95 Data acquisition 96 Data analysis 97 Results 98 Behavioral 98 ERPs 98 sLORETA 98 Discussion 101 Conclusion 103 Study 4: Affective processing within 1/10th of a second: High-Arousal is necessary for early facilitative processing of negative but not positive words 105 Introduction 107 Method 112 Participants 112 Materials 112 Procedure 113 Data acquisition 114 Data analysis 114 Results 117 Behavioral 117 ERPs 117 sLORETA 118 Discussion 122 Study 5: Remembering words in context as predicted by an Associative Read-Out Model 127 Introduction 129 Does associative spreading activate ‘false memories’? 130 Can each item’s signal be detected in an explicit memory task? 134 Simulation methods: The AROM and its predictions 137 Experimental methods: Testing the AROM’s predictions 140 Participants 140 Corpus 140 Stimuli 140 Procedure 143 Experimental and modeling results 144 Discussion 148 Conclusions 155 General Discussion: Summary and outlook 159 Sub-lexical frequencies 160 Sub-lexical frequency measures constrained the interpretation of effects! 160 Can the matching of global features be replaced by specific ones? 161 Word frequency and optical imaging 163 Optical imaging revealed greater “neural activations” to low frequency words! 163 What is “neural activation” in the IFG? 164 Lexical conflicts 167 Lexical conflicts predicted behavioral data and ACC activation! 167 Does associative-semantic competition predict IFG activation? 170 Affective word features 171 Affective lexical features elicited behavioral and ERP, but no pupil dilation effects! 171 Can semantic cohesiveness account for affective effects? 173 Associative-semantic representations 176 Modeling associations between the word stimuli of an experiment predicted false and veridical memories! 176 Going beyond measurement models of familiarity and recollection? 179 The rebirth of a mental lexicon: How to answer the challenge of fixing the structure of time? 182 Does the mind construct semantic taxonomies from associations? 186 Conclusions 189 References 191 Erklärung I Curriculum Vitae III Wissenschaftlicher Werdegang III Lehre III Vorträge III Poster V Publizierte Konferenzbeiträge und Buchkapitel VI Gutachtertätigkeiten VI Zeitschriftenartikel VIIThis dissertation investigated visual word recognition based on the theoretical framework of interactive activation models (IAMs, McClelland & Rumelhart, 1981). Study 1 provided sub-lexical frequency measures for German, which were used as control variables in the Studies 2, 4, and 5. Study 2 was the first of three studies using the lexical decision task. The optical imaging results showed that words elicit greater neural responses than nonwords in the left inferior parietal gyrus, which suggests a role of this region during the integration of orthographic, phonological and semantic representations. Greater activations for word stimuli in the superior frontal gyrus can be interpreted in terms of decision-related processes during visual word recognition. Moreover, rare words elicited greater neural activation than common words in the left inferior frontal gyrus. This word frequency effect suggests a role of this region during the selection of a semantic representation from many co-activated semantic candidates. Study 3 used an IAM to calculate the conflicts between orthographic representations, and set this model-generated measure of lexical competition into a direct relation with an event-related potentials (ERP) negativity between 400 and 600 ms post- stimulus. The electric sources of the ERP-conflict effects were attributed to the anterior cingulate cortex. The model accounted for a significant portion of item-level variance in reaction times, error rates and mean amplitudes. Study 4 showed that positive and high-arousal negative words elicit response facilitation and an early ERP effect between 80 and 120 ms post-stimulus, when compared to neutral words. The ERP-effect in high-arousal negative words was source-localized in the left fusiform and middle temporal gyri. The latter finding may be explained by the larger amount of associative relations of affective words. Study 5 captures associative relations between words for IAMs. Two words were defined as 'associated', when they co-occur significantly often together in the sentences of a large corpus. This corresponds to Hebbian learning: Items being repeatedly presented together are likely to be associated. The results of a recognition memory task showed that learned and non-learned words elicit greater 'yes' response rates when they provide a larger amount of associated items in the stimulus set. The co-occurrence statistics were further used to implement associations between words in a contextual representation layer. This IAM-model predicted which word is recognized with which probability on an item-level. Because many of the most strongly co-activated words revealed a semantic relation to the presented word (e.g., synonymy), the resulting 'Associative Read-Out Model' is the first IAM with a fully implemented semantic representation layer.Diese Dissertation untersucht die visuelle Worterkennung auf der theoretischen Grundlage des 'Interactive Activation Models' (IAM, McClelland und Rumelhart, 1981). Studie 1 stellt sub-lexikalische Häufigkeitsmaße für das Deutsche zur Verfügung: Orthographische und phonologische Silbenfrequenzen, Bigramm- Biphonemfrequenzen, sowie Buchstaben- und Phonemfrequenzen. Solche Maße dienen in den Studien 2, 4, und 5 als Kontroll-Variablen. Studie 2 ist die erste von drei Studien, welche die visuelle Worterkennung mit der lexikalischen Entscheidungsaufgabe untersucht. Die optischen Bildgebungsbefunde zeigen, dass Wörter höhere neuronale Aktivierungen im linken inferioren Parietallappen auslösen, was auf die Rolle dieser Region bei der Integration orthographischer, phonologischer und semantischer Repräsentationen hinweist. Die höheren Aktivierungen für Wörter im superioren Frontallappen weisen auf die entscheidungsrelevanten Prozesse der Worterkennung hin. Seltene Wörter lösten höhere Aktivierungen im linken inferioren Frontallappen im Vergleich zu häufigen Wörtern aus, was die Beteiligung dieser Region bei der Auswahl einer semantischen Repräsentation aus verschiedenen konfligierenden Kandidaten nahelegt. Studie 3 setzt simulierte Konflikte zwischen orthographischen Repräsentationen bei der Verarbeitung von Nichtwörtern in eine direkte Beziehung zu einer Negativierung des ereigniskorrelierten Potentials (EKP) zwischen 400 und 600 ms. Die Quellen dieser Aktivierungen wurden im anterioren cingulären Cortex verortet. Das Modell klärte signifikante Varianzanteile für Reaktionszeiten, Fehlerraten und EKP-Negativierungen auf. Studie 4 zeigt, dass positive und hocherregend negative Wörter Antworterleichterungen im Vergleich zu neutralen Wörtern und eine frühen EKP-Negativierung zwischen 80 und 120 ms nach Reizdarbietung auslösen. Der EKP-Effekt hocherregend negativer Wörter konnte im linken fusiformen und im mittleren temporalen Gyrus verortet werden, was dafür spricht, dass affektiv konnotierte Wörter mehr assoziativ verknüpfte Wörter aufweisen. Studie 5 erschließt assoziative Verknüpfungen zwischen Wörtern für IAMs. Zwei Wörter wurden als 'assoziiert' definiert, wenn sie in den Sätzen eines großen Satzkorpus signifikant häufig gemeinsam auftreten. Dies entspricht der Hebb'schen Lernregel: Wörter, die häufig gemeinsam auftreten, sind wahrscheinlich assoziiert. Die Ergebnisse einer Wiedererkennens-Gedächtnisaufgabe zeigen, dass gelernte und nicht-gelernte Wörter mehr 'Ja-'Antworten auslösen, wenn sie eine größere Anzahl assoziierte Wörter im Reizmaterial aufweisen. Die ko-okkurrenzstatistischen Maße wurden benutzt, um eine kontextuelle Modell-Repräsentationsebene mit assoziativen Verbindungsgewichten auszustatten. Das Modell sagt auf dem Item-level voraus, welches Wort mit welcher Wahrscheinlichkeit wiedererkannt wird. Da viele der am stärksten assoziierten Wörter zum präsentierten Wort eine semantische Verknüpfung aufweisen (z.B. Synonymie), ist das so gewonnene 'Associative Read-Out Model', das erste IAM mit einer semantischen Repräsentationsebene

Factors affecting daytime function in the sleep apnoea/hypopnoea syndrome

The sleep apnoea/hypopnoea syndrome (SAHS) is characterised by repetitive upper airway obstructions during sleep, which lead to recurrent hypoxaemia and brief arousals from sleep. SAHS patients suffer from excessive daytime sleepiness (EDS), cognitive impairments and decreased psychological well -being. Previous studies have examined relationships between the nocturnal events of SAHS and a limited number of daytime function measures, frequently in small, non -consecutive patient samples. Relationships found have been either weak or non -significant. This thesis examines the relationships between a wide range of nocturnal sleep and breathing variables and daytime function. Additionally, this thesis examines the use of subjective and objective measures of daytime sleepiness, to determine which tests provide the most useful information for SAHS patients.A pilot study found that neither the 103 patients' nor their partners' Epworth rating of sleepiness were strong predictors of SAHS severity. In 150 patients with a wide range of SAHS severity, relationships between nocturnal events and daytime function were examined using newer definitions of arousal and measures of sleep continuity. A broad battery of daytime tests were used including the maintenance of wakefulness test (MWT) and the short form (SF) -36. Unlike previous studies, all correlations were controlled for age and awake oxygen saturation, known to influence the variables measured. The current study also examined these correlations in an unselected patient sample with a range of disease severity. The study found a lack of strong relationships between conventional nocturnal sleep and breathing variables and daytime function. Few baseline variables significantly predicted CPAP use.Daytime function measures were compared within the 150 patients. The multiple sleep latency test (MSLT) and the MWT displayed a moderate, discordant relationship. Measures of cognitive function, psychological well -being and subjective sleepiness ii better related to the MWT than MSLT, suggesting that the MWT may be a more useful tool in assessing functional impairment in sleep apnoea.A randomised cross -over study, on 12 SANS patients, compared daytime sleepiness measured following a night's sleep at home (as performed in this thesis) versus a night in the sleep centre (standard protocol). Preliminary results indicated that daytime sleepiness, as measured by the MSLT and MWT, was not significantly different between the two study limbs. This suggests that the non -standard method of conducting the MSLT and MWT in this thesis does not explain the lack of correlational relationships between nocturnal measures and daytime sleepiness.The studies presented in this thesis demonstrate a lack of identified factors affecting daytime function in a group of unselected SANS patients. This may be due to inter - individual patient variability. Also, more sophisticated nocturnal SANS measures should be examined, as should more `real -life' daytime assessments, such as ambulatory EEG recorded during a patient's normal daily routine

Diet Overlap of Native and Translocated Northern White-Tailed Deer in Southeastern Louisiana

I used microhistological analysis of fecal pellets to estimate and compare seasonal diet compositions between free-ranging, southern and translocated. northern woodland white-tailed deer (Odocoileus virginianus) on Golden Ranch Hunting Farm, Gheens, Louisiana,. over four consecutive seasons, from January 1997 through January 1998. I analyzed pellet groups with Near Infrared Reflectance Spectroscopy (NIRS) and wet chemistry techniques to evaluate and compare crude protein levels between populations of deer and provide indices of diet quality. On average, native and translocated deer diets were 87.65% similar during the entire study, and were significantly associated during all seasons ( P \u3c 0.0000 I ). suggesting that deer fed on similar plant species in like quantities throughout the year. Few differences were found in plant selection frequencies per fecal sample. hut significant differences were detected (P 0.00 l) among deer populations in the use of Berchemia scandens and Vitis rotundifolia during spring. Northern deer also ingested a greater diversity of plants (P \u3c 0.05) during spring and winter; and fecal crude protein levels were similar (P \u3e 0.05) in all seasons except winter, when there was more (P \u3c 0.05) protein in southern deer diets. Overall. diet compositions. plant diversity. and diet quality of southern and northern deer populations were similar, suggesting that translocated deer select diets comparable to those of native animals

The potential use of sugarcane varieties for the identification of genetic markers.

Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1996.The use of genetic markers that are linked to specific traits in sugarcane has the potential to increase the efficiency of the selection of improved varieties. Conventionally, markers are identified by analysing the segregation of potential markers and traits in the progeny of single crosses. However, this approach is not practical for sugarcane breeding programmes where replicated, well characterized progenies do not exist. The objective of this project was to investigate the potential of using commercial varieties for identifying markers associated with some of the important traits in sugarcane. This approach would be far more effective than dealing with single progenies since the traits of commercial varieties have already been characterized. The DNA of fifty commercial varieties of sugarcane was amplified by RAPD PCR using forty-one arbitrary decamer primers. Analysis of the resulting banding profiles, obtained by agarose gel electrophoresis, yielded fifty-four reliable polymorphic fragments. Two approaches were used to identify putative markers linked to the traits of resistance to eldana, sugarcane mosaic virus, and smut: (1) a correlation approach which attempted to identify whether the presence of any polymorphisms could be used to imply the existence of a particular phenotypic state, and (2) multiple regression analysis, in order to determine whether polymorphisms could be used to predict the performance of the varieties for each of the traits. Both approaches appeared to identify associations between polymorphisms and the traits, although multiple regression analysis yielded the most informative results and was able to assign statistical values to the associations. Using multiple regression, the best predictive model was obtained for sugarcane mosaic virus resistance. This model consisted of four polymorphisms and had an r² of 0.40l. By dividing the resistance ratings into three groups (resistant, intermediate and susceptible), 52% of the varieties were correctly classified and only 2% of the varieties were predicted in opposite groups (i .e. predicted susceptible when actually resistant, and vice versa). The predictive model for eldana resistance consisted offour polymorphisms and had an r² of 0.347. This model classified 30% of the varieties in the correct group of three while none of the varieties were predicted in opposite groups. The predictive model for smut resistance consisted of three polymorphisms and had an r² of 0.316. This model classified 30% of the varieties in the correct group of three while 2% of the varieties were predicted in opposite groups. Further analysis of sugarcane varieties using additional polyrnorphisrns has the potential to identify markers linked to important traits. These markers could be used for marker-assisted selection to increase the efficiency of selecting for improved sugarcane genotypes for commercial release